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Toxins
Volume 10
Issue 12
10.3390/toxins10120488
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Article

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

by
Shiyong Zhang
1,2,†,
Jia Li
3,†,
Qin Qin
1,†,
Wei Liu
4,†,
Chao Bian
3,†,
Yunhai Yi
2,3,
Minghua Wang
1,
Liqiang Zhong
1,
Xinxin You
3,
Shengkai Tang
1,
Yanshan Liu
1,
Yu Huang
2,3,
Ruobo Gu
5,
Junmin Xu
5,6,
Wenji Bian
1,*,
Qiong Shi
2,3,5,* and
Xiaohui Chen
1,*
1
Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing 210017, China
2
BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China
3
Shenzhen Key Laboratory of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, Shenzhen 518083, China
4
Nanjing Institute of Fisheries Science, Nanjing 210029, China
5
BGI Zhenjiang Institute of Hydrobiology, Zhenjiang 212000, China
6
School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu 069-8501, Japan
*
Authors to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Toxins 2018, 10(12), 488; https://doi.org/10.3390/toxins10120488
Received: 11 October 2018 / Revised: 15 November 2018 / Accepted: 19 November 2018 / Published: 23 November 2018
(This article belongs to the Special Issue Emerging Marine Biotoxins)
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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. View Full-Text
Keywords: Chinese yellow catfish; whole genome sequencing; toxin genes; identification Chinese yellow catfish; whole genome sequencing; toxin genes; identification
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MDPI and ACS Style

Zhang, S.; Li, J.; Qin, Q.; Liu, W.; Bian, C.; Yi, Y.; Wang, M.; Zhong, L.; You, X.; Tang, S.; Liu, Y.; Huang, Y.; Gu, R.; Xu, J.; Bian, W.; Shi, Q.; Chen, X. Whole-Genome Sequencing of Chinese Yellow Catfish Provides a Valuable Genetic Resource for High-Throughput Identification of Toxin Genes. Toxins 2018, 10, 488. https://doi.org/10.3390/toxins10120488

AMA Style

Zhang S, Li J, Qin Q, Liu W, Bian C, Yi Y, Wang M, Zhong L, You X, Tang S, Liu Y, Huang Y, Gu R, Xu J, Bian W, Shi Q, Chen X. Whole-Genome Sequencing of Chinese Yellow Catfish Provides a Valuable Genetic Resource for High-Throughput Identification of Toxin Genes. Toxins. 2018; 10(12):488. https://doi.org/10.3390/toxins10120488

Chicago/Turabian Style

Zhang, Shiyong, Jia Li, Qin Qin, Wei Liu, Chao Bian, Yunhai Yi, Minghua Wang, Liqiang Zhong, Xinxin You, Shengkai Tang, Yanshan Liu, Yu Huang, Ruobo Gu, Junmin Xu, Wenji Bian, Qiong Shi, and Xiaohui Chen. 2018. "Whole-Genome Sequencing of Chinese Yellow Catfish Provides a Valuable Genetic Resource for High-Throughput Identification of Toxin Genes" Toxins 10, no. 12: 488. https://doi.org/10.3390/toxins10120488

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