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

• Published in: Marine biotechnology (New York, N.Y.) Vol. 26; no. 5; pp. 902 - 916
• Main Authors: Mwamburi, Samuel Mwakisha, Kawato, Satoshi, Furukawa, Miho, Konishi, Kayo, Nozaki, Reiko, Hirono, Ikuo, Kondo, Hidehiro
• Format: Journal Article
• Language: English
• Published: New York Springer US 01.10.2024; Springer Nature B.V
• Subjects: Annotations; Aquaculture; Assembly; Biomedical and Life Sciences; Engineering; Evolutionary genetics; Fatty acids; Fish; Freshwater & Marine Ecology; Gene duplication; Gene sequencing; Genomes; Genomics; Haploidy; Life Sciences; Marine fishes; Microbiology; Nucleotide sequence; Polyunsaturated fatty acids; Quality standards; Sequencing; Siganidae; Siganus fuscescens; Structure-function relationships; Venom; Zoology; Comparative genomics; Mitogenome; Hybrid assembly; Mottled spinefoot; Aquaculture
• ISSN: 1436-2228; 1436-2236; 1436-2236
• DOI: 10.1007/s10126-024-10325-9

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 .