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The use of medicinal plants for managing diabetes and related conditions has been an integral part of traditional healthcare systems throughout the world including Nagaland, India. Authentic identification of these medicinal plants is crucial for their safe and effective use. A study was aimed for authentic identification of some anti-diabetic potential ethnomedicinal plants from Nagaland, India using DNA sequence based molecular characterization by amplifying and sequencing of ITS, rbcL and matK barcode regions. DNA barcode loci from the nuclear and chloroplast genomes from 15 different ethnomedicinal anti-diabetic plants of Nagaland, India, were studied for molecular characterisation. Based on the ITS, rbcL and matK region sequences, three main discrimination methods, i.e., BLAST, Phylogenetic tree and genetic distance, were adopted to identify the species. Utilising DNA markers for identification is both highly advantageous and efficient due to its reliability and rapidity. Successful amplification across species and high blast hits (100 % identity) highlighted their potential for molecular characterisation. Phylogenetic trees constructed using various models showed distinct clades and subclades, with matK revealing hypervariability and rbcL demonstrating consistent matches. Genetic distances revealed varying levels of similarity, with certain species establishing close relationships based on pairwise comparisons. GC% variations were detected, potentially indicating nucleotide composition differences and functional constraints among species genomes. The findings of this study highlight that the ITS, rbcL , and matK regions serve as effective markers for verifying the authenticity of anti-diabetic medicinal plants indigenous to Nagaland, India. [Display omitted] • DNA markers based species identification of 15 antidiabetic plants from Nagaland. • ITS, matK and rbcL based identification complemented with phonological identification. • Consistency in rbcL and matK regions showing reliability as DNA barcode markers. • Sequence length variations attributed to genomic differences among plants. [ABSTRACT FROM AUTHOR]

• We applied liquid chromatography-tandem mass spectrometry to the analysis of historical iron gall ink recipes. • We characterised ageing markers of iron gall inks by HPLC-ESI-Q-ToF. • We highlighted different degradation trends depending on historical recipes and ageing conditions. • We proved that it is possible to use 15 µg as minimum amount of sample for the HPLC-ESI-Q-ToF analysis of iron gall inks. Several manuscripts and drawings of our historical and artistic heritage have been produced with iron gall inks. To obtain an iron gall ink, ancient treatises cite the addition of ferrous sulphate and gum Arabic to a decoction of oak galls as a basic procedure. Owing to the development of synthetic chemistry, iron gall ink recipes were improved with new materials and procedures in the late 19th and early 20th century. Notably, many conservation issues arise from the interaction between iron gall inks and the paper support of manuscripts and drawings. To date, most of the research on the topic are focused on paper preservation by non-destructive analytical methods, which provide only limited information on degradation process trends and minor components, representative of iron gall ink's recipes. In the present work, three historical recipes of iron gall inks (alizarine ink, Reid ink, modern gall ink) , dated to 19th-20th century and differing for the preparation method and additives, were characterized. The molecular markers of iron gall inks and of gallic acid degradation were detected by an optimized protocol based on high performance liquid chromatography coupled to high resolution mass spectrometry (HPLC HRMS). Furthermore, by performing ageing tests on reference materials in different indoor conditions (natural light and stored in the dark), two degradation mechanisms were observed: hydrolysis of poly-galloyl glucose species and auto-oxidation of gallic acid. Thus, different chemical profiles and ageing trends were revealed depending on the starting recipe. The procedure Limit of Detection (LOD) was estimated, improving the approaches reported so far in the literature. Finally, the strategy was successfully applied for the characterisation of the ink employed in a very degraded 16th century manuscript, granting access to the complete molecular profile of an iron gall ink with just 15 µg of sample. [Display omitted] [ABSTRACT FROM AUTHOR]

The crab genus Panopeus is characterized by a high morphological similarity among its species and the taxonomic problems that ensue. This complex situation can lead to misidentifications and mistaken comprehension of the phylogenetic relationships and species distributions. In this context, the present study morphologically and genetically (16S rRNA and COI) assessed the seven species of Panopeus recorded from the Southwestern Atlantic, with special focus on Panopeus occidentalis , whose occurrence in Brazilian waters has been under debate, and on the relationship between Panopeus austrobesus and Panopeus rugosus , where available genetic and morphological data were apparently contrasting. Although the investigated species are morphologically similar, this study describes some characters that can be used as diagnostic, such as a pigmented spot in the inner surface of the third maxilliped ischium. Phylogenetic inference and genetic distance reinforced the idea that the genus is non-monophyletic and were able to clarify the phylogenetic relationships within the genus. The integrative approach using morphological and genetic data confirmed the occurrence of six out of the seven Panopeus species reported along the Southwestern Atlantic coast, but with different geographic extents than what was previously assumed in some cases. We provide updated diagnoses for these species and also a key for their identification. [ABSTRACT FROM AUTHOR]

• We examine empirically the link between player diversity and team performance. • We focus on national soccer teams and propose an IV based on past immigration. • Our diversity measure relies on genetic distances across surname-predicted origins. • IV findings reveal a positive causal link between ancestral diversity and performance of national teams. The theoretical impact of diversity on performance is ambiguous since it leads to costs and benefits at the collective level. In this paper, we empirically assess the connection between ancestral diversity and the performance of sports teams. Focusing on football (soccer), we built a novel dataset of national teams of European countries that have participated in the European and World Championships since 1970. The ancestral diversity of national teams is measured from genetic distance scores within the team, based on information on every player's origins. Origins are recovered using a matching algorithm based on family names. Performance is measured at the match level. Identification of the causal link relies on an instrumental variable strategy based on past immigration at the country level about one generation before the competition. Our findings indicate a positive causal link between ancestral diversity and national teams' performance. We find that a one-standard increase in diversity leads to a significant increase in the goal difference of 0.77 to 1.79 goals per match (about a 1.30 goal difference per match). [ABSTRACT FROM AUTHOR]

• There can be a 'degree' of tropical nature within a short distance of a province. • T. dregeana seeds from two locations within the same province are morphologically different. • There were variations in their responses to chilling and desiccation stresses. • The prevailing climatic conditions conferred genetic variations on the seeds. In the conventional method of seed conservation, chilling- and desiccation-tolerances are requisites. However, recalcitrant-seeded species cannot meet these requisites because of their characteristics. Thus, the alternative method for the conservation of the germplasms of recalcitrant species is cryopreservation. The aim of this study was to investigate how growth environments influenced the response of Trichilia dregeana germplasms to chilling and desiccation treatments. In this study, seeds of Trichilia dregeana were harvested from two locations within the KwaZulu-Natal province of South Africa: Durban (DBN) and Pietermaritzburg (PMB). Both locations were slightly different in climatic conditions, with DBN being more humid than PMB. Embryonic axes of the seeds were subjected to rapid drying while cleaned seeds were subjected to slow drying and chilling stress for 36 h and 18 weeks, respectively. Plantlets were generated in vitro from the embryonic axes and whole seeds, using full-strength and quarter-strength of Murashige and Skoog medium, respectively. One-way analysis of variance (ANOVA) was used to test the significant differences in seed weight, length and height, shoot and root lengths, while General Linear Model analysis and Wilcoxon tests were used for water content, germination and growth parameters. PMB seeds were significantly bigger than DBN seeds, so also were shoot production, root and shoot lengths generated from the embryonic axes. All the seeds of both provenances still retained more than 50% of their shedding water after slow drying but DBN seeds showed less survival than PMB seeds. Storage of cleaned whole seeds at chilling temperatures (3, 6 and 16 °C) caused an increase in the water content of the embryonic axes across the two provenances. Tolerance of seeds stored at these temperatures was in the order 3 °C < 6 °C < 16 °C. For the three storage temperatures, survival was less in DBN seeds than in PMB seeds. Phylogenetic analysis of the ITS region of the samples from both locations showed intraspecific levels of genetic variation, and were separated by a genetic distance of 0.9%. Although the distance between the two provenances is short, the seeds obtained from both places showed different degrees of recalcitrance with DBN seeds being more sensitive to desiccation and chilling. This study also suggested that there might be genetic variations in the seeds from both populations. [ABSTRACT FROM AUTHOR]

Polygenic scores (PGSs) aggregate the effects of variants across the genome to estimate genetic liability, but have lower performance in external study populations. A new study by Ding et al. has applied a novel framework to estimate the individual-level predictive accuracy of PGSs, and demonstrates that performance reduction occurs linearly with genetic distance. [ABSTRACT FROM AUTHOR]

The present study characterized complete mitochondrial genome of Blue-spotted maskray, Neotrygon indica and studied the evolutionary relationship of the species within the Dasyatidae family. The total length of the mitogenome was 17,974 bp including 37 genes and a non-coding control region. The average frequency of nucleotides in protein-coding genes was A: 29.1 %, T: 30.2 %, G: 13.0 % and C: 27.7 % with AT content of 59.3 %. The values of AT and GC skewness were −0.018 and −0.338, respectively. Comparative analyses showed a large number of average synonymous substitutions per synonymous site (Ks) in gene NADH4 (5.07) followed by NADH5 (4.72). High values of average number of non-synonymous substitutions per non-synonymous site (Ka) were observed in genes ATPase8 (0.54) and NADH2 (0.44). Genes NADH4L and NADH2 showed high interspecific genetic distance values of 0.224 ± 0.001 and 0.213 ± 0.002, respectively. Heat map analysis showed variation in codon usage among different species of the Dasyatidae family. The phylogenetic tree showed a sister relationship between the Dasyatinae and the Neotrygoninae subfamilies. Neotrygon indica formed as a sister species to the clade consisting of N. varidens and N. orientalis. Based on the present results, Neotrygon indica could have diverged from the common ancestor of the two latter in the Plio-Pleistocene. The present study showed distinct characteristics of N. indica from its congeners through comparative mitogenomics. • The complete mitochondrial genome of the Indian Ocean Blue-spotted Maskray, Neotrygon indica was reported for the first time. • High synonymous substitutions per synonymous site (Ks) were observed in gene NADH4 (5.07) followed by NADH5. • High interspecific genetic distance values were observed in NADH4L and NADH2. • Neotrygon indica formed as a sister species to the clade consisting of N. varidens and N. orientalis. • Supported a scenario of Plio-Pleistocene allopatric speciation for the Blue-spotted maskray species. [ABSTRACT FROM AUTHOR]

In the present study the genetic variation of different Peruvian populations was investigated. The samples for this study were obtained from 669 individuals distributed among 11 populations from Peru. All samples were analyzed using 23 autosomal STR markers. The Arlequin v3.5.2.2 software was used to determine the genetic distances (Fst) of the studied populations. Notable population substructure was detected between some populations. [ABSTRACT FROM AUTHOR]

This study focuses on estimation of the inter and intra population genetic variability of 6 duck populations. Microsatellite loci were used to assess the genetic variation and population structure of 6 duck populations under a conservation program in Poland. DNA polymorphism was assessed using 24 microsatellite markers and 50 individuals from each population. Polymorphism information content (PIC), heterozygosity with 2 estimators of genetic differentiation (FST and GST), and Nei's standard genetic distance were calculated. The results showed that these 6 endangered duck populations showed high genetic polymorphism. Observed heterozygosity within populations ranged from 0.14 to 0.83, with the average value of 0.58. PIC within populations ranged from 0.038 (P-8 and P-9 lines) to 0.89 (LsA line). Average number of alleles in the studied populations ranged from 4.5 (KhO-1 line) to 7.3 (LsA line). Based on the results, the pairs of lines LsA: P-33 and P-8: P-9 were found to be the most related; and the most genetically distant group was KhO-1 line, which originated as a cross between Khaki Campbell with Orpington duck. [ABSTRACT FROM AUTHOR]

• The newly developed molecular markers accurately distinguish Gastrodia elata subpopulations, mitigating misidentification issues and safeguarding germplasm authenticity. • Genetic analysis of 743 Gastrodia elata individuals in China reveals distinct differentiation patterns among subpopulations, aiding species understanding and breeding programs. • The construction of a core germplasm collection for Gastrodia elata plays a pivotal role in conservation efforts, resource management, and the selection of optimal parental candidates for crossbreeding programs. Gastrodia elata BL (subtribe: Gastrodiinae Lindl; family: Orchidance) is a perennial herb with high medicinal value. In China, a substantial number of wild and cultivated G. elata germplasm resources have been preserved; however, many of them exhibit genetic mixing necessitating genetic differentiation for effective germplasm management. In this study, we developed 15 novel simple sequence repeats (SSRs) and applied them in combination with 7 existing SSRs to evaluate the genetic diversity and population structure of 743 G. elata accessions excluding 24 potentially redundant genotypes, from China. Through STRUCTURE analysis, 158 pure G. elata f. elata , 60 pure G. elata f. glauca , and 38 pure G. elata f. viridis accessions were identified, whereas, the remaining accessions were idenified as potential hybrids derived from diverse crossing parents. The G. elata hybrids exhibited the highest genetic diversity, followed by G. elata f. viridis and G. elata f. elata , whereas G. elata f. glauca exhibited the lowest diversity. A major genetic differentiation existed between G. elata f. glauca and the other G. elata types. The results of Mantel test revealed a positive correlation between genetic and geographic distances. However, substantial genetic exchanges or mixing were observed in the G. elata germplasm from varying geographical regions. Based on the genetic variation, a core collection comprising 297 G. elata individuals was constructed, which is a vital resource for conserving and breeding of this medicinal plant. [ABSTRACT FROM AUTHOR]

This study provides the first documentation of three deep conspecific lineages within Panulirus polyphagus in the Indian Ocean, bridging the gap in genetic research. Comparative mitogenomics between lineages (L) at both species and family levels, evolutionary relationships and heterogeneity of sequence divergence within Decapoda, and divergence time estimation were performed. The characterized mitogenomes ranged from 15,685–15,705 bp in size and exhibited a typical pancrustacean pattern. Among the three lineages, L1 predominated the Bay of Bengal, L2 the Arabian Sea, and L2.a, a less common lineage genetically closer to L2, was restricted to the latter region. A minor lineage L1.a, was observed in the Coral Triangle area. All PCGs displayed evidence of purifying selection across species and family levels. The largest genetic distance (K2P) between lineages was 9 %, notably between L1.a and L2.a. The phylogenetic tree subdivided the Achelates into Palinuridae and Scyllaridae, and the topology demonstrated a distinct pattern of lineage diversification within P. polyphagus. AliGROOVE analysis revealed no discernible divergence in Decapoda. The diversification of P. polyphagus appears to have occurred during Miocene, with further diversification in Pliocene. Furthermore, genetic stocks and population connectivity recognized here will provide valuable insight for spatial management planning of this dwindling resource. • The first mitogenomic study demonstrating the presence of cryptic, deep conspecific lineages in Panulirus polyphagus , distributed in the Indo-West Pacific. • The mitogenome-based K2P divergence between the major lineages is ~8.0 %, dating their initial divergence back to the late Miocene. • The genetic structure and population connectivity of this heavily exploited species have been revealed, indicating a unique pattern considering the extended pelagic larval duration of spiny lobsters. • Hypotheses regarding the diversification of lineages in this species have been listed. • The lineages from the Central Indo-Pacific and the Arabian Sea can be broadly categorized as two distinct genetic stocks that require separate management. [ABSTRACT FROM AUTHOR]

The genus Paris (Melanthiaceae) holds significant pharmaceutical importance and is subject to high conservation concerns. Accurate species identification plays a crucial role in effectively addressing issues related to the exploitation, utilization, and conservation of this plant lineage. Recently, high-throughput sequencing technologies have been employed to generate complete plastid genomes (plastomes) and nuclear ribosomal DNA (nrDNA) arrays as molecular markers for plant species identification. However, the lack of reference libraries poses a substantial challenge to the widespread application of this approach. In this study, we established a comprehensive reference library consisting of complete plastomes and nrDNA arrays from 153 individuals representing all medicinal and endangered Paris species. The robustness of the reference sequences in discriminating Paris species was assessed through phylogenetic and genetic distance analyses. The results demonstrate that both complete plastome and nrDNA reference sequences exhibit a high degree of consistency with species boundaries as defined by recent taxonomic revisions to the genus, thereby facilitating unambiguous species identification. The favorable performance of this reference library underscores its invaluable significance as a genetic resource for the efficient monitoring and regulation of the collection and trade of medicinal and endangered Paris species, along with associated plant products, through the utilization of high-throughput sequencing technologies. The findings of this study will make a significant contribution to enhancing the efficacy and safety assurance of Rhizoma Paridis products, as well as supporting conservation efforts for endangered Paris species. [Display omitted] • The first reference library for precise identification of Paris species is established. • The reference library will ensure the efficacy and safety of Rhizoma Paridis products. • The reference library will contribute to the conservation of endangered Paris species. [ABSTRACT FROM AUTHOR]

Mosquitoes are medically important insects, and accurate species identification is crucial to understanding vector biology, forming the cornerstone of successful vector control programs. Identification is difficult owing to morphologically similar species. Wing morphometrics can provide a simple, fast, and accurate way to classify species, and using it as a method to differentiate vector species among its cryptic congeners has been underexplored. Using a total of 227 mosquitoes and 20 landmarks per specimen, we demonstrated the utility of wing morphometrics in differentiating species two groups occurring in sympatry – Culex (Culex) vishnui group and Culex (Lophoceraomyia) subgenus, as well as explored population-level variation in the wing shape of Aedes albopictus across habitats. Cytochrome oxidase subunit I (COI) gene region was sequenced to validate the morphological and morphometric identification. Procrustes ANOVA regression and CVA based on wing shape reflected that the wing landmarks across all species differed significantly, and leave-one-out cross validation revealed an overall high accuracy of >97% for the two Culex groups. Wing morphometrics uncovered population-level variation within Aedes albopictus , but cross validation accuracy was low. Overall, we show that wing geomorphometric analysis is able to resolve cryptic Culex species (including vectors) occurring sympatrically, and is a robust tool for identifying mosquitoes reliably. • Accurate species identification is crucial to understanding vector biology. • Relevant in mosquito groups which are speciose and taxonomically challenging. • Wing morphometrics is a simple, fast and accurate way to classify species. • Able to differentiate morphologically similar species occurring in sympatry. • Culex wing shapes are positively correlated with genetic distances in our study. [ABSTRACT FROM AUTHOR]

Several mitogenomes of the genus Ganoderma have been assembled, but intraspecific comparisons of mitogenomes in Ganoderma lingzhi have not been reported. In this study, 19 G. lingzhi mitogenomes were assembled and analyzed combined with three mitogenomes of G. lingzhi from GenBank in term of the characteristics, evolution, and phylogeny. The results showed that the mitogenomes of the G. lingzhi strains are closed circular ranging from 49.23 kb to 68.37 kb. The genetic distance, selective pressure, and base variation indicate that the 14 common protein coding genes were highly conserved. The differences in introns, open reading frames, and repetitive sequences in the mitogenome were the main factors leaded to the variations in mitogenome. The introns were horizontally transferred in mitogenomes, and the differences between introns in the same insertion, which were primarily caused by the repetitive sequence, showed that the introns may be under degeneration. Besides, the frequent insertion and deletion of introns showed an evolutionary rate faster than protein coding genes. Phylogenetic analysis showed that the G. lingzhi strains gathered with high support, and those with the same intron distribution law had closer clustering relationships. [ABSTRACT FROM AUTHOR]

A new species Polacanthoderes shiraseae sp. nov. from three Antarctic regions (off Cape Darnley, off Totten Glacier, and in Lützow-Holm Bay) is described. In addition, type species of Polacanthoderes , Polacanthoderes martinezi , is redescribed. The new species is distinguished from P. martinezi by the presence of conspicuously thick lateroventral acicular spines on segments 8 and 9 and the presence of sublateral small acicular spines on segment 7. Both P. martinezi and P. shiraseae sp. nov. occasionally show intraspecific morphological variations in the position of some small acicular spines. The K2P genetic distances based on the mitochondrial cytochrome c oxidase subunit 1 gene sequences in P. shiraseae sp. nov. are 0–1.5%, equivalent to those in other echinoderid species. Phylogenetic analyses of Polacanthoderes based on the nuclear 18S rRNA and 28S rRNA gene sequences support the inclusion of the genus in Echinorhagata/Echinoderidae and suggest that the genus represents the most basal group of this order/family. [ABSTRACT FROM AUTHOR]

Mugil curema is a common species in America and some African coastal areas. It is thought to perform reproductive migrations to the open sea and possibly spawn in estuarine waters. Previous studies described it as a species complex composed of cryptic species, which could be explained by reproductive isolation and/or philopatric behavior. In order to assess genetic diversity, genetic structure and philopatry in M. curema , we sequenced and analyzed two mitochondrial genes (control region and Cytochrome Oxidase Subunit I [COI]) and 10 microsatellite loci from adult individuals from 10 locations in the Gulf of Mexico, one in the Atlantic Ocean, and three in the Mexican Pacific. The mitochondrial results showed two genetic groups: Gulf of Mexico (GOM) and Mexican Pacific (MP). There was relatively high genetic distance between the groups (4.5 % for COI and 11.7 % for the control region), but they did share haplotypes. In addition, two genetic groups were found within the MP group, which could constitute cryptic lineages. The microsatellite results showed genetic connection between GOM and MP, probably as a consequence of recent contact. The results also showed genetic structure within GOM and MP; genetic subgroups differed between the sexes in the GOM (F ST =0.348 ♂ and 0.275 ♀), but not the MP (F ST =0.233 ♂ and 0.166 ♀). The results of genetic structure and gene flow support the hypothesis of regional philopatry in males in the GOM and both sexes in the MP. The difference between regions could be explained by the fact that these are located geographically on different oceanic slopes. We recommend that areas where there is strong mixing of males and females and high genetic diversity be considered conservation priorities. [ABSTRACT FROM AUTHOR]

• A medium-density SNP chip 182,122 SNPs was designed and validated for both Camelus bactrianus and Camelus dromedarius. • The estimated inter-marker distance of 14 kb, significantly enhances the coverage of the camel genome. • The medium-density chip has been successfully genotyped using 480 camel samples, with a call rate of 99% and 96% of the being highly reliable for genotyping. • With an enhanced genome coverage, accuracy and economic efficiency the Axiom_ MaruPri SNP chip is poised to advance genomic breeding research in camels. Camels play a crucial socio-economic role in sustaining the livelihoods of millions in arid and semi-arid regions. They possess remarkable physiological attributes which enable them to thrive in extreme environments, and provide a source of meat, milk and transportation. With their unique traits, camels embody an irreplaceable source of untapped genomic knowledge. This study introduces Axiom- MaruPri , a medium-density SNP chip meticulously designed and validated for both Camelus bactrianus and Camelus dromedarius. Comprising of 182,122 SNP markers, derived from the re-sequenced data of nine Indian dromedary breeds and the double-humped Bactrian camel, this SNP chip offers 34,894 markers that display polymorphism in both species. It achieves an estimated inter-marker distance of 14 Kb, significantly enhancing the coverage of the camel genome. The medium-density chip has been successfully genotyped using 480 camel samples, achieving an impressive 99 % call rate, with 96 % of the 182,122 SNPs being highly reliable for genotyping. Phylogenetic analysis and Discriminant Analysis of Principal Components yield clear distinctions between Bactrian camels and dromedaries. Moreover, the discriminant functions substantially enhance the classification of dromedary camels into different breeds. The clustering of various camel breeds reveals an apparent correlation between geographical and genetic distances. The results affirm the efficacy of this SNP array, demonstrating high genotyping precision and clear differentiation between Bactrian and dromedary camels. With an enhanced genome coverage, accuracy and economic efficiency the Axiom_ MaruPri SNP chip is poised to advance genomic breeding research in camels. It holds the potential to serve as an invaluable genetic resource for investigating population structure, genome-wide association studies and implementing genomic selection in domesticated camelid species. [ABSTRACT FROM AUTHOR]

The Macrobrachium amazonicum complex is composed of at least the Macrobrachium amazonicum and Macrobrachium pantanalense species, with the latter described from specimens originally identified as part of an endemic M. amazonicum population in the Brazilian Pantanal region. While there may be a reproductive barrier between these two Macrobrachium species, both are phylogenetically close, with small genetic distance. However, there is currently no available biochemical information of Macrobrachium pantanalense (Na+, K+)-ATPase. Here, we report the kinetic characteristics of the gill (Na+, K+)-ATPase in two populations of M. pantanalense from Baiazinha Lagoon (Miranda, MS, Brazil) and Araguari River (Uberlândia, MG, Brazil), and compare them with Macrobrachium amazonicum populations from the Paraná-Paraguay River Basin. (Na+, K+)-ATPase activities were 67.9 ± 3.4 and 93.3 ± 4.1 nmol Pi min−1 mg−1 protein for the Baiazinha Lagoon and Araguari River populations, respectively. Two ATP hydrolyzing sites were observed for the Araguari River population while a single ATP site was observed for the Baiazinha Lagoon shrimps. Compared to the Araguari River population, a 3-fold greater apparent affinity for Mg2+ and Na+ was estimated for the Baiazinha Lagoon population, but no difference in K+ affinity and ouabain inhibition was seen. The kinetic differences observed in the gill (Na+, K+)-ATPase between the two populations of M. pantanalense , compared with those of various M. amazonicum populations, highlight interspecific divergence within the Macrobrachium genus , now examined from a biochemical perspective. [Display omitted] • (Na+, K+)-ATPase exhibits two ATP hydrolyzing sites for the Araguari River population. • Mg2+ and Na+ affinities are 3-fold greater in the Baiazinha Lagoon population. • (Na+, K+)-ATPase activity is ∼40% greater for the Araguari River population. • (Na+, K+)-ATPase activity in M. pantanalense is lower than in M. amazonicum. [ABSTRACT FROM AUTHOR]

Danzhou chicken (DZ) is a local breed in China noted for its strong adaptability, roughage resistance, strong wildness, and delicious taste, thus containing important genetic resources. In this study, genome re-sequencing data was generated from 200 DZ chickens. Combined with previously generated data from 72 additional chickens across six other exotic and local breeds, these data were used to systematically evaluate the germplasm characteristics of DZ chickens from a genomic perspective. Unlike exotic breeds, both DZ and southern local chicken varieties exhibited high genetic diversity, and the genetic distance between DZ and southern local chickens was smaller than the genetic distance between DZ and exotic chickens. A reconstructed Neighbor-Joining phylogenetic tree indicated that all sampled populations clustered into single independent populations, with DZ chickens showing clear evidence of intra-population differentiation, forming 2 subpopulations. Principal component analysis and ADMIXTURE analysis showed that DZ was significantly different from other breeds. These results indicate that DZ is a unique genetic resource that is different from other southern native and exotic chickens. The results of the study will improve our understanding of the genetic structure and current status of the DZ breed, which is of great significance in promoting the conservation of genetic resources of DZ chickens and fostering breed innovations and genetic improvement. [ABSTRACT FROM AUTHOR]

Amblyomma integrum is a large gooseberry sized longirostrate tick (when fully repleted) found in India and Sri Lanka. In Kerala (India), this tick is commonly found in the forest and its fringe areas frequently infesting deer and hence it is locally known as " maan chellu / maanunny" (deer tick). In the present study, molecular characterisation and phylogenetic analysis of A. integrum collected from the area grazed by the sambar deer (Rusa unicolor) of Kerala, south India was performed using three molecular markers viz., the mitochondrial cytochrome c oxidase subunit 1 (COI), mitochondrial 16S ribosomal RNA, and nuclear 18S ribosomal RNA genes. Cytochrome c oxidase subunit 1 (COI) gene showed better resolving ability for elucidating the evolutionary relationship of A. integrum and identified two distinct clades, viz., A and B. The Tamil Nadu isolates of south India and Marayoor isolate 1 (from Idukki district of Kerala bordering with Tamil Nadu) belonged to clade A. Majority of Wayanad isolates from Kerala, occupied clade B. The intraspecific genetic distance among the A. integrum species ranged from 0.00 to 13.34%. Between clades A and B, the genetic distance observed was 11.49%. The clade B isolates were genetically close to A. geoemydae (GD: 1.22%). Morphological variations between the clades included darker exoskeletal coloration in clade A and distinct differences in the shape of basis capitulum. Further analysis using Assemble Species by Automatic Partitioning (ASAP) and Generalized Mixed Yule Coalescent (GMYC) provided additional insights. Assemble Species by Automatic Partitioning (ASAP) identified 26 Molecular Operational Taxonomic Units (MOTUs) at a threshold distance of 5.38%, supporting the species partition of A. integrum clade B. Generalized Mixed Yule Coalescent (GMYC) analysis retained the same species complex (A. integrum - geoemydae Complex) inferred from the ASAP analyses. It could be inferred from the present study that the A. integrum clades A and B could be two different putative pseudocryptic species. [Display omitted] • Two clades of A. integrum viz., A and B were observed in the phylogeny with COI. • Clade B ticks were similar to A. integrum sensu stircto. • Exoskeletal coloration of the morpho-variant (clade A) was darker than typical one. • The basis capitulum of clade A ticks were dorsally subtriangular. • Molecular differentiation of A. integrum and A. geoemydae is difficult. [ABSTRACT FROM AUTHOR]

This paper studies the potential link between the biological evolution of populations and present-day economic interactions by estimating the correlation of shared ancestry among populations with cross-border capital and human flows. To this end, we employ the new concept of genetic distance, based on (dis)similarity of neutral gene alleles, to quantify shared ancestry. We then incorporate the genetic distance measure into an augmented gravity model, traditionally used to analyze the effect of geographical distance on bilateral exchange. Our analysis focuses on bilateral foreign direct investment (FDI) and migration across 135 countries and we use both linear regression techniques as well as the Poisson Pseudo-Maximum Likelihood Estimator to account for any non-linearities in the model. Our results show that a 1% increase in genetic distance reduces FDI flows by 0.08% while controlling for other distance constructs and factors associated with global capital and human movement. Genetic distance also has a negative effect on migration, where a 1% increase in genetic distance reduces migration flows by 0.22%, with all other things remaining constant. Our study, therefore, links shared ancestry with economic behavior, showing how historical connections are associated with current economic exchanges among nations. Additionally, recognizing that ancestral ties are outside human control, we examine policy measures that help nations overcome such distance barriers. Our findings show that strengthening a nation's institutional quality and adherence to the rule of law can effectively mitigate any negative correlation of distance constructs with economic exchanges. These insights suggest that prudent policies to foster a stable business environment are essential for any nation to attract FDI and human capital, even from geographically or genetically distant nations. • We analyze the correlation between genetic distance, FDI, and migration. • Genetic distance is factored into an augmented gravity model through shared ancestry. • Genetic distance is negatively correlated with cross-border investment and migration. • Enhancing the rule of law and institutional quality reduces the negative correlation. [ABSTRACT FROM AUTHOR]

• This study represents a rare investigation into the regional prevalence of HIV-2 viral strains in East Asia. • Phylogenetic analysis and molecular transmission network analysis were conducted to elucidate molecular characteristics and transmission patterns. • Hunan Province, China identified over a dozen cases of HIV-2 virus between 2017 and 2022. • A significant finding from the molecular transmission network analysis is the prominent role of commercial sex work within specific clusters. • These cases originated from local transmission, primarily via commercial sex, implying a potential local prevalence. To elucidate the epidemiological features of HIV-2 in Hunan Province, China, utilizing sequence analysis. Thirteen individuals diagnosed with HIV-2 infection in Hunan Province, China, from 2017 to 2023 were included in this study. Amplification of HIV-2 env and pol regions was conducted, followed by Sanger sequencing. Phylogenetic and molecular transmission network analyses were performed to delineate molecular features and transmission dynamics. All 14 individuals contracted HIV-2 through heterosexual intercourse, comprising 7 males and 7 females, with a median age of 58 years. Among them, three couples (HN001 and HN013, HN010 and HN011, HN008 and HN009) were identified, along with commercial sexual activity engagement reported for subject HN004. Notably, subjects HN001, HN003, HN008, and HN010 engaged in commercial sexual activities at the same location as subject HN004. Phylogenetic analysis of the pol gene revealed close proximity of sequences from all subjects to reference sequences from Gambia (Sub-type A). Employing a genetic distance threshold of 1.5 %, eight out of the 14 subjects formed a molecular transmission network, with HN002 and HN004 identified as central nodes. From 2017 to 2023, all HIV-2-infected individuals in Hunan Province, China, acquired the virus through identifiable routes, indicating transmission of similar HIV-2 strains among them. [ABSTRACT FROM AUTHOR]

Microhaplotypes (MHs) were first recommended by Prof. Kidd for use in forensics because they can improve human identification, kinship analysis, mixture deconvolution, and ancestry prediction. Since their introduction, extensive research has demonstrated the advantages of MHs in forensic applications and provided useful data for different populations. Currently, two databases, ALFRED (ALlele FREquency Database) and MicroHapDB (MicroHaplotype DataBase), house the published MH information and population data. We previously constructed a single nucleotide polymorphism SNP-SNP MH database (D-SNPsDB) of MHs within 50 bp on the whole human genome for 26 populations integrating basic data such as physical genome positions, mapping of variant identifiers (rsIDs), allele frequencies, and basic variant information. Building upon the previous research, we further selected MHs containing at least two variants (SNPs and/or insertions/deletions [InDels]) within a short DNA fragment (≤ 50 bp) in 26 populations based on the 1000 Genomes Project dataset (Phase 3) to construct a more comprehensive database. Subsequently, we established a user-friendly website that allows users to search the MH database (MHBase) based on their research objectives and study population to find suitable loci and provides other functions such as querying reported loci, performing online calculations using the PHASE software, and calculating ancestral-related parameters. The loci in the database are classified as SNP-based MHs, which include only SNPs, and InDel-including MHs, which contain at least one InDel. Here, we provide a detailed overview of the MHBase and an analysis of shared loci at the global and continental levels, ancestral markers, the genetic distance within loci, and mapping with the genome annotation file. The website is an accessible and useful tool for researchers engaged in marker discovery, population studies, assay development, and panel design. • A database of MHs (MHBase) with ≥2 SNPs/InDels within 50 bp in 26 populations was constructed. • We explored the forensic application potential of the database. • A website was established to access the MH database (MHBase) according to user interests. [ABSTRACT FROM AUTHOR]

Malaria infections in school-age children further make it difficult to control the disease's spread. Moreover, the genetic diversity of glutamate-rich protein, potentially a candidate for vaccine development, has not yet been investigated in the Democratic Republic of Congo. Therefore, we aimed to assess the genetic diversity of the immunodominant C-terminal repetitive region (R2) of Plasmodium falciparum glutamate-rich protein gene (pfglurp) among school-age children living in Kinshasa, DRC. We conducted nested PCR targeting R2 of pfglurp and the amplicon were directly sequenced. We summarized the prevalence of mutations of bases and amino acids and indicated the amino acid repeat sequence in the R2 region by the unit code. We then statistically analyzed whether there was a relationship between the number of mutations in the pfglurp gene and attributes. In 221 samples, haplotype 1 was the most common (n = 137, 61.99%), with the same sequence as the 3D7 strain. Regarding the number of base mutations, it was higher in urban areas than rural areas (p = 0.0363). When genetic neutrality was tested using data from 171 samples of the single strain, Tajima's D was −1.857 (p = 0.0059). In addition, FST as the genetic distance between all attributes was very small and no significant difference was observed. This study clarified the genetic mutation status and relevant patient attributes among School-age children in the DRC. We found that urban areas are more likely to harbour pfglurp mutations. Future research needs to clarify the reason and mechanism involved. [Display omitted] • DNA samples from school-age children in the DRC were analyzed. • The GLURP R2 repeat region of Plasmodium falciparum was sequenced. • The MOI of GLURP was lower in Kinshasa than in other sub-Saharan regions. • Among 221 samples, 19 haplotypes were found; over half were identical to strain 3D7. • The pfglurp mutation occurred more in urban than rural areas. [ABSTRACT FROM AUTHOR]

Bagaza virus (BAGV) is a mosquito-borne orthoflavivirus known to occur in regions of southern Europe, Africa, India and the Middle East. The virus has been associated with neurological disease and fatalities in various wild bird species. Association with human disease is not confirmed although limited serological evidence has suggested human infection. Surveillance programs for screening mosquitoes for evidence of arbovirus infection play an important role in providing information regarding the circulation and spread of viruses in specific regions. BAGV was detected in a mosquito pool during surveillance of mosquitoes collected in central South Africa between November 2019 and March 2023. Homogenized mosquito pools were screened for flaviviral RNA using conventional RT-PCR and virus isolation was attempted on positive samples. BAGV was detected and subsequently isolated using cell culture. A multiplex tiling PCR method for targeted enrichment using a PCR based or amplicon sequencing approach of the complete genome of BAGV was developed and optimized. Primers were designed using alignment of complete genome sequence data retrieved from GenBank to identify suitable primer sites that would generate overlapping fragments spanning the complete genome. Six forward primers and eight reverse primers were identified that target the complete genome and amplified nine overlapping fragments, that ranged in length from 1954 to 2039 with an overlap ranging from 71 to 711 base pairs. The design strategy included multiple forward and reverse primer pairs for the 5' and 3' ends. Phylogenetic analysis with other isolates was performed and BAGV isolate VBD 74/23/3 was shown to share high similarity with previous BAGV isolates from all regions, with genetic distance ranging from 0.026 to 0.083. VBD 74/23/3 was most closely related to previous isolates from southern Africa, ZRU96/16/2 isolated from a post-mortem sample from a pheasant in 2016 and MP-314-NA-2018 isolated from mosquitoes in northwestern Namibia with genetic distance 0.0085 and 0.016 respectively. Currently there is limited complete genome sequence data available for many of the arboviruses circulating in Africa. The multiplex tiling method provided a simple and cost-effective method for obtaining complete genome sequence. This method can be readily applied to other viruses using sequence data from publicly available databases and would have important application facilitating genomic surveillance of arboviruses in low resource countries. • Detection and isolation of Bagaza virus from a mosquito pool in central South Africa. • Evidence for circulation of Bagaza virus in central South Africa in Aedes mosquitoes. • Complete genome sequencing of Bagaza virus isolated in cell culture using multiplex PCR tiling method for target enrichment. [ABSTRACT FROM AUTHOR]

• Vandaceous orchids are commercially important orchids which fetch a high price both at national and international market. • Difficult to identify species if they are not in flowering stage, fragment/juvenile. • Internal Transcribed Spacer (ITS) of Ribosomal DNA is used for identification, authentication of these orchids. • Could identify almost all the investigated species and mapped their genetic distances among them for phylogenetic studies. Habitat destruction, indiscriminate and rampant collection of Vandaceous orchids for their ornamental and medicinal values have resulted many of the important species pushed to threatened category and to struggle for their survival in nature. Illegal trade of this commercially important group of orchids continues as these orchids are similar in shape, size and difficult to identify and classify, especially when they are not in flowering stage. To address this issue of authentic identification, molecular barcode can be a useful tool for rapid identification even from vegetative tissues which will help in preventing indiscriminate collection of the species. The present study was carried out to test the discriminatory power of Internal Transcribed Spacer (IT1 and IT2) region in barcoding and to ascertain their phylogenetic relationship among these 31 species (80 individuals) from 15 genera of Vandaceous orchids. The sequences were aligned using ClustalW and genetic distances were computed using MEGA 7.0. Data analyses suggest that ITS of nuclear ribosomal DNA is a reliable marker which can be used as an efficient barcode to identify. The species resolution by three methods stood at 95.52% by genetic distance, 79.40% by BLAST analysis and 95.52% by phylogenetic tree building method and also analyze their phylogenetic relationships among Vandaceous orchids of Nagaland. [ABSTRACT FROM AUTHOR]

The study of ABO polymorphism has contributed to the understanding of human genetic diversity. The objective of our work is to determine the phenotypic and allelic frequencies of the ABO system in the population of the Algerian Northeast, and to make a comparative study with other national and world populations. The study included 10,208 blood donors, originating from the Northeast of Algeria, the ABO grouping was carried out by serological techniques on plate and gel card, the comparison of the ABO allelic frequencies, and the genetic distances between the populations, were carried out respectively by using the R software, and the SPSS version 20 software. The order of frequency of ABO phenotypes is O > A > B > AB, with respectively 46.32%, 33.47%, 15.93% and 4.28%, while the order of frequency of ABO alleles is O > A > B with respectively 0.6820, 0.2112, 0.1068. The estimation of the genetic distances between our study population and other national, North African and world populations, allowed us to observe that our study population is very close genetically to North African populations, and the genetic differences were less pronounced with sub-Saharan populations, than with European and Asian populations. Our region has known multiple movements and population mixtures that have contributed to the genetic identity of our population, linked in part to its geographical location at the gateway to Africa, and on the southern shore of the Mediterranean, but also to several historical events such as invasions, trade, and Islamic conquests. [ABSTRACT FROM AUTHOR]

Late in 2021, the Y Chromosome Haplotype Reference Database (YHRD) added the capability to perform discrete Laplace statistical calculations on searches performed against their SWGDAM-compliant U.S. subpopulations. Because discrete Laplace is not a commonly used or reported statistic in the United States, the SWGDAM Lineage Marker Committee, responsible for maintaining the SWGDAM Interpretation Guidelines for Y-Chromosome STR Testing, evaluated the feature to assess its ease of use and applicability to U.S. casework. Discrete Laplace calculates profile probabilities based on their genetic distance from sets of ancestral alleles and can yield much more informative probability estimates than the commonly used Clopper-Pearson 95% upper confidence interval (UCI). This is especially true for rare profiles with no database observations because, unlike the 95% UCI, the discrete Laplace calculation is not based upon how many times a profile is observed in the database. However, the statistic as applied by YHRD also has some limitations, such as a requirement that the query profile is complete for the 'minimal' kit and that expanded loci beyond those included in the Y17 kit cannot be included in the calculation. Here, we explain how discrete Laplace works and demonstrate how the results compare to those generated using the 95% UCI. [ABSTRACT FROM AUTHOR]

Oysters are widespread throughout the intertidal regions, and accurate identification and monitoring of their ecological status are still difficult due to their high level of plasticity. Anthropogenic activities facilitate oyster dispersal to new habitats through the shipping and elimination of existing barriers. In this study, a combination of morphological and molecular techniques was used to clarify the identity of an oyster species occurring along the Iranian coast of the Persian Gulf. Specimens were collected from the jetties of the ports and the rocky shores along the northern Persian Gulf. Oyster identification was carried out to the lowest possible taxonomic level based on shell morphology. The phylogenetic analysis was done using the cytochrome c oxidase subunit 1 (COI) fragments. Morphological results confirmed that studied samples belong to the genus Crassostrea and showed close to the Vietnamese (Crassostrea markushuberi) species. Molecular analysis reveals that species are a sister species to a clade containing Crassostrea zhanjiangensis and Crassostrea talonata. According to the relatively high genetic distances and lack of similarity in shell characteristics, the species is considered as distant sister species of C. zhanjiangensis and C. talonata. The results showed a non-native small size of oyster in the northern Persian Gulf, which might be a new species. The relative abundance of this species in the introduced location (Imam Khomeini port) may be linked to the high adaptation capability to the new environment. [ABSTRACT FROM AUTHOR]

A fundamental characteristic of animal multicellularity is the spatial coexistence of functionally specialized cell types that are all encoded by a single genome sequence. Cell type transcriptional programs are deployed and maintained by regulatory mechanisms that control the asymmetric, differential access to genomic information in each cell. This genome regulation ultimately results in specific cellular phenotypes. However, the emergence, diversity, and evolutionary dynamics of animal cell types remain almost completely unexplored beyond a few species. Single-cell genomics is emerging as a powerful tool to build comprehensive catalogs of cell types and their associated gene regulatory programs in non-traditional model species. We review the current state of sampling efforts across the animal tree of life and challenges ahead for the comparative study of cell type programs. We also discuss how the phylogenetic integration of cell atlases can lead to the development of models of cell type evolution and a phylogenetic taxonomy of cells. Cell types are the basic functional units of multicellular organisms. So far, cell taxonomies remain Linnaean. Single-cell transcriptomic methods enable the systematic characterization of cell diversity in understudied animal lineages. These data-driven cell catalogs should allow us to organize cell diversity into evolutionary classification schemes. Single-cell sampling bias and other technical limitations can severely constrain our ability to integrate cell atlases across species. It is important to advance towards general sampling strategies and data standards. Comparative analysis of cell type atlases uncovers transcriptional similarities across species, but are confounded by pleiotropy and non-independence of gene expression patterns, particularly at large phylogenetic distances. The interrogation of cell type regulatory programs in closely related species should enable the development of quantitative models of cell type evolution and to assess the (potentially incongruent) evolutionary histories of the different components of these programs. [ABSTRACT FROM AUTHOR]

The wingless-type MMTV integration site family member-4 (Wnt4), a member of the wingless-related integration site (Wnt) family, is widely accepted as a key regulator of ovarian development in mammals. In this study, a full-length cDNA of Wnt4 (designated as Sp-Wnt4) was cloned, characterized, and functionally studied in mud crab (Scylla paramamosain). The full-length cDNA of Sp-Wnt4 consists of 2659 bp with an open reading frame (ORF) encoding 359 amino acids, a 907 bp 5′-UTR and a 672 bp 3′-UTR. Sp-Wnt4 contains 25 cysteine (Cys) residues and three potential N -glycosylation sites. Sp-Wnt4 protein shared the highest identity (98.9%) to the Wnt4 protein of Portunus trituberculatus. The phylogenetic tree showed that Sp-Wnt4 and Wnt4 protein of Malacostracan crustaceans clustered together, indicating that they had a close genetic distance. Sp-Wnt4 was expressed at a higher level in the ovary compared to other tissues, with the highest expression level at the third stage (O-III) of the ovarian development (P < 0.05). A downward trend was observed in the expression level of Sp-Wnt4 from the embryo stage to crablet stages (P < 0.05). After unilateral eyestalk ablation, the expression level of Sp-Wnt4 significantly increased in testis (14-fold) and downregulated (3.1-fold) in the gill (P < 0.05) of females. In situ hybridization (ISH) assay revealed that Sp-Wnt4 transcripts were mainly localized in the cytoplasm of oocyte cells. These findings showed that Sp-Wnt4 play crucial roles in the ovarian development of S. paramamosain. In conclusion, our study provides novel insights into the evolution and roles of the Wnt4 gene. [ABSTRACT FROM AUTHOR]

• 17 SCAR markers linked to double flower trait of petunia hybrida was developed. • A high-density genetic map was constructed with 4474 SNP markers. • The double flower genes in petunia were first mapped to a genomic region of 1.82 Mb. Double flower (DF) is one of the important ornamental traits of horticultural plants, but the molecular mechanism of its formation is still unclear. In this study, forward genetic approaches were applied to explore the key genes involved in the DF formation in petunia. We developed a total of 17 SCAR markers linked to DF, and initially mapped the DF genes onto 9 scaffolds (totally 13.3 Mb) in the genome of the DF petunia. We also constructed a genetic linkage map of petunia, which contained 4474 SNP markers, with a total genetic distance of 2022.786 cM and an average genetic distance of 0.758 cM. In QTL analysis, a QTL associated with DF trait was detected. The LOD value of the marker was 3.82–12.71, and the contribution rate was 16.0 %–44.0 %. To further shorten the mapping interval of the DF genes, we constructed a near-isogenic line (NIL) population containing 2757 plants, and used these 17 SCAR markers to screen the recombinant plants, and located the DF genes within a 2.2 Mb interval. Combined with Bacterial Artificial Chromosome (BAC) library screening, the mapping interval of the DF genes was ultimately shortened from 2.2 Mb to 1.82 Mb. Presently, research on the DF trait of petunia mainly focused on the ABC(D)E model. The fine mapping results of petunia DF genes obtained in this study provide a new idea for revealing the molecular mechanism of DF formation in petunia. [ABSTRACT FROM AUTHOR]

• We tested adenovirus and herpesvirus in iguanas of the Galapagos archipelago. • First herpesviral detected in endangered Galapagos land pink iguana. • Novel species of herpesvirus, tentatively named iguanid alphaherpesvirus 4. • No adenovirus was detected in the tested iguanas. Virus surveillance in wildlife is important to understand ing ecosystem health, taxonomy, and evolution. Nevertheless, viruses in reptiles, and specifically in squamates, continue to be understudied. Herein, we conducted a health assessment on the critically endangered Galapagos pink land iguana (Conolophus marthae) and the vulnerable Galapagos land iguana (Conolophus subcristatus). We collected oral and/or cloacal swabs from 47 clinically healthy iguanas and tested for adenovirus (cloacal swabs, n = 47) and herpesvirus (oral swabs, n = 45) using broad-spectrum PCRs. Two out of 38 (5.3 %) Galapagos pink land iguanas tested positive for herpesvirus, while no herpesvirus was detected in all Galapagos land iguanas (n = 7). Both herpesviral sequences were identical between them and divergent (61.9 % amino acid identity) when compared to the closest herpesvirus sequences available in GenBank/EMBL/DDBJ. The genetic distance between this and other herpesviruses is consistent with its classification as a novel virus species. All iguanas were negative for adenovirus. This is the first description of a herpesvirus in iguanas of the Galapagos islands, and the first report of a potential pathogen for the iconic Galapagos pink land iguana. Further research is needed to understand the implications of this virus in the conservation and management of one of the most endangered iguana species in the world. [ABSTRACT FROM AUTHOR]

Psalteriomonadidae are a small family of anaerobic free-living protists belonging to Heterolobosea, Discoba. We cultured 74 new strains of mostly amoeboid Psalteriomonadidae obtained from mainly freshwater habitats and sequenced their 18S rRNA gene. Based on the phylogenetic analysis and genetic distances, we report multiple novel species, four of which we formally describe based on the light-microscopic morphology (Psalteriomonas minuta , P. australis , P. fimbriata , and P. parva). We also examined the ultrastructure of two Psalteriomonas species using transmission electron microscopy. We transfer Sawyeria marylandensis into the genus Psalteriomonas and synonymize Sawyeria with Psalteriomonas. In addition, we studied the flagellate stage of P. marylandensis comb. nov. for the first time, using light and scanning electron microscopy. [ABSTRACT FROM AUTHOR]

• Reported a complete mtDNA genome, three D-loop sequences of IWB in NCBI GenBank. • Indian domestic pigs may have evolved from Indian wild pig matrilineal components. • Indian wild pig was most closely related to Doom and its crossbred HDK75 pig. • Indian Wild Boar showing independent cluster from other wild pig of world. • Unique duplication and insertion events can serve as signature sequence for IWB. Mitochondrial DNA (mtDNA) serves as a valuable molecular marker for constructing matrilineal genealogies and tracing the evolutionary history of animals. This study aimed to characterize the complete mitochondrial genome of the Indian wild pig (IWB) (Sus scrofa cristatus) and identify IWB-specific DNA sequences that could be used as genomic signatures to differentiate IWB from domestic Indian pigs (IDP) in forensic cases. For the purpose, three wild IWB from a rescue centre were used for the characterization of the mitochondrial genome of the IWB. The mitochondrial genome was sequenced by the primer walking technique using 30 overlapping primers. The mitochondrial genome of the IWB was found to be 16,689 bp long containing 37 genes coding for 2 rRNAs, 22 tRNAs, 13 protein coding genes, and 1 D-loop region similar to the mitogenome of other pigs. Sequence analysis of the D-loop of IWB with other IDP indicated some signature sequence for IWB like duplication and transition event from 1090th to 1099th position, deletion of a 10 bp sequence at the 755th position, insertion of (CA) at the 137th position, and substitution of AT to GA at the 638th position. These variations specially the duplication along with transition event causes creation of unique signature sequence (-ACACAAACCT-) in the IWB that could serve as signature sequences for the IWB and be used as markers for differentiation of IWB from IDP breeds in academic as well as forensic or vetero-legal cases. Overall, a total of 36 polymorphic positions were identified in the IWB, with 29 sites being unique to the IWB only and seven being common to the Doom and HDK75 pig breeds. None of the common polymorphic sites were identified in prevailing domestic pig populations. Phylogenetic analysis of the mitochondrial genome revealed the distinct separation of the IWB from IDP. The results of genetic distance evaluation showed that the Doom pig breed was the closest to the IWB. This study provides valuable insights into the mitogenome characterisation, signature sequence and genetic distance analysis of the IWB and establishes a foundation for future studies on the conservation of this protected species. [ABSTRACT FROM AUTHOR]

Azeri people are at present day mainly living in an area which comprises North (Azerbaijan) and South (Azeri Iran provinces) parts, living the biggest population in Azeri Iran provinces with about 17–20 million people. They were studied HLA-A, -B, -DRB1 and -DQB1 allele and extended haplotype frequencies in unrelated Iranian Tabriz Azeris from a rural area close to Tabriz City. The HLA extended haplotypes with highest frequencies are: 1) HLA- A*24:02-B*35:01-DRB1*11:01-DQB1*03:01, shared with Mediterraneans and southern Russians (Chuvash, which also show Mediterranean characters); and 2) HLA-A*01:02-B*08:01-DRB1*03:01-DQB1*02:01, found also in Chuvash and other Azeri samples from Tabriz. Neí's DA HLA-DRB1 genetic distances, HLA-DRB1 Neighbour-Joining dendrogram and Vista analyses show that population with closest distance is Kurdish, followed by Iranian Gorgan and Southern Russia/ North Caucasus Chuvash; probably these latter groups and Azeris were populating North Mesopotamia/ Caucasus Mts. since prehistoric times. Kurds (in Iraq and Iran) do not speak Turk while Azeris do: they are both genetically close, but they are not genetically close to present day Anatolia (Turkey) Turks who also speak Turk language and show a typical Mediterranean HLA profile. In summary, Azeri population studies show examples that genes and languages do not correlate, contradicting the postulate asserted by others. [ABSTRACT FROM AUTHOR]

On the basis of distinct lines of evidence, detailed reconstructions of the Holocene population history of the Sabana de Bogotá (SB) region, Northern South America, have been performed. Currently, there exist two competing models that support temporal continuity or, alternatively, divergence. Despite recent bioarchaeological and isotopic research that lends support to the population discontinuity model, several discrepancies remain, calling for other kinds of evidences to be explored for a more detailed picture of Holocene biocultural evolution. In this study, 15 new complete mitochondrial genomes obtained from 30 individuals recovered from several archaeological sites spanning from the late Pleistocene (11,950–11,262 cal BP) until the initial late Holocene (2941–2752 cal BP) along with published data (n = 20) from the region dating ~9000–540 cal BP were used to investigate diachronic genetic change. Genetic diversity and distance indices were calculated, and demographic models tested in an approximate Bayesian computation (ABC) framework to evaluate whether patterns of genetic affinities of the SB prehispanic populations support genetic continuity or discontinuity. The results show that mitochondrial genomes of the complete dataset fall within the Native American haplogroups A2, B2, C1b, D1 and D4h3a. Haplotype and nucleotide diversity declined over time with further evidence of genetic drift and remarkable reduction of genetic diversity during the final late Holocene. Inter-population distances and the exact test of population differentiation, as well as demographic simulations show no population differentiation and population continuity over time. Consequently, based on the analyzed data, we cannot reject the genetic continuity in the SB region as a plausible population history scenario. However, the restriction of the analyses to the Hyper Variable Region 1 of the mitochondrial genome, and the very low sample size both constitute significant limitations to infer evolutionary history. [ABSTRACT FROM AUTHOR]

In the present study, eleven novel complete mitogenomes of Boletus were assembled and compared. The eleven complete mitogenomes were all composed of circular DNA molecules, with sizes ranging from 32,883 bp to 48,298 bp. The mitochondrial gene arrangement of Boletus varied greatly from other Boletales mitogenomes, and gene position reversal were observed frequently in the evolution of Boletus. Across the 15 core protein-coding genes (PCGs) tested, atp9 had the least and rps3 had the largest genetic distances among the eleven Boletus species, indicating varied evolution rates of core PCGs. In addition, the Ka / Ks value for nad3 gene was >1, suggesting that this gene was subject to possible positive selection pressure. Comparative mitogenomic analysis indicated that the intronic region was significantly correlated with the size of mitogenomes in Boletales. Two large-scale intron loss events were detected in the evolution of Boletus. Phylogenetic analyses based on a combined mitochondrial gene dataset yielded a well-supported (BPP ≥ 0.99; BS =100) phylogenetic tree for 72 Agaricomycetes , and the Boletus species had a close relationship with Paxillus. This study served as the first report on complete mitogenomes in Boletus , which will further promote investigations of the genetics, evolution and phylogeny of the Boletus genus. [ABSTRACT FROM AUTHOR]

• The Mycobacterium tuberculosis L4.3/Latin American and Mediterranean (LAM) sublineage is the most prevalent in Tunisia. • The success of L4.3/LAM is mainly driven by a single clonal complex: TUN4.3_CC1 (61.5%). • Unlike the much less prevalent TUN4.3_CC2 (14.68%), TUN4.3_CC1 lacks the RD115 deletion. • Genotypic and genomic data reveal that TUN4.3_CC1 is long established in Tunisia. • Compelling evidence suggests that TUN4.3_CC1 has evolved locally. To explore the evolutionary history of Mycobacterium tuberculosis Latin American and Mediterranean (L4.3/LAM) sublineage in Tunisia, where it predominates. High-resolution genotyping of 252 L4.3/LAM clinical strains was undertaken, and whole-genome sequencing was performed on 31 representative isolates. Genotyping data coupled with Bayesian analyses split the Tunisian L4.3/LAM strain collection into two divergent entities (65.07% vs 34.92%): a major subpopulation, dominated by a single clonal complex (CC), TUN4.3_CC1 (94.51%); and a minor subpopulation, dominated by TUN4.3_CC2 (42.04%). TUN4.3_CC1 is clearly thriving in Tunisia, accounting for 61.5% of the L4.3/LAM sublineage. TUN4.3_CC1 displayed higher mean allelic richness compared with TUN4.3_CC2 and predominated throughout the entire region, indicating a long-established history. The very low proportion of drug resistance among TUN4.3_CC1 isolates is indicative of their intrinsic ability to spread successfully in the host population. Genomic analyses further confirmed the clear genetic separation between the two main CCs (pairwise fixation index 0.56), and suggested the relatively ancient origin of TUN4.3_CC1. Consistent with its successful expansion, TUN4.3_CC1 showed reduced mean pairwise genetic distance between genomes. These findings link the successful expansion of L4.3/LAM in Tunisia to a single long-established clone. [ABSTRACT FROM AUTHOR]

The existence of genetic diversity in Crocus sativus has globally remained a mystery till date. The study investigated PCR based DNA amplification profile of saffron using ISSR and RAPD based primers. A total of 38 amplicons were generated by ISSR primers in the range from 7 to 12 with an average of 9.50 bands per primer. 20 bands were found to be polymorphic and 18 were monomorphic with an average percentage of polymorphism as 52.48%. RAPD based amplification revealed a total 161 amplicons, 107 as polymorphic and 54 as monomorphic with an average percentage of polymorphism as 66.44%. Cumulative results of RAPD and ISSR demonstrated that Nei-Li's similarity index ranged between 0.70 and 0.97. The results of AMOVA has revealed 9% of variance among populations and 91% of variance within populations, Φ PT was found as 0.089, which indicates existence of genetic differences though limited. In conclusion, the results indicate that saffron accessions are minimally genetically differentiated, which could be capitalized in future breeding programmes to ameliorate this precious crop. [ABSTRACT FROM AUTHOR]

The striking difference in severity of SARS CoV2 infection among global population is partly attributed to viral factors. With the spike (S) and nucleocapsid (N) are the most immunogenic subunits, genetic diversity and antigenicity of S and N are key players in virulence and in vaccine development. This paper aims at identifying immunogenic targets for better vaccine development and/or immunotherapy of COVID 19 pandemic. 18 complete genomes of SARS CoV2 (n = 14), SARS CoV (n = 2) and MERS CoV (n = 2) were examined. Bioinformatics of viral genetics and protein folding allowed functional tuning of NH2 Terminal Domain (NTD) of S protein and development of epitope maps for B and T cell responses. A deletion of amino acid residues Y144 and G107 were discovered in NTD of S protein derived from Indian and French isolates resulting in altered pocket structure exclusively located in NTD and reduced affinity of NTD binding to endogenous nAbs and disrupted NTD mediated cell entry. We therefore, proposed a set of B and T cell epitopes based on Immune Epitope Database, homologous epitopes for nAbs in convalescent plasma post SARS CoV infection and functional domains of S (NTD, Receptor Binding domain and the unique polybasic Furin cleavage site at S1/S2 junction). Nevertheless, laboratory data are required to develop vaccine and immunotherapeutics. [ABSTRACT FROM AUTHOR]

• A novel Trim23 gene (MnTrim23) was identified from M. nipponense , which belongs to C-IX family. • MnTrim23 promotes the replication of WSSV and the expression of VP28. • MnTrim23 negatively regulates Relish mediated AMPs expression. • AMPs inhibits the VP28 expression and WSSV replication. The family of TRIM proteins with E3 ubiquitin ligase activity plays important roles in virus infection in vertebrates and invertebrates. In this study, a novel Trim gene shows high similarity to Trim23 (designated as MnTrim23) was identified from Macrobrachium nipponense. The MnTrim23 protein contains three conserved domains (one RING finger domain, two B-box, and one Coiled-coil region) at its N-terminal and one ARF domain at its C-terminal. The ARF domain characterizes the members of the Trim23 family. MnTrim23 belongs to C-IX family. Phylogenetic analysis shows that MnTrim23 has a closer genetic distance with other Trim23 proteins from invertebrates than that from vertebrates. MnTrim23 has higher expression level in the intestine and hepatopancreas than in the other immune tissues. The expression levels of MnTrim23 in the gills, stomach, and intestines are significantly up-regulated after white spot syndrome virus (WSSV) infection. Moreover, knockdown of MnTrim23 inhibits WSSV replication and VP28 expression, suggesting that MnTrim23 plays a positive role in WSSV infection. Further studies revealed that MnTrim23 negatively regulates the Relish transcription factor-mediated expression of antimicrobial peptides (AMPs). Synthetic AMPs inhibit VP28 expression and WSSV replication. These findings indicate that Trim23 promotes WSSV replication by inhibiting the expression of AMPs that are positively regulated by the host NF-κB signal pathway. [ABSTRACT FROM AUTHOR]

We surveyed root endophytic fungi of the coastal halophyte Suaeda salsa and detected a population of a novel species that we described here as Laburnicola rhizohalophila sp. nov. No sexual sporulating structure was observed. Instead, it produced a large amount of thalloconidia, 0–1 transverse septa, hyaline to darkly pigmented, often peanut-shaped and sometimes dumbbell-shaped, both ends enlarged with numerous oil droplets inside the hyphal cells. Surprisingly, a high degree of phenotypic and physiological intraspecific variation (e.g., salinity tolerance, growth under different carbon:nitrogen ratios, and carbon utilization pattern) was recorded. The inoculation test indicated that the isolates could successfully infect host roots and form microsclerotia-like structures in cortical cells, a typical trait of dark septate endophytes (DSEs). Furthermore, most isolates were shown to promote host seedling growth. To evaluate conspecificity and infer its phylogenetic affinity, multiloci data including nuclear rRNA loci (ITS1 and 2, partial 28S), partial RNA Polymerase II second-largest subunit (rpb2), and partial translation elongation factor-1α (tef1) were characterized. Genealogical concordance phylogenetic species recognition (GCPSR) detected a genetically isolated clade of L. rhizohalophila within the Pleosporales in the Didymosphaeriaceae. Maximum likelihood phylogenetic reconstruction revealed that the endophytic fungus was genetically close to L aburnicola dactylidis but separated by a relatively long genetic distance. Our work highlights that the pleosporalean taxa might represent an underexplored reservoir of root DSEs. • Laburnicola rhizohalophila sp. nov. is a novel root dark septate endophyte (DSE). • This new fungus shows a high degree of intraspecific variations. • Pleosporalean taxa might represent an underexplored reservoir of root DSEs. [ABSTRACT FROM AUTHOR]

The genus Phylloscopus belongs to the order Passeriformes and subfamily Phylloscopinae within the family Sylviidae. Phylloscopus , a small insectivore widely distributed in the old world, includes 66 species and 112 subspecies. We identified five new Phylloscopus mitogenomes: P. tenellipes (16,904 base pairs (bp), MK390475), P. coronatus (16,905 bp, MK533705), P. borealis (16,881 bp, MK390476), P. schwarzi (16,920 bp, MK411584), and P. borealoides (16,904 bp, MN125373). All contained 37 genes, including 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and two control regions. Seven Phylloscopus species were compared to the five new mitogenomes and the published complete P. inornatus and P. proregulus mitochondrial sequences. The genetic distance of 13 single protein-coding genes exhibited low variation within all seven Phylloscopus mitogenomes. Based on the Ka/Ks ratios, the molecular evolution patterns of single protein-coding genes were relatively consistent among Phylloscopus bird species. Phylogenetic analysis verified that subspecies of the Pale-legged Leaf Warbler P. tenellipes borealoides could be promoted to the Sakhalin Leaf Warbler P. borealoides. Gene order and genome organization information is useful to understand evolutionary relationships among Phylloscopus species. The complete mitogenomes of these five Phylloscopus species provide genetic markers for species identification, population genetics, and phylogeographic studies of birds. Unlabelled Image • Complete mitogenomes of five Phylloscopus form a typical circular molecule. • P. tenellipes , P. coronatus , P. borealis , P. schwarzi , P. borealoides were studied. • Subspecies of P. tenellipes borealoides can be promoted to P. borealoides. • Molecular evolution of single PCGs is relatively consistent among seven birds. • Gene order and genome organization help understand evolutionary relationships. [ABSTRACT FROM AUTHOR]

Species identification technology (i.e. DNA barcoding) has been recognized as an important and reliable tools, although the effectiveness of using a single universal barcode marker for plants is still questionable. The present study reports a molecular identification method to discriminate 11 plant species within genus Piper that extensively utilized in traditional healing practices in Malaysia. The plants were sampled from six locations that represents three states in northern Peninsular of Malaysia, namely Perlis, Kedah and Penang. Species discrimination was conducted using BLASTn analysis and phylogenetic inference based on Maximum Likelihood and Neighbour-Joining method for two target genes, rbcL and rpoC1. The reliability of phylogenetic tree regenerations was assessed using Disparity Index analysis. Estimation of evolutionary divergence between all samples was employed based on Maximum Composite Likelihood with Kimura 2-parameter model. The present study revealed that the DNA identification method has successfully discriminated all samples to species level and that the rbcL is the reliable marker for identification. The outcome of the present study gives a significant information on the DNA barcoding of plants within genus Piper. [ABSTRACT FROM AUTHOR]

Drought leads to serious yield losses and followed by increasing food prices. Thereby, drought tolerance is one of most important, pivotal issues for plant breeding and is determined by the very complex genetic architecture, which involves a lot of genes engaged in many cell processes. Within genomes of currently cultivated sugar beet forms, the number of favourable allelic variants is limited. However, there is a potential to identify genes related to drought tolerance deposited in genomes of wild or fodder relatives. Therefore, the goal of our study, was to identify the source of allelic variants involved in drought tolerance using a large spectrum of sugar or fodder beets and their wild relatives for analyses. Based on the drought tolerance index, calculated for morphophysiological traits, it was demonstrated that some of selected fodder beets showed the highest level of drought tolerance. The most drought tolerant fodder beet genotype did not show differences in the level of expression of genes engaged in osmoprotection and the antioxidative system, between control and drought condition, compared to sugar and wild beets. The genetic distance between selected beet forms was broad and ranged from 18 to 87%, however the most drought tolerant sugar, fodder and wild beets showed high genetic similarity and formed the common clade. Based on obtained results we propose that an adequate broad source of genes related to drought tolerance occurs in fodder beets, the crossing with which is easier, less time-consuming and more cost-effective than with wild forms of beets. • Some of fodder beets showed the higher drought tolerance than wild and sugar beets. • Genes engaged in osmoprotection and the antioxidant system are not involved in the response of fodder beet to drought. • The total genetic distance between Beta accessions was broad and ranged from 18 to 87%. • The most drought tolerant sugar, fodder and wild beets showed high genetic similarity and formed the common clade. • Appropriate source of genes related to drought tolerance for sugar beet might be fodder beet. [ABSTRACT FROM AUTHOR]

• A*02:01 , B * 07:02 , C * 07:02 , DRB1 * 07:01 , and DQB1 * 02:01 were frequent alleles in Tatars. • A * 03:01 ∼ B * 07:02 , A * 24:02 ∼ B * 13:02 , B * 07:02 ∼ DRB1 * 15:01 , B * 07:02 ∼ C * 07:02 were frequent two-locus haplotypes. • Kazakhstani Tatars may be Russian Tatars, who originated from Volga region. Kazakhstan is a transcontinental former Soviet Union republic whose present-day population comprises more than 100 ethnic groups. Insofar as Human Leukocyte Antigen (HLA) genotyping is useful for anthropological studies, data on the HLA profile of Kazakhstani Tatars are lacking. We extend our earlier findings on the unique HLA profile of distinct Kazakhstani populations by examining HLA class I and class II loci in Kazakhstani (Volga) Tatar minority population and its relatedness to those of bordering and worldwide communities. HLA class I and class II genotypes of the Kazakhstan Tatar minority were analyzed by PCR-SSP and were compared to neighboring populations using Neighbor-Joining (NJ) trees and standard genetic distances (SGD) analysis. In total, 132 HLA alleles were identified in a sample of 103 Kazakhstani Tatars, of which HLA-A*02:01 (20.1 %), - B*07:02 (12.1 %), - C*07:02 (12.7 %), - DRB1*07:01 (18.1 %), and -DQB1*02:01 (19.6 %) were the most frequent. The most frequent two-locus haplotypes were B*07:02 ∼ C*07:02 (10.6 %) B*07:02 ∼ DRB1*15:01 (06.1 %), B*07:02 ∼ DQB1*06:02 (07.1 %) , and DRB1*15:01 ∼ DQB1*06:02 (11.6 %). Considering historical data, the close relatedness of Kazakhstani Tatars to European Russians (including Russian Tatars) suggests that Kazakhstani Tatars may be Russian Tatars, who originated from the Volga region, following their massive migrations to central Asia. [ABSTRACT FROM AUTHOR]

Bitterness in citrus fruit extract is caused by changes and transformations in limonoids and the production of limonene, a bitter-tasting substance. Limonene synthase enzyme is responsible for producing limonene. This study examined the effect of low-temperature stress on the expression of the limonene synthase gene in four different citrus species: Miyagawa mandarin (Citrus unshiu), Thomson Navel Orange (Citrus sinensis var. Thomson navel), Ruby Star grapefruit (Citrus paradisi var. Ruby star), and Lisbon lemon (Citrus limon var. Lisbon). These species were grafted on two-year-old sour orange rootstocks. The experiment was carried out as a factorial in the form of a completely random design. Three temperatures were used for the cold treatment (−8, −4, 4 °C). The expression sequence of the Limonene synthase gene was predicted using bioinformatic software such as PLANT Care and PlantPan. The results showed significant variation in the frequency of amino acids in the LS gene. Leucine (11.36) and glutamic acid (7.57) had the highest frequency. The analysis of the Limonene synthase gene promoter revealed different Cis-element regions such as response elements to light, hormones, and abiotic stresses on the promoter of these genes. The gene promoter had many regions related to binding sites of MYB transcription factors, response regions to hormones, cold (Dehydrin with 15 cis-regulatory elements), and drought, emphasizing the role of this gene in abiotic stress response. The gene expression patterns of the Limonene synthase showed that the highest and lowest expression occurred at − 4 °C in Lisbon lemon (−132.28), Ruby Star grapefruit (−70.06), Thomson Navel Orange (−2.88), and Miyagawa Mandarin (−3.88), confirming the role of this gene in abiotic and biotic stress response. [Display omitted] • Impacts of freezing tolerance on the LS gene was studied in Citrus species. • LS gene expression decreased rapidly after exposure to low-temperature stress in Citrus species. • In Silico analysis indicates the state of low temperature stress in Citrus species. • In Silico data unravels the additive pattern regulatory control of gene expression in Citrus species. • The differentially expressed proteins related to promoter analysis were further explored using bioinformatic tools. [ABSTRACT FROM AUTHOR]

Mitochondrial cytochrome c oxidase subunit I (COI) sequences were utilized to infer the population genetic structure of Simulium (Gomphostilbia) atratum De Meijere, an endemic simulid species to Indonesia. Both median-joining haplotype network and maximum-likelihood tree revealed two genetic lineages (A and B) within the species, with an overlap distribution in Lombok, which is situated along Wallace's line. Genetic differentiation and gene flow with varying frequencies (F ST = 0.02–0.967; N m = 0.01–10.58) were observed between populations of S. (G.) atratum , of which population pairs of different lineages showed high genetic differentiation. Notably, the high genetic distance of up to 5.92 % observed within S. (G.) atratum in Lombok was attributed to the existence of two genetically distinct lineages. The co-occurrence of distinct lineages in Lombok indicated that Wallace's line did not act as faunistic border for S. (G.) atratum in the present study. Moreover, both lineages also exhibited unimodal distributions and negative values of neutrality tests, suggesting a pattern of population expansion. The expansion and divergence time estimation suggested that the two lineages of S. (G.) atratum diverged and expanded during the Pleistocene era in Indonesia. [Display omitted] [ABSTRACT FROM AUTHOR]

A feature of the Chinese soft-shelled turtle (Pelodiscus sinensis) is seasonal spermatogenesis; however, the underlying molecular mechanism is not well clarified. Here, we firstly cloned and characterized P. sinensis DKKL1 , and then performed comparative genomic studies, expression analysis, and functional validation. P. sinensis DKKL1 had 2 putative N-glycosylation sites and 16 phosphorylation sites. DKKL1 also had classic transmembrane structures that were extracellularly localized. DKKL1 's genetic distance was close to turtles, followed by amphibians and mammals, but its genetic distance was far from fishes. DKKL1 genes from different species shared distinct genomic characteristics. Meanwhile, they were also relatively conserved among themselves, at least from the perspective of classes. Notably, the transcription factors associated with spermatogenesis were also identified, containing CTCF , EWSR1 , and FOXL2. DKKL1 exhibited sexually dimorphic expression only in adult gonads, which was significantly higher than that in other somatic tissues (P < 0.001), and was barely expressed in embryonic gonads. DKKL1 transcripts showed a strong signal in sperm, while faint signals were detected in other male germ cells. DKKL1 in adult testes progressively increased per month (P < 0.05), displaying a seasonal expression trait. DKKL1 was significantly downregulated in testes cells after the sex hormones (17β-estradiol and 17α-methyltestosterone) and Wnt/β-catenin inhibitor treatment (P < 0.05). Likewise, the Wnt/β-catenin inhibitor treatment dramatically repressed CTCF, EWSR1, and FOXL2 expression. Conversely, they were markedly upregulated after the 17β-estradiol and 17α-methyltestosterone treatment, suggesting that the three transcription factors might bind to different promoter regions, thereby negatively regulating DKKL1 transcription in response to the changes in the estrogen and androgen pathways, and positively controlling DKKL1 transcription in answer to the alterations in the Wnt/β-catenin pathway. Knockdown of DKKL1 significantly reduced the relative expression of HMGB2 and SPATS1 (P < 0.01), suggesting that it may be involved in seasonal spermatogenesis of P. sinensis through a positive regulatory interaction with these two genes. Overall, our findings provide novel insights into the genome evolution and potential functions of seasonal spermatogenesis of P. sinensis DKKL1. • DKKL1 had a relatively conserved function across species, but also underwent functional evolution. • Expression of DKKL1 exhibited testis-biased, age variation, and seasonal variation characteristics. • DKKL1 predominantly was localized in sperm and could be used as a molecular marker for male germ cells in P. sinensis. • CTCF , EWSR1 , and FOXL2 most likely bind to different promoter regions regulating DKKL1 transcription in different pathways. • DKKL1 may be involved in seasonal spermatogenesis of P. sinensis through a positive regulation with HMGB2 and SPATS1. [ABSTRACT FROM AUTHOR]