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The genomes of living lungfishes can inform on the molecular-developmental basis of the Devonian sarcopterygian fish-tetrapod transition. We de novo sequenced the genomes of the African (Protopterus annectens) and South American lungfishes (Lepidosiren paradoxa). The Lepidosiren genome (about 91 Gb, roughly 30 times the human genome) is the largest animal genome sequenced so far and more than twice the size of the Australian (Neoceratodus forsteri)1 and African2 lungfishes owing to enlarged intergenic regions and introns with high repeat content (about 90%). All lungfish genomes continue to expand as some transposable elements (TEs) are still active today. In particular, Lepidosiren's genome grew extremely fast during the past 100 million years (Myr), adding the equivalent of one human genome every 10 Myr. This massive genome expansion seems to be related to a reduction of PIWI-interacting RNAs and C2H2 zinc-finger and Krüppel-associated box (KRAB)-domain protein genes that suppress TE expansions. Although TE abundance facilitates chromosomal rearrangements, lungfish chromosomes still conservatively reflect the ur-tetrapod karyotype. Neoceratodus' limb-like fins still resemble those of their extinct relatives and remained phenotypically static for about 100 Myr. We show that the secondary loss of limb-like appendages in the Lepidosiren-Protopterus ancestor was probably due to loss of sonic hedgehog limb-specific enhancers.

Transposable elements (TE) play critical roles in shaping genome evolution. Highly repetitive TE sequences are also a major source of assembly gaps making it difficult to fully understand the impact of these elements on host genomes. The increased capacity of long-read sequencing technologies to span highly repetitive regions promises to provide new insights into patterns of TE activity across diverse taxa. Here we report the generation of highly contiguous reference genomes using PacBio long-read and Omni-C technologies for three species of Passerellidae sparrow. We compared these assemblies to three chromosome-level sparrow assemblies and nine other sparrow assemblies generated using a variety of short- and long-read technologies. All long-read based assemblies were longer (range: 1.12 to 1.41 Gb) than short-read assemblies (0.91 to 1.08 Gb) and assembly length was strongly correlated with the amount of repeat content. Repeat content for Bell's sparrow (31.2% of genome) was the highest level ever reported within the order Passeriformes, which comprises over half of avian diversity. The highest levels of repeat content (79.2% to 93.7%) were found on the W chromosome relative to other regions of the genome. Finally, we show that proliferation of different TE classes varied even among species with similar levels of repeat content. These patterns support a dynamic model of TE expansion and contraction even in a clade where TEs were once thought to be fairly depauperate and static. Our work highlights how the resolution of difficult-to-assemble regions of the genome with new sequencing technologies promises to transform our understanding of avian genome evolution.

Homosporous lycophytes (Lycopodiaceae) are a deeply diverged lineage in the plant tree of life, having split from heterosporous lycophytes (Selaginella and Isoetes) ~400 Mya. Compared to the heterosporous lineage, Lycopodiaceae has markedly larger genome sizes and remains the last major plant clade for which no chromosome-level assembly has been available. Here, we present chromosomal genome assemblies for two homosporous lycophyte species, the allotetraploid Huperzia asiatica and the diploid Diphasiastrum complanatum. Remarkably, despite that the two species diverged ~350 Mya, around 30% of the genes are still in syntenic blocks. Furthermore, both genomes had undergone independent whole genome duplications, and the resulting intragenomic syntenies have likewise been preserved relatively well. Such slow genome evolution over deep time is in stark contrast to heterosporous lycophytes and is correlated with a decelerated rate of nucleotide substitution. Together, the genomes of H. asiatica and D. complanatum not only fill a crucial gap in the plant genomic landscape but also highlight a potentially meaningful genomic contrast between homosporous and heterosporous species.

Summary: Increasing genome size (GS) has been associated with slower rates of DNA replication and greater cellular nitrogen (N) and phosphorus demands. Despite most plant species having small genomes, the existence of larger GS species suggests that such costs may be negligible or represent benefits under certain conditions.Focussing on the widespread and diverse grass family (Poaceae), we used data on species' climatic niches and growth rates under different environmental conditions to test for growth costs or benefits associated with GS. The influence of photosynthetic pathway, life history and evolutionary history on grass GS was also explored.We found that evolutionary history, photosynthetic pathway and life history all influence the distribution of grass species' GS. Genomes were smaller in annual and C4 species, the latter allowing for small cells necessary for C4 leaf anatomy. We found larger GS were associated with high N availability and, for perennial species, low growth‐season temperature.Our findings reveal that GS is a globally important predictor of grass performance dependent on environmental conditions. The benefits for species with larger GS are likely due to associated larger cell sizes, allowing rapid biomass production where soil fertility meets N demands and/or when growth occurs via temperature‐independent cell expansion. [ABSTRACT FROM AUTHOR]

Heterophylly is a phenomenon whereby an individual plant dramatically changes leaf shape in response to the surroundings. Hygrophila difformis (Acanthaceae; water wisteria), has recently emerged as a model plant to study heterophylly because of its striking leaf shape variation in response to various environmental factors. When submerged, H. difformis often develops complex leaves, but on land it develops simple leaves. Leaf complexity is also influenced by other factors, such as light density, humidity, and temperature. Here, we sequenced and assembled the H. difformis chromosome‐level genome (scaffold N50: 60.43 Mb, genome size: 871.92 Mb), which revealed 36 099 predicted protein‐coding genes distributed over 15 pseudochromosomes. H. difformis diverged from its relatives during the Oligocene climate‐change period and expanded gene families related to its amphibious habit. Genes related to environmental stimuli, leaf development, and other pathways were differentially expressed in submerged and terrestrial conditions, possibly modulating morphological and physiological acclimation to changing environments. We also found that auxin plays a role in H. difformis heterophylly. Finally, we discovered candidate genes that respond to different environmental conditions and elucidated the role of LATE MERISTEM IDENTITY 1 (LMI1) in heterophylly. We established H. difformis as a model for studying interconnections between environmental adaptation and morphogenesis. SUMMARY STATEMENT: We investigated the genome and transcriptome of Hygrophila difformis, establishing a model for heterophylly and functions of environmental factors on phenotype. [ABSTRACT FROM AUTHOR]

Understanding genomic characteristics, such as genetic diversity and genome size, is important because they relate to species and ecotype performance. Imperata cylindrica has two ecotypes, the common type (C‐type) and the early‐flowering type (E‐type), which differ in their ecological characteristics and distribution ranges in Japan. This study aimed to elucidate the genetic diversity of the C‐type and E‐type ecotypes of I. cylindrica throughout Japan, using the multiplexed inter‐simple sequence repeat genotyping by sequencing (MIG‐seq) method. Genome‐wide single‐nucleotide polymorphism data analysis revealed that the C‐type had greater genetic diversity and clearer isolation by distance than the E‐type. Additionally, the C‐type exhibited clear genetic differentiation between the southern part of Amami Oshima and other populations, consistent with differences in its life history. The C‐type also had a smaller genome than the E‐type, which may contribute to faster plant growth and smaller seed mass, as compared with the larger genome of the E‐type. These phenomena were consistent with the characteristics of the C‐type. These results showed that the two ecotypes differ genetically, highlighting the necessity for different guidelines for each ecotype in their conservation and use for revegetation. [ABSTRACT FROM AUTHOR]

Summary Whole genome duplication (WGD) likely plays an important role in plant macroevolution, and has been implicated in diversification rate shifts, structural innovations, and increased disparity. But the general effects of WGD are challenging to evaluate, in part due to the difficulty of directly comparing morphological patterns across disparate clades. We explored relationships between WGD and the evolution of reproductive complexity across vascular plants using a metric based on the number of reproductive part types. We used multiple regression models to evaluate the relative importance of inferred WGD events, genome size, and a suite of additional variables relating to growth habit and reproductive biology in explaining part type complexity. WGD was a consistent predictor of reproductive complexity only among angiosperms. Across vascular plants generally, reproductive biology, clade identity, and the presence of bisexual strobili (those that produce microsporangiate and megasporangiate organs) were better predictors of complexity. Angiosperms are unique among vascular plants in combining frequent polyploidy with high‐reproductive complexity. Whether WGD is mechanistically linked to floral complexity is unclear, but we suggest widespread polyploidy and increased complexity were ultimately facilitated by the evolution of herbaceous growth habits in early angiosperms. [ABSTRACT FROM AUTHOR]

Background: The common Eastern bumble bee Bombus impatiens is native to North America and is the main commercially reared pollinator in the Americas. There has been extensive research on this species related to its social biology, applied pollination, and genetics. The genome of this species was previously sequenced using short-read technology, but recent technological advances provide an opportunity for substantial improvements. This species is common in agricultural and urban environments, and heavy metal contaminants produced by industrial processes can negatively impact it. To begin to identify possible mechanisms underlying responses to these toxins, we used RNA-sequencing to examine how exposure to a cocktail of four heavy metals at field-realistic levels from industrial areas affected B. impatiens worker gene expression. Results: PacBio long-read sequencing resulted in 544x coverage of the genome, and HiC technology was used to map chromatin contacts. Using Juicer and manual curation, the genome was scaffolded into 18 main pseudomolecules, representing a high quality, chromosome-level assembly. The sequenced genome size is 266.6 Mb and BRAKER3 annotation produced 13,938 annotated genes. The genome and annotation show high completeness, with ≥ 96% of conserved Eukaryota and Hymenoptera genes present in both the assembly and annotated genes. RNA sequencing of heavy metal exposed workers revealed 603 brain and 34 fat body differentially expressed genes. In the brain, differentially expressed genes had biological functions related to chaperone activity and protein folding. Conclusions: Our data represent a large improvement in genomic resources for this important model species—with 10% more genome coverage than previously available, and a high-quality assembly into 18 chromosomes, the expected karyotype for this species. The new gene annotation added 777 new genes. Altered gene expression in response to heavy metal exposure suggests a possible mechanism for how these urban toxins are negatively impacting bee health, specifically by altering protein folding in the brain. Overall, these data are useful as a general high quality genomic resource for this species, and provide insight into mechanisms underlying tissue-specific toxicological responses of bumble bees to heavy metals. [ABSTRACT FROM AUTHOR]

Encarsia sophia, a heteronomous hyperparasitoid wasp, is a well-known biological control agent, but its genomic information is limited, hindering molecular investigations and understanding of multitrophic interactions. In this study, we present a chromosome-level genome assembly for E. sophia using Illumina, PacBio HiFi, and Hi-C technologies. The assembled genome size is 398.3 Mb, with a contig N50 of 1.0 Mb and a scaffold N50 of 74.0 Mb. The BUSCO completeness score is 97.1%, and genome coverage reaches 99.1%. Utilizing Hi-C assisted assembly, the genome was organized into five chromosomes, with a mounting rate of 95.1%. Repetitive sequences make up 54.6% of the genome, and 14,914 protein-coding genes were predicted, with 95.5% functionally annotated. The high-quality genome assembly of E. sophia is a significant achievement, marking the first complete genome for a heteronomous hyperparasitoid wasp. This milestone offers valuable insights into the evolution and host interactions of heteronomous hyperparasitoids, laying the foundation for extensive research in biological control. [ABSTRACT FROM AUTHOR]

The Patagonian toothfish (Dissostichus eleginoides) belongs to the Actinopterygii class, and the suborder Notothenioidei, which lives in cold waters in the Southern Hemisphere. We performed assembly and annotation, and we integrated the Illumina short-read sequencing for polishinng, PacBio long-read sequencing for contig-level assembly, and Hi-C sequencing technology to obtain high-quality of chromosome-level genome assembly. The final assembly analysis resulted in a total of 495 scaffolds, a genome size of 844.7 Mbp and an N50 length of 36 Mbp. Among these data, we confirmed 24 scaffolds exceeded 10 Mbp and classified as chromosome-level. The completeness of BUSCO rate was over 97%. A total gene set of 32,224 was identified. Furthermore, we analyzed the presence of AFGP genes, classified into Antarctic and sub-Antarctic categories through phylogenetic analysis. This study provides a useful resource for the genomic analysis of Patagonian toothfish and genetic insights into the comparison with Antarctic fishes. [ABSTRACT FROM AUTHOR]

SUMMARY: Among flowering plants, genome size varies remarkably, by >2200‐fold, and this variation depends on the loss and gain of noncoding DNA sequences that form distinct heterochromatin complexes during interphase. In plants with giant genomes, most chromatin remains condensed during interphase, forming a dense network of heterochromatin threads called interphase chromonemata. Using super‐resolution light and electron microscopy, we studied the ultrastructure of chromonemata during and after replication in root meristem nuclei of Nigella damascena L. During S‐phase, heterochromatin undergoes transient decondensation locally at DNA replication sites. Due to the abundance of heterochromatin, the replication leads to a robust disassembly of the chromonema meshwork and a general reorganization of the nuclear morphology visible even by conventional light microscopy. After replication, heterochromatin recondenses, restoring the chromonema structure. Thus, we show that heterochromatin replication in interphase nuclei of giant‐genome plants induces a global nuclear reorganization. Significant Statement: The replication of giant plant genomes requires a global chromatin reorganization in interphase nuclei. [ABSTRACT FROM AUTHOR]

SUMMARY: Carrot (Daucus carota) is one of the most popular and nutritious vegetable crops worldwide. However, significant yield losses occur every year due to leaf blight, a disease caused by a fungal pathogen (Alternaria dauci). Past research on resistance to leaf blight disease in carrots has been slow because of the low‐quality genome assemblies of both carrot and the pathogen. Here, we report the greatly improved assemblies and annotations of telomere‐to‐telomere (T2T) reference genomes of carrot DH13M14 (451.04 Mb) and A. dauci A2016 (34.91 Mb). Compared with the previous carrot genome versions, our assembly featured notable improvements in genome size, continuity, and completeness of centromeres and telomeres. In addition, we generated a time course transcriptomic atlas during the infection of carrots by A. dauci and captured their dynamic gene expression reprogramming during the interaction process. During infection, A. dauci genes encoding effectors and enzymes responsible for the degradation of plant cell wall components, e.g., cellulose and pectin, were identified, which appeared to increase pathogenic ability through upregulation. In carrot, the coordinated gene expression of components of pattern‐ and effector‐triggered immunity (PTI and ETI) in response to A. dauci attack was characterized. The biosynthesis or signal transduction of plant hormones, including JA, SA, and ethylene, was also involved in the carrot response to A. dauci. This work provides a foundation for understanding A. dauci pathogenic progression and carrot defense mechanisms to improve carrot resistance to leaf blight disease. The Carrot Database (CDB) developed also provides a useful resource for the carrot community. Significance Statement: Here, we report the improved assemblies and annotations of telomere‐to‐telomere (T2T) reference genomes of carrot and its leaf blight pathogen Alternaria dauci. Genome‐wide alterations in gene expression in both carrot and A. dauci during carrot leaf blight disease provide a foundation for understanding A. dauci pathogenic progression and carrot defense mechanisms to improve carrot resistance to leaf blight disease. [ABSTRACT FROM AUTHOR]

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Gaultheria Kalm ex L. (Ericaceae), a type of evergreen shrub, known as a natural source of methyl salicylate, possesses rich germplasm resources, strong habitat adaptability, significant ornamental value, and noteworthy pharmacological activities. However, due to the paucity of whole genomic information, genetically deep research in these areas remains limited. Consequently, we intend to obtain genome data through high-throughput sequencing, gene annotation, flow cytometry, transcription factors prediction and genetic marker analysis for a representative species of this genus, with Gaultheria prostrata selected for our study. In this study, we preliminarily obtained the genome of G. prostrata through next-generation sequencing methods. Utilizing 47.94 Gb of high-quality sequence data (108.95× coverage), assembled into 114,436 scaffolds, with an N50 length of 33,667 bp. The genome size assembled by SOAPdenovo, approximately 417 Mb, corresponded closely to predictions by flow cytometry (440 Mb) and k -mer analysis (447 Mb). The genome integrity was evaluated using BUSCO with 91%. The heterozygosity ratio was 0.159%, the GC content was 38.85%, and the repetitive regions encompassed over 34.6% of the genome. A total of 26,497 protein-coding genes have been predicted and annotated across Nr, Swissprot, GO, KEGG, and Pfam databases. Among these, 14,377 and 2,387 genes received functional annotation in Nr and Swissprot, respectively; 21,895, 24,424, and 22,330 genes were similarly annotated in GO, KEGG, and Pfam. Moreover, A total of 279,785 SSRs were identified and 345,270 primers for these SSRs were designed. Within the various nucleotide types of SSRs, AG/CT and AAG/CTT constituted the predominant dinucleotide and trinucleotide repeat types in G. prostrata. In addition, 1,395 transcription factors (TFs) from 75 TF families, 462 transcription regulators (TRs) from 33 TR families and 840 protein kinase (PKs) from 118 PK families were identified in this genome. We also performed phylogenetic analyses of G. prostrata and related species, including estimation of divergence times and expansion and contraction analyses, followed by positive selection analyses of orthologous gene pairs of G. prostrata and its close relative Vaccinium corymbosum. These results provide a reference for in-depth study of genus Gaultheria , contributing to future functional and comparative genomics analyses and providing supporting data for the development of molecular markers. [ABSTRACT FROM AUTHOR]

Aerobic composting is a key strategy to the sustainable use of livestock manure, which is however constrained by the slow kinetics. Microbe-aided thermophilic composting provides an attractive solution to this problem. In this study, we identified key thermophilic bacteria capable of accelerating manure composting based on the deciphering of manure bacterial community evolution in a thermophilic system. High-throughput sequencing showed a significant evolution of manure bacterial community structure with the increasing heating temperature. Firmicutes were substantially enriched by the heating, particularly some known thermotolerant bacterial species, such as Novibacillus thermophiles , Bacillus thermolactis , and Ammoniibacillus agariperforans. Correspondingly, through function prediction, we found bacterial taxa with cellulolytic and xylanolytic activities were significantly higher in the thermophilic process relative to the initial stage. Subsequently, a total of 47 bacteria were isolated in situ and their phylogenetic affiliation and degradation capacity were determined. Three isolates were back inoculated to the manure, resulting in shortened composting process from 5 to 3 days with Germination Index increased up to 134%, and improved compost quality particularly in wheat growth promoting. Comparing to the mesophilic and thermophilic Bacillus , the genomes of the three isolates manifested some features similar to the thermophiles, including smaller genome size and mutation of specific genes that enhance heat tolerance. This study provide robust evidence that microbe-aided thermophilic composting is capable to accelerate manure composting and improve the quality of compost, which represents a new hope to the sustainable use of manure from the meat industry. [ABSTRACT FROM AUTHOR]

Background: In evolutionary biology, identifying and quantifying inter-lineage genome size variation and elucidating the underlying causes of that variation have long been goals. Repetitive elements (REs) have been proposed and confirmed as being among the most important contributors to genome size variation. However, the evolutionary implications of genome size variation and RE dynamics are not well understood. Results: A total of 35 Ensifera insects were collected from different areas in China, including nine species of crickets and 26 species of katydids. The genome sizes of seven species were then determined using flow cytometry. The RepeatExplorer2 pipeline was employed to retrieve the repeated sequences for each species, based on low-coverage (0.1 X) high-throughput Illumina unassembled short reads. The genome sizes of the 35 Ensifera insects exhibited a considerable degree of variation, ranging from 1.00 to 18.34 pg. This variation was more than 18-fold. Similarly, the RE abundances exhibited considerable variation, ranging from 13.66 to 61.16%. In addition, the Tettigonioidea had larger genomes and contained significantly more REs than did the Grylloidea genomes. Analysis of the correlation between RE abundance and the genome size of 35 Ensifera insects revealed that the abundance of REs, transposable elements (TEs), long terminal repeats (LTRs), and long interspersed nuclear elements (LINEs) are significantly correlated with genome size. Notably, there is an inflection point in this correlation, where species with increasingly large genomes (e.g., > 5–10 pg) have repeats that contribute less to genome expansion than expected. Furthermore, this study revealed contrasting evolutionary directions between the Tettigonioidea and Grylloidea clades in terms of the expansion of REs. Tettigonioidea species exhibit a gradual increase in ancestral genome size and RE abundance as they diverge, while Grylloidea species experience sustained genome contraction. Conclusions: This study reveals extensive variation in genome size and RE abundance in Ensifera insects, with distinct evolutionary patterns across two major groups, Tettigonioidea and Grylloidea. This provides valuable insights into the variation in genome size and RE abundance in Ensifera insects, offering a comprehensive understanding of their evolutionary history. [ABSTRACT FROM AUTHOR]

Summary Genome merging is a common phenomenon causing a wide range of consequences on phenotype, adaptation, and gene expression, yet its broader implications are not well‐understood. Two consequences of genome merging on gene expression remain particularly poorly understood: dosage effects and evolution of expression. We employed Chlamydomonas reinhardtii as a model to investigate the effects of asymmetric genome merging by crossing a diploid with a haploid strain to create a novel triploid line. Five independent clonal lineages derived from this triploid line were evolved for 425 asexual generations in a laboratory natural selection experiment. Utilizing fitness assays, flow cytometry, and RNA‐Seq, we assessed the immediate consequences of genome merging and subsequent evolution. Our findings reveal substantial alterations in genome size, gene expression, protein homeostasis, and cytonuclear stoichiometry. Gene expression exhibited expression‐level dominance and transgressivity (i.e. expression level higher or lower than either parent). Ongoing expression‐level dominance and a pattern of ‘functional dominance’ from the haploid parent was observed. Despite major genomic and nucleo‐cytoplasmic disruptions, enhanced fitness was detected in the triploid strain. By comparing gene expression across generations, our results indicate that proteostasis restoration is a critical component of rapid adaptation following genome merging in Chlamydomonas reinhardtii and possibly other systems. [ABSTRACT FROM AUTHOR]

Land hermit crabs are a group of shell-carrying crabs that have evolved remarkable terrestrial adaptations in behavior, morphology, physiology, and biochemistry. However, the genetic mechanisms underlying these adaptations remain unclear. In addition, usually it is very difficult to get good genome assemblies for crustaceans. In this study, we managed to assemble the first chromosome-level genome for a land hermit crab (Coenobita brevimanus) with careful manual curation. The final assembly spans 4.74 Gb, with the contig N50 of 1.75 Mb and scaffold N50 of 42.95 Mb, encompassing 117 chromosomes that account for 96.54% of the genome. The evaluations including genome BUSCO (95.26%), Merqury qv (35.88) and the mapping ratio of pair-end short reads (99.48%) showed the high-continuity of C. brevimanus genome assembly, making it the genome with the highest quality in crustaceans with genome size bigger than 3 Gb. The availability of this chromosome-scale genome of crustaceans represents a valuable resource for the land hermit crab, which represents an independent water-to-land transition evolutionary event in the animal kingdom. [ABSTRACT FROM AUTHOR]

Grasses are considered one of the most important angiosperm groups in economic terms. The Setaria sphacelata complex is an intriguing species with considerable variation in genome size (GS). It is currently being explored from a genomic perspective especially because of its great adaptability under winter periods. Repetitive DNA sequences are known to contribute significantly to GS diversity, which in turn can play a role in impacting the ecology and evolution of a species. This study is aimed to characterize the GS and repetitive elements of different germplasm accessions of S. sphacelata. We analyzed 540 plants from 70 accessions collected worldwide. Flow cytometry was used for GS estimation, together with chromosome counting, fluorescent in situ hybridization (FISH), and bioinformatic analysis. Most (i.e., 80%) accessions were tetraploids (2n = 4x = 36) with GS ranging from 3.0 to 3.7 pg/2C. Additionally, a low number of diploids (2n = 2x = 18; ∼1.6 to 2 pg/2C), pentaploids (2n = 5x = 45: ∼4 pg/2C), hexaploids (2n = 6x = 54; ∼4.4 pg/2C), and octoploids (2n = 8x = 72; ∼6 pg/2C,) were detected. The greatest variation was found in accessions from South Africa. RepeatExplorer2 showed that 39% and 43% of the genomes of two diploid accessions comprised repetitive sequences, with Ty3/gypsy retrotransposons being the most abundant repeats. However, variation in the percentage of two Ty3/gypsy sublineages, Athila and Ogre, suggests different process of amplification and deletion of repeats during the evolution of the species complex. In contrast, FISH revealed some satellite repeats with a conserved localized distribution in pericentromeric regions between accessions. Although differences in the distribution of the FISH signals over the chromosomes were observed between the different ploidy levels, the data suggest that increases in the ploidy level were associated with the occurrence of hybridization and DNA loss. Core Ideas: This study characterized the genome size of worldwide accessions of the forage crop Setaria sphacelata.Plants ranging from diploids to octaploids were detected.The greatest genome size variation was found in accessions from South Africa.Transposable elements constitution of Australian diploid accessions was analyzed.Genome downsizing and satellite repeats with a conserved distribution are present in the species. Plain Language Summary: Grasses are one of the most significant angiosperm groups, present worldwide. In this context, studying genome size and cytogenetics is essential for understanding their adaptive capabilities. In this study, we characterized the genome size and repetitive elements of different germplasm accessions of Setaria sphacelata, an intriguing species. Most plants were tetraploids (2n = 4x = 36), with a smaller number of diploids (2n = 2x = 18), pentaploids (2n = 5x = 45), hexaploids (2n = 6x = 54), and octoploids (2n = 8x = 72) also detected. The greatest variation was found in accessions from South Africa, and molecular cytogenetics revealed some satellite repeats with a conserved localized distribution in the pericentromeric regions. Overall, our findings highlight the complex genetic and evolutionary factors that contribute to the diversity of S. sphacelata. [ABSTRACT FROM AUTHOR]

Brevibacillus brevis FJAT-0809-GLX has a broad spectrum of antimicrobial activity. Understanding the molecular basis of biocontrol ability of B. brevis will allow us to develop effective microbial agents for sustainable agriculture. In this study, we present the complete and annotated genome sequence of FJAT-0809-GLX. The complete genome size of B. brevis FJAT-0809-GLX was 6,137,019 bp, with 5688 predicted coding sequences (CDS). The average GC content of 47.38%, and there were 44 copies of the rRNAs operon (16S, 23S and 5S RNA), and 127 tRNA genes. A total of 11,162 genes were functionally annotated with the COG, GO, and KEGG databases, and 123 genes belonged to CAZymes. Genomic secondary metabolite analysis indicated 13 clusters encoding potential new antimicrobials. FJAT-0809-GLX was designated as B. brevis according to average nucleotide polymorphism (ANI) and phylogenetic analysis. The pangenome consisted of 7141 homologous genes, and 4469 homologous genes shared by B. brevis FJAT-0809-GLX, B. brevis NBRC100599, B. brevis DSM30, and B. brevis NCTC2611. The number of unique homologous genes of B. brevis FJAT-0809-GLX (419 genes) and B. brevis NBRC100599 (480 genes) were much more than those in B. brevis DSM30 (13 genes), and B. brevis NCTC2611 (6 genes). Nine gene clusters encoding for secondary metabolite biosynthesis were compared in the genome of B. brevis FJAT-0809-GLX with those of B. brevis NBRC100599, B. brevis DSM30 and B. brevis NCTC2611, and the gene clusters encoding for lantipeptide and transatpks-otherks only existed in genome of B. brevis FJAT-0809-GLX. The 11 BbPks genes were included in the B. brevis FJAT-0809-GLX genome, which contained the conserved PS-DH domain. The relative expression of BbPksL, BbPksM2, BbPksM3, BbPksN3, BbPksN4 and BbPksN5 reached a maximum at 120 h and then decreased at 144 h. Our results provided detailed genomic and Pks genes information for the FJAT-0809-GLX strain, and lid a foundation for studying its biocontrol mechanisms. [ABSTRACT FROM AUTHOR]

Background and Aims Thallium (Tl) is extremely toxic to all life forms and is an emerging pollutant. Plants in the Brassicaceae family, including edible crops, have an enhanced capacity for Tl accumulation, even from soils with low thallium concentration. The most extreme Tl hyperaccumulator is Biscutella laevigata , capable of attaining >32 000 μg Tl g−1 dry weight (DW) in its leaves. Methods Biscutella laevigata from a non-metallicolous accession (Feltre, Italy) and a metallicolous accession (Les Malines, France) were subjected to a dosing experiment in hydroponics (0, 5 and 30 μ m Tl), followed by synchrotron-based micro-X-ray fluorescence analysis to elucidate tissue- and cellular-level Tl distribution. Key Results Flow cytometric data on the two accessions showed that the Feltre accession has a genome size twice of that of the Les Malines accession (256 and 125 pg per 2 C , respectively), suggesting that they are phylogenetically distant populations. The Feltre accession did not accumulate Tl (125 μg Tl g−1 DW on average in leaves) at the 5 µ m Tl dose level, whereas the Les Malines accession had a mean of 1750 μg Tl g−1 DW, with peaks of 24 130 μg Tl g−1 DW, at the 30 µ m Tl dose level. At 30 µ m Tl, the non-metallicolous accession did not grow, and at 5 µ m Tl it showed reduced biomass compared with the metallicolous one. In the Les Malines accession, the synchrotron-based micro-X-ray fluorescence analysis revealed that Tl was localized in the vacuoles of epidermal cells, especially underneath trichomes and in trichome basal cells. Thallium also occurred in solid crystalline deposits (3–5 µm in size, ~40 wt% Tl) that were found mainly in foliar margins and under trichome bases. Conclusions Biscutella laevigata is an attractive model for studying Tl hypertolerance and hyperaccumulation on account of the extreme expression of this trait and its marked intraspecific variability. [ABSTRACT FROM AUTHOR]

Blastomyces dermatitidis and Blastomyces gilchristii are cryptic species of fungi that cause blastomycosis, an often severe disease involving pulmonary infection capable of systemic dissemination. While these species appear morphologically identical, differences exist in the genetic makeup, geographical range, and possibly the clinical presentation of infection. Here, we show genetic divergence between the cryptic species through both a Blastomyces species tree constructed from orthologous protein sequences and whole genome single-nucleotide variant phylogenomic analysis. Following linked-read sequencing and de novo genome assembly, we characterized and compared the genomes of 3 B. dermatitidis and 3 B. gilchristii isolates. The B. gilchristii genomes (73.25–75.4 Mb) were ∼8 Mb larger than the B. dermatitidis genomes (64.88–66.61 Mb). Average nucleotide identity was lower between genomes of different species than genomes of the same species, yet functional classification of genes suggested similar proteomes. The most striking difference involved long terminal repeat retrotransposons. Although the same retrotransposon elements were detected in the genomes, the quantity of elements differed between the 2 species. Gypsy retrotransposon content was significantly higher in B. gilchristii (38.04–39.26 Mb) than in B. dermatitidis (30.85–32.40 Mb), accounting for the majority of genome size difference between species. Age estimation and phylogenetic analysis of the reverse transcriptase domains suggested that these retrotransposons are relatively ancient, with genome insertion predating the speciation of B. dermatitidis and B. gilchristii. We postulate that different trajectories of genome contraction led to genetic incompatibility, reproductive isolation, and speciation, highlighting the role of transposable elements in fungal evolution. [ABSTRACT FROM AUTHOR]

The two invasive Reynoutria species, Reynoutria japonica var. japonica and Reynoutria sachalinensis, and their hybrid Reynoutria x bohemica are often misidentified by managers and nonspecialists. The taxonomic confusions are all the more exacerbated by the infraspecific variability of introduced populations in terms of morphology, genetic diversity, and ploidy level. We resolved the identity of North‐Eastern French invasive populations using 4582 single‐nucleotide polymorphisms (SNPs) from a RADseq analysis, DNA contents estimated by flow cytometry, and 12 vegetative morphometric variables. The SNPs supported only one single genotype for R. japonica over 11 localities, while the nine localities of Reynoutria x bohemica were represented by one genotype each. Estimation of genome size using DAPI staining and flow cytometry revealed only octoploid cytotypes for R. japonica and hexaploid cytotypes for R. x bohemica, whereas R. sachalinensis was represented by tetraploid and hexaploid cytotypes. Among morphometric variables, no single one allows for a clear differentiation of the three taxa. We propose a combination of characters to easily and quickly identify these three invasive taxa based on six vegetative criteria including leaf and apex length, as well as leaf shape, leaf base, and apex shape, and the extrafloral nectaries on the node. [ABSTRACT FROM AUTHOR]

Reynoutria multiflora is a widely used medicinal plant in China. Its medicinal compounds are mainly stilbenes and anthraquinones which possess important pharmacological activities in anti‐aging, anti‐inflammatory and anti‐oxidation, but their biosynthetic pathways are still largely unresolved. Here, we reported a near‐complete genome assembly of R. multiflora consisting of 1.39 Gb with a contig N50 of 122.91 Mb and only one gap left. Genome evolution analysis revealed that two recent bursts of long terminal repeats (LTRs) contributed significantly to the increased genome size of R. multiflora, and numerous large chromosome rearrangements were observed between R. multiflora and Fagopyrum tataricum genomes. Comparative genomics analysis revealed that a recent whole‐genome duplication specific to Polygonaceae led to a significant expansion of gene families associated with disease tolerance and the biosynthesis of stilbenes and anthraquinones in R. multiflora. Combining transcriptomic and metabolomic analyses, we elucidated the molecular mechanisms underlying the dynamic changes in content of medicinal ingredients in R. multiflora roots across different growth years. Additionally, we identified several putative key genes responsible for anthraquinone and stilbene biosynthesis. We identified a stilbene synthase gene PM0G05131 highly expressed in roost, which may exhibit an important role in the accumulation of stilbenes in R. multiflora. These genomic data will expedite the discovery of anthraquinone and stilbenes biosynthesis pathways in medicinal plants. [ABSTRACT FROM AUTHOR]

As an important halophyte in the Yellow River Delta, the Amaranthaceae C3Suaeda salsa (L.) Pall. has attracted much attention for the "red carpet" landscape, and could be simply divided into red and green phenotypes according to the betacyanin content in the fleshy leaves. However, S. salsa has not been sequenced yet, which limited people's understanding of this species at the molecular level. We constructed a high‐quality chromosome‐scale reference genome by combining high‐throughput sequencing, PacBio single molecule real‐time sequencing, and Hi‐C sequencing techniques with a genome size of 445.10 Mb and contigs N50 of 2.94 Mb. Through the annotation of the S. salsa genome, 298.76 Mb of the repetitive sequences and 23 965 protein‐coding genes were identified, of which the proportion of long terminal repeats type in the repetitive sequences was the most abundant, about 50.74% of the S. salsa genome. Comparative genomics indicated that S. salsa underwent a whole‐genome duplication event about 146.15 million years ago (Ma), and the estimated divergence time between S. salsa and Suaeda aralocaspica was about 16.9 Ma. A total of four betacyanins including betanidin, celosianin II, amaranthin and 6′‐O‐malonyl‐celosianin II were identified and purified in both phenotypes, while two significantly up‐regulated betacyanins (celosianin II and amaranthin) may be the main reason for the red color in red phenotype. In addition, we also performed transcriptomics and metabolomics in both phenotypes to explore the molecular mechanisms of pigment synthesis, and a series of structural genes and transcription factors concerning with betacyanin production were selected in S. salsa. [ABSTRACT FROM AUTHOR]

The evolutionary processes that underlie variation in plant genome size have been much debated. Abiotic factors are thought to have played an important role, with negative and positive correlations between genome size and seasonal or stressful climatic conditions being reported in several systems. In turn, variation in genome size may influence plant traits which affect interactions with other organisms, such as herbivores. The mechanisms underlying evolutionary linkages between plant genome size and biotic and abiotic factors nonetheless remain poorly understod. To address this gap, we conducted phylogenetically controlled analyses testing for associations between genome size, climatic variables, plant traits (defenses and nutrients), and herbivory across 29 oak (Quercus) species. Genome size is significantly associated with both temperature and precipitation seasonality, whereby oak species growing in climates with lower and less variable temperatures but more variable rainfall had larger genomes. In addition, we found a negative association between genome size and leaf nutrient concentration (found to be the main predictor of herbivory), which in turn led to an indirect effect on herbivory. A follow‐up test suggested that the association between genome size and leaf nutrients influencing herbivory was mediated by variation in plant growth, whereby species with larger genomes have slower growth rates, which in turn are correlated with lower nutrients. Collectively, these findings reveal novel associations between plant genome size and biotic and abiotic factors that may influence life history evolution and ecological dynamics in this widespread tree genus. [ABSTRACT FROM AUTHOR]

Amphibians represent a diverse group of tetrapods, marked by deep divergence times between their three systematic orders and families. Studying amphibian biology through the genomics lens increases our understanding of the features of this animal class and that of other terrestrial vertebrates. The need for amphibian genomic resources is more urgent than ever due to the increasing threats to this group. Amphibians are one of the most imperiled taxonomic groups, with approximately 41% of species threatened with extinction due to habitat loss, changes in land use patterns, disease, climate change, and their synergistic effects. Amphibian genomic resources have provided a better understanding of ontogenetic diversity, tissue regeneration, diverse life history and reproductive modes, anti-predator strategies, and resilience and adaptive responses. They also serve as essential models for studying broad genomic traits, such as evolutionary genome expansions and contractions, as they exhibit the widest range of genome sizes among all animal taxa and possess multiple mechanisms of genetic sex determination. Despite these features, genome sequencing of amphibians has significantly lagged behind that of other vertebrates, primarily due to the challenges of assembling their large, repeat-rich genomes and the relative lack of societal support. The emergence of long-read sequencing technologies, combined with advanced molecular and computational techniques that improve scaffolding and reduce computational workloads, is now making it possible to address some of these challenges. To promote and accelerate the production and use of amphibian genomics research through international coordination and collaboration, we launched the Amphibian Genomics Consortium (AGC, https://mvs.unimelb.edu.au/amphibian-genomics-consortium) in early 2023. This burgeoning community already has more than 282 members from 41 countries. The AGC aims to leverage the diverse capabilities of its members to advance genomic resources for amphibians and bridge the implementation gap between biologists, bioinformaticians, and conservation practitioners. Here we evaluate the state of the field of amphibian genomics, highlight previous studies, present challenges to overcome, and call on the research and conservation communities to unite as part of the AGC to enable amphibian genomics research to "leap" to the next level. [ABSTRACT FROM AUTHOR]

The aim of this study was to investigate the reference population size required to obtain substantial prediction accuracy within‐ and across‐lines and the effect of using a multi‐line reference population for genomic predictions of maternal traits in pigs. The data consisted of two nucleus pig populations, one pure‐bred Landrace (L) and one Synthetic (S) Yorkshire/Large White line. All animals were genotyped with up to 30 K animals in each line, and all had records on maternal traits. Prediction accuracy was tested with three different marker data sets: High‐density SNP (HD), whole genome sequence (WGS), and markers derived from WGS based on pig combined annotation dependent depletion‐score (pCADD). Also, two different genomic prediction methods (GBLUP and Bayes GC) were compared for four maternal traits; total number piglets born (TNB), total number of stillborn piglets (STB), Shoulder Lesion Score and Body Condition Score. The main results from this study showed that a reference population of 3 K–6 K animals for within‐line prediction generally was sufficient to achieve high prediction accuracy. However, when the number of animals in the reference population was increased to 30 K, the prediction accuracy significantly increased for the traits TNB and STB. For multi‐line prediction accuracy, the accuracy was most dependent on the number of within‐line animals in the reference data. The S‐line provided a generally higher prediction accuracy compared to the L‐line. Using pCADD scores to reduce the number of markers from WGS data in combination with the GBLUP method generally reduced prediction accuracies relative to GBLUP using HD genotypes. The BayesGC method benefited from a large reference population and was less dependent on the different genotype marker datasets to achieve a high prediction accuracy. [ABSTRACT FROM AUTHOR]

An intense black pigmented halotolerant yeast GUBPC1, was obtained from the solar salterns of Nerul, Goa-India. The isolate could tolerate 0 to 20 % NaCl. FE-SEM analysis revealed its polymorphic nature, exhibiting oval cells at higher salt concentrations and filamentous spindle like shapes at lower concentrations. Initially, the cells appear oval, yeast like in shape but gradually after 15 days of incubation, it becomes elongated and undergoes budding, exhibiting various budding patterns, from single polar bud to bipolar buds with annellidic ring, to lateral buds and eventually forming filamentous hyphae. The intracellular black pigment was identified as melanin based on ultraviolet–visible spectroscopy analysis. The molecular identification of the culture showed closest similarity with Hortaea werneckii. Plant polymer-degrading enzymatic activities such as cellulase, laccase, chitinase, xylanase, pectinase, amylase and protease were exhibited by the isolate GUBPC1. To further understand and explore its biotechnological potential, we performed whole-genome sequencing and analysis. The obtained genome size was 26.93 Mb with 686 contigs and a GC content of 53.24 %. We identified 9383 protein-coding genes, and their functional annotation revealed the presence of 435 CAZyme genes and 16 functional genes involved in secondary metabolite synthesis, thus providing a basis for its potential value in various biotechnological applications. [ABSTRACT FROM AUTHOR]

Field‐collected specimens were used to obtain nine high‐quality genome assemblies from a total of 10 insect species native to prairies and savannas of central Illinois (USA): Mellilla xanthometata (Lepidoptera: Geometridae), Stenolophus ochropezus (Coleoptera: Carabidae), Forcipata loca (Hemiptera: Cicadellidae), Coelinius sp. (Hymenoptera: Braconidae), Thaumatomyia glabra (Diptera: Chloropidae), Brachynemurus abdominalus (Neuroptera: Myrmeleontidae), Catonia carolina (Hemiptera: Achilidae), Oncometopia orbona (Hemiptera: Cicadellidae), Flexamia atlantica (Hemiptera: Cicadellidae) and Stictocephala bisonia (Hemiptera: Membracidae). Sequencing library preparation from single specimens was successful despite extremely small DNA yields (<0.1 μg) for some samples. Additional sequencing and assembly workflows were adapted to each sample depending on the initial DNA yield. PacBio circular consensus (CCS/HiFi) or continuous long reads (CLR) libraries were used to sequence DNA fragments up to 50 kb in length, with Illumina sequenced linked‐reads (TellSeq libraries) and Omni‐C libraries used for scaffolding and gap‐filling. Assembled genome sizes ranged from 135 MB to 3.2 GB. The number of assembled scaffolds ranged from 47 to >13,000, with the longest scaffold per assembly ranging from ~23 to 439 Mb. Genome completeness was high, with BUSCO scores ranging from 85.5% completeness for the largest genome (Stictocephala bisonia) to 98.8% completeness for the smallest genome (Coelinius sp.). The unique content was estimated using RepeatMasker and GenomeScope2, which ranged from 50.7% to 75.8% and roughly decreased with increasing genome size. Structural annotation predicted a range of 19,281–72,469 protein models for sequenced species. Sequencing costs per genome at the time ranged from US$3–5k, averaged ~1600 CPU‐hours on a high‐performance cluster and required approximately 14 h of bioinformatics analyses with samples using PacBio HiFi data. Most assemblies would benefit from further manual curation to correct possible scaffold misjoins and translocations suggested by off‐diagonal or depleted signals in Omni‐C contact maps. [ABSTRACT FROM AUTHOR]

The article in the Journal of Plant Pathology discusses the complete genome sequence of the endophytic Bacillus subtilis GUCC4, a potential biocontrol agent for managing Nigrospora pathogens that cause leaf blight disease in passion fruit. The study highlights the strain's inhibitory effects on N. sphaerica, its biocontrol determinants such as amylase and protease, and its capacity to synthesize secondary metabolites with antifungal properties. The genome annotation reveals 4,446 protein-coding genes and 14 secondary metabolite biosynthetic gene clusters, emphasizing GUCC4's potential as an eco-friendly alternative to synthetic fungicides for plant disease management. [Extracted from the article]

Lacticaseibacillus casei KACC92338 was originally isolated from Korean raw milk. The antioxidant activities and protective effect in vitro of this strain were evaluated extensively. The results showed that KACC92338 can tolerate hydrogen peroxide up to 2 mM and cell-free supernatant (CFS) had higher scavenging rates for DPPH, hydroxyl radical, reducing power, and iron chelating activities with 95.61 ± 1.59%, 34.10 ± 1.93%, 2.220 ± 0.82 and 81.06 ± 1.06%, respectively. Meanwhile, the CFS showed a protective effect on yeast cells against 10 mM hydrogen peroxide with a survival rate of 76.05 ± 5.65%. To explore the probiotic potential of KACC92338, whole genome assembly and gene clusters with probiotic properties were further analyzed. The genome size was 3,050,901 bp with a 47.96% GC ratio, and 63 contigs. The genome contains 3,048 genes composed of 2,981 coding sequences and 67 RNAs (including 57 tRNAs +9 rRNAs +1 tmRNA). Average Nucleotide Identity and genome-based taxonomy showed that the KACC92338 genome had close similarity with L. casei strains with 96% ANI. Functional annotation by EggNOG and KEGG revealed the presence of numerous genes putatively involved in carbohydrate- and amino acid-transport and metabolism, genetic information processing, and signaling and cellular processes. Additionally, several genes conferring probiotic characteristics such as tolerance to stress, heat, cold, acid, bile salts, oxidative stress, immunomodulation, and adhesion to intestinal epithelium were identified. Notably absent were acquired antibiotic resistance genes, virulence, and pathogenic factors, that prove KACC92338 is a safe strain. Besides, the defense mechanisms of KACC92338 include six prophage regions and three clustered regularly interspaced short palindromic repeat (CRISPR) arrays as acquired immune systems against mobile elements. Further, the BAGEL4 database determined antimicrobial bacteriocin clusters of class IIb: sakacin-P, Enterolysin_A, sactipeptides, and Enterocin X, which suggests the strain could exhibit a wide range of antimicrobial functions. Together, these findings show that the L. casei KACC92338 strain can be a potential probiotic candidate in producing functional fermented foods-, health care- and skin care products-with antioxidant properties. However, a few more mechanistic studies are necessary on the safety assurance and potential application of the strain as a probiotic agent. [ABSTRACT FROM AUTHOR]

Soil microbial growth, a vital biogeochemical process, governs both the accrual and loss of soil carbon. Here, we investigate the biogeography of soil microbiome potential growth rates and show that microbiomes in resource-rich (high organic matter and nutrients) and acid-neutral soils from cold and humid regions exhibit high potential growth. Conversely, in resource-poor, dry, hot, and hypersaline soils, soil microbiomes display lower potential growth rates, suggesting trade-offs between growth and resource acquisition or stress tolerance. In addition, the potential growth rates of soil microbiomes positively correlates with genome size and the number of ribosomal RNA operons but negatively correlates with optimum temperature, biomass carbon-to-phosphorus and nitrogen-to-phosphorus ratios. The spatial variation of microbial potential growth rates aligns with several macroecological theories. These findings not only enhance our understanding of microbial adaptation to diverse environments but also aid in realistically parameterizing microbial physiology in soil carbon cycling models. Soil microbial growth controls carbon sequestration. Here, the authors show that resource-rich, neutral soils from cold and humid areas have higher growth potential than resource-poor, hypersaline soil from dry and hot regions, demonstrating diverse microbial adaptations. [ABSTRACT FROM AUTHOR]

Consisting of trees, climbers and herbs exclusively in the intertidal environments, mangrove forest is one of the most extreme and vulnerable ecosystems of our planet and has long been of great interest for biologists and ecologists. Here, we first assembled the chromosome-scale genome of a climber mangrove plant, Dalbergia candenatensis. The assembled genome size is approximately 474.55 Mb, with a scaffold N50 of 48.1 Mb, a complete BUSCO score of 98.4%, and a high LTR Assembly Index value of 21. The genome contained 283.46 Mb (59.74%) repetitive sequences, and 29,554 protein-coding genes were predicted, of which 87.54% were functionally annotated in five databases. The high-quality genome assembly and annotation presented herein provide a valuable genomic resource that will expedite genomic and evolutionary studies of mangrove plants and facilitate the elucidation of molecular mechanisms underlying the salt- and water-logging-tolerance of mangrove plants. [ABSTRACT FROM AUTHOR]

Fokienia hodginsii (F. hodginsii), belonging to the genus Fokienia of the Cupressaceae. F. hodginsii has significant application value due to its wood properties and great research value in evolutionary studies as a gymnosperm. However, the genome of F. hodginsii remains unknown due to the large size of gymnosperms genome. Pacific Bioscience sequencing, Hi‐C mapping, whole‐genome Bisulfite Sequencing (BS‐Seq), long‐read isoform sequencing (Iso‐Seq), direct RNA sequencing (DRS), quantitative proteomics, and metabonomics analysis are employed to facilitate genome assembly, gene annotation, and investigation into epigenetic mechanisms. In this study, the 10G F. hodginsii genome is assembled into 11 chromosomes. Furthermore, 50 521 protein‐coding genes are annotated and determined that 65% of F. hodginsii genome comprises repetitive sequences. It is discovered that transposable element (TE)‐including introns is associated with higher expression. The DNA methylome of F. hodginsii reveals that xylem has a higher DNA methylation level compared to callus. Moreover, DRS reveals the significant alterations in RNA full‐length ratio, which potentially associated with poly(A) length (PAL) and alternative polyadenylation (APA). Finally, the morphology measurement and metabonomics analysis revealed the difference of 14 cultivars. In summary, the genomes and epigenetics datasets provide a molecular basis for callus formation in the gymnosperm family. [ABSTRACT FROM AUTHOR]

ABSTRACT Magnolia sieboldii K. Koch (M. sieboldii) stands as an elegant tree species within the Magnoliaceae family, esteemed for its exquisite beauty, cultural significance and economic advantages. The species faces challenges in seed germination under natural conditions, primarily attributed to morphological dormancy. Despite its significance, the molecular mechanisms governing M. sieboldii seed germination remain elusive, compounded by the absence of genomic resources specific to this species. In this study, we present the first chromosome‐scale genome assembly of M. sieboldii, with a total genome size of 2.01 Gb, including 1096 scaffolds assigned to 19 chromosomes (N50 = 102.4 Mb). Phylogenetic analyses, incorporating 13 plant species, illuminate the evolutionary independence of Magnoliids from monocots and eudicots, positioning them as a sister clade. Through RNA‐seq analysis, we identify pivotal genes and pathways contributing to seed dormancy and germination. In addition, our investigation delves into the the far‐red‐impaired response (FAR1) transcription factor gene family, revealing their enrichment throughout evolution and their involvement in the intricate process of seed germination. This comprehensive genome sequencing initiative offers invaluable insights into the biological attributes of M. sieboldii, with a specific emphasis on unravelling the complexities of seed dormancy and germination. [ABSTRACT FROM AUTHOR]

Lanternfish not only boast the most abundant biomass among marine fish species but also play a vital role in marine ecosystems. As one of the lanternfish species with the highest global catch, the skinnycheek lanternfish (Benthosema pterotum) is widely distributed in the Indo-Pacific region, playing a pivotal role in the marine biological pump. This study constructed the first chromosome-level genome of B. pterotum using a combination of short-read sequencing, PacBio, and Hi-C sequencing technologies. The genome size of B. pterotum is 1,272.53 Mb, with a contig N50 of 810 Kb and a scaffold N50 of 54.49 M. More than 99.65% of contigs were successfully anchored onto 24 pseudochromosomes, and 95.7% of BUSCO genes were identified within the genome, demonstrating the high level of completeness in genome assembly. A total of 24,934 protein-coding genes were predicted, of which 99.02% were functionally annotated. The successful assembly of a high-quality genome for B. pterotum provides valuable genetic resources for better understanding its biological characteristics and potentially those of all lanternfish species. [ABSTRACT FROM AUTHOR]

The diatom Paralia guyana is a tychoplanktonic microalgal species that represents one of the early diverging diatoms. P. guyana can thrive in both planktonic and benthic habitats, making a significant contribution to the occurrence of red tide events. Although a dozen diatom genomes have been sequenced, the identity of the early diverging diatoms remains elusive. The understanding of the evolutionary clades and mechanisms of ecological adaptation in P. guyana is limited by the absence of a high-quality genome assembly. In this study, the first high-quality genome assembly for the early diverging diatom P. guyana was established using PacBio single molecular sequencing. The assembled genome has a size of 558.85 Mb, making it the largest diatom genome on record, with a contig N50 size of 26.06 Mb. A total of 27,121 protein-coding genes were predicted in the P. guyana genome, of which 22,904 predicted genes (84.45%) were functionally annotated. This data and analysis provide innovative genomic resources for tychoplanktonic microalgal species and shed light on the evolutionary origins of diatoms. [ABSTRACT FROM AUTHOR]

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Cyamophila willieti (Hemiptera: Psyllidae) is a significant pest that adversely affects the growth of Styphnolobium japonicum and its variant, Styphnolobium japonicum f. pendula. Despite its impact, research on this species remains limited. In this study, we successfully assembled a chromosome-level genome for Cyamophila willieti using a comprehensive approach that integrated Illumina sequencing, PacBio sequencing, and Hi-C technology. The genome size was determined to be 361.61 Mb, with a scaffold N50 length of 28.90 Mb. Additionally, the genome was mapped to 13 chromosomes (N = 12 A + X), and a total of 15,841 genes were predicted, with 90.38% of them functionally annotated. In summary, the high-quality genome of Cyamophila willieti provides valuable data to support further research, including pest management strategies. [ABSTRACT FROM AUTHOR]

Background : Garuga Roxb. is a genus endemic to southwest China and other tropical regions in Southeast Asia facing risk of extinction due to the loss of tropical forests and changes in land use. Conducting a genome survey of G. forrestii contribute to a deeper understanding and conservation of the genus. Results: This study utilized genome survey of G. forrestii generated approximately 54.56 GB of sequence data, with approximately 112 × coverage. K-mer analysis indicated a genome size of approximately 0.48 GB, smaller than 0.52GB estimated by flow cytometry. The heterozygosity is of about 0.54%, and a repeat rate of around 51.54%. All the shotgun data were assembled into 339,729 scaffolds, with an N50 of 17,344 bp. The average content of guanine and cytosine was approximately 35.16%. A total of 330,999 SSRs were detected, with mononucleotide repeats being the most abundant at 70.16%, followed by dinucleotide repeats at 20.40%. We conducted a preliminary ploidy assessment using Smudgeplot and observed a clear bimodal distribution in G. forrestii at 1/2 relative coverage depth and total coverage depth (2n), suggesting a potential diploid genome structure. A pseudo chromosome of G. forrestii and a gemone of Boswellia sacra were used as reference genome to perform a primer population resequencing analysis within three Garuga species. Principal component analysis (PCA) indicated three distinct groups, but genome wide phylogenetics represented conflicting both between the dataset of different reference genomes and between maternal and nuclear genome. Conclusion: In summary, the genome of G. forrestii is small, and the phylogenetic relationships within the Garuga genus are complex. The genetic data presented in this study holds significant value for comprehensive whole-genome analyses, the evaluation of population genetic diversity, investigations into adaptive evolution, the advancement of artificial breeding efforts, and the support of species conservation and restoration initiatives. Ultimately, this research contributes to reinforcing the conservation and management of natural ecosystems, promoting biodiversity conservation, and advancing sustainable development. [ABSTRACT FROM AUTHOR]

Background: The family Lauraceae is subdivided into six main lineages: Caryodaphnopsideae, Cassytheae, Cryptocaryeae, Hypodaphnideae, Laureae, and Neocinnamomeae. However, phylogenetic relationships among these lineages have been debatable due to incongruence between trees constructed using nuclear ribosomal DNA (nrDNA) sequences and chloroplast (cp) genomes. As with cp DNA, the mitochondrial (mt) DNA of most flowering plants is maternally inherited, so the phylogenetic relationships recovered with mt genomes are expected to be consistent with that from cp genomes, rather than nrDNA sequences. Results: The mitogenome of Machilus yunnanensis, with a length of 735,392 bp, has a very different genome size and gene linear order from previously published magnoliid mitogenomes. Phylogenomic reconstructions based on 41 mt genes from 92 Lauraceae mitogenomes resulted in highly supported relationships: sisterhood of the Laureae and a group containing Neocinnamomeae and Caryodaphnopsideae, with Cassytheae being the next sister group, followed by Cryptocaryeae. However, we found significant incongruence among the mitochondrial, chloroplast, and nuclear phylogenies, especially for the species within the Caryodaphnopsideae and Neocinnamomeae lineages. Time-calibrated phylogenetic analyses showed that the split between Caryodaphnopsideae and Neocinnamomeae dated to the later Eocene, around 38.5 Ma, Laureae originated in the Late Cretaceous, around 84.9 Ma, Cassytheae originated in the mid-Cretaceous around 102 Ma, and Cryptocaryeae originated in the Early Cretaceous around 116 Ma. From the Late Cretaceous to the Paleocene, net diversification rates significantly increased across extant clades of major lineages, and both speciation rates and net diversification rates continued steady growth towards the present. Conclusions: The topology obtained here for the first time shows that mt genes can be used to support relationships among lineages of Lauraceae. Our results highlight that both Caryodaphnopsideae and Neocinnamomeae lineages are younger than previously thought, likely first diversifying in the Eocene, and species in the other extant lineages of Lauraceae dates in a long-time span from the Early Cretaceous to the Eocene, and the climate of a period of about 90 million years was relatively warm, while the extant species of Lauraceae then continuously diversified with global cooling from the Eocene to the present day. [ABSTRACT FROM AUTHOR]

Highly pathogenic Burkholderia pseudomallei is the causative agent of melioidosis, a neglected tropical disease endemic in Southeast Asian tropical region. This bacterium encompasses diverse virulence factors which further undergo dynamic gene-expression flux as it transits through distinct environmental niches within the host which may lead to manifestation of differential clinical symptoms. B. pseudomallei, is classified as a Tier 1 select agent in the United States and regarded as a risk group 3 organism in India with the potential to be used as bioweapon. Considering these facts, it is vital to uncover both physiological and genetic heterogeneity of B. pseudomallei, particularly to identify any novel virulence factors that may contribute to pathogenicity. B. pseudomallei strain CM000113 was isolated from a clinical case in India, characterized it for its physiological, biochemical, and prominently genetic traits through WGS. It has a type 2 morphotype with faster doubling time and high biofilm producing capacity as compared to Pseudomonas aeruginosa. The genome size is 7.3 Mbp and it is phylogenetically close to B. pseudomallei strain Mahidol 1106a and Burkholderia mallei Turkey 2. We observed genetic heterogeneity, as key virulence factors that were identified shows sequence dissimilarity with reference strains. Additionally, presence of genomic islands, harbouring two virulence factors, GmhA and GmhB2, associated with pathogenesis indicates possibility of horizontal gene transfer. These results emphasize the need for an extensive study focusing the genome of B. pseudomallei and its associated heterogeneity, to identify molecular biomarkers aiding to develop point-of-care diagnostic kits for early diagnosis of melioidosis. [ABSTRACT FROM AUTHOR]

Background: Milk is an excellent growth medium for microorganisms due to its nutritive composition. Microorganisms have been implicated in bovine mastitis (BM) in dairy cows as well as causing infections in animals and humans. Despite extensive endeavours to manage BM, this condition continues to persist as the most prevalent and economically burdensome problem affecting dairy cattle on a global scale. Non-aureus staphylococci (NAS) species such as Staphylococcus haemolyticus, S. epidermidis, and S. xylosus are currently the predominant microbiological agents identified as the main cause of subclinical udder infections and are also considered opportunistic pathogens in cases of clinical mastitis in dairy cows. Therefore, it is crucial to elucidate the genetic profile of these species. The primary objective of this study was to characterise three phenotypically determined multidrug-resistant NAS environmental strains (NWU MKU1, NWU MKU2, and NWU MKS3) obtained from dairy cows milk via whole-genome sequencing. Results: The results confirmed that the three isolates were S. haemolyticus with genome sizes of 2.44, 2.56, and 2.56 Mb and a G + C content of 32.8%. The genomes contained an array of antibiotic resistance genes that may potentially confer resistance to a range of antibiotic classes, such as macrolides, fluoroquinolones, aminoglycosides, cephalosporins, tetracyclines, peptides, and phenicol. Furthermore, all the genomes carried virulence genes, which are responsible for several functions, such as adhesion, enzyme and toxin production. The genomes of these organisms contained signatures encoding mobile genetic elements such as prophages and insertion sequences. Conclusion: These findings indicate there is a need for diligent monitoring with improved management practices and quality control strategies on farms to safeguard milk production systems and human health. [ABSTRACT FROM AUTHOR]

Background: Aquatic viruses act as key players in shaping microbial communities. In polar environments, they face significant challenges such as limited host availability and harsh conditions. However, due to the restricted accessibility of these ecosystems, our understanding of viral diversity, abundance, adaptations, and host interactions remains limited. Results: To fill this knowledge gap, we studied viruses from atmosphere-close aquatic ecosystems in the Central Arctic and Northern Greenland. Aquatic samples for virus-host analysis were collected from ~60 cm depth and the submillimeter surface microlayer (SML) during the Synoptic Arctic Survey 2021 on icebreaker Oden in the Arctic summer. Water was sampled from a melt pond and open water before undergoing size-fractioned filtration, followed by genome-resolved metagenomic and cultivation investigations. The prokaryotic diversity in the melt pond was considerably lower compared to that of open water. The melt pond was dominated by a Flavobacterium sp. and Aquiluna sp., the latter having a relatively small genome size of 1.2 Mb and the metabolic potential to generate ATP using the phosphate acetyltransferase-acetate kinase pathway. Viral diversity on the host fraction (0.2–5 µm) of the melt pond was strikingly limited compared to that of open water. From the 1154 viral operational taxonomic units (vOTUs), of which two-thirds were predicted bacteriophages, 17.2% encoded for auxiliary metabolic genes (AMGs) with metabolic functions. Some AMGs like glycerol-3-phosphate cytidylyltransferase and ice-binding like proteins might serve to provide cryoprotection for the host. Prophages were often associated with SML genomes, and two active prophages of new viral genera from the Arctic SML strain Leeuwenhoekiella aequorea Arc30 were induced. We found evidence that vOTU abundance in the SML compared to that of ~60 cm depth was more positively correlated with the distribution of a vOTU across five different Arctic stations. Conclusions: The results indicate that viruses employ elaborate strategies to endure in extreme, host-limited environments. Moreover, our observations suggest that the immediate air-sea interface serves as a platform for viral distribution in the Central Arctic. Dvb_jZZ1H7pg55rxrDSVb2 Video Abstract [ABSTRACT FROM AUTHOR]

Fusarium ear rot (FER), caused by the fungal pathogen Fusarium verticillioides, stands as one of the most economically burdensome and pervasive diseases affecting maize worldwide. Its impact on food security is particularly pronounced due to the production of fumonisins, toxic secondary metabolites that pose serious health risks, especially for livestock. FER disease severity is complex and polygenic, with few resistance (R) genes being identified for use in breeding resistant varieties. While FER is the subject of several breeding programs, only a few studies have investigated entire populations of F. verticillioides with corresponding virulence data to better understand and characterize the pathogenomics. Here, we sequenced and compared the genomes of 50 Fusarium isolates (43 F. verticillioides and 7 other Fusarium spp.) that were used to inoculate a diverse maize population. Our objectives were to elucidate the genome size and composition of F. verticillioides, explore the variable relationship between fumonisin production and visual disease severity, and shed light on the phylogenetic relationships among the isolates. Additionally, we conducted a comparative analysis of the nucleotide variants (SNPs) and the isolates' effectoromes to uncover potential genetic determinants of pathogenicity. Our findings revealed several promising leads, notably the association of certain gene groups, such as pectate lyase, with disease severity. These genes should be investigated further as putative alleles for breeding resistant maize varieties. We suggest that, beyond validation of the alleles identified in this study, researchers validate each phenotypic dataset on an individual basis, particularly if considering fumonisin concentrations and when using diverse populations. Our study underscores the importance of genomic analysis in tackling FER and offers insights that could inform the development of resilient maize cultivars. By leveraging advances in genomics and incorporating pathogen populations into breeding programs, resistance to FER can be advanced. [ABSTRACT FROM AUTHOR]

AbstractThe complete mitochondrial genomes of octocorals typically range from 18.5 kb to 20.5 kb in length and include 14 protein-coding genes (PCGs), two ribosomal RNA genes and one tRNA. To date, seven different gene orders (A–G) have been described, yet comprehensive investigations of the actual number of arrangements, as well as comparative analyses and evolutionary reconstructions of mitochondrial genome evolution within the whole class Octocorallia, have been often overlooked. Here, we considered the complete mitochondrial genomes available for octocorals and explored their structure and gene order variability. Our results updated the actual number of mitochondrial gene order arrangements so far known for octocorals from 7 to 14 and allowed us to explore and preliminarily discuss the role of some of the structural and functional factors in the mitogenomes. We performed comparative mitogenomic analyses on the existing and novel octocoral gene orders, considering different mitogenomic structural features such as genome size, GC percentage, AT and GC skewness. The mitochondrial gene order history mapped on a recently published nuclear loci phylogeny showed that the most common rearrangement events in octocorals are inversions, inverted transpositions and transpositions. Furthermore, gene order rearrangement events were restricted only to some regions of the tree. Overall, different rearrangement events arose independently and from the ancestral and most common gene order, instead of being derived from other rearranged orders. Finally, our data demonstrate how the study of mitochondrial gene orders can be used to explore the evolution of octocorals and in some cases can be used to assess the phylogenetic placement of certain taxa. [ABSTRACT FROM AUTHOR]

The planthopper Nilaparvata muiri is a sister species to N. lugens (Hemiptera: Delphacidae), a notorious insect pest in Asian rice fields. N. muiri and N. lugens have a different host preference despite the similarities in many biological features. To better understand the adaptive evolution of planthoppers, comprehensive genomic information on N. muiri and N. lugens are urgently needed. In this study, we used ultra-low input PacBio HiFi libraries and Hi-C sequencing technologies to assemble a reference genome of a single N. muiri at the chromosomal level. The genome size was determined to be 531.62 Mb with a contig N50 size of 2.47 Mb and scaffold N50 size of 38.37 Mb. Totally, 96.61% assembled sequences were anchored to the 15 pseudo-chromosomes. BUSCO analysis yielded an Insecta completeness score of 98.6%. A total of 22,057 protein-coding genes were annotated, and 168.16 Mb repetitive sequences occupying 31.63% of genome were pinpointed. The assembled genome is valuable for evolutionary and genetic studies of planthoppers, and may provide sights to pest control. [ABSTRACT FROM AUTHOR]

Jujube (Ziziphus jujuba Mill.) is a valuable tree species with economic, edible, medicinal, and ecological conservation benefits. In this study, we used PacBio HiFi sequencing and Hi-C technology to assemble chromosome-level genomes of two cultivated Jujubes, namely 'Lingwuchangzao' and 'Shiguang'. The genome sizes of 'Lingwuchangzao' and 'Shiguang' were 385.66 Mb and 394.12 Mb, respectively, with contig N50 sizes of 30.62 Mb and 4.30 Mb. These genomes contained 31,082 and 31,015 protein-coding genes, with repeat element contents of 42.11% and 42.33%, respectively. Phylogenetic analysis revealed that 'Lingwuchangzao' was sister to 'Shiguang' and followed by 'Dongzao'. Additionally, comparative analysis of gene families among 'Lingwuchangzao', 'Shiguang', 'Dongzao', 'Junzao', and 'Suanzao' identified 15,988 (57.98%) core gene families, 11,191 (40.59%) disposable gene families, and 394 (1.43%) private gene families. Overall, the assembly of the genomes of these two cultivated Jujube varieties provides valuable genetic information for Jujube evolution, functional genomics research, and molecular breeding. [ABSTRACT FROM AUTHOR]

Simple Summary: To obtain more female individuals in the breeding population of R. dybowskii, it is important to explore the sex determination mechanism based on whole genome analysis. In this study, we analyzed the genome survey of male individuals of R. dybowskii using next-generation sequencing technology. The estimated genome size of R. dybowskii was approximately 3585.05 M. The total size of contigs and scaffolds was 3,748,543,415 and 3,765,862,278 bp, respectively. The N50 length of contigs and scaffolds was 31,988 and 336,385,783, respectively. The Dmrt1 gene with an 18,893 bp length was obtained from the scaffolding genomes of R. dybowskii. Sequence alignment to Dmrt1 revealed that the two male-specific DNA markers (MSM-222 and MSM-261) were not located on Dmrt1. This indicated that Dmrt1 may not be the only key gene for sex determination in R. dybowskii. Rana dybowskii is one of the important aquaculture species in Northeast China. The fallopian tubes of female R. dybowskii are used to prepare oviductus ranae (an important traditional Chinese medicine). Therefore, R. dybowskii females have higher economical value than males. An increasing female R. dybowskii population can increase the benefits from R. dybowskii culture. However, the genome of amphibians is complex, making it difficult to investigate their sex determination mechanism. In this study, we analyzed the genome of male R. dybowskii using next-generation sequencing technology. A total of 200,046,452,400 bp of clean data were obtained, and the K-mer analysis indicated that the depth was 50×. The genome size of R. dybowskii was approximately 3585.05 M, with a heterozygosity rate, repeat sequence ratio, and genome GC content of 1.15%, 68.96%, and approximately 43.0%, respectively. In total, 270,785 contigs and 498 scaffolds were generated. The size of the contigs and scaffolds was 3,748,543,415 and 3,765,862,278 bp, respectively, with the N50 length of 31,988 and 336,385,783. The longest contig and scaffold were of the size 137,967,485 and 1,808,367,828 bp, respectively. The number of contigs and scaffolds > 10K nt was 99,620 and 451, respectively. Through annotation, 40,913 genes were obtained, including 156,609 CDS (i.e., 3.83 CDS per gene). Sequence alignment was performed with the assembled scaffolding genome in this study. Two and one fragment had high homology with two male-specific DNA molecular markers of R. dybowskii discovered previously (namely, MSM-222 and MSM-261, respectively). In addition, the Dmrt1 gene of R. dybowskii was obtained with a length of 18,893 bp by comparison and splicing. The forward primers amplifying MSM-222 and MSM-261 were located at 322–343 and 14,501–14,526 bp of Dmrt1, respectively. However, sequence alignment revealed that MSM-222 and MSM-261 were not located on Dmrt1, and only some homologous parts were observed. This indicated that in addition to Dmrt1, other important genes may play a crucial role in the sex determination mechanism of R. dybowskii. Our study provided a foundation for the subsequent high-quality genome construction and provided important genomic resources for future studies on R. dybowskii. [ABSTRACT FROM AUTHOR]