LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons

Chromosome-level genome assembly of cultivated strawberry 'Seolhyang' (Fragaria × ananassa)

Cultivated strawberry (Fragaria × ananassa) belongs to the family Rosaceae and is an allo-octoploid species (2n = 8×  = 56). Using PacBio Revio long reads of 'Seolhyang', we completed telomere-to-telomere phased genome assemblies with a size of 797 Mb with a contig N50 of 27.04 Mb. Benchmarking of the universal single-copy orthologs (BUSCO) analysis detected 99.1% conserved genes in the assembly. In addition, the average long terminal repeat assembly index (LAI) was 17.28, with high genome continuity. In this study, we identified 50 of the possible 56 telomeres across 28 chromosomes. The 'Seolhyang' genome was annotated using RNA-Seq data representing various F. × ananassa tissues from the NCBI sequence read archive, which resulted in 129,184 genes.

Chromosome-level genome assembly and annotation of the maize weevil (Sitophilus zeamais Motschulsky)

The maize weevil, Sitophilus zeamais Motschulsky, is one of the most destructive pests of stored grains worldwide, posing a significant threat to global food security. To better understand the biology, resistance mechanism, and adaptive evolution of this species, we presented a high-quality chromosome-level genome assembly of S. zeamais using PacBio sequencing and Hi-C technologies. The size of the final assembled genome was 693.21 Mb with scaffold N50 of 61.03 Mb, and 631.97 Mb were successfully anchored into 11 pseudochromosomes. In total, 15,161 protein-coding genes were annotated, of which 98.89% obtained functional descriptions. Additionally, 377.50 Mb of sequences were identified as repeat elements, accounting for 54.46% of the genome. BUSCO analysis revealed a high level of completeness in both the genome assembly and annotation, with scores of 98.17% and 97.22%, respectively. The chromosome-level genome of S. zeamais provides valuable genomic insights that deepen our understanding of the evolution and ecology of Sitophilus species, while also contributing to the development of targeted and innovative control strategies for stored-product pests.

Assembling chromosome-level genomes of male and female Chanodichthys mongolicus using PacBio HiFi reads and Hi-C technologies

Chanodichthys mongolicus, a carnivorous fish belonging to the Cyprinidae family (Erythroculter), is widely distributed in reservoirs and lakes across China. However, the lack of research on whole genome assembly has impeded advancements in genetic studies for this species. In this study, we employed PacBio sequencing and Hi-C technology to assemble high-quality genomes for both female and male Chanodichthys mongolicus at the chromosome level. The assembly results revealed a male genome size of 1.10 GB with a scaffold N50 of 43 Mb, while the female genome was 1.09 GB with a scaffold N50 of 42 Mb. Both assemblies consist of 24 chromosomes and demonstrate an average genome integrity of 98.5%, as assessed by BUSCO. We annotated the male genome using a combination of ab initio predictions, protein homology comparisons, and RNAseq data, resulting in the identification of 33,581 genes, of which 88.15% were predicted to have functional roles. These findings provide a valuable resource for future research on the genetic breeding and genome evolution of Chanodichthys mongolicus.

A chromosome-scale and haplotype-resolved genome assembly of tetraploid blackberry (Rubus L. subgenus Rubus Watson)

Blackberries (Rubus spp.) are globally consumed and well known for their rich anthocyanin and antioxidant content and distinct flavors. Improving blackberries has been challenging due to genetic complexity of traits and limited genomic resources. The blackberry genome has been particularly challenging to assemble due to its polyploid nature. Here, we present the first chromosome-scale and haplotype-phased assembly for the primocane-fruiting, thornless tetraploid blackberry selection BL1 (Rubus L. subgenus Rubus Watson). The genome assembly was generated using Oxford Nanopore Technology and Hi-C scaffolding, resulting in a 919 Mb genome distributed across 27 pseudochromosomes, with an N50 of 35.73 Mb. This assembly covers >92% of the genome length and contains over 98% of complete BUSCOs. Approximately, 58% of the assembly consists of repetitive sequences, with long terminal repeats being the most abundant class. A total of 87,968 protein-coding genes were predicted, of which, 82% were functionally annotated. Genome mining and RNA-Seq analyses identified possible candidate genes and transcription factors related to thornlessness and the key structural genes and transcription factors for anthocyanin biosynthesis. Activator genes including PAP1 and TTG1 and repressor genes such as ANL2 and MYBPA1 play an important role in the fine tuning of anthocyanin production during blackberry development. Resequencing of seven tetraploid blackberry cultivars/selections with different horticultural characteristics revealed candidate genes that could impact fruiting habit and disease resistance/susceptibility. This tetraploid reference genome should provide a valuable resource for accelerating genetic analysis of blackberries and facilitating the development of new improved cultivars with enhanced horticultural and nutritional traits.

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.

Telomere-to-telomere genome assembly reveals insights into the adaptive evolution of herbivore-defense mediated by volatile terpenoids in Oenanthe javanica

Releasing large quantities of volatiles is a defense strategy used by plants to resist herbivore attack. Oenanthe javanica, a perennial herb of the Apiaceae family, has a distinctive aroma due to volatile terpenoid accumulation. At present, the complete genome and genetic characteristics of volatile terpenoids in O. javanica remain largely unclear. Here, the telomere-to-telomere genome of O. javanica, with a size of 1012.13 Mb and a contig N50 of 49.55 Mb, was established by combining multiple sequencing technologies. Comparative genome analysis revealed that O. javanica experienced a recent species-specific whole-genome duplication event during the evolutionary process. Numerous gene family expansions were significantly enriched in the terpenoid biosynthesis process, monoterpenoid, and diterpenoid biosynthesis pathways, which resulted in abundant volatile substance accumulation in O. javanica. The volatile terpenoids of O. javanica showed repellent effects on herbivores. Terpenoid biosynthesis was activated by wounding signals under exogenous stimuli. The TPS gene family was significantly expanded in O. javanica compared to those in other species, and the members (OjTPS1, OjTPS3, OjTPS4, OjTPS5, OjTPS7, OjTPS16, OjTPS18, OjTPS30 and OjTPS58) responsible for different terpenoid biosynthesis were functionally characterized. These results reveal the genome evolution and molecular characteristics of volatile terpenoids in the process of plant-herbivore interactions. This study also provides genomic resources for genetic and molecular biology research on O. javanica and other plants.

Pangenome analysis reveals yield- and fiber-related diversity and interspecific gene flow in Gossypium barbadense L

Gossypium barbadense is renowned for its superior fiber quality, particularly its extra-long fibers, although its fiber yield is lower compared to G. hirsutum. Here, to further reveal fiber-related genomic variants of G. barbadense, we de novo assemble 12 genomes of G. barbadense that span the wild-to-domesticated continuum, and construct a graph-based pangenome by integrating these assemblies and 17 publicly available tetraploid cotton genome assemblies. We uncover the divergent evolutionary trajectories and subsequent exchanges between G. barbadense and G. hirsutum through investigation of structural variants (SVs). We perform the SV-based GWAS analysis in G. barbadense and identify four, three, and seven candidate SVs for fiber length, fiber strength, and lint percentage, respectively. Furthermore, we detect the underlying candidate genes and uncover the origin and distribution of favorable alleles, and reveal the tradeoff between lint percentage and fiber quality. These pangenome and trait-associated SVs provide insights into and resources for improving cotton fiber.

Chromosome-level genome assembly of Sambus kanssuensis (Coleoptera: Buprestidae)

Sambus kanssuensis Ganglbauer, 1890 (Coleoptera: Buprestidae), distributed in Gansu and Sichuan Provinces of China, is a phytophagous pest that feeds on the toxic plant Buddleja. However, the genomic resources of this beetle remain unknown, which impedes the understanding of its ecological adaptations. Consequently, this study presents a complete, well-assembled, and annotated genome of S. kanssuensis. The assembled results indicate a genome size of 312.42 Mb, comprising 206 scaffolds, with an N50 of 34.04 Mb; 98.68% of the assembly sequences were anchored to 11 chromosomes, including one sex chromosome. The genome contains 12,723 protein-coding genes, of which 11,977 have been annotated. BUSCO analysis revealed that the completeness of the chromosome-level genome is 97.9%. This chromosome-level genome provides valuable data for further investigations into detoxification mechanisms, ecological adaptations, population genetics, and the evolution of Buprestidae.

Chromosome-scale genome assembly of the fire blight resistant Malus fusca accession MAL0045, donor of FB_Mfu10

The wild apple, Malus fusca accession MAL0045, is highly resistant to fire blight disease, caused by the bacterial pathogen, Erwinia amylovora. A major resistance locus, FB_Mfu10 was identified on chromosome 10 of MAL0045 including other contributory loci on chromosomes 16, 4, and 15. Here, we report a chromosome-scale genome assembly of MAL0045 to facilitate the studies of its fire blight resistance. PacBio sequencing and Illumina sequencing for Hi-C contig anchorage were employed to obtain the genome. A total of 669.46 Mb sequences were anchored onto 17 chromosomes, taking up 99.75% of total contig length. Contigs anchored onto chromosomes were further ordered and orientated, where a total of 637.67 Mb sequences were anchored onto chromosomes in proper order and orientation, resulting in a final anchoring ratio of 95.25%. The BUSCO score of this assembly is 97.46%. Further, a total of 47,388 genes were predicted via ab initio, homology-based, and RNAseq methodologies. The availability of this genome will facilitate functional and comparative genomics studies, especially about the donors of fire blight resistance in Malus.

High-quality assembly of the chromosomal genome for Flemingia macrophylla reveals genomic structural characteristics

Flemingia macrophylla, a prominent shrub species within the Fabaceae family, is widely distributed across China and Southeast Asia. In addition to its ecological importance, it possesses notable medicinal value, with its roots traditionally used for treating rheumatism, enhancing blood circulation, and alleviating joint pain. We employed Nanopore sequencing platforms to generate a high-quality reference genome for F. macrophylla, with an assembled genome size of 1.01 Gb and a contig N50 of 59.43 Mb. A total of 33,077 protein-coding genes were predicted, and BUSCO analysis indicated a genome completeness of 99%. Phylogenomic analyses showed that F. macrophylla is most closely related to Cajanus cajan among the sampled taxa, with an estimated divergence time of 13.2-20.0 MYA. Evidence of whole-genome duplication (WGD) events was detected in F. macrophylla, C. cajan, and P. vulgaris, with these species sharing two WGD events. The unique gene families in F. macrophylla are associated with strong resistance to both abiotic and biotic stress, supporting its remarkable ecological adaptability. Furthermore, gene family expansion analysis revealed a significant enrichment of genes related to secondary metabolites biosynthesis, providing a molecular basis for its high medicinal value. In summary, this study provides a foundational genomic resource for F. macrophylla, offering valuable insights into its genetic architecture, evolutionary history, and potential applications in medecine and agriculture. The comprehensive analyses lay the groundwork for future research into the species's medicinal properties and evolutionary biology.

Chromosome-level genome assembly for clubrush (Scirpus × mariqueter) endemic to China

Scirpus × mariqueter (Tang & F.T.Wang) Tatanov, which is endemic to eastern estuaries in China, is a tidal zone-engineering species with great promise for managing greenhouse gases and enhancing ecosystem resilience against invasive species. Although S. mariqueter is widely recognized as a hybrid species derived from Bolboschoenus planiculmis (F. Schmidt) T.V. Egorova and Schoenoplectus triqueter (L.) Palla, its speciation remains highly controversial. The lack of a reference genome is the major cause of this ambiguity. We generated the first chromosome-level genome assembly for S. mariqueter combining PacBio long-reads, Illumina short-reads, and the Hi-C method. The genome assembly consisted of 227.75 Mb (contig N50: 3.89 Mb). We also constructed a haploid karyotype comprising 54 pseudochromosomes. The average size of these pseudochromosomes was small (4.05 Mb). Thirty-two pseudochromosomes were assembled to a telomere to telomere level. Repetitive elements represented approximately 54.12% of the genome. We predicted and annotated 25,239 protein-coding genes. The overall BUSCO score was 95.10%, with notably few duplicated genes (1.70%). This high-quality genome provides critical data for future studies.

Haplotype-resolved chromosome-level genome sequence of Elsholtzia splendens (Nakai ex F.Maek.)

Elsholtzia splendens, a perennial herb native to East Asia, is valued for its ornamental and medicinal uses, particularly in treating inflammatory and febrile conditions. Recent studies have highlighted its antibacterial, anti-inflammatory, antidepressant, antithrombotic, and lipid-lowering properties of its compounds. Additionally, E. splendens shows potential for phytoremediation owing to its ability to hyperaccumulate copper (Cu), lead (Pb), zinc (Zn), and cadmium (Cd). However, its role in remediation conflicts with its medicinal use because of the risk of heavy metal accumulation. Genome sequencing will be key to boosting beneficial compound production and reducing heavy metal risks. In this study, we generated a high-resolution, haplotype-resolved, chromosome-scale genome sequence of E. splendens using PacBio Revio long-read, Illumina short-read, and Hi-C sequencing technologies. The haplotype genome assemblies, spanned 275.4 and 265.0 Mbp with a scaffold N50 of 33.9 and 33.8 Mbp for haplotype 1 and 2, respectively. This assembly provides valuable insights into medicinal compound biosynthesis and supports genetic conservation efforts, facilitating future genetic and biotechnological applications of E. splendens for medicinal and ecological uses.

A telomere-to-telomere genome assembly of Camellia nitidissima

Camellia nitidissima is the model species of the Camellia sect. Chrysantha Chang, the only lineage within the genus Camellia known to produce golden-yellow flowers. This species holds high aesthetic, germplasm and medical value. Unfortunately, due to excessive collection and habitat loss, C. nitidissima is classified as a critically endangered plant. In this study, we assembled a telomere-to-telomere (T2T) genome of C. nitidissima by incorporating PacBio HiFi and Hi-C data. The assembled genome consisted of 15 pseudo-chromosomes, with a total size estimated to be 2.72 Gb. The GC content and repetitive sequences occupied 38.05% and 84.38% of the assembled genome, respectively. In total, 35,701 protein-coding genes were annotated. Multiple evaluation methods confirmed the contiguity (contig N50: 81.74 Mb), completeness (BUSCOs: 98.80%) and high LTR Assembly Index (LAI: 14.57) of the genome. This high-quality T2T genome will provide valuable insights into the genomic characteristics of C. nitidissima and facilitate conservation efforts as well as functional genomic studies in Camellia sect. Chrysantha species.

Chromosome-level genome assembly of the parasitoid wasp Aenasius arizonensis

Aenasius arizonensis is an important solitary endoparasitoid successfully used for biocontrol of cotton mealybug. However, lacking genomic resources has limited molecular-level investigations. Our exploration produced a superior genomic assembly of A. arizonensis from the chromosome level by combining MGISEQ short reads, Hi-C scaffolding, and PacBio Revio sequencing techniques. The genome measured 398.69 Mb, including a contig N50 of 4.73 Mb, a BUSCO completeness level of 97.07%, and a scaffold N50 of 35.96 Mb. Hi-C data were further utilized cluster and anchor 98.66% of the genome sequences into 11 chromosomes. Approximately, 165.90 Mb, representing about 41.61% of the genome, was identified as repeat elements. Non-coding sequence annotation identified 171 rRNAs, 117 small RNAs, 331 regulatory RNAs, and 872 tRNAs. Genome annotation reveals 11,727 protein-coding genes, with 10,842 (92.45%) genes functionally annotated. In summary, our chromosome-level genome assembly serves as a significant resource for advancing research on Encyrtidae parasitoids.

Two haplotype-resolved telomere-to-telomere genome assemblies of Xanthoceras sorbifolium

Yellowhorn (Xanthoceras sorbifolium) is widely used in northern China for landscaping, desertification control, and oil production. However, the lack of high-quality genomes has hindered breeding and evolutionary studies. Here, we present the first haplotype-resolved, telomere-to-telomere (T2T) yellowhorn genomes of PBN-43 (white single-flowered) and PBN-126 (white double-flowered) using PacBio HiFi and Hi-C data. These assemblies range from 464.34 Mb to 468.97 Mb and include all centromeres and telomeres. Genome annotation revealed that an average of 67.99% (317.09 Mb) of yellowhorn genomic regions consist of repetitive elements across all haplotypes. The number of protein-coding genes ranges from 35,039 to 35,174 among assemblies, representing an average 50.16% increase over the first published yellowhorn genome. Additionally, 93.90% of the annotated genes have functional annotations. We found yellowhorn experienced an LTR-RT burst during the last 0.45-0.48 Mya. These data provide a resource for investigating genomic variations, phylogenetic relationships, duplication modes, and the distribution of nucleotide-binding leucine-rich repeat (NLR) genes, and support further research into yellowhorn breeding.

An annotated near-complete sequence assembly of the Magnaporthe oryzae 70-15 reference genome

Magnaporthe oryzae is a devastating fungal pathogen that causes substantial yield losses in rice and other cereal crops worldwide. A high-quality genome assembly is critical for addressing challenges posed by this pathogen. However, the current widely used MG8 assembly of the M. oryzae strain 70-15 reference genome contains numerous gaps and unresolved repetitive regions. Here, we report a complete 44.82 Mb high-quality nuclear genome and a 35.95 kb circular mitochondrial genome for strain 70-15, generated using deep-coverage PacBio high-fidelity sequencing (HiFi) and high-resolution chromatin conformation capture (Hi-C) data. Notably, we successfully resolved one or both telomere sequences for all seven chromosomes and achieved telomere-to-telomere (T2T) assemblies for chromosomes 2, 3, 4, 6, and 7. Based on this T2T assembly, we predicted 12,100 protein-coding genes and 493 effectors. This high-quality T2T assembly represents a significant advancement in M. oryzae genomics and provides an enhanced reference for studies in genome biology, comparative genomics, and population genetics of this economically important plant pathogen.

A telomere-to-telomere gap-free assembly integrating multi-omics uncovers the genetic mechanism of fruit quality and important agronomic trait associations in pomegranate

Pomegranate is an important perennial fruit tree distributed worldwide. Reference genomes with gaps and limit gene identification controlling important agronomic traits hinder its functional genomics and genetic improvements. Here, we reported a telomere-to-telomere (T2T) gap-free genome assembly of the distinctive cultivar 'Moshiliu'. The Moshiliu reference genome was assembled into eight chromosomes without gaps, totalling ~366.71 Mb, with 32 158 predicted protein-coding genes. All 16 telomeres and eight centromeres were characterized; combined with FISH analysis, we revealed the atypical telomere units in pomegranate as TTTTAGGG. Furthermore, a total of 16 loci associated with 15 important agronomic traits were identified based on GWAS of 146 accessions. Gene editing and biochemical experiments demonstrated that a 37.2-Kb unique chromosome translocation disrupting the coding domain sequence of PgANS was responsible for anthocyanin-less, knockout of PgANS in pomegranate exhibited a defect in anthocyanin production; a unique repeat expansion in the promoter of PgANR may affected its expression, resulting in black peel; notably, the G → A transversion located at the 166-bp coding domain of PgNST3, which caused a E56K mutation in the PgNST3 protein, closely linked with soft-seed trait. Overexpression of PgNST3A in tomato presented smaller and softer seed coats. The E56K mutation in PgNST3 protein, eliminated the binding ability of PgNST3 to the PgMYB46 promoter, which subsequently affected the thickness of the inner seed coat of soft-seeded pomegranates. Collectively, the validated gap-free genome, the identified genes controlling important traits and the CRISPR-Cas9-mediated gene knockout system all provided invaluable resources for pomegranate precise breeding.

Haplotype-resolved genome reveals haplotypic variation and the biosynthesis of medicinal ingredients in Areca catechu L

Areca catechu, as a traditional Chinese medicine, contains a high concentration of therapeutic compounds. However, the biosynthesis of these compounds is largely unexplored. We present a haplotype-resolved genome assembly and annotation for A. catechu, with chromosome-level genome sizes of 2.45 Gb (Ac. Hap1) and 2.49 Gb (Ac. Hap2). A comparative analysis of the haplotypes revealed significant divergence, including multiple Mb-level large inversions. Furthermore, A. catechu shared two whole genome duplications with other palm plants and its genome size had increased due to the insertion of transposons within the last 2.5 million years. By integrating transcriptomics and metabolomics, two tandem genes (AcGNMT1 and AcGNMT2) were negatively associated with guvacine and trigonelline in gene-metabolite interaction network. AcGNMT1, AcGNMT2 and their three homologous genes were involved in the conversion of guvacine to arecoline. Further analyses tested the function of AcUGT71CE15, AcUGT74CJ38, AcUGT87EE5 and AcUGT83S982 as glucosyltransferases, and AcUGT78AP14 was identified as a rhamnosyltransferase involved in flavonol glycosylation. Our study provides a high-quality genome of A. catechu, characterizes the arecoline biosynthetic pathway and expands the understanding of the diversity of UDP-glucosyltransferase and UDP-rhamnosyltransferase, offering insights into the potential of A. catechu for the biosynthesis of bioactive compounds.

MangroveDB: A Comprehensive Online Database for Mangroves Based on Multi-Omics Data

Mangroves are dominant flora of intertidal zones along tropical and subtropical coastline around the world that offer important ecological and economic value. Recently, the genomes of mangroves have been decoded, and massive omics data were generated and deposited in the public databases. Reanalysis of multi-omics data can provide new biological insights excluded in the original studies. However, the requirements for computational resource and lack of bioinformatics skill for experimental researchers limit the effective use of the original data. To fill this gap, we uniformly processed 942 transcriptome data, 386 whole-genome sequencing data, and provided 13 reference genomes and 40 reference transcriptomes for 53 mangroves. Finally, we built an interactive web-based database platform MangroveDB (https://github.com/Jasonxu0109/MangroveDB), which was designed to provide comprehensive gene expression datasets to facilitate their exploration and equipped with several online analysis tools, including principal components analysis, differential gene expression analysis, tissue-specific gene expression analysis, GO and KEGG enrichment analysis. MangroveDB not only provides query functions about genes annotation, but also supports some useful visualization functions for analysis results, such as volcano plot, heatmap, dotplot, PCA plot, bubble plot, population structure, and so on. In conclusion, MangroveDB is a valuable resource for the mangroves research community to efficiently use the massive public omics datasets.

Cotton transposon-related variome reveals roles of transposon-related variations in modern cotton cultivation

INTRODUCTION

Transposon plays a vital role in cotton genome evolution, contributing to the expansion and divergence of genomes within the Gossypium genus. However, knowledge of transposon activity in modern cotton cultivation is limited.

OBJECTIVES

In this study, we aimed to construct transposon-related variome within Gossypium genus and reveal role of transposon-related variations during cotton cultivation. In addition, we try to identify valuable transposon-related variations for cotton breeding.

METHODS

We utilized graphical genome construction to build up the graphical transposon-related variome. Based on the graphical variome, we integrated t-test, eQTL analysis and Mendelian Randomization (MR) to identify valuable transposon activities and elite genes. In addition, a convolutional neural network (CNN) model was constructed to evaluate epigenomic effects of transposon-related variations.

RESULTS

We identified 35,980 transposon activities among 10 cotton genomes, and the diversity of genomic and epigenomic features was observed among 21 transposon categories. The graphical cotton transposon-related variome was constructed, and 9,614 transposon-related variations with plasticity in the modern cotton cohort were used for eQTL, phenotypic t-test and Mendelian Randomization. 128 genes were identified as gene resources improving fiber length and strength simultaneously. 4 genes were selected from 128 genes to construct the elite gene panel whose utility has been validated in a natural cotton cohort and 2 accessions with phenotypic divergence. Based on the eQTL analysis results, we identified transposon-related variations involved in cotton's environmental adaption and human domestication, providing evidence of their role in cotton's adaption-domestication cooperation.

CONCLUSIONS

The cotton transposon-related variome revealed the role of transposon-related variations in modern cotton cultivation, providing genomic resources for cotton molecular breeding.

The genomic insights of intertidal adaptation in Bryopsis corticulans

Many marine green algae thrive in intertidal zones, adapting to complex light environments that fluctuate between low underwater light and intense sunlight. Exploring their genomic bases could help to comprehend the diversity of adaptation strategies in response to environmental pressures. Here, we developed a novel and practical strategy to assemble high-confidence algal genomes and sequenced a high-quality genome of Bryopsis corticulans, an intertidal zone macroalga in the Bryopsidales order of Chlorophyta that originated 678 million years ago. Comparative genomic analyses revealed a previously overlooked whole genome duplication event in a closely related species, Caulerpa lentillifera. A total of 100 genes were acquired through horizontal gene transfer, including a homolog of the cryptochrome photoreceptor CRY gene. We also found that all four species studied in Bryopsidales lack key photoprotective genes (LHCSR, PsbS, CYP97A3, and VDE) involved in the xanthophyll cycle and energy-dependent quenching processes. We elucidated that the expansion of light-harvesting antenna genes and the biosynthesis pathways for siphonein and siphonaxanthin in B. corticulans likely contribute to its adaptation to intertidal light conditions. Our study unraveled the underlying special genetic basis of Bryopsis' adaptation to intertidal environments, advancing our understanding of plant adaptive evolution.

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.

The chromosome-level genome of Centella asiatica provides insights into triterpenoid biosynthesis

Centella asiatica is a well-known herbal plant that makes a significant contribution to the treatment of various chronic ailments. Triterpenoid saponins are the main active components extracted from C. asiatica, which have rich pharmacological activity. However, only a few studies have systematically elucidated the molecular mechanism underlying the biosynthesis of triterpenoid saponins in C. asiatica. Here, we report a chromosome-level reference genome of C. asiatica, by using Illumina, PacBio HiFi, and Hi-C technologies. The assembled genome exhibits high quality with a size of 455 Mb and a contig N50 of 36 Mb. A total of 26,479 protein-coding genes were predicted. Comparative genomic analysis revealed that the gene families involved in triterpenoid saponin biosynthesis, including squalene synthase (SS) and farnesyl diphosphate synthase (FPS), rapidly expanded in the C. asiatica genome. In particular, we have discovered two whole-genome duplication events in C. asiatica genomes. A further comprehensive analysis of the metabolome and transcriptome was performed using different tissues of C. asiatica in order to identify the key genes associated with triterpenoid saponin biosynthesis. Consequently, seven enzyme genes were considered to play important roles in triterpenoid biosynthesis. Subsequent functional characterization of CaOSC4 demonstrated that it is responsible for the biosynthesis of three ursane-type triterpenoids in C. asiatica. Our research establishes a genomic data platform that can be employed in the excavation of genes and precision breeding in C. asiatica. Additionally, the results offer new insights into the biosynthesis of triterpenoid saponins.

Trichaptum biforme (Pallidohirschioporus biformis) genome decoding provides insights into carbohydrate degradation and polysaccharide synthesis

Trichaptum biforme is a white-rot fungus that plays a key role in the process of cellulose degradation. In this study, we employed a suite of techniques to sequence the genome of T. biforme, and achieved high-quality assembly and detailed annotation. The genome spans 50.71 Mb, comprises 13 chromosomal pseudomolecules, and encodes 15,302 predicted genes, exhibiting a BUSCO completeness of 96.30 %. Comparative genomic analysis has elucidated the similarities in gene composition and the differences in evolutionary pressure between T. biforme and T. abietinum. Phylogenetic analysis revealed the evolutionary position of T. abietinum and indicates that their divergence time is 21.20 million years ago (MYAs). Bioinformatic analysis revealed 375 genes encoding carbohydrate-active enzymes (CAZymes), of which 144 CAZymes were predicted to interact with 18 polysaccharide synthases. In conclusion, this work reports for the first time the genome of T. biforme, providing a comprehensive understanding of its complex functions, and elucidating the genetic basis of its ability to degrade lignocellulose.

Pan-genomic analysis highlights genes associated with agronomic traits and enhances genomics-assisted breeding in alfalfa

Alfalfa (Medicago sativa L.), a globally important forage crop, is valued for its high nutritional quality and nitrogen-fixing capacity. Here, we present a high-quality pan-genome constructed from 24 diverse alfalfa accessions, encompassing a wide range of genetic backgrounds. This comprehensive analysis identified 433,765 structural variations and characterized 54,002 pan-gene families, highlighting the pivotal role of genomic diversity in alfalfa domestication and adaptation. Key structural variations associated with salt tolerance and quality traits were discovered, with functional analysis implicating genes such as MsMAP65 and MsGA3ox1. Notably, overexpression of MsGA3ox1 led to a reduced stem-leaf ratio and enhanced forage quality. The integration of genomic selection and marker-assisted breeding strategies improved genomic estimated breeding values across multiple traits, offering valuable genomic resources for advancing alfalfa breeding. These findings provide insights into the genetic basis of important agronomic traits and establish a solid foundation for future crop improvement.

Evolutionary history of magnoliid genomes and benzylisoquinoline alkaloid biosynthesis

Benzylisoquinoline alkaloids (BIAs) are important metabolites synthesized in early-diverging eudicots and magnoliids, yet the genetic basis of BIA biosynthesis in magnoliids remains unclear. Here, we decode the genomes of two magnoliid species, Saruma henryi and Aristolochia manshuriensis, and reconstruct the ancestral magnoliid karyotype and infer the chromosomal rearrangement history following magnoliid diversification. Metabolomic, transcriptomic, and phylogenetic analyses reveal the intermediate chemical components and genetic basis of BIA biosynthesis in A. manshuriensis. Although the core enzymes involved in BIA synthesis appear to be largely conserved between early-diverging eudicots and magnoliids, the biosynthetic pathways in magnoliids seem to exhibit greater flexibility. Significantly, our investigation of the evolutionary history of BIA biosynthetic genes revealed that almost all were duplicated before the emergence of extant angiosperms, with only early-diverging eudicots and magnoliids preferentially retaining these duplicated genes, thereby enabling the biosynthesis of BIAs in these groups.

The telomere-to-telomere genome assembly of the wild mulberry, Morus mongolica

Morus mongolica is a wild mulberry native to China and North Korea. In the current study, we assembled a high-quality telomere-to-telomere genome sequence of M. mongolica using NGS, HiFi, ONT, and Hi-C technologies. The genome was determined to be 341.88 Mb in size with a contig N50 of 23.82 Mb. The numbers of telomeres and centromeres were 28 and 14, with average lengths of 9.86 kb and 1.91 Mb, accounting for 0.08% and 7.84% of the total genome, respectively. A total of 21,657 protein-coding genes and 186.50 Mb repeat sequences were annotated. Genome integrity evaluation by BUSCO revealed a completeness score of 99.44% and a quality value of 46.7. Collinearity analysis between M. mongolica and either Morus alba or Morus notabilis showed that the breakage and fusion of chromosomes in Morus occurred at the centromere region of M. notabilis, which provided important genomic evidence for the evolution and chromosome breakage-fusion mechanism of Morus species.

Insights into convergent evolution of cosexuality in liverworts from the Marchantia quadrata genome

Sex chromosomes are expected to coevolve with their respective sex, potentially disfavoring their co-occurrence as cosexuality evolves. This effect is expected to be stronger where sex chromosomes are restricted to one sex, such as in plants expressing sex in their haploid stage. We assess this hypothesis in liverworts with U/V sex chromosomes, ancestral dioicy, and several independent transitions to monoicy (cosexuality). We report the chromosome-level genome assembly of Marchantia quadrata, which recently evolved monoicy, and perform comparative genomic analyses with its dioicous relative M. polymorpha. We find that monoicy evolved via retention of the V chromosome as a small ninth chromosome, complete loss of the U chromosome, and translocation of key U-linked genes to autosomes, among which the major sex-determining gene (Feminizer) acquired environmental/developmental regulation. Our findings parallel recent observations on Ricciocarpos natans, which evolved monoicy independently, suggesting genetic constraints that may make transitions to monoicy predictable in liverworts.

Chromosome-level genome assembly of an important ethnic medicinal plant Callicarpa nudiflora

Callicarpa nudiflora is one of high medicinal and economic value plants in China, which was recorded in Chinese pharmacopoeia (2020 edition) and widely used to treat tropical bacterial infections, acute infectious hepatitis, and internal and external bleeding. In this study, we assembled the C. nudiflora genome with a size of approximately 597.82 Mb and a contig N50 length of 34.14 Mb. A total of 98.61% of the assembled sequences were anchored to 17 pseudo-chromosomes by using PacBio long reads and Hi-C sequencing data. We totally predicted 31,266 protein-coding genes, of which 92.45% could be annotated in databases such as NR, GO, KOG, and KEGG. In addition, we identified 2,303 rRNAs, 884 MicroRNAs and 531 tRNAs from the genome. The chromosome-scale genome represents a crucial resource for investigating the molecular mechanisms underlying the biosynthesis of medicinal components and facilitates the exploration and conservation of C. nudiflora.

Zygotic activation of transposable elements during zebrafish early embryogenesis

Although previous studies have shown that transposable elements (TEs) are conservatively activated to play key roles during early embryonic development, the details of zygotic TE activation (ZTA) remain poorly understood. Here, we employ long-read sequencing to precisely identify that only a small subset of TE loci are activated among numerous copies, allowing us to map their hierarchical transcriptional cascades at the single-locus and single-transcript level. Despite the heterogeneity of ZTA across family, subfamily, locus, and transcript levels, our findings reveal that ZTA follows a markedly different pattern from conventional zygotic gene activation (ZGA): ZTA occurs significantly later than ZGA and shows a pronounced bias for nuclear localization of TE transcripts. This study advances our understanding of TE activation by providing a high-resolution view of TE copies and creating a comprehensive catalog of thousands of previously unannotated transcripts and genes that are activated during early zebrafish embryogenesis. Among these genes, we highlight two that are essential for zebrafish development.

The genome of giant waterlily provides insights into the origin of angiosperms, leaf gigantism, and stamen function innovation

As some of the earliest evolving flowering plants, waterlilies offer unique insights into angiosperm evolution. Giant Amazonian waterlilies (genus Victoria) are of particular interest due to their production of the world's largest floating leaves and gigantic flowers that entrap pollinating beetles. Here, we report chromosome-level genome assemblies of Victoria cruziana and three related waterlilies: Euryale ferox, Nymphaea mexicana, and Brasenia schreberi. We found an ancient whole-genome duplication event specific to the Nymphaeales. We reveal major gene duplication and loss events throughout the evolution of angiosperms, with substantial implications for flower development and the biosynthesis of floral volatile organic compounds (FVOCs) in waterlilies. Importantly, we report a unique division of labor in the stamen function of V. cruziana linked to beetle attraction by FVOCs. This is related to the ultra-high expression of VicSABATHa along with Vicchitinase, possibly linked to protection from damage by trapped beetles. Overexpression of VicSABATHa in tobacco leaves reveals a capacity to produce volatile fatty acids, confirming its role in their catalytic synthesis. Overall, these findings provide novel insights into the evolution and adaptations of waterlilies and flowering plants in general.

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.

High-quality genome of allotetraploid Avena barbata provides insights into the origin and evolution of B subgenome in Avena

Avena barbata, a wild oat species within the genus Avena, is a widely used model for studying plant ecological adaptation due to its strong environmental adaptability and disease resistance, serving as a valuable genetic resource for oat improvement. Here, we phased the high-quality chromosome-level genome assembly of A. barbata (6.88 Gb, contig N50 = 53.74 Mb) into A (3.57 Gb with 47,687 genes) and B (3.31 Gb with 46,029 genes) subgenomes. Comparative genomics and phylogenomic analyses clarified the evolutionary relationships and trajectories of A, B, C and D subgenomes in Avena. We inferred that the A subgenome donor of A. barbata was Avena hirtula, while the B subgenome donor was probably an extinct diploid species closely related to Avena wiestii. Genome evolution analysis revealed the dynamic transposable element (TE) content and subgenome divergence, as well as extensive structure variations across A, B, C, and D subgenomes in Avena. Population genetic analysis of 211 A. barbata accessions from distinct ecotypes identified several candidate genes related to environmental adaptability and drought resistance. Our study provides a comprehensive genetic resource for exploring the genetic basis underlying the strong environmental adaptability of A. barbata and the molecular identification of important agronomic traits for oat breeding.

The chromosomal-level genome assembly and annotation of pen shell Atrina pectinata

The pen shell Atrina pectinata is a bivalve recognized for its outstanding large adductor muscle and developed byssus. Now, it becomes threatened in East Asia, requiring special attention for artificial breeding to boost yield. However, the lack of high-quality genomes hinders our understanding of its reproductive biology, which resulting in the artificial breeding in pen shell is still a scientific technological problem. Here, we produced a high-quality chromosome-level genome assembly of A. pectinata combing the PacBio, Illumina, and high-resolution chromosome conformation capture sequencing. The final assembly has a size of 951.01 Mb with a scaffold N50 of 52.64 Mb, 98.87% of sequence was anchored onto 17 chromosomes, with a BUSCO evaluation integrity score of 98.8%. We successfully identified 29,326 protein-coding genes and 24,708 genes (84.25%) were functionally annotated. The BUSCO evaluation integrity score for the predicted protein-coding genes was 97.7%. This work promotes the applicability of the A. pectinata genome, laying a solid foundation for future investigations into genomics and biology within this species.

Haplotype-resolved genomes of Trichophyton mentagrophytes and Trichophyton tonsurans

Dermatophytes have posed a significant health concern due to their ability to parasitize human and animal skin, hair, and nails, causing a spectrum of dermatological conditions. However, the absence of high-quality genomes hinders our understanding of the dermatophytes. In this study, we utilized the circular consensus sequencing (CCS) technology to generate haplotype-resolved, nearly-complete genomes for two representative dermatophytes, Trichophyton mentagrophytes and Trichophyton tonsurans. Total sizes of the genomes ranged from 23.8 Mb to 25.2 Mb, with the contig N50 lengths of 6.47 Mb and 12.65 Mb, respectively. Each genome assembly was gapless and possessed three pseudochromosomes, with two achieving telomere-to-telomere (T2T) level. BUSCO analysis of the assemblies revealed approximately 99% of genome completeness. More than 7500 protein-coding genes were identified, and over 99% of the genes were well annotated through multiple gene function databases. Approximately 10% of the genomes were covered by repeats, particularly retrotransposons. Our findings provided valuable genomic resources of dermatophytes, paving the way for developing more effective medical interventions and public health strategies against Trichophyton infections.

Chromosome-level genome assembly and annotation of Anthurium amnicola

Anthurium amnicola is in the monocot family Araceae, subfamily Pothoideae and is a contributing species in Hawaii floriculture industry hybrids. To support future genetic improvements to this commodity, we sequenced and assembled the A. amnicola genome to chromosome-scale using PacBio HiFi and short-read Hi-C sequencing. A total of 98.51% of the 4.79 Gb genome is anchored into 15 chromosomes, with 99.2% gene completeness and a high LTR assembly index (LAI) score of 21.73, indicative of a complete, high-quality assembly. Annotation reveals the presence of 20,380 protein-coding genes, with 78.52% of the genome composed of repetitive sequences, predominantly long terminal repeat retrotransposons (LTR-RT). Phylogenetic analysis identified evolutionary relationships between A. amnicola and representative species in the Araceae and other plant families. This study provides the first reference genome sequence for the neotropical genus Anthurium and insights into Araceae evolution, benefiting the floriculture industry and evolutionary studies.

Chromosome-level genome assembly of the crofton weed (Ageratina adenophora)

Crofton weed (Ageratina adenophora), a significant invasive species, extensively disrupts ecosystem stability, leading to considerable economic losses. However, genetic insights into its invasive mechanisms have been limited by a lack of genomic data. In this study, we present the successful de novo assembly of the triploid genome of A. adenophora, leveraging long-read PacBio Sequel, optical mapping, and Hi-C sequencing. Our assembly resolved into a haplotype-resolved genome comprising 51 chromosomes, with a total size of ~3.82 Gb and a scaffold N50 of 70.8 Mb. BUSCO analysis confirmed the completeness of 97.71% of genes. Genome annotation revealed 3.16 Gb (76.44%) of repetitive sequences and predicted 123,134 protein-coding genes, with 99.03% functionally annotated. The high-quality reference genome will provide valuable genomic resources for future studies on the evolutionary dynamics and invasive adaptations of A. adenophora.

Analysis of allohexaploid wheatgrass genome reveals its Y haplome origin in Triticeae and high-altitude adaptation

Phylogenetic origin of the Y haplome present in allopolyploid Triticeae species remains unknown. Here, we report the 10.47 Gb chromosome-scale genome of allohexaploid Elymus nutans (StStYYHH). Phylogenomic analyses reveal that the Y haplome is sister to the clade comprising V and Jv haplomes from Dasypyrum and Thinopyum. In addition, H haplome from the Hordeum-like ancestor, St haplome from the Pseudoroegneria-like ancestor and Y haplome are placed in the successively diverged clades. Resequencing data reveal the allopolyploid origins with St, Y, and H haplome combinations in Elymus. Population genomic analyses indicate that E. nutans has expanded from medium to high/low-altitude regions. Phenotype/environmental association analyses identify MAPKKK18 promoter mutations reducing its expression, aiding UV-B adaptation in high-altitude populations. These findings enhance understanding of allopolyploid evolution and aid in breeding forage and cereal crops through intergeneric hybridization within Triticeae.

An chromosome-level haplotype-resolved genome assembly and annotation of pitaya (Selenicereus polyrhizus)

Pitaya, (Selenicereus spp.), a fruit originating from North and Central America and extensively cultivated in China and Vietnam, holds significant economic value. Utilizing PacBio HiFi sequencing and Oxford Nanopore Technologies ultra-long sequencing, aided by Hi-C data, we have assembled a chromosome-level haplotype-resolved genome. The sizes of the two haplotype genomes were determined to be 1.477 Gb (hap1, contig N50 = 133.35 Mb) and 1.442 Gb (hap2, contig N50 = 132.57 Mb), with 96.7% (hap1) and 98.4% (hap2) respectively allocated to 11 pseudochromosomes. Hap1 comprises 58.94% repeat sequences and predicts a total of 29,139 protein-coding gene models and 18,378 non-coding RNAs. Hap2 comprises 58.37% repeat sequences and predicts a total of 28,538 protein-coding gene models and 19,458 non-coding RNAs. Notably, 93.5% and 93.6% of protein-coding genes were annotated for the two haplotypes. The high-quality genome assembly presented in this study provides a valuable resource for future ecological, evolutionary, biological, and breeding research in pitaya.

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.

A nuclear tRNA-derived fragment triggers immunity in Arabidopsis

In Arabidopsis, effector-triggered immunity (ETI) against avirulent Pseudomonas syringae pv. tomato (Pst) correlates with the rapid, Dicer-Like 1 (DCL1)-dependent nuclear accumulation of a 31-nt 5'-tRNA fragment derived from Asp-tRNA (tRF31Asp2). Several tRFs, including tRF31Asp2, are induced at early stages of infection and associate with AGO2 in the nucleus. Infiltrating Arabidopsis leaves with synthetic tRF31Asp2 induces over 500 defense-associated genes, conferring immunity against virulent and avirulent Pst as well as aphids, while tRF31Asp2 depletion compromises resistance to avirulent Pst. The biological activity of tRF31Asp2 requires its 5' sequence and predicted stem-loop structure, and its loading into AGO2 or related clade members may contribute to activating defense responses. Chromatin affinity precipitation-sequencing revealed that tRF31Asp2 binds specific sequences in defense genes and the Gypsy superfamily of LTR retrotransposons, particularly at their primer binding sites (PBS). tRF31Asp2 binding appears to modulate transcriptional reprogramming, inducing neighboring tRF-responsive defense genes while suppressing active retrotransposons. Since Gypsy retrotransposon proliferation is primed by tRNA binding at PBS, tRF31Asp2 may exploit a similar mechanism to coordinate defense responses. Together, these findings reveal a role for DCL1 and tRF31Asp2 in regulating plant immunity and transcriptional dynamics at defense-associated loci and retrotransposons.

Chromosome-Level Genome Assembly of the Loach Goby Rhyacichthys aspro Offers Insights Into Gobioidei Evolution

The percomorph fish clade Gobioidei is a suborder that comprises over 2200 species distributed in nearly all aquatic habitats. To understand the genetics underlying their species diversification, we sequenced and annotated the genome of the loach goby, Rhyacichthys aspro, an early-diverging group, and compared it with nine additional Gobioidei species. Within Gobioidei, the loach goby possesses the smallest genome at 594 Mb, and a rise in species diversity from early-diverging to more recently diverged lineages is mirrored by enlarged genomes and a higher presence of transposable elements (TEs), particularly DNA transposons. These DNA transposons are enriched in genic and regulatory regions and their copy number increase is strongly correlated with substitution rate, suggesting that DNA repair after transposon excision/insertion leads to nearby mutations. Consequently, the proliferation of DNA transposons might be the crucial driver of Gobioidei diversification and adaptability. The loach goby genome also points to mechanisms of ecological adaptation. It contains relatively few genes for lateral line development but an overrepresentation of synaptic function genes, with genes putatively under selection linked to synapse organisation and calcium signalling, implicating a sensory system distinct from other Gobioidei species. We also see an overabundance of genes involved in neurocranium development and renal function, adaptations likely connected to its flat morphology suited for strong currents and an amphidromous life cycle. Comparative analyses with hill-stream loaches and the European eel reveal convergent adaptations in body shape and saltwater balance. These findings shed new light on the loach goby's survival mechanisms and the broader evolutionary trends within Gobioidei.

A telomere-to-telomere genome assembly coupled with multi-omic data provides insights into the evolution of hexaploid bread wheat

The complete assembly of vast and complex plant genomes, like the hexaploid wheat genome, remains challenging. Here we present CS-IAAS, a comprehensive telomere-to-telomere (T2T) gap-free Triticum aestivum L. genome, encompassing 14.51 billion base pairs and featuring all 21 centromeres and 42 telomeres. Annotation revealed 90.8 Mb additional centromeric satellite arrays and 5,611 rDNA units. Genome-wide rearrangements, centromeric elements, transposable element expansion and segmental duplications were deciphered during tetraploidization and hexaploidization, providing a comprehensive understanding of wheat subgenome evolution. Among them, transposable element insertions during hexaploidization greatly influenced gene expression balances, thus increasing the genome plasticity of transcriptional levels. Additionally, we generated 163,329 full-length cDNA sequences and proteomic data that helped annotate 141,035 high-confidence protein-coding genes. The complete T2T reference genome (CS-IAAS), along with its transcriptome and proteome, represents a significant step in our understanding of wheat genome complexity and provides insights for future wheat research and breeding.

The genome and GeneBank genomics of allotetraploid Nicotiana tabacum provide insights into genome evolution and complex trait regulation

Nicotiana tabacum is an allotetraploid hybrid of Nicotiana sylvestris and Nicotiana tomentosiformis and a model organism in genetics. However, features of subgenome evolution, expression coordination, genetic diversity and complex traits regulation of N. tabacum remain unresolved. Here we present chromosome-scale assemblies for all three species, and genotype and phenotypic data for 5,196 N. tabacum germplasms. Chromosome rearrangements and epigenetic modifications are associated with genome evolution and expression coordination following polyploidization. Two subgenomes and genes biased toward one subgenome contributed unevenly to complex trait variation. Using 178 marker-trait associations, a reference genotype-to-phenotype map was built for 39 morphological, developmental and disease resistance traits, and a novel gene regulating leaf width was validated. Signatures of positive and polygenic selection during the process of selective breeding were detected. Our study provides insights into genome evolution, complex traits regulation in allotetraploid N. tabacum and the use of GeneBank-scale resources for advancing genetic and genomic research.

Genomic Insights into Post-Domestication Expansion and Selection of Body Size in Ponies

Horse domestication revolutionizes human civilization by transforming transportation, agriculture, and warfare patterns. Despite extensive studies on modern domestic horse origins, the intricate demographic history and genetic signatures underlying pony size remain unexplored. Here, a high-quality genome assembly of the Chinese Debao pony is presented, and 452 qualified individuals from 64 horse breeds worldwide are extensively analyzed. The authors' results reveal the conservation of ancient components in East Asian horses and close relationships between Asian horses and Western pony lineages. Genetic analyses suggest an Asian paternal origin for European pony breeds. These pony-sized horses share close genetic affinities, potentially attributed to their early expansion and adaptation to local environments. In addition, promising cis-regulatory elements influencing horse withers height by regulating genes such as RFLNA and FOXO1 are identified. Overall, this study provides insightful perspectives on the dispersal history and genetic determinants underlying body size in ponies, offering broader implications for horse population management and improvement.

Haplotype-resolved genome assembly of the tetraploid Youcha tree Camellia meiocarpa Hu

Camellia meiocarpa Hu, a member of Youcha species in the genus Camellia, is an important woody edible Youcha plant with high ecological and economic value. The haplotype-resolved genome assembly of this tetraploid species can shed light on genomic evolution and the functional divergence among subgenomes and haplotypes. In this study, we achieved the first chromosome-level haplotype-resolved genome assembly using PacBio HiFi, Hi-C, and Illumina sequencing. The scaffolds, with an N50 of 44.46 Mb and 41.40 Mb, were mapped to 60 chromosomes and four distinct haplotypes, each with unique transposon features. The haplotypes varied in length (2967.25 Mb to 3041.66 Mb) and contained 51,336 to 52,631 protein-coding genes, 99.4% of which were annotated. Non-coding RNAs and repetitive elements were identified across haplotypes. This comprehensive genomic resource will enhance molecular and genetic studies, aiding in the conservation and utilization of Youcha.

High-quality genome assembly of the azooxanthellate coral Tubastraea coccinea (Lesson, 1829)

Coral reefs are among the most biodiverse and economically significant ecosystems globally, yet they are increasingly degrading due to global climate change and local human activities. The sun coral Tubastraea coccinea (T. coccinea) an obligate heterotroph lacking symbiotic zooxanthellae, exhibits remarkable tolerance to conditions that cause bleaching and mortality in zooxanthellate species. With its extensive low-latitude distribution across multiple oceans, T. coccinea has become a highly invasive species, adversely impacting native species, degrading local ecosystems, and causing significant socio-economic challenges that demand effective management. Despite substantial research efforts, the molecular biology of T. coccinea remains insufficiently characterized. To address this gap, we generated a draft genome assembly for T. coccinea using PacBio Hi-Fi long-read sequencing. The assembly spans 875.9 Mb with a scaffold N50 of 694.3 kb and demonstrates high completeness, with a BUSCO score of 97.4%. A total of 37,307 protein-coding sequences were identified, 95.2% of which were functionally annotated through comparisons with established protein databases. This reference genome provides a valuable resource for understanding the genetic structure of T. coccinea, advancing research into its adaptive mechanism to environmental changes, and informing conservation and management strategies to mitigate its invasive impact.

Chromosome-scale genome assembly of Trigonella corniculata (L.)L. (Nagauri pan /Kasuri methi), an important spice

Trigonella corniculata (L) L. or Nagauri pan /Kasuri methi, is an important spice crop with high nutraceutical potential. We report the de novo chromosome-scale assembly of T. corniculata genome using high coverage PacBio, Illumina and Hi-C reads. The assembly spans 798 Mb (Megabases) in 282 scaffolds with a scaffold N50 of 99.6 Mb. More than 98% of the sequence length is captured in eight different pseudomolecules with an average length of 98 Mb. A BUSCO score of over 97% is suggestive of the high degree of completeness and contiguity of the genome. A total of 64,801 protein-coding genes are predicted. Genome-wide Simple Sequence Repeats (99,149) have been identified and wet lab validated at forty-eight loci. The chromosome-scale genome assembly of T. corniculata and the SSR markers identified in this study will provide a strong foundation for future structural and functional genomics studies in T. corniculata and other fenugreek species.

Chromosome-level genome assembly of the threatened ornamental plant Hibiscus yunnanensis

Hibiscus yunnanensis S.Y. Hu is an endangered species of the genus Hibiscus (Malvaceae), which has high potential economic value. However, the absence of a high-quality reference genome impedes the study of the ecology and molecular biology of H. yunnanensis. Here, we present a high-quality chromosome-level assembly of H. yunnanensis using BGI-DIPSEQ, Nanopore, and Hi-C sequencing. The assembled genome size is 2.2 Gb with a contig N50 of 12.1 Mb and a scaffold N50 of 137.1 Mb. Approximately 99.2% of the assembly is anchored into 17 pseudochromosomes, and a BUSCO analysis indicates a completeness score of 99.6%. Furthermore, we identify 42,085 protein-coding genes, of which 96.4% are functionally annotated. This genome resource provides a foundation for future studies on unique traits, including drought-tolerant, savanna-adapted, and long-flowering traits. Its ability to flower in winter, along with its automatic selfing and lack of delayed inbreeding depression, makes it an excellent model for studying style curvature mechanism and its adaptive significance in the Malvaceae.

Chromosome-level genome assembly and annotation of the White-spotted spinefoot Siganus canaliculatus

The White-spotted spinefoot S. canaliculatus, is an economically important marine fish in South China and featured by possessing poisonous glands in its fin spines. However, the unavailability of the S. canaliculatus genome has been a serious obstacle to genetic breeding as well as basic researches such as uncovering genomic basis underlying its toxigenic glands. Here, we presented a chromosome-level genome assembly coupled with good annotation of S. canaliculatus using multiple omics technologies. The assembled genome size was 547.39 Mb, with a contig N50 and scaffold N50 length of 21.41 Mb and 21.79 Mb, respectively. Approximately 95.32% (521.76 Mb) of assembled sequences were placed into 24 pseudochromosomes with the support of Hi-C contact map. Furthermore, around 16.37% of the genome was composed of repetitive elements. The quality of the assembly assessed using BUSCO showed that 98.6% of BUSCO genes were identified as complete. 25,323 protein-coding genes were predicted after integration of three kinds of evidence, of which 96.96% were functionally annotated in at least one of nine protein databases. In sum, the chromosome-level genome assembly and annotation provide fundamental resources for genetic breeding and molecular mechanism related studies of S. canaliculatus.