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De Novo Assembly and Annotation of the Siganus fuscescens (Houttuyn, 1782) Genome: Marking a Pioneering Advance for the Siganidae Family

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Abstract

This study presents the first draft genome of Siganus fuscescens, and thereby establishes the first whole-genome sequence for a species in the Siganidae family. Leveraging both long and short read sequencing technologies, i.e., Oxford Nanopore and Illumina sequencing, we successfully assembled a mitogenome spanning 16.494 Kb and a first haploid genome encompassing 498 Mb. The assembled genome accounted for a 99.6% of the estimated genome size and was organized into 164 contigs with an N50 of 7.2 Mb. This genome assembly showed a GC content of 42.9% and a high Benchmarking Universal Single-Copy Orthologue (BUSCO) completeness score of 99.5% using actinopterygii_odb10 lineage, thereby meeting stringent quality standards. In addition to its structural aspects, our study also examined the functional genomics of this species, including the intricate capacity to biosynthesize long-chain polyunsaturated fatty acids (LC-PUFAs) and secrete venom. Notably, our analyses revealed various repeats elements, which collectively constituted 17.43% of the genome. Moreover, annotation of 28,351 genes uncovered both shared genetic signatures and those that are unique to S. fuscescens. Our assembled genome also displayed a moderate prevalence of gene duplication compared to other fish species, which suggests that this species has a distinctive evolutionary trajectory and potentially unique functional constraints. Taken altogether, this genomic resource establishes a robust foundation for future research on the biology, evolution, and the aquaculture potential of S. fuscescens.

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Data Availability

No datasets were generated or analyzed during the current study.

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Funding

This research was partly supported by the Science and Technology Research Partnership for Sustainable Development (SATREPS JPMJSA1806).

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Authors and Affiliations

  1. Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Konan 4-5-7, Minato-ku, Tokyo, 108-8477, Japan

    Samuel Mwakisha Mwamburi, Satoshi Kawato, Miho Furukawa, Kayo Konishi, Reiko Nozaki, Ikuo Hirono & Hidehiro Kondo

  2. Department of Fisheries, Kenya Marine and Fisheries Research Institute, P.O BOX 81651-80100, Mombasa, Kenya

    Samuel Mwakisha Mwamburi

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  1. Samuel Mwakisha Mwamburi
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Contributions

Samuel Mwakisha Mwamburi, Satoshi Kawato, and Hidehiro Kondo were responsible for conceptualization. Samuel Mwakisha Mwamburi, Kayo Konishi, and Reiko Nozaki designed the methodology. Samuel Mwakisha Mwamburi, Satoshi Kawato, and Miho Furukawa performed formal analysis and data curation. Samuel Mwakisha Mwamburi was responsible for writing original draft and visualization. Satoshi Kawato, Hidehiro Kondo, and Ikuo Hirono participated in review and editing. Hidehiro Kondo supervised the project.

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Mwamburi, S.M., Kawato, S., Furukawa, M. et al. De Novo Assembly and Annotation of the Siganus fuscescens (Houttuyn, 1782) Genome: Marking a Pioneering Advance for the Siganidae Family. Mar Biotechnol (2024). https://doi.org/10.1007/s10126-024-10325-9

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