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

【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15362 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17338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TYRP 1、CDKN 2 A、SLC 45 A 2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。

【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 15362 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 17338 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 TYRP 1,CDKN 2 A and SLC 45 A 2 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.