Chromosome-level genome assembly and annotation of the male Andinoacara rivulatus

Chromosome-level genome assembly of the cyprinid fish Onychostoma lini using PacBio HiFi and Hi-C sequencing

Onychostoma lini is an ecologically and economically important cyprinid species endemic to the mountain rivers of southern China. Wild populations have sharply declined due to habitat fragmentation, hydropower development, and overexploitation, yet genomic information remains unavailable, hindering studies on its diversity, adaptation, and conservation. Here, we assembled the first chromosome-level genome of O. lini using PacBio HiFi long-read sequencing, Illumina short-read polishing, and Hi-C scaffolding. The 907.5 Mb assembly achieved a contig N50 of 32.83 Mb and a scaffold N50 of 34.89 Mb, with 99.93% of sequences anchored to 25 chromosomes. Repetitive elements occupied 387.36 Mb, representing 42.69% of the genome. We predicted 28,597 protein-coding genes, 99.05% of which were functionally annotated in NR, KEGG, InterPro, SwissProt, and GO databases. BUSCO analysis identified 97.9% complete orthologs, confirming assembly completeness and annotation accuracy. This high-quality reference genome provides a foundational resource for investigating cyprinid evolution, environmental adaptation, and molecular breeding, and supports the conservation of O. lini .

Chromosome-level genome assembly and annotation of the endemic and endangered karst medicinal plant Corydalis saxicola

This high-quality chromosome-level genome assembly of C. Saxicola will serve as a valuable resource for understanding the ecology, genetics, and evolution of the endangered herbaceous plant and will help towards its cultivation.

Chromosome-level genome assembly of the bitterling Rhodeus sinensis (Acheilognathidae) reveals genomic signatures associated with its mussel-dependent reproductive system.

Bitterlings (Acheilognathidae) exhibit a unique reproductive strategy characterized by symbiotic embryonic development inside the gill cavities of freshwater unionid mussels. Despite extensive ecological and physiological research on this system, genomic resources for bitterlings have remained limited, hindering comparative and evolutionary studies. Here, we present a high-quality, chromosome-level genome assembly for Rhodeus sinensis, a widely distributed bitterling species in the Korean Peninsula. By combining PacBio Continuous Long Read (CLR) sequencing, Illumina short reads, and Hi-C scaffolding, we generated a 0.77 Gb genome assembly with a scaffold N50 of 30.06 Mb. The final assembly comprises 24 chromosome-scale scaffolds, accounting for 98.3% of the assembled genome, with a BUSCO completeness score of 96.3% against the Actinopterygii_odb10. Comparative genomic analyses identified prominent expansions in gene families associated with alcohol metabolism, lipid catabolism, and oxidative stress responses. These genomic signatures of metabolic rewiring suggest a potential fuel flexibility, which may serve as a critical adaptive mechanism to mitigate the severe hypoxic stress encountered within the host mussel's gill environment. Ultimately, our chromosome-level genome assembly and findings provide a robust genomic foundation, contributing to a deeper understanding of the extreme physiological adaptations and unique life-history evolution within the Acheilognathidae.

Chromosome-Level Genome Assembly of Solanum carolinense

Horsenettle (Solanum carolinense L.) is a noxious weed widely distributed across North America and increasingly invasive in other regions. Its strong environmental adaptability, complex defense strategies, and distinctive reproductive traits make it an important model for studying plant–herbivore coevolution. However, the absence of high-quality genomic resources has limited deeper investigation into its adaptive evolutionary mechanisms. In this study, we generated a chromosome-level reference genome assembly for S. carolinense using an integrated approach combining PacBio HiFi long-read sequencing, Illumina second-generation sequencing, and Hi-C chromatin interaction scaffolding. The final genome assembly had a total length of 915.40 Mb, with a contig N50 of 51.06 Mb and a scaffold N50 of 73.17 Mb; 96.05% of the sequences were successfully anchored onto 12 pseudochromosomes. The genome was characterized by a high proportion of repetitive sequences (73.64%) and substantial heterozygosity (1.13%), consistent with a highly repetitive and moderately high heterozygous genome. BUSCO analysis indicated that the chromosome-level genome assembly of S. carolinense reached a completeness score of 94.8%. A total of 32,206 protein-coding genes were annotated, of which 97.95% received functional annotations. The evaluation of the annotated protein-coding gene set returned a completeness value of 94.9%. This reference genome provides a valuable resource for advancing research on the adaptive evolution of weedy Solanaceae species, supports the development of more effective management strategies for this troublesome species, and offers a technical reference for assembling other highly heterozygous weed genomes.

A chromosome scale reference genome of an arid adapted ungulate, Gazella subgutturosa.

Genome assembly and Full-length transcriptome of Malabar Red Snapper, Lutjanus malabaricus

The Malabar red snapper (Lutjanus malabaricus) is a high-value marine food fish of growing economic and aquaculture importance across the Indo-Pacific. Despite its significance, genomic resources for this species have remained scarce, hindering the application of genomic tools for selective breeding. Here, we present the first chromosome-level genome assemblies and full-length transcriptome of L. malabaricus. Using PacBio HiFi long-read sequencing and Hi-C scaffolding, we generated high-quality assemblies for unsexed, male, and female individuals, each approximately 1.0 Gb in size and anchored to 24 chromosomes. The assemblies exhibited exceptional contiguity (N50 ≈ 42 Mb) and completeness (BUSCO > 99%), with karyotyping confirming 2n = 48 telocentric chromosomes. Genome annotation identified ~25,000 protein-coding genes, and repeat sequences accounted for almost half of the genome, comparable to other reef-associated teleosts. Comparative analyses of the male and female assemblies revealed strong chromosomal synteny and localized sex-associated regions, suggesting a polygenic or complex mechanism of sex determination. The accompanying multi-tissue full-length transcriptome supports functional and developmental studies. Together, these genomic and transcriptomic datasets provide a comprehensive molecular foundation for population genetics, comparative genomics, and selective breeding in L. malabaricus.