| Chromosomal-level assembly of yellow catfish genome using third-generation DNA sequencing and Hi-C analysis | |
| Gong, Gaorui1; Dan, Cheng1; Xiao, Shijun2; Guo, Wenjie1; Huang, Peipei3; Xiong, Yang1; Wu, Junjie1; He, Yan1; Zhang, Jicheng2; Li, Xiaohui1; Chen, Nansheng4,5; Gui, Jian-Fang1; Mei, Jie1 | |
| Corresponding Author | Gui, Jian-Fang(jfgui@ihb.ac.cn) ; Mei, Jie(jmei@mail.hzau.edu.cn) |
| 2018-09-20 | |
| Source Publication | GIGASCIENCE
 |
| ISSN | 2047-217X |
| Volume | 7Issue:11Pages:9 |
| Abstract | Background: The yellow catfish, Pelteobagrus fulvidraco, belonging to the Siluriformes order, is an economically important freshwater aquaculture fish species in Asia, especially in Southern China. The aquaculture industry has recently been facing tremendous challenges in germplasm degeneration and poor disease resistance. As the yellow catfish exhibits notable sex dimorphism in growth, with adult males about two- to three-fold bigger than females, the way in which the aquaculture industry takes advantage of such sex dimorphism is another challenge. To address these issues, a high-quality reference genome of the yellow catfish would be a very useful resource. Findings: To construct a high-quality reference genome for the yellow catfish, we generated 51.2 Gb short reads and 38.9 Gb long reads using Illumina and Pacific Biosciences (PacBio) sequencing platforms, respectively. The sequencing data were assembled into a 732.8 Mb genome assembly with a contig N50 length of 1.1 Mb. Additionally, we applied Hi-C technology to identify contacts among contigs, which were then used to assemble contigs into scaffolds, resulting in a genome assembly with 26 chromosomes and a scaffold N50 length of 25.8 Mb. Using 24,552 protein-coding genes annotated in the yellow catfish genome, the phylogenetic relationships of the yellow catfish with other teleosts showed that yellow catfish separated from the common ancestor of channel catfish similar to 81.9 million years ago. We identified 1,717 gene families to be expanded in the yellow catfish, and those gene families are mainly enriched in the immune system, signal transduction, glycosphingolipid biosynthesis, and fatty acid biosynthesis. Conclusions: Taking advantage of Illumina, PacBio, and Hi-C technologies, we constructed the first high-quality chromosome-level genome assembly for the yellow catfish P. fulvidraco. The genomic resources generated in this work not only offer a valuable reference genome for functional genomics studies of yellow catfish to decipher the economic traits and sex determination but also provide important chromosome information for genome comparisons in the wider evolutionary research community. |
| Keyword | yellow catfish PacBio Hi-C genomics chromosomal assembly |
| DOI | 10.1093/gigascience/giy120 |
| Funding Organization | China Agriculture Research System ; China Agriculture Research System ; China Agriculture Research System ; China Agriculture Research System ; Fundamental Research Funds for the Central Universities ; Fundamental Research Funds for the Central Universities ; Fundamental Research Funds for the Central Universities ; Fundamental Research Funds for the Central Universities ; China Agriculture Research System ; China Agriculture Research System ; China Agriculture Research System ; China Agriculture Research System ; Fundamental Research Funds for the Central Universities ; Fundamental Research Funds for the Central Universities ; Fundamental Research Funds for the Central Universities ; Fundamental Research Funds for the Central Universities ; China Agriculture Research System ; China Agriculture Research System ; China Agriculture Research System ; China Agriculture Research System ; Fundamental Research Funds for the Central Universities ; Fundamental Research Funds for the Central Universities ; Fundamental Research Funds for the Central Universities ; Fundamental Research Funds for the Central Universities ; China Agriculture Research System ; China Agriculture Research System ; China Agriculture Research System ; China Agriculture Research System ; Fundamental Research Funds for the Central Universities ; Fundamental Research Funds for the Central Universities ; Fundamental Research Funds for the Central Universities ; Fundamental Research Funds for the Central Universities |
| Indexed By | SCI ; SCI |
| Language | 英语 |
| Funding Project | China Agriculture Research System[CARS-46] ; Fundamental Research Funds for the Central Universities[2662017PY013] |
| WOS Research Area | Science & Technology - Other Topics |
| WOS Subject | Multidisciplinary Sciences |
| WOS ID | WOS:000456731400001 |
| WOS Keyword | MARKERS ; GENE ; DIFFERENTIATION ; TRANSCRIPTOME ; MANIPULATION ; ANNOTATION ; DIVERGENCE ; PROGRAM ; TOPHAT ; TOOL |
| Publisher | OXFORD UNIV PRESS |
| Funding Organization | China Agriculture Research System ; China Agriculture Research System ; China Agriculture Research System ; China Agriculture Research System ; Fundamental Research Funds for the Central Universities ; Fundamental Research Funds for the Central Universities ; Fundamental Research Funds for the Central Universities ; Fundamental Research Funds for the Central Universities ; China Agriculture Research System ; China Agriculture Research System ; China Agriculture Research System ; China Agriculture Research System ; Fundamental Research Funds for the Central Universities ; Fundamental Research Funds for the Central Universities ; Fundamental Research Funds for the Central Universities ; Fundamental Research Funds for the Central Universities ; China Agriculture Research System ; China Agriculture Research System ; China Agriculture Research System ; China Agriculture Research System ; Fundamental Research Funds for the Central Universities ; Fundamental Research Funds for the Central Universities ; Fundamental Research Funds for the Central Universities ; Fundamental Research Funds for the Central Universities ; China Agriculture Research System ; China Agriculture Research System ; China Agriculture Research System ; China Agriculture Research System ; Fundamental Research Funds for the Central Universities ; Fundamental Research Funds for the Central Universities ; Fundamental Research Funds for the Central Universities ; Fundamental Research Funds for the Central Universities |
| Citation statistics | |
| Document Type | 期刊论文 |
| Identifier | http://ir.ihb.ac.cn/handle/342005/28734 |
| Collection | 其他_期刊论文 |
| Corresponding Author | Gui, Jian-Fang; Mei, Jie |
| Affiliation | 1.Huazhong Agr Univ, Coll Fisheries, Key Lab Freshwater Anim Breeding, Minist Agr, Wuhan 430070, Hubei, Peoples R China 2.Wuhan Frasergen Bioinformat, Wuhan 430075, Hubei, Peoples R China 3.Univ Chinese Acad Sci, Chinese Acad Sci, State Key Lab Freshwater Ecol & Biotechnol, Inst Hydrobiol, Wuhan 430072, Hubei, Peoples R China 4.Chinese Acad Sci, Oceanol, Qingdao 266071, Shandong, Peoples R China 5.Simon Fraser Univ, Dept Mol Biol & Biochem, Burnaby, BC, Canada |
| Recommended Citation GB/T 7714 | Gong, Gaorui,Dan, Cheng,Xiao, Shijun,et al. Chromosomal-level assembly of yellow catfish genome using third-generation DNA sequencing and Hi-C analysis[J]. GIGASCIENCE,2018,7(11):9. |
| APA | Gong, Gaorui.,Dan, Cheng.,Xiao, Shijun.,Guo, Wenjie.,Huang, Peipei.,...&Mei, Jie.(2018).Chromosomal-level assembly of yellow catfish genome using third-generation DNA sequencing and Hi-C analysis.GIGASCIENCE,7(11),9. |
| MLA | Gong, Gaorui,et al."Chromosomal-level assembly of yellow catfish genome using third-generation DNA sequencing and Hi-C analysis".GIGASCIENCE 7.11(2018):9. |
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