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Updated: Aug 26, 2026

Spatially Resolved, Integrated Single-Cell Multiomic Profiling of the Transcriptome and Epigenomic Targets in Frozen Tissue Sections
Published on: June 12, 2026
Chromosome level genome assembly and full-length transcriptome of blacktip trevally (Caranx heberi)
Mudagandur S Shekhar1, Vinaya Kumar Katneni2, Sudheesh K Prabhudas1
1ICAR-Central Institute of Brackishwater Aquaculture, 75, Santhome High Road, MRC Nagar, Chennai, 600028, Tamil Nadu, India.
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.
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