基于PacBio三代测序的高质量汶上芦花鸡基因组的组装

doi:10.16431/j.cnki.1671-7236.2023.10.001

中国畜牧兽医 ›› 2023, Vol. 50 ›› Issue (10): 3869-3881.doi: 10.16431/j.cnki.1671-7236.2023.10.001

基于PacBio三代测序的高质量汶上芦花鸡基因组的组装

薛倩^1,2, 邢伟杰^1,2, 李国辉^1,2, 周成浩^1,2, 张会永^1,2, 殷建玫^1,2, 蒋一秀^1,2, 朱云芬^1,2, 韩威^1,2

1. 江苏省家禽科学研究所科技创新有限公司, 扬州 225125;
2. 江苏省家禽科学研究所, 扬州 225125

收稿日期:2022-12-14 出版日期:2023-10-05 发布日期:2023-09-26
通讯作者: 韩威 E-mail:hanwei830@163.com
作者简介:薛倩,E-mail:yzxueqian@163.com;邢伟杰,E-mail:2331962146@qq.com
基金资助:
江苏省重点研发计划(现代农业)专项(BE2019353)；江苏省自然科学基金面上项目(BK20221285)

Assembly of High-quality Wenshang Barred Chickens Genome Based on PacBio Third-Generation Sequencing

XUE Qian^1,2, XING Weijie^1,2, LI Guohui^1,2, ZHOU Chenghao^1,2, ZHANG Huiyong^1,2, YIN Jianmei^1,2, JIANG Yixiu^1,2, ZHU Yunfen^1,2, HAN Wei^1,2

1. Science and Technology Innovation Co., Ltd., Poultry Institute of Jiangsu Province, Yangzhou 225125, China;
2. Poultry Institute of Jiangsu Province, Yangzhou 225125, China

Received:2022-12-14 Online:2023-10-05 Published:2023-09-26

摘要/Abstract

摘要： 【目的】汶上芦花鸡为中国唯一的芦花羽地方鸡品种资源,芦花基因可伴性遗传,芦花羽性状可用于雏鸡的自别雌雄。试验旨在丰富家鸡基因组信息,获取汶上芦花鸡全基因组序列,为鸡伴性芦花羽分子机制研究提供材料。【方法】以汶上芦花鸡为试验动物,基于BGI MGISEQ构建小片段文库进行基因组特征评估,利用PacBio三代测序技术、Hi-C技术组装及构建汶上芦花鸡全基因组信息数据库,利用生物信息学方法对获得的基因组序列进行组装和功能注释。【结果】试验共获得BGI二代测序数据量59.70 Gb;获得PacBio三代测序数据量31.13 Gb,reads平均长度为15 362 bp;获得Hi-C数据量95.37 Gb;拼接和初步组装得到基因组大小为1.12 Gb,经Hi-C辅助组装后,共有1.07 Gb的序列挂载到41条染色体上,挂载率95.62%,基因组contigs N50为9.61 Mb,scaffold N50为91.29 Mb,BUSCO评估为98.50%,基因组连续性和完整度良好;预测基因组有22.57%的重复序列,有426个tRNAs、56个rRNAs、260个miRNAs和308个 snRNAs;共预测得到蛋白编码基因17 338 个,其中96.00%的基因在数据库中得到了功能注释;组装获得汶上芦花鸡Z染色体长度约88.23 Mb,预测并注释到蛋白编码基因742个,这些基因显著富集于氨基酸、脂肪等代谢相关通路,在汶上芦花鸡Z染色体上准确定位了TYRP1、CDKN2A、SLC45A2等羽色相关基因。【结论】研究获得了汶上芦花鸡高质量染色体水平基因组,丰富了家鸡基因组遗传信息,准确定位了Z染色体上一些羽色相关基因。研究结果可为从全基因组水平挖掘汶上芦花鸡优异性状调控机制奠定基础。

关键词: 汶上芦花鸡; 基因组组装; PacBio三代测序技术; 基因组注释; Z染色体; 伴性芦花羽

Abstract: 【Objective】 Wenshang Barred chickens is the only barred chicken breed in the abundant Chinese native chicken resources.The barred-related gene is sex-linked,so the trait could be used for automatical sexing of chicks.This study was aimed to enrich the genome information of domestic chickens,and obtain the whole genome sequence information in Wenshang Barred chickens,so as to provide materials for studying the molecular mechanism of sex-linked barred feather in chickens.【Method】 Wenshang Barred chicken was used as material to construct a small fragment library based on BGI MGISEQ for genomic characterization assessment.The whole genome information database of Wenshang Barred chickens was assembled and constructed by PacBio and Hi-C sequencing technology.The obtained genome sequences were assembled and annotated based on bioinformatics methods.【Result】 A total of 59.70 Gb BGI second-generation sequencing data were obtained.31.13 Gb of PacBio data were obtained with an average reads length of 15 362 bp.The obtained Hi-C data was 95.37 Gb.Splicing and initial assembly resulted in a genome size of 1.12 Gb.After Hi-C auxiliary assembly,a total of 1.07 Gb sequence could be attached to 41 chromosomes,with a mount rate of 95.62%.The contigs N50 and scaffold N50 of the genome were 9.61 and 91.29 Mb,respectively.BUSCO was assessed at 98.50%.So the continuity and integrity of the genome were good.The assembled genome was predicted to have 22.57% repeats,with 426 tRNAs,56 rRNAs,260 miRNAs and 308 snRNAs.A total of 17 338 protein-coding genes were predicted,and 96.00% of them were annotated in the gene function databases.The length of chromosome Z in Wenhang Barred chickens was 88.23 Mb,and 742 protein-coding genes were predicted and annotated,which were significantly enriched in as amino acid and fat related metabolism pathways.The positions of feather color related genes such as TYRP1,CDKN2A and SLC45A2 were accurately located on chromosome Z in Wenhang Barred chickens.【Conclusion】 In this study,high quality chromosome level genome of Wenshang Barred chickens was obtained,which enriched the genetic information of the domestic chicken genome.Some feather color related genes on chromosome Z were accurately located.The results would provide a basis for exploring the regulation mechanism of superior traits in Wenshang Barred chickens at the genome-wide level.

Key words: Wenshang Barred chickens; genome assembly; PacBio third generation sequencing technology; genome annotation; chromosome Z; sex-linked barred feather

中图分类号:

S831.2

薛倩, 邢伟杰, 李国辉, 周成浩, 张会永, 殷建玫, 蒋一秀, 朱云芬, 韩威. 基于PacBio三代测序的高质量汶上芦花鸡基因组的组装[J]. 中国畜牧兽医, 2023, 50(10): 3869-3881.

XUE Qian, XING Weijie, LI Guohui, ZHOU Chenghao, ZHANG Huiyong, YIN Jianmei, JIANG Yixiu, ZHU Yunfen, HAN Wei. Assembly of High-quality Wenshang Barred Chickens Genome Based on PacBio Third-Generation Sequencing[J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(10): 3869-3881.

参考文献

[1] HILLIER L D W,MILLER W,BIRNEY E,et al.Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution[J].Nature,2004,32(7018):695-716.
[2] LI M,SUN C,XU N,et al.De novo assembly of 20 chicken genomes reveals the undetectable phenomenon for thousands of core genes on microchromosomes and subtelomeric regions[J].Molecular Biology and Evolution,2022,39(4):msac066.
[3] LAWAL R A,HANOTTE O.Domestic chicken diversity:Origin,distribution,and adaptation[J].Animal Genetics,2021,52(4):385-394.
[4] 蒋海涛,谭万芝.汶上芦花鸡品种资源调查研究[J/OL].畜牧兽医科学(电子版),2020,13:2. JIANG H T,TAN W Z.Investigation on breed resources of Wenshang Luhua chicken[J/OL].Graziery Veterinary Sciences(Electronic Version),2020,13:2.(in Chinese)
[5] SCHWOCHOW T D,RING H,SUNDSTRÖM E,et al.The evolution of Sex-linked barring alleles in chickens involves both regulatory and coding changes in CDKN2A[J].PLoS Genetics,2017,13(4):e1006665.
[6] HELLSTRÖM A R,SUNDSTRÖM E,GUNNARSSON U,et al.Sex-linked barring in chickens is controlled by the CDKN2A/B tumour suppressor locus[J].Pigment Cell & Melanoma Research,2010,23(4):521-530.
[7] CHEN Y,CHEN Y,SHI C,et al.SOAPnuke:A MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data[J].Gigascience,2018,7(1):1-6.
[8] ALTSCHUL S F,GISH W,MILLER W,et al.Basic local alignment search tool[J].Journal of Molecular Biology,1990,215(3):403-410.
[9] BINGHANG L,SHI Y,YUAN J,et al.Estimation of genomic characteristics by analyzing K-mer frequency in de novo genome projects[J].Quantitative Biology,2013,35(s1-3):62-67.
[10] DURAND N C,SHAMIM M S,MACHOL I,et al.Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments[J].Cell Systems,2016,3(1):95-98.
[11] BURTON J N,ADEY A,PATWARDHAN R P,et al.Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions[J].Nature Biotechnology,2013,31(12):1119-1125.
[12] DUDCHENKO O,BATRA S S,OMER A D,et al.De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds[J].Science,2017,356(6333):92-95.
[13] HOLT C,YANDELL M.MAKER2:An annotation pipeline and genome-database management tool for second-generation genome projects[J].BMC Bioinformatics,2011,12:491.
[14] HAAS B J,DELCHER A L,MOUNT S M,et al.Improving the arabidopsis genome annotation using maximal transcript alignment assemblies[J].Nucleic Acids Research,2003,31(19):5654-5666.
[15] LOWE T M,EDDY S R.tRNAscan-SE:A program for improved detection of transfer RNA genes in genomic sequence[J].Nucleic Acids Research,1997,25(5):955-964.
[16] GRIFFITHS J S,MOXON S,MARSHALL M,et al.Rfam:Annotating non-coding RNAs in complete genomes[J].Nucleic Acids Research,2005,33(Database issue):D121-D124.
[17] NAWROCKI E P,EDDY S R.Infernal 1.1:100-fold faster RNA homology searches[J].Bioinformatics,2013,29(22):2933-2935.
[18] RHIE A,MCCARTHY S A,FEDRIGO O,et al.Towards complete and error-free genome assemblies of all vertebrate species[J].Nature,2021,592(7856):737-746.
[19] HUANG Z,XU Z,BAI H,et al.Evolutionary analysis of a complete chicken genome[J].Proceedings of the National Academy of Sciences of the United States of America,2023,120(8):e2216641120.
[20] 吴日富,瞿浩,严霞,等.家鸡羽色性状遗传调控机制研究进展[J].中国畜牧兽医,2022,49(5):1806-1816. WU R F,QU H,YAN X,et al.Research progress on the genetic regulation mechanism of feather color traits in domestic chickens[J].China Animal Husbandry & Veterinary Medicine,2022,49(5):1806-1816.(in Chinese)
[21] CIESLAK M,REISSMANN M,HOFREITER M,et al.Colours of domestication[J].Biological Reviews of the Cambridge Philosophical Society,2011,86(4):885-899.
[22] 陈海雁,陈向东,俞黎姗.黑色素形成机理、生物学功能和应用开发的研究进展[J].生物资源,2020,42(6):652-659. CHEN H Y,CHEN X D,YU L S,et al.Biosynthesis,function and applications of melanin[J].Biotic Resources,2020,42(6):652-659.(in Chinese)
[23] 李青芝,陈宇旭,周琳,等.脊椎动物TYR基因的序列特征与正选择位点鉴定[J].广东农业科学,2014,41(23):7. LI Q Z,CHEN Y X,ZHOU L,et al.Sequence features and selective pressure of the TYR genes in vertebrates[J].Guangdong Agricultural Sciences, 2014,41(23):7.(in Chinese)
[24] 宋素芳,宋幸辉,蔺成刚,等.SLC45A2基因在"豫粉1号"浅芦花羽色中的表达及酪氨酸对其在黑色素细胞中表达量的影响[J].中国畜牧杂志,2019,55(9):64-67. SONG S F,SONG X H,LIN C G,et al.Expression of SLC45A2 in columbian plume color of "Yufen Ⅰ" chicken and effect of tyrosine on its expression in melanocytes[J].Chinese Journal of Animal Science,2019,55(9):64-67.(in Chinese)
[25] GUNNARSSON U,HELLSTRÖM A R,TIXIER-BOICHARD M,et al.Mutations in SLC45A2 cause plumage color variation in chicken and Japanese quail[J].Genetics,2007,175(2):867-877.

基于PacBio三代测序的高质量汶上芦花鸡基因组的组装

Assembly of High-quality Wenshang Barred Chickens Genome Based on PacBio Third-Generation Sequencing

PDF

可视化

摘要/Abstract

引用本文

使用本文

参考文献

相关文章 2

编辑推荐

Metrics

本文评价

[1]	高绪莉, 杨佳林, 刘玮, 韩海霞, 雷秋霞, 周艳, 刘杰, 曹顶国, 陈甫, 李福伟. 暗斑蛋7 d内的变化规律及暗斑对蛋品质影响的研究[J]. 中国畜牧兽医, 2021, 48(7): 2397-2403.
[2]	李福伟, 韩海霞, 雷秋霞, 周艳, 高金波, 刘玮, 曹顶国. 汶上芦花鸡催乳素基因外显子2的遗传变异及其与繁殖性状的相关性分析[J]. 中国畜牧兽医, 2014, 41(9): 184-188.