Aug 2026· Scientific Data· Vol 13· 0 citations· 45 references
Medicine
TL;DR
The comprehensive genomic and transcriptomic resources developed in this study will facilitate the domestication and aquaculture development of C. heberi, as well as support research on its nutritional potential, ecological adaptations, and evolutionary biology.
Abstract
Caranx heberi (Bennett, 1830) commonly known as the blacktip trevally belongs to the family Carangidae and is a potential brackishwater aquaculture species. However, the limited genomic resources are hindering the efforts to study its genetic traits and their molecular basis. To bridge this gap, we generated a high-quality reference genome employing multiple sequencing strategies including PacBio Hifi reads (135x), Illumina short reads (150x), and Hi-C chromosome conformation capturing (180x). The high-quality genome assembly consisted of 159 scaffolds summing to 618.71 Mb and an N50 value of 26.72 Mb. Among these, 24 chromosome level scaffolds covered 97.5% of the total assembly. The genome contained 20.94% of repeat elements and 30,354 protein encoding genes. In addition, full-length transcriptomes were generated using the PacBio IsoSeq approach from seven tissues (gill, kidney, liver, muscle, heart, spleen, and intestine). The comprehensive genomic and transcriptomic resources developed in this study will facilitate the domestication and aquaculture development of C. heberi, as well as support research on its nutritional potential, ecological adaptations, and evolutionary biology.
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.
Shubha Vij, V. Nguyen, Kathiresan Purushothaman et al.· Scientific Data· 0 citations
This chromosome-scale genome assembly and annotation of anise hyssop provides a foundational genomic resource for comparative and functional genomics within the genus Agastache and the Lamiaceae family.
Triosteum pinnatifidum
is a perennial herbaceous plant endemic to East Asia, whose roots, leaves, and fruits have long been utilized in traditional herbal medicine, thereby demonstrating substantial medicinal value. The root of
T. pinnatifidum
(commonly referred to as “Tianwangqi”) exhibits multiple pharmacological effects: enhancing Qi-blood circulation, dispelling wind-dampness, tonifying the spleen and stomach, and relieving inflammation and pain. However, the absence of a reference genome has impeded genetic research on this species. In the present study, we report a high-quality chromosome-level genome assembly of
T. pinnatifidum
generated using PacBio HiFi long-read sequencing and Hi-C scaffolding technologies. The final assembled genome spans 698.94 Mbp with a contig N50 of 46.55 Mbp, which was successfully anchored onto 9 chromosomes. Genome annotation revealed that repetitive sequences account for 65.84% of the genome, and a total of 26,027 protein-coding genes were predicted, among which 98.19% were functionally annotated. The final gene set of
T. pinnatifidum
exhibited a BUSCO completeness of 98.5%, indicating a high level of assembly accuracy and completeness. This genome assembly not only contributes to the genetic conservation of
Triosteum
L. species but also provides a valuable genomic resource for evolutionary studies within the Caprifoliaceae family.
Hai-Rui Liu, Huan Liu, Yao Wei et al.· Scientific Data· 0 citations
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
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
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
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