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The Qinling Mountains in East Asia serve as the geographical boundary between the north and south of China and are also indicative of climatic differences, resulting in rich ecological and species diversity. However, few studies have focused on the responses of plants to geological and climatic changes in the Qinling Mountains and adjacent regions. Therefore, we investigated the evolutionary origins and phylogenetic relationships of three Pedicularis species in there to provide molecular evidence for the origin and evolution of plant species. Ecological niche modeling was used to predict the geographic distributions of three Pedicularis species during the last interglacial period, the last glacial maximum period, and current and future periods, respectively. Furthermore, the distribution patterns of climate fluctuations and the niche dynamics framework were used to assess the equivalence or difference of niches among three Pedicularis species. The results revealed that the divergence of three Pedicularis species took place in the Miocene and Holocene periods, which was significantly associated with the large-scale uplifts of the Qinling Mountains and adjacent regions. In addition, the geographic distributions of three Pedicularis species have undergone a northward migration from the past to the future. The most important environmental variables affecting the geographic distributions of species were the mean diurnal range and annual mean temperature range. The niche divergence analysis suggested that the three Pedicularis species have similar ecological niches. Among them, P. giraldiana showed the highest niche breadth, covering nearly all of the climatic niche spaces of P. dissecta and P. bicolor. In summary, this study provides novel insights into the divergence and origins of three Pedicularis species and their responses to climate and geological changes in the Qinling Mountains and adjacent regions. The findings have also provided new perspectives for the conservation and management of Pedicularis species. [ABSTRACT FROM AUTHOR]

Mitochondrial genomes provide new insights that help elucidating biological features, genetic evolution, and classification of protozoans. Theileria uilenbergi (T. uilenbergi), transmitted by Haemaphysalis qinghaiensis and H. longicornis, is considered as highly pathogenic to sheep and goats in China. This study reports and outlines features of its mitochondrial genome. The T. uilenbergi mitochondrial genome is a linear monomeric molecule of 6.0 kb length, which encodes three protein-coding genes named cytochrome c oxidase I (cox1), cytochrome b (cob), and cytochrome c oxidase III (cox3), as well as six large subunit (LSU) rRNA gene fragments, and ends in terminal inverted repeats (TIRs). The array structure and organization of the mitochondrial genome of T. uilenbergi is identical to that of T. parva. Phylogenetic analysis based on the amino acid sequences of cox1, cob, and cox3 genes suggests that T. uilenbergi is distantly related to the group of transforming Theileria species such as T. parva. This study contributes to a comprehensive understanding of the phylogeny and evolution of the mitochondrial genome of piroplasms and provides useful information of diagnostic marker for T. uilenbergi. [ABSTRACT FROM AUTHOR]

The genus Shewanella comprises a group of marine-dwelling species with worldwide distribution. Several species are regarded as causative agents of food spoilage and opportunistic pathogens of human diseases. In this study, a standard multilocus sequence analysis (MLSA) based on six protein-coding genes (gyrA, gyrB, infB, recN, rpoA and topA) was established as a rapid and accurate identification tool in fifty-nine type Shewanella strains. This method yielded sufficient resolving power in regard to enough informative sites, adequate sequence divergences and distinct interspecies branches. The stability of phylogenetic topology was supported by high bootstrap values and concordance with different methods. The reliability of the MLSA scheme was further validated by identical phylogenies and high correlations of genomes. The MLSA approach provided a robust system to exhibit evolutionary relationships in the Shewanella genus. The split network tree proposed twelve distinct monophyletic clades with identical G+C contents and high genetic similarities. Eighty-six tested strains were investigated to explore the population biology of the Shewanella genus in China. The most prevalent Shewanella species were Shewanella algae, Shewanella xiamenensis, Shewanella chilikensis, Shewanella indica, Shewanella seohaensis and Shewanella carassii. The strains frequently isolated from clinical and food samples highlighted the importance of increasing the surveillance of Shewanella species. Combined with the genetic, genomic and phenotypic analyses, Shewanella upenei should be considered a synonym of S. algae, and Shewanella pacifica should be reclassified as a synonym of Shewanella japonica. IMPORTANCE The MLSA scheme based on six housekeeping genes (HKGs) (gyrA, gyrB, infB, recN, rpoA and topA) is well established as a reliable tool for taxonomic, evolutionary and population diversity analyses of the genus Shewanella in this study. The standard MLSA method allows researchers to make rapid, economical and precise identification of Shewanella strains. The robust phylogenetic network of MLSA provides profound insight into the evolutionary structure of the genus Shewanella. The population genetics of Shewanella species determined by the MLSA approach plays a pivotal role in clinical diagnosis and routine monitoring. Further studies on remaining species and genomic analysis will enhance a more comprehensive understanding of the microbial systematics, phylogenetic relationships and ecological status of the genus Shewanella. [ABSTRACT FROM AUTHOR]

To evaluate the applicability of 23 autosomal STR loci (D10S1248, D11S4463, D12ATA63, D14S1434, D17S1301, D18S853, D1GATA113, D1S1627, D6S1017, D20S1082, D20S482, D17S974, D22S1045, D1S1677, D2S1776, D2S441, D3S4529, D4S2408, D9S1122D5S2500, D6S474, D18S51, D9S2157) included in DNA Typer™ 25 Kit for individual identification and parentage testing, allele frequencies and forensic efficiency parameters were first obtained from healthy, unrelated 506 Chongqing Tujia individuals. A total of 1012 alleles were identified in 23 STR loci, and allele frequencies ranged from 0.001 to 0.5761. The combined power of discrimination (CPD) and the combined power of exclusion (CPE) of the 23 STR loci were 0.999999999999999999999753 and 0.99999967, respectively. These results suggested that 23 autosomal STR loci could be used as an effective tool for forensic application in Chongqing Tujia population. Comprehensive comparisons were conducted based on the analysis of genetic distance, principal component analysis (PCA), multidimensional scaling plot (MDS), and phylogenetic tree to explore the interpopulation genetic relationship. Our results revealed that Chongqing Tujia keeps the more relatively genetic similarity with Hunan Han, Hubei Tujia, and Sichuan Han, which could be interpreted by that those populations were originated from the same ethnic ancestor or genetic communication were happened in adjacent areas. [ABSTRACT FROM AUTHOR]

Contradiction between growing plantation economic demand and agro-ecological degradation has always restricted sustainable development of agricultural countries. This study applied the unit inventory analysis to evaluate the productions and discharges of farmland non-point source (FNPS) nitrogen (TN) and phosphorus (TP) among China's nine national-level agricultural districts over 1999–2019. On this basis, we quantified the evolutionary relationship between plantation economic output and FNPS pollution based on optimal regression fitting. The results showed that over 1999–2019, farmland cumulative TN and TP discharges for the whole China were approximately 15807 × 104 t and 1312 × 104 t, with prominent district heterogeneity. According to FNPS discharge magnitudes, China's agricultural districts can be classified into three categories: high, moderate and slight discharge zones. Huang-Huai-Hai Plain and Middle-lower Yangtze Plain were identified as the main severely-polluted districts. Mineral fertilizer is the primary contributor to FNPS pollution. Annual FNPS load showed a trend of increasing followed by decreasing, and the peak interval was recorded in 2014–2016. Spatiotemporal dynamics in FNPS discharge intensities were disparate from that in discharge magnitudes. SC has the highest TN discharge intensity, with an annual average intensity of 0.068 t/ha, followed by MLYP (0.044 t/ha) and HHHP (0.041 t/ha). HHHP has the highest TP discharge intensity, with an annual average intensity of 0.0051 t/ha, followed by SC (0.0038 t/ha) and MLYP (0.0031 t/ha). District-based agro-ecological restoration strategies were accordingly proposed considering FNPS discharge magnitude and intensity concurrently. In most agricultural districts, with the growing economic output in plantation, the FNPS load showed an increase followed by a decrease or to leveling off. Furthermore, with the increasing TN/TP economic partial productivity, the FNPS TN/TP discharge intensities reached the climax, then declined or tended to be flattening out. [Display omitted] • Farmland FNPS nutrient pollution in China was inspected. • China's annual FNPS loads showed a trend of increasing followed by decreasing. • District-based agro-ecological restoration strategies were proposed considering three scenarios. • Evolutionary relation between FNPS pollution and economic development was explored. • Correlation between FNPS discharge intensity and fertilizer partial productivity was examined. [ABSTRACT FROM AUTHOR]

The knowledge of origin and evolution of cultivated soybeans is one of the basic issues in both biology and agronomy of the crop. In order to investigate the nuclear and cytoplasmic genetic diversity, geographic differentiation and genetic relationship among geographic ecotypes of cultivated (Glycine max) and wild (G. soja) soybeans, the allelic profiles at 60 nuclear simple-sequence repeat (nuSSR) loci and 11 chloroplastic SSR (cpSSR) loci evenly distributed on whole genome of 393 landraces and 196 wild accessions from nation-wide growing areas in China were analyzed. (i) The genetic diversity of the wild soybean was obviously larger than that of the cultivated soybean, with their nuSSR and cpSSR alleles as 1067 vs. 980 and 57 vs 44, respectively. Of the 980 nuclear alleles detected in the cultivated soybean, 377 new ones (38.5%) emerged, while of the 44 chloroplastic alleles in the cultivated soybean, seven new ones (15.9%) emerged after domestication. (ii) Among the cultivated geographic ecotypes, those from southern China, including South-Central China, Southwest China and South China possessed relatively great genetic diversity than those from northern China, while among the wild geographic ecotypes, the Middle and Lower Changjiang Valleys wild ecotype showed the highest genetic diversity. (iii) The analysis of molecular variance, association analysis between geographic grouping and molecular marker clustering and analysis of specific-present alleles of ecotypes demonstrated that the geographic differentiation of both cultivated and wild soybeans associated with their genetic differentiation, or in other words, had their relevant genetic bases. (iv) The cluster analysis of all accessions clearly showed that the wild accessions from Middle and Lower Changjiang Valleys and South-Central & Southwest China had relatively small genetic distances with all cultivated accessions. The UPGMA dendrogram among geographic ecotypes further showed that the genetic distances between all cultivated ecotypes and the Middle and Lower Changjiang Valleys wild ecotype were smaller than those with other wild ones, including their local wild counterparts. Therefore, it is inferred that the wild ancestors in southern China, especially those from Middle and Lower Changjiang Valleys might be the common ancestor of all the cultivated soybeans. [ABSTRACT FROM AUTHOR]

Eucommia ulmoides is an important traditional medicinal plant and as a common herb for orthopedic treatment in China. In this study, we reported and analyzed the complete chloroplast genome of E. ulmoides. The chloroplast genome length of E. ulmoides was 163,586 bp in size that has the typical quadripartite structure. It contained a large single-copy (LSC) region of 86,773 bp, a small single-copy (SSC) region of 14,167 bp and separated by two inverted repeat (IRa and IRb) regions of 31,323 bp. The overall GC content of the circular genome was 38.4% while A of 30.8% (50,496 bp), T of 30.8% (50,414 bp), C of 19.2% (31,341 bp), G of 19.2% (31,335 bp). In the chloroplast genome, 135 genes had been found, which included 89 protein-coding (PC) genes, 38 transfer RNA (tRNA) genes and 8 ribosomal RNA (rRNA) genes. Phylogenetic relationship analysis shown that Eucommia ulmoides was clustered with Aucuba japonica in the evolutionary relationship by the Maximum-Likelihood (ML) method. [ABSTRACT FROM AUTHOR]

Perilla frutescens is well known for its high α-linolenic acid (ALA) accumulation and medicinal values in the world. In this study, the complete chloroplast genome of P. frutescens was reported. The chloroplast genome length of P. frutescens was 152,602 bp, which was circular in shape with a characteristic quadripartite structure. It contained a large single-copy (LSC) region of 83,706 bp, a small single-copy (SSC) region of 17,546 bp and separated by two inverted repeat (IR) regions of 25,675 bp. The overall nucleotide content of the chloroplast genome was 38.1% G + C content. This chloroplast genome contained 139 genes, which included 94 protein-coding genes (PCGs), 37 transfer RNA (tRNAs), and 8 ribosome RNA (rRNAs). Phylogenetic and evolutionary relationship have shown that P. frutescens was closely related to P. setoyensis in the family Lamiaceae using the maximum-likelihood (ML) method. [ABSTRACT FROM AUTHOR]

Xanthium sibiricum is a common and annual the Traditional Chinese Medicine for many years in China. In this study, we presented the complete chloroplast genome of X. sibiricum. The chloroplast genome size was 151,897 bp in length that contained a large single-copy region (LSC) of 83,847 bp, a small single-copy region (SSC) of 17,890 bp and two inverted repeat regions (IR) of 25,080 bp. The overall nucleotide composition of the chloroplast genome is: 31.2% of A, 31.3% T, 18.5% C and 19.0% G, with a total G + C content of the chloroplast genome 37.5% and A + T of 62.5%. The chloroplast genome of X. sibiricum contains 133 genes, which included 88 protein-coding genes (PCG), 37 transfer RNA (tRNAs), and 8 ribosome RNA (rRNAs). Phylogenetic neighbour-joining (NJ) analysis result shown that the position of X. sibiricum closely related to X. strumarium in evolutionary relationship. [ABSTRACT FROM AUTHOR]

The muskrat Ondatra zibethicus is native to North America, However it has successfully dispersed into most areas of northeast China in the past decades, which may lead to potential impact on endemic eco-system. We determined and annotated the whole mtDNA genome of the muskrat O. zibethicus to better understand the evolutionary relationship of this invasive species with other Rodentia distributed in China. The complete mitogenome is 16,351 bp in length, includes 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region. We built the phylogenetic tree of muskrat and other 11 most closely related Rodentia species. [ABSTRACT FROM AUTHOR]

Background: R2R3-MYB is a class of transcription factor crucial in regulating secondary cell wall development during wood formation. The regulation of wood formation in gymnosperm has been understudied due to its large genome size. Using Single-Molecule Real-Time sequencing, we obtained full-length transcriptomic libraries from the developmental stem of Cunninghamia lanceolata, a perennial conifer known as Chinese fir. The R2R3-MYB of C. lanceolata (hereafter named as ClMYB) associated with secondary wall development were identified based on phylogenetic analysis, expression studies and functional study on transgenic line., Results: The evolutionary relationship of 52 ClMYBs with those from Arabidopsis thaliana, Eucalyptus grandis, Populus trichocarpa, Oryza sativa, two gymnosperm species, Pinus taeda, and Picea glauca were established by neighbour-joining phylogenetic analysis. A large number of ClMYBs resided in the woody-expanded subgroups that predominated with the members from woody dicots. In contrast, the woody-preferential subgroup strictly carrying the members of woody dicots contained only one candidate. The results suggest that the woody-expanded subgroup emerges before the gymnosperm/angiosperm split, while most of the woody-preferential subgroups are likely lineage-specific to woody dicots. Nine candidates shared the same subgroups with the A. thaliana orthologs, with known function in regulating secondary wall development. Gene expression analysis inferred that ClMYB1/2/3/4/5/26/27/49/51 might participate in secondary wall development, among which ClMYB1/2/5/26/27/49 were significantly upregulated in the highly lignified compression wood region, reinforcing their regulatory role associated with secondary wall development. ClMYB1 was experimentally proven a transcriptional activator that localised in the nucleus. The overexpression of ClMYB1 in Nicotiana benthamiana resulted in an increased lignin deposition in the stems. The members of subgroup S4, ClMYB3/4/5 shared the ERF-associated amphiphilic repression motif with AtMYB4, which is known to repress the metabolism of phenylpropanoid derived compounds. They also carried a core motif specific to gymnosperm lineage, suggesting divergence of the regulatory process compared to the angiosperms., Conclusions: This work will enrich the collection of full-length gymnosperm-specific R2R3-MYBs related to stem development and contribute to understanding their evolutionary relationship with angiosperm species., (© 2021. The Author(s).)

Babesia gibsoni (B. gibsoni), an intracellular apicomplexan protozoan, poses great threat to canine health. Currently, little information is available about the B. gibsoni (WH58) endemic to Wuhan, China. Here, the mitochondrial (mt) genome of B. gibsoni (WH58) was amplified by five pairs of primers and sequenced and annotated by alignment with the reported mt genome sequences of Babesia canis (B. canis, KC207822), Babesia orientalis (KF218819), Babesia bovis (AB499088), and Theileria equi (AB499091). The evolutionary relationships were analyzed with the amino acid sequences of cytochrome c oxidase I (cox1) and cytochrome b (cob) genes in apicomplexan parasite species. Additionally, the mt genomes of Babesia, Theileria, and Plasmodium spp. were compared in size, host infection, form, distribution, and direction of the protein-coding genes. The full size of the mt genome of B. gibsoni (WH58) was 5865 bp with a linear form, containing terminal-inverted repeats on both ends, six large subunit ribosomal RNA fragments, and three protein-coding genes: cox1, cob, and cytochrome c oxidase III (cox3). Babesia, Theileria, and Plasmodium spp. had a similar mt genome size of about 6000 bp. The mt genomes of parasites that cause canine babesiosis showed a slightly smaller size than the other species. Moreover, Babesia microti (R1 strain) was about 11,100 bp in size, which was twice larger than that of the other species. The mt form was linear for Babesia and Theileria spp. but circular for Plasmodium falciparum and Plasmodium knowlesi. Additionally, all the species contained the three protein-coding genes of cox1, cox3, and cob except Toxoplasma gondii (RH strain) which only contained the cox1 and cob genes. The phylogenetic analysis indicated that B. gibsoni (WH58) was more identical to B. gibsoni (AB499087), B. canis (KC207822), and Babesia rossi (KC207823) and most divergent from Babesia conradae in Babesia spp. Despite the highest similarity to B. gibsoni (AB499087) reported in Japan, B. gibsoni (WH58) showed notable differences in the sequence of nucleotides and amino acids and the property in virulence to host and in vitro cultivation. This study compared the mt genomes of the two B. gibsoni isolates and other parasites in the phylum Apicomplexa and provided new insights into their differences and evolutionary relationships.