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

IF 2.6 3区 生物学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY
Samuel Mwakisha Mwamburi, Satoshi Kawato, Miho Furukawa, Kayo Konishi, Reiko Nozaki, Ikuo Hirono, Hidehiro Kondo
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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.

Abstract Image

Siganus fuscescens (Houttuyn, 1782) 基因组的全新组装和注释:标志着 Siganidae 科取得了开创性的进展。
本研究首次提出了Siganus fuscescens的基因组草案,从而建立了Siganidae科物种的首个全基因组序列。利用长短读测序技术,即牛津纳米孔测序技术和 Illumina 测序技术,我们成功地组装了一个跨度为 16.494 Kb 的有丝分裂基因组和一个包含 498 Mb 的第一单倍体基因组。组装的基因组占估计基因组大小的 99.6%,并被组织成 164 个等位基因,N50 为 7.2 Mb。该基因组的 GC 含量为 42.9%,使用 actinopterygii_odb10 线系的基准通用单拷贝同源物(BUSCO)完整性得分高达 99.5%,从而达到了严格的质量标准。除了结构方面,我们的研究还考察了该物种的功能基因组学,包括生物合成长链多不饱和脂肪酸(LC-PUFAs)和分泌毒液的复杂能力。值得注意的是,我们的分析发现了各种重复元件,它们共占基因组的 17.43%。此外,对 28,351 个基因的注释发现了 S. fuscescens 共有的遗传特征和特有的遗传特征。与其他鱼类相比,我们组装的基因组还显示出适度的基因重复率,这表明该物种具有独特的进化轨迹和潜在的独特功能限制。总之,这一基因组资源为今后研究鱼腥鲑的生物学、进化和水产养殖潜力奠定了坚实的基础。
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来源期刊
Marine Biotechnology
Marine Biotechnology 工程技术-海洋与淡水生物学
CiteScore
4.80
自引率
3.30%
发文量
95
审稿时长
2 months
期刊介绍: Marine Biotechnology welcomes high-quality research papers presenting novel data on the biotechnology of aquatic organisms. The journal publishes high quality papers in the areas of molecular biology, genomics, proteomics, cell biology, and biochemistry, and particularly encourages submissions of papers related to genome biology such as linkage mapping, large-scale gene discoveries, QTL analysis, physical mapping, and comparative and functional genome analysis. Papers on technological development and marine natural products should demonstrate innovation and novel applications.
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