Abstract

Trachidermus fasciatus is a roughskin sculpin fish widespread across the coastal areas of East Asia. Due to environmental destruction and overfishing, the population of this species is under threat. In order to protect this endangered species, it is important to have the genome sequenced. Reference genomes are essential for studying population genetics, domestic farming, and genetic resource protection. However, currently, no reference genome is available for Trachidermus fasciatus, and this has greatly hindered the research on this species. In this study, we integrated nanopore long-read sequencing, Illumina short-read sequencing, and Hi-C methods to thoroughly assemble the Trachidermus fasciatus genome. Our results provided a chromosome-level high-quality genome assembly with a predicted genome size of 542.6 Mbp (2n = 40) and a scaffold N50 of 24.9 Mbp. The BUSCO value for genome assembly completeness was higher than 96%, and the single-base accuracy was 99.997%. Based on EVM-StringTie genome annotation, a total of 19,147 protein-coding genes were identified, including 35,093 mRNA transcripts. In addition, a novel gene-finding strategy named RNR was introduced, and in total, 51 (82) novel genes (transcripts) were identified. Lastly, we present here the first reference genome for Trachidermus fasciatus; this sequence is expected to greatly facilitate future research on this species.

Highlights

  • The roughskin sculpin (Trachidermus fasciatus) is a small, carnivorous, and catadromous fish that has been found across the coastal areas of China, Korea, and Japan [1,2].Historically, roughskin sculpin has been named one of the four most famous fishes in China and has been treated as a valuable food source by the Chinese population [3]

  • It had been reported that the karyotype of this species is 2n = 40 ([6]), and more recently, the genetic diversity [7] and genomic signature [8] of Trachidermus fasciatus had been studied, which might be important for its conservation management

  • For Illumina sequencing, we obtained more than 350 million reads for both genome and Hi-C sequencing (Table 3), which contains more than 50 billion nucleotide bases

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Summary

Introduction

The roughskin sculpin (Trachidermus fasciatus) is a small, carnivorous, and catadromous fish that has been found across the coastal areas of China, Korea, and Japan [1,2]. Roughskin sculpin has been named one of the four most famous fishes in China and has been treated as a valuable food source by the Chinese population [3]. It had been reported that the karyotype of this species is 2n = 40 ([6]), and more recently, the genetic diversity [7] and genomic signature [8] of Trachidermus fasciatus had been studied, which might be important for its conservation management. A reference genome of this species is important for both the development of a farming system and future genetic studies. Its mitochondrial genome has been previously identified [9], the nuclear genome sequence is still unavailable

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