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Chromosome level assembly reveals a unique immune gene organization and signatures of evolution in the common pheasant.

染色体水平组装揭示了常见野鸡独特的免疫基因组织和进化特征。

  • 影响因子:0
  • DOI:10.1111/1755-0998.13296
  • 作者列表:"He C","Zhao L","Xiao L","Xu K","Ding J","Zhou H","Zheng Y","Han C","Akinyemi F","Luo H","Yang L","Luo L","Yuan H","Lu X","Meng H
  • 发表时间:2021-04-01
Abstract

:The common pheasant Phasianus colchicus, belonging to the order Galliformes and family Phasianidae, is the most widespread species. Despite a long history of captivity, the domestication of this bird is still at a preliminary stage. Recently, the demand for accelerating its transformation to poultry for meat and egg production has been increasing. In this study, we assembled high quality, chromosome scale genome of the common pheasant by using PacBio long reads, next-generation short reads, and Hi-C technology. The primary assembly has contig N50 size of 1.33 Mb and scaffold N50 size of 59.46 Mb, with a total size of 0.99 Gb, resolving most macrochromosomes into single scaffolds. A total of 23,058 genes and 10.71 Mb interspersed repeats were identified, constituting 30.31% and 10.71% of the common pheasant genome, respectively. Our phylogenetic analysis revealed that the common pheasant shared common ancestors with turkey about 24.7-34.5 million years ago (Ma). Rapidly evolved gene families, as well as branch-specific positively selected genes, indicate that calcium-related genes are potentially related to the adaptive and evolutionary change of the common pheasant. Interestingly, we found that the common pheasant has a unique major histocompatibility complex B locus (MHC-B) structure: three major inversions occurred in the sequence compared with chicken MHC-B. Furthermore, we detected signals of selection in five breeds of domestic common pheasant, several of which are production-oriented.

摘要

: 常见的野山鱼秋水仙,属于g目和pha科,是分布最广的物种。尽管饲养历史悠久,但这只鸟的驯化仍处于初步阶段。最近,加快其向禽肉和蛋生产的转化的需求一直在增加。在这项研究中,我们利用PacBio长读、下一代短读和Hi-C技术组装了普通野鸡的高质量染色体规模基因组。初级组装体的contig N50大小为1.33 Mb,支架N50大小为59.46 Mb,总大小为0.99 Gb,将大多数宏染色体解析为单个支架。鉴定了总共23,058个基因和10.71个Mb穿插重复,分别构成普通野鸡基因组的30.31% 和10.71%。我们的系统发育分析发现,大约2470-3450万年前 (Ma),普通野鸡与土耳其有着共同的祖先。快速进化的基因家族,以及分支特异性的阳性选择基因,表明与钙相关的基因与普通野鸡的适应性和进化变化潜在相关。有趣的是,我们发现普通野鸡具有独特的主要组织相容性复合体B基因座 (mhc-b) 结构: 与鸡mhc-b相比,序列中发生了三种主要倒位。此外,我们还检测了国内常见野鸡的五个品种的选择信号,其中几个品种是生产导向的。

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