Genome assembly of the common pheasant Phasianus colchicus, a model for speciation and ecological genomics
Genome assembly of the common pheasant Phasianus colchicus, a model for speciation and ecological genomics
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雉鸡的基因组组装，物种形成和生态基因组学模型
DOI：
10.1093/gbe/evz249
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发表时间：
2019
影响因子：
3.3
通讯作者：
王标
中科院分区：
文献类型：
--
作者：
刘阳;刘思敏;张楠;陈德;阙品甲;Jacob Hoglund;张正旺;王标
普通雉鸡（Phasianus colchicus）属于鸡形目和雉科，有30个亚种分布在古北界的原生地，并已被引入欧洲，北美和澳大利亚。它是一种重要的狩猎鸟类，经常受到野生动物管理，也是研究物种形成，地理学和当地适应的模式物种。然而，普通雉鸡的基因组资源普遍缺乏。我们使用Illumina HiSeq平台对普通雉鸡亚种的雄性个体进行测序。我们通过过滤掉所生成的原始数据的低质量读段获得了94.88 Gb的可用序列。这导致了1.02 Gb的最终组装，这等于估计的基因组大小。以鸡为模型的BUSCO分析表明，93.3%的基因是完整的。重叠群N50和支架N50的大小分别为178 kb和10.2 Mb。这些都表明我们获得了高质量的基因组组装。我们通过从头算和基于同源性的预测注释了16，485个蛋白质编码基因和123.3 Mb（占基因组的12.05%）的重复序列。此外，我们还对中国7个代表亚种的另外45个个体应用了RAD测序方法，并确定了4，376，351个新的单核苷酸多态性（SNP）标记。利用这一前所未有的数据集，我们揭示了中国普通雉鸡的地理种群结构和遗传渐渗。我们的研究结果提供了第一个高质量的参考基因组的普通雉鸡和一个有价值的全基因组SNP数据库的研究人口基因组学和人口统计学的历史。
The common pheasant (Phasianus colchicus) in the order Galliformes and the family Phasianidae, has 30 subspecies distributed across its native range in the Palearctic realm and has been introduced to Europe, North America, and Australia. It is an important game bird often subjected to wildlife management as well as a model species to study speciation, biogeography, and local adaptation. However, the genomic resources for the common pheasant are generally lacking. We sequenced a male individual of the subspeciestorquatusof the common pheasant with the Illumina HiSeq platform. We obtained 94.88 Gb of usable sequences by filtering out low-quality reads of the raw data generated. This resulted in a 1.02 Gb final assembly, which equals the estimated genome size. BUSCO analysis using chicken as a model showed that 93.3% of genes were complete. The contig N50 and scaffold N50 sizes were 178 kb and 10.2 Mb, respectively. All these indicate that we obtained a high-quality genome assembly. We annotated 16,485 protein-coding genes and 123.3 Mb (12.05% of the genome) of repetitive sequences by ab initio and homology-based prediction. Furthermore, we applied a RAD-sequencing approach for another 45 individuals of seven representative subspecies in China and identified 4,376,351 novel single nucleotide polymorphism (SNPs) markers. Using this unprecedented data set, we uncovered the geographic population structure and genetic introgression among common pheasants in China. Our results provide the first high-quality reference genome for the common pheasant and a valuable genome-wide SNP database for studying population genomics and demographic history.