LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons

An improved chromosomal-scale genome assembly of the Tanaka's snailfish (Liparis tanakae)

As one of the top predators in the Yellow Sea, the Tanaka's snailfish (Liparis tanakae) plays an important ecological role in maintaining the structure and function of the ecosystem. This species also has fast and strong adaptability to external pressures such as climate change and fishing activities. To facilitate further molecular evolution researches of L. tanakae, we generated a chromosome-scale genome assembly in this study. The final assembly yielded 574.44 Mb in total length, with a scaffold N50 of 24.64 Mb, and anchored 97.87% of the sequences into 24 pseudo-chromosomes. Our assembly was 20.18 Mb longer than the reference genome (Tanakav1) in total length, with higher scaffold N50 and fewer scaffolds. The BUSCO score of 97.3% and Merqury quality value of 36.98 revealed high completeness and accuracy of our assembly. The genome contained 20,933 predicted protein-coding genes and 28.28% of the assembly was annotated as repetitive sequences. This study significantly advances the genomic resources for L. tanakae and facilitates future adaptation and evolution researches of this species.

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.

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.

Haplotype-resolved genome assembly and genome-wide association study identifies the candidate gene closely related to sugar content and tuber yield in Solanum tuberosum

As an important noncereal food crop grown worldwide, the genetic improvement of potato in tuber yield and quality is largely constrained due to the lacking of a high-quality reference genome and understanding of the regulatory mechanism underlying the formation of superior alleles. Here, a chromosome-scale haplotype-resolved genome assembled from an anther-cultured progeny of 'Ningshu 15', a tetraploid variety featured by its high starch content and drought resistance was presented. The assembled genome size was 1.653 Gb, with a contig N50 of approximately 1.4 Mb and a scaffold N50 of 61 Mb. The long terminal repeat assembly index score of the two identified haplotypes of 'Ningshu 15' was 11.62 and 11.94, respectively. Comparative genomic analysis revealed that positive selection occurred in gene families related to starch, sucrose, fructose and mannose metabolism, and carotenoid biosynthesis. Further genome-wide association study in 141 accessions identified a total number of 53 quantitative trait loci related to fructose, glucose, and sucrose content. Among them, a tonoplast sugar transporter encoding gene, StTST2, closely associated with glucose content was identified. Constitutive expression of StTST2 in potato and Arabidopsis increased the photosynthetic rate, chlorophyll and sugar content, biomass tuber and seed production in transgenic plants. In addition, co-immunoprecipitation assays demonstrated that StTST2 directly interacted with SUT2. Our study provides a high-quality genome assembly and new genetic locus of potato for molecular breeding.

Chromosome-level genome assembly of scalloped spiny lobster Panulirus homarus homarus

Lobsters, aquatic organisms of significant economic value, hold an important position in the global aquaculture and fisheries industries. However, due to overfishing and ecological change, the populations of certain lobster species have declined dramatically, prompting conservation efforts in various countries. However, limited genomics research has restricted our capacity to conserve and exploit lobster germplasm resources. Here, we present a chromosome-level reference genome for Panulirus homarus homarus constructed using PacBio long-read sequencing and Hi-C data. The genome assembly size was 2.61 Gb, with a contig N50 of 5.43 Mb, and a scaffold N50 of 36.69 Mb. The assembled sequences were anchored to 73 chromosomes, covering 96.05% of the total genome. A total of 25,580 protein-coding genes were predicted, and 99.98% of the genes were functionally annotated using various protein databases. The high-quality genome assembly provides a valuable resource for studying the biology and evolutionary history of P. h. homarus, and could facilitate sustainable resource management, aquaculture, and conservation of the species.

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 of the estuarine Corbicula flumnalis from the Yangtze River estuary in China

Corbicula clams are of important economic values. Corbicula clams have diverse reproductive characteristics, inhabiting both freshwater and estuary. Here, we constructed a chromosome-level genome of the estuarine C. fluminalis from China by combining HiFi sequencing and Hi-C technology. The assembled genome is 1,140.30 Mb with a scaffold N50 length of 58.80 Mb, and is anchored onto 19 pseudo-chromosomes. A total of 25,363 protein-coding genes were identified and 94.03% of the identified genes were annotated. Approximately 63.50% of the genome is consisted of repetitive elements. The genome synteny between C. fluminalis and Mercenaria mercenaria is highly conserved. The chromosome genome assembly of C. fluminalis is a valuable resource for active ingredient research, phylogenomic studies and comparative genomics of the Corbicula clams and related species.

Chromosome-Level Genome Assembly and Genomic Analysis of the Hybrid Grouper ShanHu (Epinephelus fuscoguttatus ♀ × Epinephelus polyphekadion ♂)

Groupers are important aquaculture species, and hybridization is an effective breeding method for genetic improvement and to enhance production efficiency in groupers. The ShanHu grouper (Epinephelus fuscoguttatus ♀ × Epinephelus polyphekadion ♂) is a hybrid grouper with potential for aquaculture development and research value. Using Illumina and PacBio sequencing platforms, as well as PacBio SMRT technology and Hi-C auxiliary mounting technology, the whole genome sequencing and assembly of the ShanHu grouper were completed, resulting in a chromosome-level genome information for this hybrid grouper. The genome assembly has a total length of 1.17 Gb with a scaffold N50 of 46.12 Mb, and 171 contigs were anchored into 24 chromosomes. Additionally, its repeat sequences and non-coding RNAs were annotated and 26,102 genes were predicted. Through comparative genomic analysis of the hybrid species ShanHu grouper and its parents, we found that comparative genomic analyses revealed centric inversion structural variations on the chromosomes of the hybrid ShanHu grouper in relation to the brown-marbled grouper and the camouflage grouper. Furthermore, the gene families of the hybrid species have expanded in pathways related to immunity and growth development. This study is the first to provide complete genomic information for a hybrid grouper, offering its full genetic information, exploring the genetic variations in the genomes of hybrid offspring, and providing data references for foundational theoretical research and grouper production practices.

Chromosome-level genome assembly and annotation of Gypsophila vaccaria

Gypsophila vaccaria Sm., a member of the Caryophyllaceae family, is known for its dry mature seeds, which are widely used in traditional Chinese medicine as "Wang Bu Liu Xing". This study presents a high-quality, chromosome-scale genome assembly of G. vaccaria, integrating Hi-C technology with PacBio and Illumina sequencing data. The final assembled genome measures 1.09 Gb in total length, with a contig N50 of 9.73 Mb and a scaffold N50 of 73.3 Mb, and complete benchmarking universal single-copy orthologs (BUSCO) for the genome and protein modes were 95.9% and 94.9%. Notably, 99.93% of the sequences are anchored to 15 pseudo-chromosomes. A total of 21,795 protein-coding genes were predicted, and repetitive elements were found to constitute 80.43% of the assembled genome. This chromosome-level genome assembly serves as an invaluable resource for future research, including functional genomics and molecular breeding of G. vaccaria.

Chromosome-level genome assembly of a high-yield Chinese soybean variety Mengdou1137 unlocks genetic potential of disease and lodging resistance

KEY MESSAGE

We assembled the genome of Mengdou1137 with high quality and revealed the specific disease resistance genes and a large number of genomic variations related to agronomic traits. As a cornerstone in the global agricultural landscape, soybean stands as a pivotal oilseed crop, underpinning both nutritional and industrial applications. The burgeoning development of novel soybean varieties significantly propels the crop's industrialization, offering enhanced traits that cater to diverse agricultural and commercial needs. In this study, we present the de novo assembly of the genome a high-yield Chinese soybean variety Mengdou1137, employing an integrated approach of both long-read and short-read sequencing technologies to achieve comprehensive genomic insights. Achieving a notable assembly with a genome size of 999.99 Mb, our work features a contig N50 of 14.92 Mb and a scaffold N50 of 50.26 Mb, successfully anchoring 98.24% of sequences across the 20 chromosomes. Through meticulous comparative analysis with existing soybean genomes, our research unveiled 115 Mengdou1137-specific disease resistance genes alongside a substantial array of agronomical trait-associated genomic variants. Among the salient genomic features, we identified a favorable haplotype of the dwarf gene PH13, a critical determinant of plant stature, underscoring its potential for breeding compact soybean varieties with lodging resistance. This high-quality assembly of the Mengdou1137 genome not only enriches the repository of soybean genetic resources but also paves the way for future innovations in soybean breeding and trait improvement, offering valuable insights for the enhancement of this crucial agricultural commodity.

Chromosome-level assembly of Pseudopodoces humilis genome: A resource for avian evolutionary studies

Pseudopodoces humilis is a small passerine bird predominantly found in the mid-latitude regions of the Tibetan Plateau in Asia. A chromosome-level reference genome assembly for P. humilis was generated using PacBio CLR with Hi-C. The final genome assembly spans approximately 1.096 Gb, consisting of 1,968 contigs with a Contig N50 of 32.246 Mb, and was evaluated to be 95.60% complete using BUSCO. Hi-C chromosome mapping resulted in 33 chromosome sequences, which enabled the ordering and orientation of 329 contigs, with chromosome lengths ranging from 2.08 Mb to 152.13 Mb, covering 95.85% of the total genome sequence. Repetitive sequences comprised 144.91 Mb of the genome. A total of 381 tRNA, 507 non-coding RNA (ncRNA), and 205 rRNA were identified. In addition, we identified 17,108 protein-coding genes and 29,473 proteins, comprising a total of 17,236,726 amino acids. This high-quality genome assembly provides a strong genomic foundation for exploring critical questions in evolutionary genetics, phylogenomics, and the molecular mechanisms of adaptation - key areas for understanding biodiversity and species resilience amidst changing environments.

New insights into the cold tolerance of upland switchgrass by integrating a haplotype-resolved genome and multi-omics analysis

BACKGROUND

Switchgrass (Panicum virgatum L.) is a bioenergy and forage crop. Upland switchgrass exhibits superior cold tolerance compared to the lowland ecotype, but the underlying molecular mechanisms remain unclear.

RESULTS

Here, we present a high-quality haplotype-resolved genome of the upland ecotype "Jingji31." We then conduct multi-omics analysis to explore the mechanism underlying its cold tolerance. By comparative transcriptome analysis of the upland and lowland ecotypes, we identify many genes with ecotype-specific differential expression, particularly members of the cold-responsive (COR) gene family, under cold stress. Notably, AFB1, ATL80, HOS10, and STRS2 gene families show opposite expression changes between the two ecotypes. Based on the haplotype-resolved genome of "Jingji31," we detect more cold-induced allele-specific expression genes in the upland ecotype than in the lowland ecotype, and these genes are significantly enriched in the COR gene family. By genome-wide association study, we detect an association signal related to the overwintering rate, which overlaps with a selective sweep region containing a cytochrome P450 gene highly expressed under cold stress. Heterologous overexpression of this gene in rice alleviates leaf chlorosis and wilting under cold stress. We also verify that expression of this gene is suppressed by a structural variation in the promoter region.

CONCLUSIONS

Based on the high-quality haplotype-resolved genome and multi-omics analysis of upland switchgrass, we characterize candidate genes responsible for cold tolerance. This study advances our understanding of plant cold tolerance, which provides crop breeding for improved cold tolerance.

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.

The complete reference genome of Tartary buckwheat and its mutation library provide important resources for genetic studies and breeding

Tartary buckwheat (TB), Fagopyrum tataricum, is an important medicinal and edible crop with a worldwide distribution. However, reference genomes with gaps and mutant population scarcity have hindered functional genomics and genetic improvement of TB. Here, we present a telomere-to-telomere (T2T) gap-free genome assembly of the elite TB inbred line Guiku1 and its ethyl-methyl-sulfonate (EMS)-induced phenotypically rich mutation library. The Guiku1 gap-free genome spans 453.83 Mb, containing 43,441 predicted protein-coding genes. The mutation library includes 751 mutants with stably heritable phenotypes. Whole-genome resequencing of 320 mutants identified 105,682 single-nucleotide polymorphisms (SNPs) and 21,461 insertions/deletions (indels), affecting the protein-coding sequences of 25,986 genes. Genes responsible for the pink stem and petiole mutant trait and flavonoid content variation were identified using forward- and reverse-genetics approaches, respectively. Collectively, the T2T gap-free genome of Guiku1 and its EMS mutation library provide important resources for functional genomics studies and the genetic improvement of TB.

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.

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.

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.

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.

A study of repetitive sequences in the genome of Sinopodisma qinlingensis

The family Acrididae characterized by a remarkable genome size and a significant proportion of repetitive sequences. In this study, we find a considerable characteristics by examining the Sinopodisma qinlingensis, which has an average genome size within the range observed in Acrididae. The genome size of S. qinlingensis was determined to be 11.37 pg for females and 10.95 pg for males using flow cytometry. The analysis of low-coverage sequencing data revealed that the total repeat content of the genome was 63.58%, with long terminal repeat (LTR) elements accounting for 17.74% of the genome contents. Phylogenetic analysis of the reverse transcriptase (RT) domains, which are found within LTR and LINE sequences with consistent conserved motifs, showed that LTR elements belong to multipl within a monophyletic branch. This finging suggests that LTR elements did not originate independently, but rather shared a common evolutionary history. Additionally, the content of Ty3-Gypsy sequences within LTR elements was found to be significantly increased. Fluorescence in situ hybridisation (FISH) showed that most satellite DNA and LTR elements exhibited an aggregated distribution pattern on the chromosome.

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.

Chromosome-level genomes of Arctic and Antarctic mosses: Aulacomnium turgidum and Polytrichastrum alpinum

Bryophytes play a crucial role in the ecosystems of polar regions. These simple plants are among the predominant vegetation types in both Arctic and Antarctic landscapes, where they contribute significantly to biodiversity and ecological stability. Here, we report the chromosome-level genomes of two polar moss species, the Arctic Aulacomnium turgidum and Antarctic Polytrichastrum alpinum. Utilizing a combination of Illumina short reads, Nanopore long reads, and Hi-C data, we assembled genomes of 277.84 Mb for A. turgidum and 498.33 Mb for P. alpinum, respectively. These assemblies were anchored to 11 chromosomes for A. turgidum and 8 chromosomes for P. alpinum. Both species exhibited a sex chromosome with distinct genomic characteristics. Gene annotations revealed 25,999 protein-coding genes in A. turgidum and 28,070 in P. alpinum. The high completeness of the gene space was validated via BUSCO, achieving impressive scores of 98.2% and 98.0%. These high-quality genomes provide critical resources for studying the adaptive evolution and stress tolerance mechanisms of mosses in extreme polar environments.

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.

Chromosome-level genome assembly and annotation of Chinese herring (Ilisha elongata)

The Chinese herring (Ilisha elongata) is a commercially and scientifically significant fish species. In this study, we conducted high-precision whole-genome sequencing using two high-throughput platforms: second-generation MGI and third-generation PacBio. Hi-C technology assisted in assembling the contig sequences onto 24 chromosomes, resulting in a high-quality chromosome-level genome map with excellent continuity and coverage. The completed genome size was approximately 815 Mb, with a contig N50 of 4.82 Mb, scaffold N50 of 32.61 Mb, and a chromosome mounting rate of 95.32%. SNP and InDel purity rates were 0.003% and 0.012%, respectively, and the genome assembly completeness was 96.68%, assessed by BUSCO. Repetitive sequences were annotated via ab initio and homology predictions, identifying 295.7 Mb of repetitive sequences, constituting 35.08% of the genome. A total of 26,381 protein-coding genes were predicted, with 24,596 functionally annotated.

Chromosomal-level genome assembly of Trichogramma dendrolimi (Trichogrammatidae: Hymenoptera)

Trichogramma dendrolimi is an essential egg parasitic wasp with a broad host range and has been widely used for controlling agricultural and forestry pests. Despite the availability of fragmented genomes of Trichogramma, a high-quality, chromosome-level genome reference is not yet available for this diverse genus. In this study, we assembled a high-quality chromosome-level genome of T. dendrolimi using PacBio CLR long sequencing and further scaffolded it with Hi-C technologies. The genome size was 216.24 Mb, featuring a N50 of 39.07 Mb, and 98.79% of scaffolds were anchored to five chromosomes. In addition, we annotated 12,902 protein-coding genes and 60.74 Mb repeat sequences for this genome assembly. In conclusion, our chromosome-level genome assembly provided important genomic resources that benefit the utilization of Trichogramma parasitoids in pest control.

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.

High-Quality Genome Assembly and Transcriptome of Rhododendron platypodum Provide Insights into Its Evolution and Heat Stress Response

R. platypodum (Rhododendron platypodum) is an endangered alpine species with a highly restricted distribution in the southwestern region of China, which possesses significant ornamental and horticultural value. In this study, the high-quality genome assembly of R. platypodum at the chromosomal level is reported. The total genome size was determined to be 642.25 Mb, with a contig N50 of 25.64 Mb, and it contains 36,522 predicted genes. Comparative genomic analysis between R. platypodum and other species revealed the expansion of gene families, such as those related to transition metal ion binding and sodium ion transport, as well as the contraction of gene families involved in the recognition of pollen and pollen-pistil interaction. These findings might explain the adaptation of R. platypodum to rocky habitats and contribute to its endangered status. Furthermore, a heat stress experiment was conducted on R. platypodum, followed by transcriptome sequencing and physiological co-analysis to construct a co-expression network. This analysis identified the candidate gene TAR1-A and other transcription factors exhibiting differential expression under heat stress. The whole-genome sequencing, transcriptome analysis, and physiological co-analysis of R. platypodum provide valuable resources for its conservation and offer insights into its mechanisms of heat stress.

Allelic variation and duplication of the dmrt1 were associated with sex chromosome turnover in three representative Scatophagidae fish species

Fish species of the family Scatophagidae possessing known candidate sex-determining genes (male-specific dmrt1Ys), offer suitable models for studying sex chromosome evolution. Here, we analyzed sex chromosome turnover events in three representative fish species of the family Scatophagidae, belonging to the genera Scatophagus and Selenotoca, which diverged 12.8 million years ago (Mya). Prior to the divergence of Sc. argus and Sc. tetracanthus 7.2 Mya, their dmrt1Y was differentiated from its locus, the truncated dmrt1ΔX, through allelic variation. The Y chromosome (Chr1) of Sc. tetracanthus is the result of the fusion of the original Y chromosome (Chr4) with an autosome (Chr13). The Se. multifasciata dmrt1Y arose from a duplication of dmrt1 on Chr4 and then translocated to the new Y chromosome (Chr18). The divergent evolutionary trajectories of the dmrt1Ys were accompanied by sex chromosome turnover in these three species. The sex chromosomes of the Scatophagidae family have evolved rapidly, albeit not randomly.

Draft genome assembly of the largemouth bass (Micropterus salmoides)

OBJECTIVE

Largemouth bass (Micropterus salmoides, LMB) is an important species in aquaculture, and the annual production is rapidly increasing. Genetic and breeding studies related to LMB have promising applications, and a high-quality genome assembly is essential for interpreting genetic and sequencing data. In this study, we sequenced the genome of a male LMB using the PacBio Sequel platform, high-throughput chromosome conformation capture (Hi-C), and paired-end Illumina sequencing. Additionally, Full-length transcript sequencing was performed using isoform sequencing (Iso-Seq). Following the assembly and annotation, a draft assembly for male LMB was obtained.

DATA DESCRIPTION

This work generated PacBio data of 164.5 Gb, Hi-C data of 113.4 Gb, Illumina data of 54.7 Gb, and Iso-Seq data of 22.8 Gb. The assembly revealed that the LMB genome has a total length of 877.7 Mb, with an N50 of 37.2 Mb, comprising 23 chromosomes and 202 scaffolds. Annotation results indicated that 32.8% of the genome consists of repetitive sequences, containing 23,952 coding genes with an average gene length of 17,328 bp.

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.

Genomic evidence for low genetic diversity but purging of strong deleterious variants in snow leopards

BACKGROUND

Long-term persistence of species with low genetic diversity is the focus of widespread attention in conservation biology. The snow leopard, Panthera uncia, is a big cat from high-alpine regions of Asia. However, its subspecies taxonomy, evolutionary history, evolutionary potential, and survival strategy remain unclear, which greatly hampers their conservation.

RESULTS

We sequence a high-quality chromosome-level genome of the snow leopard and the genomes of 52 wild snow leopards. Population genomics reveal the existence of two large genetic lineages in global snow leopards, the northern and southern lineages, supported by the biogeography. The Last Glacial Maximum drove the divergence of two lineages. Microclimate differences and large rivers between the western and central Himalayas likely maintain the differentiation of two lineages. EPAS1 is positively selected in the southern lineage with almost fixed amino acid substitutions and shows an increased allele frequency with elevation. Compared to the southern lineage, the northern lineage exhibits a lower level of genomic diversity and higher levels of inbreeding and genetic load, consistent with its recent population decline. We find that snow leopards have extremely low genomic diversity and higher inbreeding than other Carnivora species; however, strong deleterious mutations have been effectively purged in snow leopards by historical population bottlenecks and inbreeding, which may be a vital genetic mechanism for their population survival and viability.

CONCLUSIONS

Our findings reveal the survival strategy of a species with low genetic diversity and highlight the importance of unveiling both genetic diversity and genetic burden for the conservation of threatened 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.

Integrated genomic and transcriptomic analyses reveal the genetic and molecular mechanisms underlying hawthorn peel color and seed hardness diversity

Hawthorn (Crataegus pinnatifida) fruit peel color and seed hardness are key traits that significantly impact economic value. We present here the high-quality chromosome-scale genomes of two cultivars, including the hard-seed, yellow-peel C. pinnatifida "Jinruyi" (JRY) and the soft-seed, red-peel C. pinnatifida "Ruanzi" (RZ). The assembled genomes comprising 17 chromosomes are 809.1 Mb and 760.5 Mb in size, achieving scaffold N50 values of 48.5 Mb and 46.8 Mb for JRY and RZ, respectively. Comparative genomic analysis identifies 3.6-3.8 million single nucleotide polymorphisms, 8.5-9.3 million insertions/deletions, and approximately 30 Mb of presence/absence variations across different hawthorn genomes. Through integrating differentially expressed genes and accumulated metabolites, we filter candidate genes CpMYB114 and CpMYB44 associated with differences in hawthorn fruit peel color and seed hardness, respectively. Functional validation confirms that the CpMYB114-CpANS regulates anthocyanin biosynthesis in hawthorn peels, contributing to the observed variation in peel color. CpMYB44-CpCOMT is significantly upregulated in JRY and is verified to promote lignin biosynthesis, resulting in the distinction in seed hardness. Overall, this study reveals the new insights into understanding of distinct peel pigmentation and seed hardness in hawthorn and provides an abundant resource for molecular breeding.

Telomere-to-telomere gapless genome assembly of Triplophysa yaopeizhii

The genus Triplophysa exhibits remarkable adaptability to the unique environment found at the Qinghai-Tibet Plateau (QTP). Higher quality genomes are helpful to the study of the adaptability to the extreme environment in the plateau. This study utilized PacBio HiFi, Ultra-long ONT, and Hi-C sequencing of Triplophysa yaopeizhii to construct the first telomere-to-telomere (T2T) gapless genome assembly of the genus Triplophysa. The genome size is 671.58 Mb, with a contig N50 length of 26.04 Mb. The sequences were anchored onto 25 chromosomes with all centromeres and telomeres. Furthermore, 293.98 Mb (43.77%) of repetitive sequences and 26,487 protein-coding genes were identified. Comparative analyses with the genomes of closely related species demonstrated high completeness, continuity, and accuracy of the genome. The genomic quality was further substantiated by the QV of 31.82 with 96.60% of BUSCO. This study provides a valuable genetic resource of the genus Triplophysa and serves as an essential reference for elucidating the adaptive genetic mechanisms of plateau fish to the high altitude.

The chromosome-scale genomes of two cultivated safflowers (Carthamus tinctorius) provide insights into the genetic diversity resulting from domestication

KEY MESSAGE

Two cultivated safflowers from distinct areas elucidate the genetic diversity present in the linoleic acid biosynthesis, flowering time and flavonoid biosynthesis. The process of domestication facilitates the adaptation of crops to agricultural environments. In this study, we selected two representative safflower cultivars that has been domesticated in two distinct areas in China as samples to investigate their genetic diversity due to local environmental adaption. Yunhong-7 is a locally bred safflower (Carthamus tinctorius) cultivar, that has been currently widely cultivated in Yunnan Province, Southwest China, and Anhui-1 is a safflower cultivar that was locally bred in Anhui Province, East China. We firstly generated the chromosome-scale genome assembly for yunhong-7 cultivar by combining PacBio and Hi-C technologies. Through comparative genomic analysis, we identified structural variations (SVs) between yunhong-7 and anhui-1, which revealed their genetic differences in the pathways of fatty acid biosynthesis, circadian rhythm and flavonoid biosynthesis. Subsequently, a total of 40 non-redundant fatty acid desaturase 2 (FAD2) genes (39 for yunhong-7 and 20 for anhui-1) were identified, revealing the presence of copy-number variation and major genes change between yunhong-7 and anhui-1. The presented results suggested that changes in SVs may induce alterations in the expression of flowering-related genes, which could explain the observed early flowering phenotype in yunhong-7 compared to anhui-1. We identified a total of 197 non-redundant UDP-glucuronosyltransferases (UGT) genes. Based on prokaryotic expression system, we investigated the catalytic functions of two unique UGT genes (CtUGT.18 and CtUGT.191). The current study increases our knowledge of genetic diversity among crop cultivars resulting from distinct domestication processes and thus could contribute to the advancement of traits research and the safflower breeding.

Genomic insights and the conservation potential of captive breeding: The case of Chinese alligator

Despite 40 years of conservation of the critically endangered Chinese alligator (Alligator sinensis), the genomic underpinnings of its status remained uncharted. Genome sequencing data of 244 individuals uncovered relatively low overall genomic diversity/heterozygosity and long runs of homozygosity, with captive populations exhibiting higher heterozygosity and smaller inbreeding coefficients compared to wild individuals. The decreased level of inbreeding in the captive population demonstrates the contribution of the large captive breeding population. The estimated recent effective population size was around a few dozen. To combat challenges of inbreeding depression and reduced adaptability, we used genome-wide SNP-based kinship analysis on captive populations to enable a genome-informed breeding program that minimizes inbreeding. Long-term field monitoring revealed that the Chinese government greatly advanced the conservation of A. sinensis through conservation measures and reintroduction programs. Our research enriches the understanding of the Chinese alligator's genetic landscape, offering invaluable genomic resources for breeding and conservation strategies.

REPrise: de novo interspersed repeat detection using inexact seeding

BACKGROUND

Interspersed repeats occupy a large part of many eukaryotic genomes, and thus their accurate annotation is essential for various genome analyses. Database-free de novo repeat detection approaches are powerful for annotating genomes that lack well-curated repeat databases. However, existing tools do not yet have sufficient repeat detection performance.

RESULTS

In this study, we developed REPrise, a de novo interspersed repeat detection software program based on a seed-and-extension method. Although the algorithm of REPrise is similar to that of RepeatScout, which is currently the de facto standard tool, we incorporated three unique techniques into REPrise: inexact seeding, affine gap scoring and loose masking. Analyses of rice and simulation genome datasets showed that REPrise outperformed RepeatScout in terms of sensitivity, especially when the repeat sequences contained many mutations. Furthermore, when applied to the complete human genome dataset T2T-CHM13, REPrise demonstrated the potential to detect novel repeat sequence families.

CONCLUSION

REPrise can detect interspersed repeats with high sensitivity even in long genomes. Our software enhances repeat annotation in diverse genomic studies, contributing to a deeper understanding of genomic structures.

Chromosome-scale genome assembly of Zoysia japonica uncovers cold tolerance candidate genes

Zoysiagrass stands out as a crucial native turfgrass due to its exceptional abiotic stress tolerance, extensive adaptability, and high ornamental value. In this study, we generated a high-quality chromosome-level genome assembly of Compadre (COM) zoysiagrass, leveraging PacBio SMRT sequencing and Hi-C scaffolding technologies. The resulting genome assembly (312.42 Mb) is anchored on 20 chromosomes, with a Scaffold N50 of 18.72 Mb. In total, 49,074 genes and 306,768 repeat sequences were annotated in the assembled genome. The first chromosome-scale genome of Zoysia japonica 'Compadre' provides a critical genetic resource for cold-tolerant turfgrass breeding through identifying stress-responsive candidate genes. Additionally, we have successfully established a cell nucleus extraction and library construction protocol tailored for zoysiagrass ATAC-seq technology, and a total of 80 low temperature tolerance candidate genes were preliminarily identified via ATAC-seq and RNA-seq profiling, thereby initiating the exploration of turfgrass epigenomics.

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.

Comparative genomics provides insights into chromosomal evolution and immunological adaptation in horseshoe bats

Horseshoe bats are natural hosts of zoonotic viruses, yet the genetic basis of their antiviral immunity is poorly understood. Here we generated two new chromosomal-level genome assemblies for horseshoe bat species (Rhinolophus) and three close relatives, and show that, during their diversification, horseshoe bats underwent extensive chromosomal rearrangements and gene expansions linked to segmental duplications. These expansions have generated new adaptive variations in type I interferons and the interferon-stimulated gene ANXA2R, which potentially enhance antiviral states, as suggested by our functional assays. Genome-wide selection screens, including of candidate introgressed regions, uncover numerous putative molecular adaptations linked to immunity, including in viral receptors. By expanding taxon coverage to ten horseshoe bat species, we identify new variants of the SARS-CoV-2 receptor ACE2, and report convergent functionally important residues that could explain wider patterns of susceptibility across mammals. We conclude that horseshoe bats have numerous signatures of adaptation, including some potentially related to immune response to viruses, in genomic regions with diverse and multiscale mutational changes.

Haplotype-resolved and chromosome-level reference genome assembly of Diospyros deyangensis provides insights into the evolution and juvenile growth of persimmon

The Diospyros genus , which includes both wild and cultivated species such as Diospyros lotus and Diospyros kaki, represents a diverse genetic pool with significant agricultural value. In this study, we present a high-quality, haplotype-resolved, chromosome-level genome assembly for Diospyros deyangensis (hereinafter referred to as 'Deyangshi'), an autotetraploid wild species notable for its short juvenile phase, by integrating high-fidelity single-molecule, nanopore sequencing, and high-throughput chromosome conformation capture techniques. The assembled genome size is ~3.01 Gb, anchored onto 60 pseudochromosomes. Comparative genomic analysis revealed that the D. deyangensis genome underwent an additional whole-genome duplication (WGD) event following the eudicots shared ancient hexaploidy event. Resequencing and clustering on 63 samples representing 11 geographically diverse Diospyros accessions revealed significant genetic differentiation between D. deyangensis and D. kaki, as well as between D. kaki and other Diospyros species using population genomic analyses, suggesting that D. kaki followed an independent evolutionary pathway. Additionally, we identified DdELF4 (EARLY FLOWERING 4) from the 'Deyangshi' backcross population using bulked segregant RNA sequencing (BSR-seq) with 50 early-flowering and 50 non-early-flowering individuals. Overexpression of DdELF4 in Arabidopsis resulted in delayed flowering and downregulation of FT gene expression, indicating its role as a flowering repressor. This high-quality genome assembly of 'Deyangshi' provides an essential genomic resource for the Diospyros genus, particularly for breeding programs focused on developing early-flowering persimmon varieties.