Whole-Genome Sequencing of Chinese Yellow Catfish Provides a Valuable Genetic Resource for High-Throughput Identification of Toxin Genes

Abstract

Naturally derived toxins from animals are good raw materials for drug development. As a representative venomous teleost, Chinese yellow catfish (Pelteobagrus fulvidraco) can provide valuable resources for studies on toxin genes. Its venom glands are located in the pectoral and dorsal fins. Although with such interesting biologic traits and great value in economy, Chinese yellow catfish is still lacking a sequenced genome. Here, we report a high-quality genome assembly of Chinese yellow catfish using a combination of next-generation Illumina and third-generation PacBio sequencing platforms. The final assembly reached 714 Mb, with a contig N50 of 970 kb and a scaffold N50 of 3.65 Mb, respectively. We also annotated 21,562 protein-coding genes, in which 97.59% were assigned at least one functional annotation. Based on the genome sequence, we analyzed toxin genes in Chinese yellow catfish. Finally, we identified 207 toxin genes and classified them into three major groups. Interestingly, we also expanded a previously reported sex-related region (to ≈6 Mb) in the achieved genome assembly, and localized two important toxin genes within this region. In summary, we assembled a high-quality genome of Chinese yellow catfish and performed high-throughput identification of toxin genes from a genomic view. Therefore, the limited number of toxin sequences in public databases will be remarkably improved once we integrate multi-omics data from more and more sequenced species.

Genome Sequencing of the Japanese Eel (Anguilla japonica) for Comparative Genomic Studies on tbx4 and a tbx4 Gene Cluster in Teleost Fishes

“…Chinese yellow catfish ( Pelteobagrus fulvidraco ) secretes venom through its fin spines, which has been proposed by us to be essential for the development of marine drugs [36]. Eeltail catfish (Siluriformes), scorpionfish and stonefish (Scorpaeniformes) also have venomous fin spines that can severely injure other animals [37].…”

“…Many fishes have developed fin spines for defense or hunting purposes. In our previous reports [36,56,57], we predicted several toxin genes from the venom glands of fin spines in Chinese yellow catfish using a combination of genomic, transcriptomic, and proteomic sequencing. The contribution of more toxins to future drugs seems to be more promising [57], and we will therefore sequence and analyze more fish species with fin spines.…”

“…Genomic DNA (for the genome sequencing) and total RNA (for the transcriptome sequencing) were extracted from the muscle samples as previously described [36]. For whole-genome sequencing, we constructed seven paired-end sequencing libraries, including three short-insert (270, 500, and 800 bp) and four long-insert (2, 5, 10, and 20 kb).…”

“…After that, SSPACE was used to elongate the scaffolds produced by Gapcloser1.10. These steps were described in detail in our previous studies [12,18,36]. We also manually filtered those redundant scaffolds caused by the high heterozygosity.…”

Emerging Marine Biotoxins

“…These include short sequence tags that can be used to elucidate full-length peptide sequences to identify natural toxins like conotoxins from the venom of the cone snail Conus geographus by NMR spectroscopy [13], or the use of novel sequencing approaches to identify a diversity of toxin-related peptide sequences by means of computational processing, comprising of structural phylogenetic analysis, model prediction, and the dynamics simulation of peptide–receptor interaction [14]. Sequencing approaches have been also used to characterize the whole-genome of Chinese Yellow Catfish, providing a valuable genetic resource for high-throughput identification of toxin genes [15].…”