An improved pig reference genome sequence to enable pig genetics and genomics research
An improved pig reference genome sequence to enable pig genetics and genomics research
复制标题
DOI：
10.1093/gigascience/giaa051
复制
发表时间：
2020-06-01
期刊：
影响因子：
9.2
通讯作者：
Archibald, Alan L.
中科院分区：
文献类型：
--
作者：
Warr, Amanda;Affara, Nabeel;Archibald, Alan L.
背景资料：家猪（Sus scrofa）作为食物来源和生物医学模型都很重要，因为它在大小，解剖学，生理学，代谢，病理学和药理学方面与人类相似。使用较旧的基于克隆的测序方法建立的纯种杜洛克母猪的参考基因组草案（Sscrofa 10.2）是不完整的，未解决的冗余，短程顺序和方向错误，以及相关的错误组装基因限制了其实用性。结果如下：我们提出了2个注释的高度连续的染色体水平的基因组组件创建与最近的长读技术和全基因组鸟枪策略，1为同一杜洛克女性（Sscrofa 11.1）和1为远交，复合品种男性（USMARCv1.0）。这两个组件的连续性和准确性都比Sscrofa 10.2高得多（>90倍）。结论：这些高度连续的组装加上另外11个短读组装的注释，为这种重要的农业和生物医学模式物种的遗传组成提供了前所未有的视角。我们建议将改良的杜洛克组装体（Sscrofa11.1）作为猪基因组研究的参考基因组。
Background: The domestic pig (Sus scrofa) is important both as a food source and as a biomedical model given its similarity in size, anatomy, physiology, metabolism, pathology, and pharmacology to humans. The draft reference genome (Sscrofa10.2) of a purebred Duroc female pig established using older clone-based sequencing methods was incomplete, and unresolved redundancies, short-range order and orientation errors, and associated misassembled genes limited its utility. Results: We present 2 annotated highly contiguous chromosome-level genome assemblies created with more recent long-read technologies and a whole-genome shotgun strategy, 1 for the same Duroc female (Sscrofa11.1) and 1 for an outbred, composite-breed male (USMARCv1.0). Both assemblies are of substantially higher (>90-fold) continuity and accuracy than Sscrofa10.2. Conclusions: These highly contiguous assemblies plus annotation of a further 11 short-read assemblies provide an unprecedented view of the genetic make-up of this important agricultural and biomedical model species. We propose that the improved Duroc assembly (Sscrofa11.1) become the reference genome for genomic research in pigs.