A high-quality chromosome-level genome assembly was generated by integrating MGI DNBSEQ-T7 short-read, PacBio Sequel II long-read, and Hi-C scaffolding technologies to facilitate research on adaptive evolution in Heteroptera.
Abstract
Corizus hyoscyami (Heteroptera: Rhopalidae) is a widely distributed and highly polyphagous insect, making it a relevant species for understanding the evolution of herbivory and host adaptation in true bugs. However, the genome of Corizus hyoscyami has not yet been sequenced, limiting investigations into its biological characteristics. In this study, a high-quality chromosome-level genome assembly was generated by integrating MGI DNBSEQ-T7 short-read, PacBio Sequel II long-read, and Hi-C scaffolding technologies. The assembly was assessed to be 97.6% complete by BUSCO. The final genome was assembled into a size of 1.47 Gb, with a contig N50 of 1.61 Mb and a scaffold N50 of 198.34 Mb. The GC content was determined to be 34%, and 94.90% of the sequences were anchored onto 6 chromosome-level scaffolds, representing the major chromosomal elements of the genome. Repetitive sequences accounted for 69.79% of the genome, and 18,540 protein-coding genes were annotated. This genome assembly is expected to facilitate research on adaptive evolution in Heteroptera.
This genome provides a foundational resource for investigating the molecular basis of evolutionary mechanisms, genetic breeding, and conservation genomics of male Andinoacara rivulatus, with direct implications for sustainable aquaculture and the global ornamental fish trade.
Zhen Yuan, Qi Liu, Hong-Wei Yan et al.· Scientific Data· 0 citations
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
.
Xuan Xie, Li Zou, Zhonggui Xie et al.· Scientific Data· 0 citations
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.
Rawon Jeong, Jeonghun Kim, Young-Suk Ho· G3· 0 citations
Conifers, which comprise nearly two-thirds of extant gymnosperm species, are ecologically and economically important but remain genomically understudied because of their exceptionally large, repeat-rich genomes. Here, we report a chromosome-level assembly of the haploid genome of Cupressus sempervirens generated using PacBio HiFi reads and scaffolded with optical and genetic maps. The 10 Gb assembly shows exceptional contiguity for a conifer genome (contig N50 = 29.8 Mb) and was organized into 11 pseudomolecules. Iso-Seq-supported annotation identified 42,980 protein-coding genes. Repetitive elements account for over 80% of the genome, with LTR retrotransposons alone representing 52.5%. Transposable elements (TE) are pervasive in both intergenic and genic regions and have a major impact on gene architecture: TE insertions within introns generate ultra-long introns, often exceeding 100 kb, and drive gene size expansion. Analyses of LTR retrotransposon dynamics indicate that genome enlargement in C. sempervirens was driven not by recent transpositional bursts, but by the long-term accumulation and incomplete removal of ancient LTR retrotransposons. Consistent with this pattern, paleogenomic reconstruction across representative gymnosperms found no evidence of whole-genome duplication in the Cupressus lineage. This reference genome provides a valuable resource for studying conifer genome evolution, gene structure, and traits of agronomic and ecological interest, including cypress pollinosis.
Cravero Charlotte, L. Isabelle, Choisne Nathalie et al.· bioRxiv· 0 citations
The European leaf-toed gecko (Euleptes europaea) is a small, nocturnal gecko endemic to the western Mediterranean. As a phylogenetically distinctive member of the Gondwanan family Sphaerodactylidae, it represents an important species for studying Mediterranean island biogeography, adaptation, and reptile genome evolution. The species also occupies a key position for investigating the evolution of sex chromosomes, as geckos exhibit remarkable diversity and frequent transitions in sex-determination systems. We present a chromosome-level genome assembly of Euleptes europaea generated as part of the Vertebrate Genomes Project. The 1.8 Gb assembly has a scaffold N50 of 102.3 Mb (contig N50 27 Mb), with 21 chromosome-scale scaffolds corresponding to the known karyotype (2n = 42). The primary assembly has a BUSCO completeness of 97.80% (95.60% as single-copy), a k-mer completeness of 96.00%, and a k-mer quality value (QV) of 61.20. Repetitive elements account for 53.20% of the genome and genome annotation identified 18,633 protein-coding genes. This high-quality reference genome will facilitate studies of genome evolution, island adaptation, and sex chromosome evolution across geckos and other reptiles.
J. Paris, L. Abueg, S. Pelan et al.· bioRxiv· 0 citations
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.
Ming Lei, Jing Wang, S. Sooranna et al.· Scientific Data· 0 citations
We use cookies to run the site and, with your consent, for analytics and to show ads.
See our Cookie Policy.
