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

Shiyong Zhang,Shiyong Zhang,Yanshan Liu,Jia Li,Ruobo Gu,Yunhai Yi,Junmin Xu,Junmin Xu,Liqiang Zhong,Qiong Shi,Qiong Shi,Xinxin You,Chao Bian,Wenji Bian,Qin Qin,Shengkai Tang,Xiaohui Chen,Yu Huang,Minghua Wang,Wei Liu

doi:10.3390/toxins10120488

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.

Highlights

As one venomous bony fish in the order of Siluriformes, Chinese yellow catfish (Pelteobagrus fulvidraco) has been an economically important freshwater species in China because of its good meat quality [1]
Our results demonstrated that the genome-level benchmarking value was
After alignment searching of public databases, we found that these genes were annotated as “fragmental,” which means these genes do not have full structures

Summary

Introduction

As one venomous bony fish in the order of Siluriformes, Chinese yellow catfish (Pelteobagrus fulvidraco) has been an economically important freshwater species in China because of its good meat quality [1]. In 2016, the Chinese yellow catfish production in China was over 300,000 tons with an elevation of 20% from the previous year [2]. In our previous study [3], we reported a novel multi-omics pipeline to predict toxin genes from the venom glands of Chinese yellow catfish based on transcriptomic and proteomic sequencing. We performed whole genome sequencing of this venomous teleost to provide another valuable genetic resource for high-throughput identification of toxin genes. As we discussed before [3], aquatic venoms have been largely ignored as a resource for potential pharmaceuticals, there are more aquatic venomous species than the total of venomous terrestrial animals [3]. The limited number of toxin sequences [3,4] has been an obstacle for development of novel marine drugs

Methods

Results

Discussion

Conclusion