Chromosomal-level assembly of yellow catfish genome using third-generation DNA sequencing and Hi-C analysis.
Chromosomal-level assembly of yellow catfish genome using third-generation DNA sequencing and Hi-C analysis.
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利用第三代DNA测序和Hi - C分析进行黄颡鱼基因组的染色体水平组装
DOI：
10.1093/gigascience/giy120
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发表时间：
2018-11-01
期刊：
影响因子：
9.2
通讯作者：
Mei J
中科院分区：
文献类型：
--
作者：
Gong G;Dan C;Xiao S;Guo W;Huang P;Xiong Y;Wu J;He Y;Zhang J;Li X;Chen N;Gui JF;Mei J
黄颡鱼（Pelteobagrus fulvidraco）是亚洲，特别是中国南方重要的淡水养殖鱼类，属于志卢形目。近年来，水产养殖业面临着种质退化和抗病性差的巨大挑战。由于黄鲶鱼在生长过程中表现出明显的性别二态性，成年雄性比雌性大两到三倍，水产养殖业如何利用这种性别二态性是另一个挑战。为了解决这些问题，高质量的黄鲶鱼参考基因组将是一个非常有用的资源。为了构建高质量的黄颡鱼参考基因组，我们使用Illumina和Pacific Biosciences （PacBio）测序平台分别生成了51.2 Gb的短序列和38.9 Gb的长序列。测序数据被组装成一个732.8 Mb的基因组组装体，其中contig N50长度为1.1 Mb。此外，我们利用Hi-C技术鉴定了contig之间的接触，然后将contig组装成支架，得到了一个包含26条染色体的基因组组装体，支架N50长度为25.8 Mb。黄鲶鱼与其他硬骨鱼的系统发育关系表明，黄鲶鱼在大约8190万年前从通道鲶鱼的共同祖先中分离出来。我们在黄颡鱼中发现了1717个待扩增的基因家族，这些基因家族主要富集于免疫系统、信号转导、鞘糖脂生物合成和脂肪酸生物合成。利用Illumina， PacBio和Hi-C技术，我们构建了黄颡鱼P. fulvidraco的第一个高质量染色体水平基因组组装。本工作所获得的基因组资源不仅为黄颡鱼的功能基因组学研究提供了有价值的参考基因组，以破译黄颡鱼的经济性状和性别决定，而且为更广泛的进化研究界的基因组比较提供了重要的染色体信息。
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. 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 ∼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. 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.
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影响因子：
14.9
作者：
Flicek P;Amode MR;Barrell D;Beal K;Billis K;Brent S;Carvalho-Silva D;Clapham P;Coates G;Fitzgerald S;Gil L;Girón CG;Gordon L;Hourlier T;Hunt S;Johnson N;Juettemann T;Kähäri AK;Keenan S;Kulesha E;Martin FJ;Maurel T;McLaren WM;Murphy DN;Nag R;Overduin B;Pignatelli M;Pritchard B;Pritchard E;Riat HS;Ruffier M;Sheppard D;Taylor K;Thormann A;Trevanion SJ;Vullo A;Wilder SP;Wilson M;Zadissa A;Aken BL;Birney E;Cunningham F;Harrow J;Herrero J;Hubbard TJ;Kinsella R;Muffato M;Parker A;Spudich G;Yates A;Zerbino DR;Searle SM
通讯作者：
Searle SM
影响因子：
4.9
作者：
Bao W;Kojima KK;Kohany O
通讯作者：
Kohany O
影响因子：
14.9
作者：
Harris, MA;Clark, J;White, R
通讯作者：
White, R
影响因子：
48
作者：
Chin, Chen-Shan;Peluso, Paul;Schatz, Michael C.
通讯作者：
Schatz, Michael C.
YY超雄性和XY全雄性黄颡鱼（Pelteobagrus fulvidraco (Richardson)）规模化养殖的性别比遗传调控
影响因子：
3
作者：
Liu, Hanqin;Guan, Bo;Chen, Hongxi
通讯作者：
Chen, Hongxi