Synteny and Collinearity in Plant Genomes

Construction of the super pan-genome for the genus Actinidia reveals structural variations linked to phenotypic diversity

Kiwifruits, belonging to the genus Actinidia, are acknowledged as one of the most successfully domesticated fruits in the twentieth century. Despite the rich wild resources and diverse phenotypes within this genus, insights into the genomic changes are still limited. Here, we conducted whole-genome sequencing on seven representative materials from highly diversified sections of Actinidia, leading to the assembly and annotation of 14 haplotype genomes with sizes spanning from 602.0 to 699.6 Mb. By compiling these haplotype genomes, we constructed a super pan-genome for the genus. We identified numerous structural variations (SVs, including variations in gene copy number) and highly diverged regions in these genomes. Notably, significant SV variability was observed within the intronic regions of the MED25 and TTG1 genes across different materials, suggesting their potential roles in influencing fruit size and trichome formation. Intriguingly, our findings indicated a high genetic divergence between two haplotype genomes, with one individual, tentatively named Actinidia × leiocacarpae, from sect. Leiocacarpae. This likely hybrid with a heterozygous genome exhibited notable genetic adaptations related to resistance against bacterial canker, particularly through the upregulation of the RPM1 gene, which contains a specific SV, after infection by Pseudomonas syringae pv. actinidiae. In addition, we also discussed the interlineage hybridizations and taxonomic treatments of the genus Actinidia. Overall, the comprehensive pan-genome constructed here, along with our findings, lays a foundation for examining genetic compositions and markers, particularly those related to SVs, to facilitate hybrid breeding aimed at developing desired phenotypes in kiwifruits.

Genome sequence of the wild species, Spinacia tetrandra, including a phased sequence of the extensive sex-linked region, revealing partial degeneration in evolutionary strata with unusual properties

Genetic degeneration is a striking feature of Y chromosomes, often involving losses of many genes carried on the X chromosome. However, the time course of gene losses remains unclear. Sex chromosomes of plants evolved more recently than animals' highly degenerated ones, making them ideal for studying degeneration timing. To investigate Spinacia sex chromosome evolution and the time course of degeneration, we compared genome sequences of cultivated Spinacia oleracea, with a small Y-linked region on Chr4, with its two wild relatives. In spinach and its closest relative Spinacia turkestanica, the Y duplication region (YDR) introduced a male-determining factor into Chr4's low-recombining pericentromeric region. In other words, a turnover event occurred in these species' recent common ancestor. The homologous Chr4 of the more distantly related S. tetrandra has a c. 133 Mb completely sex-linked and partially degenerated region, possibly reflecting the ancestral state. Sequence divergence analysis suggests that two 'evolutionary strata' evolved shortly before the two Spinacia lineages split. Consistent with the turnover hypothesis, the YDR of the other two Spinacia species is not within the S. tetrandra older stratum. We discuss the unexpected findings in S. tetrandra that genetic degeneration, genomic rearrangements, and repetitive sequence density are all greatest in the younger stratum.

Chromosome-level assemblies of the White bream Parabramis pekinensis

White bream Parabramis pekinensis is an omnivorous fish belong to Cyprinidae that is widespread in Asia. In this study, we presented chromosome-level genome assemblies of P. pekinensis by using PacBio HiFi long reads and Hi-C technology. We assembled high-quality genome of 1.03 Gb with scaffold N50 length of 40.04 Mb, and a total of 98.31% of the assembled sequences were anchored to 24 chromosomes. BUSCO analysis revealed that the genome assembly has a high-level completeness of 98.35% gene coverage. A total of 26,542 protein-coding genes were predicted, of which 92.61% were functionally annotated. The phylogenetic analysis indicated that the lineage leading to P. pekinensis was diverged from the lineage to Megalobrama amblycephala approximately 7.6 million years ago. The high-quality genome assembly provide valuable resources for evolutionary study and genetic breeding of genus Parabramis.

Genome-wide identification and functional characterization of LBD gene family in four Cymbidium species (Orchidaceae) and potential regulatory role of CsiLBD27 in floral development of Cymbidium sinense

BACKGROUND

The Lateral Organ Boundaries Domain (LBD) gene family, encompassing plant-specific LOB domain proteins, plays essential roles in various aspects of plant growth and development, and has continuously diversified its functions across numerous species. However, studies on LBD genes in the Orchidaceae family remain limited. To our knowledge, this is the first systematic investigation of the LBD gene family in Cymbidium, a genus that exhibits remarkable species and trait diversity within the Orchidaceae.

RESULTS

In this study, we identified 122 LBD genes within the genomes of four Cymbidium species, distributed on 20 chromosomes. These genes were classified into class I (109 members, including 16 in subclass Ic/d) and class II (13 members), with protein lengths ranging from 94-477 amino acids. Promoter sequences of CymLBD genes revealed various cis-elements significant for light, hormonal, biotic, and abiotic stress responses. Transcriptomic analysis revealed tissue- and stage-specific expression of CymLBD genes in Cymbidium, and RT-qPCR and yeast one-hybrid assays indicated that CsiLBD27 may regulate floral patterning by directly binding to the CsiSEP3 promoter and activating its transcription. Under ABA treatment, the genes CsiLBD13, CsiLBD19, and CsiLBD21 displayed tissue-specific expression changes, suggesting hormone-responsive regulation. In Cymbidium ensifolium, 16 CenLBD genes were differentially expressed, while in Cymbidium mannii, 9 CmaLBD gene expression exist obvious circadian rhythm. GO and KEGG enrichment of 1074 and 399 predicted target genes, respectively, indicating a diverse range of functions for LBDs.

CONCLUSIONS

Collectively, this study provides the first comprehensive insight into the evolutionary dynamics, regulatory mechanisms, and functional roles of LBD genes in Cymbidium. These findings offer a valuable genetic resource for understanding floral and vegetative development in Orchidaceae and uncover potential novel functions of LBD genes.

The superoxide dismutase (SOD) gene family in perennial ryegrass: Characterization and roles in heat stress tolerance

Perennial ryegrass (Lolium perenne) is a cool-season forage and turfgrass widely cultivated in warm and subtropical regions worldwide due to its ease of cultivation, resilience, and low maintenance costs. However, high temperatures severely impact its growth. Superoxide dismutase (SOD) is a key enzyme in plant stress responses, playing a crucial role in regulating reactive oxygen species (ROS) homeostasis. In this study, eight SOD genes were identified in perennial ryegrass. Bioinformatics analyses provided detailed insights into their chromosomal locations, phylogenetic relationships, conserved motifs, and cis-acting regulatory elements. Transcriptomic data revealed that these LpSOD genes exhibit distinct tissue-specific expression patterns and temperature response profiles. The enzymatic activity experiments of the purified LpSOD proteins revealed the effects of pH and temperature on the superoxide dismutase activity of LpSODs. Functional complementation tests using yeast mutants demonstrated that LpMSD1.1, LpCSD1, LpCSD2, and LpCSD3 rescue the high-temperature-sensitive phenotypes of yeast SOD gene deletion mutants. This study represents the first genome-wide analysis of the LpSOD gene family, laying a foundation for a better understanding of their functional roles in the high-temperature response of perennial ryegrass.

A chromosome-level genome assembly of Ficus benjamina, a fig tree with great ecological and ornamental value

Ficus benjamina, the weeping fig, is one of the most widely distributed and cultivated figs, with important ecological functions and landscape value. However, the lack of a reference genome has hindered molecular and functional research on this well-known fig-tree. Here we present a chromosome-scale genome assembly and annotation for F. benjamina, based on a combination of Illumina short-reads, PacBio subreads, and Hi-C sequencing data. The genome consists of 13 pseudochromosomes that contain 362.73 Mb of assembled sequences, with a contig N50 length of 25.76 Mb and a complete BUSCO score of 98.10%. In total, 28,840 protein-coding genes were identified, of which 96.22% were functionally annotated. Our study provides the first chromosome-level genome of F. benjamina, providing an important resource for exploring the genetic basis of its ecological and horticultural characters.

Genomic structure of yellow lupin (Lupinus luteus): genome organization, evolution, gene family expansion, metabolites and protein synthesis

Yellow lupin (Lupinus luteus) gives valuable high-quality protein and has good sustainability due to its ability in nitrogen fixation and exudation of organic acids, which reduces the need for chemical-based phosphate fertilization in acid soils. However, the crop needs further improvements to contribute in a major way to sustainable agriculture and food security.In this study, we present the first chromosome-level genome assembly of L. luteus. The results provide insights into its genomic organization, evolution, and functional attributes. Using integrated genomic approaches, we unveil the genetic bases governing its adaptive responses to environmental stress, delineating the intricate interplay among alkaloid biosynthesis, mechanisms of pathogen resistance, and secondary metabolite transporters. Our comparative genomic analysis of closely related species highlights recent speciation events within the Lupinus genus, exposing extensive synteny preservation alongside notable structural alterations, particularly chromosome translocations. Remarkable expansions of gene families implicated in terpene metabolism, stress responses, and conglutin proteins were identified, elucidating the genetic basis of L. luteus' superior nutritional profile and defensive capabilities. Additionally, a diverse array of disease resistance-related (R) genes was uncovered, alongside the characterization of pivotal enzymes governing quinolizidine alkaloid biosynthesis, thus shedding light on the molecular mechanisms underlying "bitterness" in lupin seeds.This comprehensive genomic analysis serves as a valuable resource to improve this species in terms of resilience, yield, and seed protein levels to contribute to food and feed to face the worldwide challenge of sustainable agriculture and food security.

Three cytochrome P450 enzymes consecutively catalyze the biosynthesis of furanoclerodane precursors in Salvia species

Salvia species native to the Americas are rich in valuable bioactive furanoclerodanes like the psychoactive salvinorin A found in Salvia divinorum, which is used in the treatment of opioid addiction. However, relatively little is known about their biosynthesis. To address this, we investigated the biosynthesis of salviarin, the most abundant furanoclerodane structure in the ornamental sage Salvia splendens. Using a self-organizing map and mutual rank analysis of RNA-seq co-expression data, we identified three cytochrome P450 enzymes responsible for the consecutive conversion of kolavenol into the salviarin precursors: annonene, hardwickiic acid, and hautriwaic acid. Annonene and hardwickiic acid have been proposed as intermediates in the biosynthesis of salvinorin A, and we therefore tested for a common evolutionary origin of the furanoclerodane pathway in these Salvia species by searching for homologous genes in available data for S. divinorum. The enzymes encoded by orthologous genes from S. divinorum displayed kolavenol synthase, annonene synthase, and hardwickiic acid synthase activity, respectively, supporting the view that these are intermediate steps in the biosynthesis of salvinorin A. We further investigated the origin of annonene synthase and the role of gene duplication in the evolution of this specific activity. Our work shows how S. splendens can serve as a model species for the study of furanoclerodane biosynthesis in Salvia species, contributes to understanding the evolution of specialized metabolism in plants, and provides new tools for the production of salvinorin A in biotechnological chassis.

Novel repetitive elements in plant-specific tails of Gγ proteins as the functional unit in G-protein signaling in crops

Heterotrimeric G-proteins act as molecular switches in signal transduction in response to stimuli in all eukaryotes. However, what specifies G-protein signaling in plants and how the mechanism evolved and diverged remain unsolved. Here, we found that the recently evolved tails of three Gγ subunits, Dense and erect panicle 1 (DEP1), G-protein gamma subunit 2 of type C (GGC2), and Grain size 3 (GS3), determine their distinct functions and specify grain size in rice (Oryza sativa L.). These Gγ subunits originated and expanded by an ancestral σ duplication ∼130 million years ago (mya) and a pancereal ρ duplication ∼70 mya in monocots, increasing genome complexity and inspiring functional innovations. In particular, through the comprehensive creation of artificial chimeric Gγ proteins, we found that this signaling selectivity is driven by repetitive elements and a link region hidden in plant-specific Gγ tails, allowing crops to switch from positive regulation to negative control. Unlike the tails, the conserved Gγ heads did not bias the signaling specificity; however, the change in the interaction between the mutated Gβ and Gγ affected the subsequent downstream signal transduction and grain size. Manipulating G-protein signaling also affects organ size in maize (Zea mays) and is expected to constitute a general mechanism for crop improvement. Collectively, these findings reveal that plant-specific Gγ tails drive signaling selectivity and serve as valuable targets for optimizing crop traits through G-protein manipulation.

Telomere-to-telomere gap-free genome assembly provides genetic insight into the triterpenoid saponins biosynthesis in Platycodon grandiflorus

Platycodon grandiflorus has been widely used in Asia as a medicinal herb and food because of its anti-inflammatory and hepatoprotective properties. P. grandiflorus has important clinical value because of the active triterpenoid saponins in its roots. However, the biosynthetic pathway of triterpenoid saponins in P. grandiflorus remains unclear, and the related genes remain unknown. Therefore, in this study, we assembled a high-quality and integrated telomere-to-telomere P. grandiflorus reference genome and combined time-specific transcriptome and metabolome profiling to identify the cytochrome P450s (CYPs) responsible for the hydroxylation processes involved in triterpenoid saponin biosynthesis. Nine chromosomes were assembled without gaps or mismatches, and nine centromeres and 18 telomere regions were identified. This genome eliminated redundant sequences from previous genome versions and incorporated structural variation information. Comparative analysis of the P. grandiflorus genome revealed that P. grandiflorus underwent a core eudicot γ-WGT event. We screened 211 CYPs and found that tandem and proximal duplications may be crucial for the expansion of CYP families. We outlined the proposed hydroxylation steps, likely catalyzed by the CYP716A/72A/749A families, in platycodin biosynthesis and identified three PgCYP716A, seven PgCYP72A, and seven PgCYP749A genes that showed a positive correlation with platycodin biosynthesis. By establishing a T2T assembly genome, transcriptome, and metabolome resource for P. grandiflorus, we provide a foundation for the complete elucidation of the platycodins biosynthetic pathway, which consequently leads to heterologous bioproduction, and serves as a fundamental genetic resource for molecular-assisted breeding and genetic improvement of P. grandiflorus.

Genomic insights into the domestication and genetic basis of yield in papaya

Papaya (Carica papaya L.) is an important tropical and subtropical fruit crop, and understanding its genome is essential for breeding. In this study, we assembled a high-quality genome of 344.17 Mb for the newly cultivated papaya 'Zihui', which contains 22 250 protein-coding genes. By integrating 201 resequenced papaya genomes, we identified four distinct papaya groups and a 34 Mb genomic region with strong domestication selection signals. Within these regions, two key genes associated with papaya yield were discovered: Cp_zihui06549, encoding a leucine-rich receptor-like protein kinase, and Cp_zihui06768, encoding the accumulation of photosystem one 1 (APO1) protein. Heterologous expression of Cp_zihui06549 in tomato confirmed that the total number of fruits in transgenic lines more than doubled compared to wild-type plants, resulting in a significant yield increase. Furthermore, we constructed a pan-genome of papaya and obtained a 77.41 Mb nonreference sequence containing 1543 genes. Within this pan-genome, 2483 variable genes, we detected, including four genes annotated as the 'terpene synthase activity' Gene Ontology term, which were lost in cultivars during domestication. Finally, gene retention analyses were performed using gene presence and absence variation data and differentially expressed genes across various tissues and organs. This study provides valuable insights into the genes and loci associated with phenotypes and domestication processes, laying a solid foundation for future papaya breeding efforts.

Pangenome analysis reveals structural variation associated with seed size and weight traits in peanut

Peanut (Arachis hypogaea L.) is an important oilseed and food legume crop, with seed size and weight being critical traits for domestication and breeding. However, genomic rearrangements like structural variations (SVs) underlying seed size and weight remain unclear. Here we present a comprehensive pangenome analysis utilizing eight high-quality genomes (two diploid wild, two tetraploid wild and four tetraploid cultivated peanuts) and resequencing data of 269 accessions with diverse seed sizes. We identified 22,222 core or soft-core, 22,232 distributed and 5,643 private gene families. The frequency of SVs in subgenome A is higher than in subgenome B. We identified 1,335 domestication-related SVs and 190 SVs associated with seed size or weight. Notably, a 275-bp deletion in gene AhARF2-2 results in loss of interaction with AhIAA13 and TOPLESS, reducing the inhibitory effect on AhGRF5 and promoting seed expansion. This high-quality pangenome serves as a fundamental resource for the genetic enhancement of peanuts and other legume crops.

Genomic and Methylomic Signatures Associated With the Maintenance of Genome Stability and Adaptive Evolution in Two Closely Allied Wolf Spiders

Pardosa spiders, belonging to the wolf spider family Lycosidae, play a vital role in maintaining the health of forest and agricultural ecosystems due to their function in pest control. This study presents chromosome-level genome assemblies for two allied Pardosa species, P. laura and P. agraria. Both species' genomes show a notable expansion of helitron transposable elements, which contributes to their large genome sizes. Methylome analysis indicates that P. laura has higher overall DNA methylation levels compared to P. agraria. DNA methylation may not only aids in transposable element-driven genome expansion but also positively affects the three-dimensional organisation of P. laura after transposon amplification, thereby potentially enhancing genome stability. Genes associated with hyper-differentially methylated regions in P. laura (compared to P. agraria) are enriched in functions related to mRNA processing and energy production. Furthermore, combined transcriptome and methylome profiling has uncovered a complex regulatory interplay between DNA methylation and gene expression, emphasising the important role of gene body methylation in the regulation of gene expression. Comparative genomic analysis shows a significant expansion of cuticle protein and detoxification-related gene families in P. laura, which may improve its adaptability to various habitats. This study provides essential genomic and methylomic insights, offering a deeper understanding of the relationship between transposable elements and genome stability, and illuminating the adaptive evolution and species differentiation among allied spiders.

Genome-Wide Identification and Evolution-Profiling Analysis of Heat Shock Protein Gene Family in Poaceae Barnhart

Heat shock proteins (HSPs) function as molecular chaperones to maintain protein homeostasis and repair denatured proteins, counteracting abiotic stresses. Despite their functional importance, a systematic bioinformatics analysis of the HSP gene family was lacking in Poaceae. In this study, we revealed that HSPs are widely distributed from algae to eudicots, with varying numbers in Poaceae including Oryza, Triticum, and Panicum. Gene duplication events, particularly dispersed duplication (DSD), tandem duplication (TD), and genome polyploidization, have probably driven the increased number of HSP genes and the expansion of HSP family proteins. Gene Ontology (GO) annotation analyses suggested their conserved functions. Promoter cis-acting element analyses indicated that their expression levels were tightly regulated by abiotic stresses. We validated that many collinear HSP genes are indeed regulated by the cold stress by analyzing the published RNA-seq data in rice, maize, and wheat, and performing RT-qPCR in rice. Our findings shed light on the role of HSPs in the abiotic stress response, laying the groundwork for further exploration of HSP functions in Poaceae.

Genome of a stage-dependent cave-dwelling frog reveals the genetic mechanism of an extremely divergent biphasic life cycle

Cave-dwelling species offer unique insights into adaptive evolution. The stage-dependent cave frog, Oreolalax rhodostigmatus (Orho), exhibits troglomorphic traits as a tadpole in Karst caves, transitioning to a troglophilic/trogloxenic lifestyle after metamorphosis, characterized by developed pigment and eyes. We present the Orho genome (3.16 Gb, 26,192 protein-coding genes), revealing extensive expansion and positive selection in gene families associated with olfactory, taste, visual, and pain perceptions. Orho tadpoles exhibit suppressed visual function while retaining crystalline lens development. Adult eyes demonstrate high light-induced plasticity in the visual cycle. Orho tadpoles display both developmental and light-induced melanogenesis, which is associated with distinctive tyrosinases. A stage-dependent amphibian-specific tyrosinase subfamily, reported here, underpins their ontogenetic pigmentation. Additionally, prominent hepatic fat storage and genetic/transcriptional variations in lipid metabolism genes characterize tadpole development. These findings unveil the molecular mechanisms behind Orho's stage-dependent cave adaptation, which differs mechanistically from cavefishes, offering valuable insights into the highly divergent biphasic life cycle.

Novel and diverse features identified in the genomes of bacteria isolated from a hydrothermal vent plume

Hydrothermal vent plumes (HVPs), formed by high-temperature vent emissions, are rich in compounds that support chemosynthesis and serve as reservoirs of microbial diversity and genetic innovation. Through turbulence, mixing, and interaction with subsea currents, vent communities are thought to disperse across ocean basins. In this study, we focused on the plume of the Moytirra hydrothermal vent field, a relatively unexplored site, to investigate its microbial inhabitants. We cultured bacteria from the Moytirra HVP using 11 different media types and performed complete genome sequencing on 12 isolates. Our analyses revealed four putatively novel species from the Thalassobaculum, Sulfitobacter, Idiomarina, and Christiangramia genera. Comparative genomics identified unique genomic islands containing biosynthetic gene clusters, including a novel Non-Ribosomal Peptide Synthetase/Polyketide Synthase cluster, toxin-antitoxin systems, and evidence of horizontal gene transfer facilitated by prophages. These findings underscore the potential of HVPs as a source of novel microbial species and biotechnologically relevant genes, contributing to our understanding of the biodiversity and genetic complexity of these extreme environments.IMPORTANCEHydrothermal vents are dynamic environments that offer unique nutrients for chemosynthetic organisms to drive biology in the deep-sea. The dynamics of these ecosystems are thought to drive genomic innovation in resident populations. Hydrothermal vent plumes (HVPs) mix with surrounding water, carrying local microbiota with them and dispersing for hundreds of kilometers. This study isolated bacteria from a HVP to capture a genomic snapshot of the microbial community, revealing four putatively novel species of bacteria within three taxonomic classes. The addition of these genomes to public databases provides valuable insights into the genomic function, architecture, and novel biosynthetic gene clusters of bacteria found in these extreme environments.

Genomic signatures associated with the evolutionary loss of egg yolk in parasitoid wasps

Trait regression and loss have occurred repeatedly in numerous lineages in response to environmental changes. In parasitoid wasps, a megadiverse group of hymenopteran insects, yolk protein reduction or loss has been observed in many species, likely linked to the transition from ectoparasitism to endoparasitism. However, the genetic basis of this trait and the impact of its loss on genome evolution remain poorly understood. Here, we performed a comparative genomic analysis of 64 hymenopteran insects. The conserved insect yolk protein gene vitellogenin (Vg) underwent five independent loss events in four families, involving 23 of the analyzed endoparasitoid species. Whole-genome alignment suggested that Vg loss occurred during genome rearrangement events. Analysis of Vg receptor gene (VgR) loss, selection, and structural variation in lineages lacking Vg demonstrated functional biases in the patterns of gene loss. The ectoparasitism to endoparasitism transition did not appear to be the primary driver of Vg loss or the subsequent VgR evolution. Together, these findings reveal the genomic changes underlying a unique trait loss in parasitoid wasps. More broadly, this study enhances our understanding of yolk protein loss evolution outside the class Mammalia, highlighting a potential evolutionary trend arising from the availability of an alternative nutrient source for embryonic development.

Still waters run deep in large-scale genome rearrangements of morphologically conservative Polyplacophora

A major question in animal evolution is how genotypic and phenotypic changes are related, and another is when and whether ancient gene order is conserved in living clades. Chitons, the molluscan class Polyplacophora, retain a body plan and general morphology apparently little changed since the Palaeozoic. We present a comparative analysis of five reference quality genomes, including four de novo assemblies, covering all major chiton clades, and an updated phylogeny for the phylum. We constructed 20 ancient molluscan linkage groups (MLGs) and show that these are relatively conserved in bivalve karyotypes, but in chitons they are subject to re-ordering, rearrangement, fusion, or partial duplication and vary even between congeneric species. The largest number of novel fusions is in the most plesiomorphic clade Lepidopleurida, and the chitonid Liolophura japonica has a partial genome duplication, extending the occurrence of large-scale gene duplication within Mollusca. The extreme and dynamic genome rearrangements in this class stands in contrast to most other animals, demonstrating that chitons have overcome evolutionary constraints acting on other animal groups. The apparently conservative phenome of chitons belies rapid and extensive changes in genome.

A wheat CC-NBS-LRR protein Ym1 confers WYMV resistance by recognizing viral coat protein

Ym1 is the most widely utilized gene for wheat yellow mosaic virus (WYMV) disease control in worldwide wheat breeding. Here, we successfully isolated the responsible gene for Ym1. It encodes a typical CC-NBS-LRR type R protein, which is specifically expressed in root and induced upon WYMV infection. Ym1-mediated WYMV resistance is likely achieved by blocking viral transmission from the root cortex into steles, thereby preventing systemic movement to aerial tissues. Ym1 CC domain is essential for triggering cell death. Ym1 specifically interacts with WYMV coat protein, and this interaction leads to nucleocytoplasmic redistribution, a process for transitioning Ym1 from an auto-inhibited to an activated state. The activation subsequently elicits hypersensitive responses and establishes WYMV resistance. Ym1 is likely introgressed from the sub-genome Xn or Xc of polyploid Aegilops species. The findings highlight an exogenous-introgressed and root-specifically expressed R gene that confers WYMV resistance by recognizing the viral component.

A pangenome reference of wild and cultivated rice

Oryza rufipogon, the wild progenitor of Asian cultivated rice Oryza sativa, is an important resource for rice breeding1. Here we present a wild-cultivated rice pangenome based on 145 chromosome-level assemblies, comprising 129 genetically diverse O. rufipogon accessions and 16 diverse varieties of O. sativa. This pangenome contains 3.87 Gb of sequences that are absent from the O. sativa ssp. japonica cv. Nipponbare reference genome. We captured alternate assemblies that include heterozygous information missing in the primary assemblies, and identified a total of 69,531 pan-genes, with 28,907 core genes and 13,728 wild-rice-specific genes. We observed a higher abundance and a significantly greater diversity of resistance-gene analogues in wild rice than in cultivars. Our analysis indicates that two cultivated subpopulations, intro-indica and basmati, were generated through gene flows among cultivars in South Asia. We also provide strong evidence to support the theory that the initial domestication of all Asian cultivated rice occurred only once. Furthermore, we captured 855,122 differentiated single-nucleotide polymorphisms and 13,853 differentiated presence-absence variations between indica and japonica, which could be traced to the divergence of their respective ancestors and the existence of a larger genetic bottleneck in japonica. This study provides reference resources for enhancing rice breeding, and enriches our understanding of the origins and domestication process of rice.

Genome-wide identification and expression analysis of epigenetic regulator gene families in the medicinal mushroom Ganoderma lucidum

Epigenetic regulator (ER) genes, crucial for fungal growth and development, remain largely unexplored in Ganoderma lucidum, a medicinal mushroom valued for its bioactive compounds. This study identified 81 ER genes in G. lucidum, distributed across 12 chromosomes and classified into six families: 3 chromatin remodelers, 4 DNA methyltransferases, 7 histone acetyltransferases, 22 histone deacetylases, 23 histone methyltransferases, and 22 histone demethyltransferases. Comparative and phylogenetic analyses with other species revealed conserved orthologs and species-specific clusters. Gene duplication analysis suggested whole-genome duplication expanded ER gene families, primarily histone demethyltransferases under purifying selection. Additionally, gene structure, motif, and domain analyses revealed family-specific intron/exon organization and conserved domains. Transcriptome profiling across four developmental stages (mycelium, primordia, young and mature fruiting body) revealed dynamic stage-specific expression patterns, suggesting their developmental significance. The result of qRT-PCR validated the expression patterns for 18 ER genes, laying foundation for future research exploring epigenetic regulation in fungal development and bioactive compound production.

SOI: robust identification of orthologous synteny with the Orthology Index and broad applications in evolutionary genomics

With the explosive growth of whole-genome datasets, accurate detection of orthologous synteny has become crucial for reconstructing evolutionary history. However, current methods for identifying orthologous synteny face great limitations, particularly in scaling with varied polyploidy histories and accurately removing out-paralogous synteny. In this study, we developed a scalable and robust approach, based on the Orthology Index (OI), to effectively identify orthologous synteny. Our evaluation across a large-scale empirical dataset with diverse polyploidization events demonstrated the high reliability and robustness of the OI method. Simulation-based benchmarks further validated the accuracy of our method, showing its superior performance against existing methods across a wide range of scenarios. Additionally, we explored its broad applications in reconstructing the evolutionary histories of plant genomes, including the inference of polyploidy, identification of reticulation, and phylogenomics. In conclusion, OI offers a robust, interpretable, and scalable approach for identifying orthologous synteny, facilitating more accurate and efficient analyses in plant evolutionary genomics.

Phylogenomics and adaptive evolution of the Colletotrichum gloeosporioides species complex

The Colletotrichum gloeosporioides species complex (CGSC) is one of the most devastating fungal phytopathogens, and is composed of three main clades: Kahawae, Musae, and Theobromicola. Despite the diversity of CGSC, there is limited understanding on their evolutionary mechanisms. By analysing 49 newly assembled genomes, we found that the expansion of transposable elements, especially long terminal repeat retrotransposons, facilitates the expansion of genome size and genetic variation. In-depth analyses suggested that an intra-chromosomal inversion may have been the driving force behind the divergence of Kahawae clade from its ancestor. Within the Kahawae clade, the narrow-hosted quarantine species C. kahawae has undergone extensive chromosomal rearrangements mediated by repetitive sequences, generating highly dynamic lineage-specific genomic regions compared to the closely related broad-hosted species C. cigarro. The findings of this study highlight the role of chromosomal rearrangements in promoting genetic diversification and host adaptation, and provide new perspectives for understanding the evolution of phytopathogenic fungi.

Understanding the Regulation Activities of Transposons in Driving the Variation and Evolution of Polyploid Plant Genome

Transposon is the main component of the eukaryotic genome, and more and more plant genome data show that transposons are diverse in regulating genome structure, variation, function and evolution, with different transposition mechanisms in the genome. Hybridization and polyploidy play an important role in promoting plant speciation and evolution, and recent studies have shown that polyploidy is usually accompanied by the expansion of transposons, which affect the genome size and structure of polyploid plants. Transposons can insert into genes and intergenic regions, resulting in great differences in the overall genome structure of closely related plant species, and it can also capture gene segments in the genome to increase the copy number of genes. In addition, transposons influence the epigenetic modification state of the genome and regulate the expression of the gene, while plant phenotype, biological and abiotic stress response are also regulated by transposons. Overall, transposons play an important role in the plant genome, especially polyploid plant genome, adaptation and evolution.

Chromosome-scale genome assembly and annotation of Xenocypris argentea

Xenocypris argentea is a small to medium-sized freshwater cyprinid fish. It distributes widely in the rivers and lakes of China, and is often used as a tool fish for water quality improvement and optimizing aquaculture structures. In recent years, natural populations of X. argentea have decreased rapidly due to human activities, yet little is known about the genetics and genomics of this fish. In the present work, we reported a chromosome-level reference genome of X. argentea based on PacBio HiFi, Hi-C and Illumina paired-end sequencing technologies. The assembled genome was 984.96 Mb in length, with a contig N50 of 36.02 Mb. Using Hi-C interaction information, 99.47% of the contigs were anchored onto 24 chromosomes, and 18 of the chromosomes were gap-free. Further analysis identified 560.27 Mb of repeat sequences and 28,533 protein-coding genes in the genome, of which, 95.62% (27,284) genes were functionally annotated. This high-quality genome offers an invaluable resource for population genetics and phylogeny, comparative genomics, adaptive evolution and functional exploration of X. argentea.

Evolutionary History of Bilaterian FoxP Genes: Complex Ancestral Functions and Evolutionary Changes Spanning 2R-WGD in the Vertebrate Lineage

Human and fly FoxP homologs are well-known for their roles in the development of cognitive abilities. These findings have led to the hypothesis that the ancestral function of FoxP was in the development of cognitive neural circuits. However, complex brains in human and fly evolved independently, and the similar cognitive function of FoxP in human and fly may thus be interpreted as a result of convergent evolution. In addition, the 4 gnathostome FoxP paralogs also possess diverse developmental functions unrelated to neurodevelopment, which might have been overlooked in comparative studies of invertebrate FoxP homologs. To resolve these uncertainties, we set out to improve the phylogenetic reconstruction of vertebrate FoxP homologs and broaden the taxonomic sampling of gene expression profiling to include an invertebrate chordate, ambulacrarian deuterostomes, and a spiralian protostome. Using phylogenetic analysis combined with synteny mapping, we elaborated the hypothesis that the 4 FoxP paralogs arose through the 2R-WGD events shared by all gnathostome species. Based on this evolutionary scenario, we examined the FoxP expression pattern in amphioxus development and concluded that FoxP already had complex developmental functions across all germ layers in the chordate ancestor. Moreover, in sea urchin, hemichordate, and catenulid flatworm, FoxP was expressed in the gut prominently, in addition to the anterior neurogenic ectoderm. This surprising similarity shared among these distantly related species implies that FoxP may have a significant function in gut development in addition to the neural development function in the last common ancestor of bilaterians.

A chromosome-level genome assembly and annotation of the Pseudorasbora elongata (Cypriniformes: Cyprinidae)

Pseudorasbora elongata is a unique small fish species endemic to China, distinguished by its striking body coloration resembling a "Chinese ink brush." Due to environmental changes and anthropogenic factors, its wild populations have declined, and it has been listed multiple times as an endangered species. However, the absence of a chromosomal-level reference for P. elongata has hindered our understanding of its population genetics and conservation biology. To address this gap, we present a chromosome-level genome assembly of P. elongata, generated using PacBio HiFi reads, Oxford Nanopore Technologies, and Hi-C data. We get a genome size of 1.4 Gb with a contig N50 of 34.4 Mb and a scafold N50 of 53.7 Mb. Telomeric sequences were identified at the ends of 42 telomeres across 25 chromosomes. Notably, we observed a high degree of collinearity between our assembly and the Pseudorasbora parva genome. This study provides valuable insights into the genetics, genomics, and evolutionary history of P. elongata, offering a foundation for future research and enabling the development of genetic conservation strategies.

Identification of the GATA transcription factor family in tea plant (Camellia sinensis) and the characterizations in nitrogen metabolism

GATA transcription factor is a widely existing regulatory factor in biology and participates in many plant physiological processes. In tea plants (Camellia sinensis), the GATA Transcription Factor family has not been explored. In this study, 40 GATA genes were identified in tea plants, with a focus on CsGATA12 and 17, whose expression patterns were correlated with nitrogen deficiency, nitrogen forms and nitrogen concentration. Among them, CsGATA17 is highly correlated with theanine and ethylamine contents in response to high nitrogen levels. Transcriptional regulation confirmed that CsGATA17 acts as a transcriptional activator to positively regulate CsAlaDC (alanine decarboxylase) to promote theanine synthesis in leaves with high nitrogen levels. This interaction was simulated and visualized by molecular docking and ultimately confirmed by EMSA. This study expands our understanding of GATA factors in tea plants and reveals the role of CsGATA17 in nitrogen metabolism and theanine regulation.

Chromosomal-Level Genome Suggests Adaptive Constraints Leading to the Historical Population Decline in an Extremely Endangered Plant

Increased human activity and climate change have significantly impacted wild habitats and increased the number of endangered species. Exploring evolutionary history and predicting adaptive potential using genomic data will facilitate species conservation and biodiversity recovery. Here, we examined the genome evolution of a critically endangered tree Pellacalyx yunnanensis, a plant species with extremely small populations (PSESP) that is narrowly distributed in Xishuangbanna, China. The species has neared extinction due to economic exploitation in recent decades. We assembled a chromosome-level genome of 334 Mb, with the N50 length of 20.5 Mb. Using the genome, we discovered that P. yunnanensis has undergone several population size reductions, leading to excess deleterious mutations. The species may possess low adaptive potential due to reduced genetic diversity and the loss of stress-responsive genes. We estimate that P. yunnanensis is the basal species of its genus and diverged from its relatives during global cooling, suggesting it was stranded in unsuitable environments during periods of dramatic climate change. In particular, the loss of seed dormancy leads to germination under unfavourable conditions and reproduction challenges. This dormancy loss may have occurred through genetic changes that suppress ABA signalling and the loss of genes involved in seed maturation. The high-quality genome has also enabled us to reveal phenotypic trait evolution in Rhizophoraceae and identify divergent adaptation to intertidal and inland habitats. In summary, our study elucidates mechanisms underlying the decline and evaluates the adaptive potential of P. yunnanensis to future climate change, informing future conservation efforts.

Genome-Wide Identification and Expression Analysis Unveil the Involvement of the Succinic Semialdehyde Dehydrogenase (SSADH) Gene Family in Banana Low Temperature Stress

Banana (Musa spp.) is susceptible to low-temperature stress and other environmental stresses, which can hinder the growth and development. Succinic semialdehyde dehydrogenase (SSADH) is critical for GABA biosynthesis and plays a crucial role in plants. However, the SSADH genes of bananas have not been studied. This study found 19 MaSSADHs, 18 MbSSADHs, and 18 MiSSADHs from the banana genome. According to the phylogenetic tree, these genes can be categorized into five branches. This study cloned the MaSSADH1-14 from banana. The subcellular localization assays of MaSSADH1-14 in tobacco leaves confirmed that the presence of SSADH was not only localized mitochondrion but also localized chloroplast. The cis-elements of the SSADH gene family are related to the potential regulation of the banana SSADH gene family; their involvement in diverse stress responses. Transcriptomic data was utilized to examine the effect of MaSSADH genes under cold stress in bananas. The results of RT-qPCR were consistent with transcriptome data. These results showed that most MaSSADHs are passively responsive to low-temperature treatment. In addition, transient overexpression of MaSSADH1-14 in Nicotiana benthamiana leaves resulted in the content of GABA increasing, indicating that MaSSADH1-14 may be involved in the accumulation of GABA of banana. Collectively, these results improve knowledge of the SSADH gene family in banana and establish a basis for comprehending its biological roles in response to low temperatures.

Integrative omics reveals mechanisms of biosynthesis and regulation of floral scent in Cymbidium tracyanum

Flower scent is a crucial determiner in pollinator attraction and a significant horticultural trait in ornamental plants. Orchids, which have long been of interest in evolutionary biology and horticulture, exhibit remarkable diversity in floral scent type and intensity. However, the mechanisms underlying floral scent biosynthesis and regulation in orchids remain largely unexplored. In this study, we focus on floral scent in Cymbidium tracyanum, a wild species known for its strong floral fragrance and as a primary breeding parent of commercial Cymbidium hybrids. We present a chromosome-level genome assembly of C. tracyanum, totaling 3.79 Gb in size. Comparative genomic analyses reveal significant expansion of gene families associated with terpenoid biosynthesis and related metabolic pathways in C. tracyanum. Integrative analysis of genomic, volatolomic and transcriptomic data identified terpenoids as the predominant volatile components in the flowers of C. tracyanum. We characterized the spatiotemporal patterns of these volatiles and identified CtTPS genes responsible for volatile terpenoid biosynthesis, validating their catalytic functions in vitro. Dual-luciferase reporter assays, yeast one-hybrid assays and EMSA experiments confirmed that CtTPS2, CtTPS3, and CtTPS8 could be activated by various transcription factors (i.e., CtAP2/ERF1, CtbZIP1, CtMYB2, CtMYB3 and CtAP2/ERF4), thereby regulating the production of corresponding monoterpenes and sesquiterpenes. Our study elucidates the biosynthetic and regulatory mechanisms of floral scent in C. tracyanum, which is of great significance for the breeding of fragrant Cymbidium varieties and understanding the ecological adaptability of orchids. This study also highlights the importance of integrating multi-omics data in deciphering key horticultural traits in orchids.

Identification and Characterization of Histone Modification Gene Families and Their Expression Patterns During Pod and Seed Development in Peanut

Histone methylation and acetylation play potential roles in plant growth and development through various histone modification (HM) genes. However, studies of HM genes are still limited in peanut (Arachis hypogaea L.), a globally important oilseed crop. Here, comprehensive identification and investigation of HM genes were performed using the whole genome of peanut, and a total of 207 AhHMs encoding 108 histone methyltransferases, 51 histone demethylases, 16 histone acetylases, and 32 histone deacetylases were identified. Detailed analysis of these AhHMs, including chromosome locations, gene structures, protein motifs, and protein-protein interactions, was performed. Tandem, segmental, transposed, dispersed, and whole-genome duplications were involved in the evolution and expansion of the HM gene families in peanut. Ka/Ks analysis indicated that the AhHMs underwent purifying selection. The expression profiles of the 207 AhHMs were investigated during the pod and seed development stages on the basis of the transcriptome sequencing results. Quantitative real-time PCR confirmed that eight AhHMs were differentially expressed during pod and seed development. These results provide data support for further studying the epigenetic mechanism of peanut histones, deepen the understanding of seed development, and provide a new direction for the cultivation of more high-yield and high-quality peanut varieties.

Chromosome-level genome assembly of a specialist walnut pest Atrijuglans aristata

Gelechioidea represents the most diverse superfamily of tiny boring pests in Lepidoptera that pose a serious threat to agricultural and forestry economic crops. However, the lack of high-quality genome of highly specialized species makes it difficult to draw general conclusions about the mechanism of the close binding relationship between pests and crops. In this study, based on second- and third-generation sequencing reads, we constructed a chromosome-level genome for the Atrijuglans aristata, a specialized boring pest, that specifically harms the green husk of cultivated walnuts. The genome is 480.99 Mb and spans 31 pseudo-chromosomes, including Z and a portion of W chromosome. Contig N50 and scaffold N50 of the genome are 2.68 Mb and 16.01 Mb respectively. The BUSCO completeness achieves 95.6% with a total of 22,542 protein-coding genes are annotated. As the first sequenced genome of Stathmopodidae family, this high-quality genome provides a genetic basis for the mining of genes for important functional traits in A. aristata, as well as an important reference for the study of host adaptation of the (insect) specialists.

A Chromosome-level genome assembly of the American bullfrog (Aquarana catesbeiana)

The American bullfrog (Aquarana catesbeiana) is both an economically important aquaculture species and a globally distributed invasive organism with high environmental adaptability. In this study, we present a high-quality chromosome-level genome assembly for the species, comprising 13 chromosomes with a total length of 6.32 Gb and a scaffold N50 of 691.8 Mb. Genome completeness was evaluated at 95.5% using BUSCO and 99.9% using Merqury. Repetitive sequences accounted for 79.51% of the genome. Through a combination of RNA-seq, Ab initio and homology-based gene prediction, we identified 32,382 protein-coding genes, with 98.96% of these genes functionally annotated. This chromosome-level assembly provides an important resource for future studies on the evolution, functional genomics and molecular breeding of the American bullfrog.

Genomes of two indigenous clams Anomalocardia flexuosa (Linnaeus, 1767) and Meretrix petechialis (Lamarck, 1818)

Clam digging has a long history in Hong Kong, but unregulated clam digging activities depletes clam populations and threatens the ecosystem. Population genomics is useful to unravel the connectivity of clams at different geographical locations and to provide necessary conservation measures; and yet, only limited number of clams in Hong Kong have genomic resources. Here, we present chromosomal-level genome assemblies for two clams commonly found in Hong Kong, Anomalocardia flexuosa and Meretrix petechialis, using a combination of PacBio HiFi and Omni-C reads. For A. flexuosa, we assembled the genome into 19 pseudochromosomes with a genome size of 1.09 Gb (scaffold N50 = 58.5 Mb), and BUSCO scores of 94.4%. A total of 20,881 gene models were also predicted using the transcriptomes generated in this study. For M. petechialis, the genome was mainly assembled into 19 pseudochromosomes with a genome size of 1.04 Gb (scaffold N50 = 53.5 Mb), and BUSCO scores of 95.7%. A total of 20,084 gene models were also predicted using the transcriptomes generated in this study. The two new genomic resources established in this study will be useful for further study of biology, ecology, and evolution of clams, as well as setting up a foundation for evidence-informed decision making in conservation measures and implementation.

Chromosome-level genome assembly of Z strain European corn borer Ostrinia nubilalis (Lepidoptera: Crambidae)

European corn borer Ostrinia nubilalis (Hübner) is the most important pest of maize around world, and an ideal model for the sympatric host races, evolutionary and speciation research. In this study, we assembled a chromosome-level genome of Z strain O. nubilalis by the integrated Illumina short reads, PacBio Revio long reads, and Hi-C sequencing data. The chromosome-level genome was 480.04 Mb in total length with a contig N50 length of 16.51 Mb, which 98.59% genome anchored into 31 chromosomes. For the annotation, 1,046,695 repeat sequences in length of 212.07 Mb, 1,550 non-coding RNAs (including 1,208 tRNAs, 179 rRNAs, 62 miRNAs, 81 snRNAs, and 20 snoRNAs), and 17,145 protein-coding genes were identified. And 100% genes were functional annotated by SwissProt, NR, eggNOG, Go, and KEGG database. This genome provides a valuable genomics resource to elucidate the host plant adaptation, thermal adaptation, diapause induction, Bacillus thuringiensis toxin resistance, sexual communication, sympatric host races, and speciation process of O. nubilalis.

Chromosome-level genome assembly of Iodes seguinii and its metabonomic implications for rheumatoid arthritis treatment

Iodes seguinii is a woody vine known for its potential therapeutic applications in treating rheumatoid arthritis (RA) due to its rich bioactive components. Here, we achieved the first chromosome-level assembly of the nuclear genome of I. seguinii using PacBio HiFi and chromatin conformation capture (Hi-C) sequencing data. The initial assembly with PacBio data produced contigs with an N50 length of 9.71 Mb, and Hi-C data anchored these contigs into 13 chromosomes, achieving a total length of 273.58 Mb, closely matching the estimated genome size. Quality assessments, including BUSCO, long terminal repeat assembly index, transcriptome mapping rates, and sequencing coverage, confirmed the high quality, completeness, and continuity of the assembly, identifying 115.28 Mb of repetitive sequences, 1062 RNA genes, and 25,270 protein-coding genes. Additionally, we assembled and annotated the 150,599 bp chloroplast genome using Illumina sequencing data, containing 121 genes including key DNA barcodes, with maturase K (matK) proving effective for species identification. Phylogenetic analysis positioned I. seguinii at the base of the Lamiales clade, identifying significant gene family expansions and contractions, particularly related to secondary metabolite synthesis and DNA damage repair. Metabolite analysis identified 84 active components in I. seguinii, including the discovery of luteolin, with 119 targets predicted for RA treatment, including core targets like AKT1, toll-like receptor 4 (TLR4), epidermal growth factor receptor (EGFR), tumor necrosis factor (TNF), TP53, NFKB1, janus kinase 2 (JAK2), BCL2, mitogen-activated protein kinase 1 (MAPK1), and spleen-associated tyrosine kinase (SYK). Key active components such as flavonoids and polyphenols with anti-inflammatory activities were highlighted. The discovery of luteolin, in particular, underscores its potential therapeutic role. These findings provide a valuable genomic resource and a scientific basis for the development and application of I. seguinii, addressing the genomic gap in the genus Iodes and the order Icacinales and underscoring the need for further research in genomics, transcriptomics, and metabolomics to fully explore its potential.

Pangeneric genome analyses reveal the evolution and diversity of the orchid genus Dendrobium

Orchids constitute one of the most diverse families of angiosperms, yet their genome evolution and diversity remain unclear. Here we construct and analyse chromosome-scale de novo assembled genomes of 17 representative accessions spanning 12 sections in Dendrobium, one of the largest orchid genera. These accessions represent a broad spectrum of phenotypes, lineages and geographical distributions. We first construct haplotype-resolved genomes for a Dendrobium hybrid and uncover haplotypic variations and allelic imbalance in the heterozygous genome, demonstrating the significance of diverse ancestry. At Dendrobium genus-wide scale, we further elucidate phylogenetic relationships, evolutionary dynamics, entire gene repertoire, and the mechanisms of preserving ancient genetic variants and rapid recent genome evolution for habitat adaption. We also showcase distinctive evolutionary trajectories in MADS-box and PEBP families over 28 Ma. These results considerably contribute to unearthing the mystery of orchid origin, evolution and diversification, laying the foundation for efficient use of genetic diversity in breeding.

Genome sequencing of three Polyscias species reveals common features in terpene synthase gene family evolution in these species

The genus Polyscias, part of the Araliaceae family, is known for its significant ornamental and medicinal value, as well as its rich variety of metabolites. These plants are primarily found in tropical regions, particularly in Southeast Asia and the Pacific islands. The diverse geographical environments have led to the emergence of many unique and endangered species, although there is limited genomic information available about them. In this study, we generated high-quality reference genomes for three endangered species: two that are endemic to Hawai'i, Polyscias cf. bisattenuata and Polyscias lallanii, and one more widespread species, Polyscias macgillivrayi. We identified a total of 51,083, 60,881, and 29,060 genes in these three species, respectively. Whole-genome duplication analysis indicated that all three species underwent a common duplication event. By examining the phylogenetic and structural characteristics of the terpene synthase gene family in these species and closely related species, we identified several gene clusters that play crucial roles in metabolite synthesis. A variety of mono- and sesquiterpenoids were detected, with several of these compounds having been validated in previous studies. Our findings provide a foundation for further genetic and biochemical investigations of Polyscias, which may aid in the conservation of these endangered species.

Species-specific circular RNA circDS-1 enhances adaptive evolution in Talaromyces marneffei through regulation of dimorphic transition

Thermal adaptability is a crucial characteristic for mammalian pathogenic fungi that originally inhabit natural ecosystems. Thermally dimorphic fungi have evolved a unique ability to respond to host body temperature by shifting from mycelia to yeast. The high similarity of protein-coding genes between these fungi and their relatives suggests the indispensable but often overlooked roles of non-coding elements in fungal thermal adaptation. Here, we systematically delineated the landscape of full-length circRNAs in both mycelial and yeast conditions of Talaromyces marneffei, a typical thermally dimorphic fungus causing fatal Talaromycosis, by optimizing an integrative pipeline for circRNA detection utilizing next- and third-generation sequencing. We found T. marneffei circRNA demonstrated features such as shorter length, lower abundance, and circularization-biased splicing. We then identified and validated that circDS-1, independent of its parental gene, promotes the hyphae-to-yeast transition, maintains yeast morphology, and is involved in virulence regulation. Further analysis and experiments among Talaromyces confirmed that the generation of circDS-1 is driven by a T. marneffei-specific region in the flanking intron of circDS-1. Together, our findings not only provide fresh insights into the role of circRNA in fungal thermal adaptation but also reveal a novel molecular mechanism for the adaptive evolution of functional circRNAs derived from intronic mutations.

Proteomic analyses reveal the key role of gene co-option in the evolution of the scaly-foot snail scleritome

Biomineralization, a key driving force underlying dramatic morphological diversity, is widely adopted by metazoans to incorporate inorganic minerals into their organic matrices. The scaly-foot snail Chrysomallon squamiferum from deep-sea hot vents uniquely possesses hundreds of sclerites on its foot in addition to a coiled shell, providing an exclusive case to study the formation of evolutionarily novel hard parts. Here, we identified the matrix proteins present in the exoskeletons of C. squamiferum and Gigantopelta aegis, a confamilial species from the same vent habitat but lacking sclerites, to uncover the genes and proteins presumably involved in the sclerite formation processes. Comparative multi-omics analyses suggest that C. squamiferum co-opted a diverse range of metazoan biocalcifying proteins through sclerite formation in a possibly deep homology scenario, and the up-regulated biomineralization-related genes in the foot imply alternative sources of sclerite proteins. The sclerite-secreting epithelium employs and utilizes genes considerably older than those in the mantle, which supports the predominant contribution of co-option in C. squamiferum sclerite formation. Our results highlight the importance of gene co-option in shaping novel hard parts in C. squamiferum and indicate that lineage-specific gene incorporation is a possible key factor leading to the rapid evolution of a novel hard structure in this vent-endemic species.

A chromosome-level genome assembly of the male darkbarbel catfish (Pelteobagrus vachelli) using PacBio HiFi and Hi-C data

The darkbarbel catfish (Pelteobagrus vachelli), a species of significant economic value in China's aquaculture sector, is widely utilized in hybrid yellow catfish production due to its exceptional growth rate. The growth rate of male P. vachelli is significantly higher compared to females, making all-male breeding a promising market opportunity. Therefore, the analysis of the male P. vachelli genome provides crucial genetic information for hybrid breeding and all-male breeding. Utilizing PacBio Hifi long-read sequencing and Hi-C technologies, we present a high-quality, chromosome-level genome assembly for the male P. vachelli. The assembly covers 728.88 Mb with 99.92% of the sequence distributed across 26 chromosomes. The contig N50 is 5.60 Mb, and the scaffold N50 is 28.76 Mb. The completeness of the P. vachelli genome assembly is highlighted by a BUSCO score of 97.45%. The genome is estimated to encode 25,121 protein-coding genes, with 93.46% annotated functionally and a BUSCO score of 96.40%. Repeat elements constitute approximately 38.97% of the genome. This comprehensive genome assembly represents an invaluable resource for advancing hybrid breeding, comparative genomics, and evolutionary studies in catfish and related species.

Phylogeny and Functional Differentiation of the Terpene Synthase Gene Family in Angiosperms with Emphasis on Rosa chinensis

Terpenes are pivotal for plant growth, development, and adaptation to environmental stresses. With the advent of extensive genomic data and sophisticated bioinformatics tools, new insights into the evolutionary dynamics and functional diversification of terpene synthases (TPSs) have emerged. Despite genome-wide identifications of the TPS family in certain species, comprehensive cross-species analyses remain scarce. In this study, we conducted a genome-wide identification and subgroup classification of TPS families across 115 angiosperms with available genomic sequences. Our phylogenomic synteny network analysis elucidated the complex evolutionary history of TPS genes, revealing notable expansions and contractions among subgroups. Specifically, TPS-a showed significant expansion, while TPS-b was variably lost in some Poaceae, indicating adaptive responses. TPS-c maintained considerable conservation across species, whereas TPS-e/f diverged into distinct evolutionary trajectories despite functional overlap, with TPS-e further splitting into two angiosperm-specific clades. The TPS-g subgroup displayed lineage-restricted distribution, primarily in super-rosids and monocots. Notably, TPS-d and TPS-h subgroups were absent in angiosperms. Employing Rosa chinensis as a case study, we identified RcTPS23, a conserved bifunctional terpene synthase, highlighting the utility of cross-species synteny data in functional prediction. This comprehensive analysis elucidates the phylogenetic and functional landscape of TPS subgroups in angiosperms, providing a robust framework for predicting TPS function and guiding further functional investigations.

On the way to diploidization and unexpected ploidy in the grass Sporobolus section Spartina mesopolyploids

Plant history is characterized by cyclical whole genome duplication and diploidization with important biological and ecological consequences. Here, we explore the genome history of two related iconic polyploid grasses (Sporobolus alterniflorus and S. maritimus), involved in a well-known example of neopolyploid speciation. We report particular genome dynamics where an ancestral Sporobolus genome (n = 2x = 20) duplicated 9.6-24.4 million years ago (MYA), which was followed by descending dysploidy resulting in a genome with an unexpected base chromosome number (n = 15). This diploidized genome duplicated again 2.1-6.2 MYA to form a tetraploid lineage (2n = 4x = 60), thus reshuffling the ploidy of these species previously thought hexaploids. We also elucidate the mechanism accompanying the speciation between S. maritimus (2n = 60) and S. alterniflorus (2n = 62), resulting from chromosome restructuring, and identify key adaptive genes in the corresponding regions. This represents critical findings to decipher molecular mechanisms underlying species expansion, adaptation to environmental challenge and invasiveness.

The origin, evolution, and translocation of sex chromosomes in Silurus catfish mediated by transposons

BACKGROUND

Sex chromosome (SC) evolution is a longstanding topic of focus in evolutionary biology. Teleosts often exhibit rapid turnover of SCs and sex-determining (SD) genes, alongside a diverse range of SC differentiation mechanisms.

RESULTS

On the basis of new chromosome-scale assemblies of three Silurus species (S. microdorsalis, S. glanis, and S. lanzhouensis) and two outgroup species (Pterocryptis cochinchinensis and Kryptopterus bicirrhis), along with our previous assemblies of S. meridionalis and S. asotus, we traced the evolution of SC in the Silurus genus (Siluriformes), following the fate of the known SD gene amhr2y. Phylogenetic analysis showed that amhr2y occurred at least before the divergence of Pterocryptis, Kryptopterus, and Silurus and lost in P. cochinchinensis and K. bicirrhis. Chr24 has become the SC in the ancestor of five Silurus species due to the duplication-and-translocation of amhr2 mediated by LTR transposon. Then, a proto Y was formed and maintained with a shared 60 kb male-specific region of the Y chromosome (MSY) by transposable elements (TEs) expansion and gene gathering. Due to the continuous TEs accumulation, genes other than amhr2y in MSYs have degenerated or been lost, while non-recombinant regions continue to expend, forming MSYs of different sizes in different Silurus species (from 320 to 550 kb). Two turnover events, one homologous (from the left arm to the right arm of Chr24) and one nonhomologous (from Chr24 to Chr5), occurring among five Silurus species were possibly mediated by hAT and Helitron transposons.

CONCLUSIONS

Our results on the dynamic evolutionary trajectory of SD gene amhr2y, MSYs, and SCs in Silurus catfish indicated the variability and diversity of fish SCs and confirmed that frequent turnover is an important way to maintain the homology and low differentiation of fish SCs.

Evidence for evolution of a new sex chromosome within the haploid-dominant Marchantiales plant lineage

Sex chromosomes have evolved independently in numerous lineages across the Tree of Life, in both diploid-dominant species, including many animals and plants, and the less studied haploid-dominant plants and algae. Strict genetic sex determination ensures that individuals reproduce by outcrossing. However, species with separate sexes (termed dioecy in diploid plants, and dioicy in haploid plants) may sometimes evolve different sex systems, and become monoicous, with the ability to self-fertilize. Here, we studied dioicy-monoicy transitions in the ancient liverwort haploid-dominant plant lineage, using three telomere-to-telomere gapless chromosome-scale reference genome assemblies from the Ricciaceae group of Marchantiales. Ancestral liverworts are believed to have been dioicous, with U and V chromosomes (chromosome 9) determining femaleness and maleness, respectively. We confirm the finding that monoicy in Ricciocarpos natans evolved from a dioicous ancestor, and most ancestrally U chromosomal genes have been retained on autosomes in this species. We also describe evidence suggesting the possible re-evolution of dioicy in the genus Riccia, with probable de novo establishment of a sex chromosome from an autosome (chromosome 5), and further translocations of genes from the new sex chromosome to autosomes. Our results also indicated that micro-chromosomes are consistent genomic features, and may have evolved independently from sex chromosomes in Ricciocarpos and Riccia lineages.

Genome-wide identification, characterization and expression analysis of tubulin gene family in Populus deltoides

BACKGROUND

Tubulin proteins, the main components of microtubules in all eukaryotes, are involved in numerous aspects of plant morphogenesis and adaptation to the environment. In woody plants, microtubules are closely associated with the orientation of cellulose microfibril deposition in the secondary xylem cells and thereby exert an influence on the strength and flexibility of wood. Three major types of tubulin proteins-α-, β- and γ-tubulin-are ubiquitously present in all flowering plants, with α- and β- tubulin serving as basic subunits of microtubules and γ-tubulin directing microtubule nucleation. Compared with herbaceous plants, information on tubulin gene family has been limited in forest trees. This study aimed to characterize the tubulin gene family in the model forest tree Populus deltoides.

RESULT

Based on the whole genome sequence of P. deltoides, 25 PdTubulin genes were identified, including 6 PdTUAs, 17 PdTUBs, and 2 PdTUBGs were identified, with an uneven distribution across 14 chromosomes. Unlike Arabidopsis, which has only three pairs of tubulin paralogs, nearly all PdTubulin were paralogous duplicates, primarily generated by p-whole genome duplication (WGD), γ-WGD, or segmental duplication, indicating multiple rounds of gene family expansion. After the duplication events, the number of TUA genes in Populus was more strictly constrained compared to TUB genes. All paralogous and orthologous tubulin pairs have been under strong purifying selection. Expression analysis revealed that each PdTubulin gene was preferentially expressed in one of three organs: root, leaf, or stem. 5 PdTUB paralogs exhibited similar expression patterns, suggesting potential redundancy. Additionally, expression analysis in male and female floral buds across developmental stages indicated that different members might be involved in sex-specific processes.

Genome-Wide Identification and Expression Analyses of Glycoside Hydrolase Family 18 Genes During Nodule Symbiosis in Glycine max

Glycoside hydrolase family 18 (GH18) proteins can hydrolyze the β-1,4-glycosidic bonds of chitin, which is a common structure component of insect exoskeletons and fungal cell walls. In this study, 36 GH18 genes were identified and subjected to bioinformatic analysis based on the genomic data of Glycine max. They were distributed in 16 out of 20 tested soybean chromosomes. According to the amino acid sequences, they can be further divided into five subclades. Class III chitinases (22 members) and class V chitinases (6 members) are the major two subclades. The amino acid size of soybean GH18 proteins ranges from 173 amino acids (aa) to 820 aa and the molecular weight ranges from 19.46 kDa to 91.01 kDa. From an evolutionary perspective, soybean GH18 genes are closely related to Medicago (17 collinear loci with soybean) and Lotus (23 collinear loci with soybean). Promoter analysis revealed that GH18 genes could be induced by environmental stress, hormones, and embryo development. GmGH18-15, GmGH18-24, and GmGH18-33 were screened out due to their nodulation specific expression and further verified by RT-qPCR. These results provide an elaborate reference for the further characterization of specific GH18 genes, especially during nodule formation in soybean.

Genome assembly, gene content, and plastic gene expression responses to salinity changes in the Brackishwater Clam (Corbicula japonica) from a dynamic estuarine environment

Estuaries are dynamic transition zones between marine and freshwater environments, where salinity varies greatly on spatial and temporal scales. The temporal salinity fluctuations of these habitats require organisms to rapidly regulate ionic concentrations and osmotic pressure to survive in these dynamic conditions. Understanding the extent of plasticity of euryhaline animals is vital for predicting their responses and resilience to salinity change. We generated the first high-resolution genome and transcriptome sequences of C. japonica. In comparison with 11 other molluscan genomes, the C. japonica genome displayed striking expansions of putative neuron-related genes and gene families. The involvement of these genes in the glutamate/GABA-glutamine and glycine cycle suggests a possible contribution to the excitation of neuronal networks, particularly under high salinity conditions. This study contributes to our understanding of mechanisms underlying the rapid responses of estuarine species to changing conditions and raises many intriguing hypotheses and questions for future investigation.

A chromosome-level genome assembly of the Peruvian Algarrobo (Neltuma pallida) provides insights on its adaptation to its unique ecological niche

The dry forests of northern Peru are dominated by the legumous tree Neltuma pallida which is adapted to hot arid and semiarid conditions in the tropics. Despite having been successfully introduced in multiple other areas around the world, N. pallida is currently threatened in its native area, where it is invaluable for the dry forest ecosystem and human subsistence. A major tool for enhancing ecosystem conservation and understanding the adaptive properties of N. pallida to dry forest ecosystems is the construction of a reference genome sequence. Here, we report on a high-quality reference genome for N. pallida. The final genome assembly size is 403.7 Mb, consisting of 14 pseudochromosomes and 63 scaffolds with an N50 size of 26.2 Mb and a 34.3% GC content. Use of Benchmarking Universal Single Copy Orthologs revealed 99.2% complete orthologs. Long terminal repeat elements dominated the repetitive sequence content which was 51.2%. Genes were annotated using N. pallida transcripts, plant protein sequences, and ab initio predictions resulting in 22,409 protein-coding genes encoding 24,607 gene models. Comparative genomic analysis showed evidence of rapidly evolving gene families related to disease resistance, transcription factors, and signaling pathways. The chromosome-scale N. pallida reference genome will be a useful resource for understanding plant evolution in extreme and highly variable environments.