梅花鹿与欧洲马鹿染色体水平基因组的比较研究

doi:10.11843/j.issn.0366-6964.2021.02.010

摘要/Abstract

摘要： 旨在从基因组层面揭示梅花鹿与欧洲马鹿的起源进化，找到与进化过程相关的信号通路并与表型进行关联。本试验以成年雌性梅花鹿与成年雄性欧洲马鹿染色体水平基因组作为研究对象，利用比较基因组学的方法对梅花鹿和欧洲马鹿基因组进行染色体共线性分析，获得两个物种间基因组序列的同源关系和基因组发生的染色体倒位现象，并对被倒位截断和在倒位内部未被截断的两类基因分别进行GO和KEGG功能富集分析；同时对两个物种染色体上的基因进行共线性分析，识别二者基因组间的直系同源区域，检测直系同源基因，估算两个物种的分化时间。结果显示，梅花鹿与欧洲马鹿基因组表现出同源性，有27条染色体的同源性在95%以上；通过基因组的比对确定了梅花鹿的23号染色体是X染色体；而对染色体倒位的统计及基因的GO和KEGG功能富集分析发现，梅花鹿基因组共有37 847个倒位，片段长度为1~5 kb的倒位数目最多；而倒位涉及基因的GO功能富集的生物学过程及分子功能有嗅觉中化学刺激的检测、嗅觉感觉、嗅觉感受器活动、信号传感器活动；KEGG富集的是嗅觉传导信号通路。而梅花鹿与欧洲马鹿基因共线性分析共检测出79个同源区段，12 629个直系同源基因，利用同源基因的同义突变率（Ks）估算出梅花鹿与欧洲马鹿的分化时间是0.318 MYA （millions of years ago）。本研究利用比较基因组学的方法，获得了梅花鹿与欧洲马鹿基因组间的同源关系以及两个物种染色体倒位现象，通过功能富集分析发现，染色体倒位与嗅觉表型有关，为鹿属动物染色体进化的研究提供新的理论基础。

关键词: 梅花鹿, 欧洲马鹿, 染色体水平基因组, 比较基因组学

Abstract: The purpose of this study was to reveal the origin and evolution of sika deer and red deer at the genome level, to find the signal pathways related to the evolution process and to explore their correlation with the phenotypes. The chromosome-level genomes of adult female sika deer and adult male red deer were used as research objects and the comparative genomics was used to perform the analysis of chromosome collinearity. The homologous relationship of genomic sequences and the phenomenon of chromosome inversion between the two species were obtained. The functional enrichment analysis of GO and KEGG were carried out for the two kinds of genes which were truncated by inversion and untruncated inside the inversion, respectively. At the same time, the collinearity analysis of genes on chromosomes of the two species were performed to identify the orthologous regions between the two genomes, detect the orthologous genes and estimate the divergence time of two species. The results showed the homology between the genomes of sika deer and red deer, and 27 chromosomes had a homology of more than 95%. We also identified sika deer chromosome 23 as the X chromosome by the alignment. By statistical analysis of chromosomal inversion and functional enrichment of genes involved in the inversions by GO and KEGG, there were 37 847 inversions in sika deer genome and the number of inverted fragments in 1-5 kb was the largest. The biological processes and molecular functions of GO functional enrichment of genes involved in inversion included detection of chemical stimulus involved in sensory perception of smell, sensory perception of smell, olfactory receptor activity, signal transducer activity. The signal pathway of KEGG enrichment was olfactory transduction. A total of 79 homologous regions and 12 629 orthologous genes were detected by collinearity analysis, and the divergence time between sika deer and red deer was estimated to be 0.318 MYA by using the synonymous mutation rate (Ks). In this study, the comparative genomic was used to find the homology relationship between sika deer and red deer genomes, and the phenomenon of chromosome inversion in two species were obtained. Through functional enrichment analysis, it was found that chromosome inversion was related to olfactory phenotype, which provided a new theoretical basis for the study of chromosome evolution in Cervus.

Key words: sika deer, red deer, chromosome-level genome, comparative genomics

中图分类号:

S825.2

唐丽昕, 王天骄, 刘华淼, 张然然, 邢秀梅. 梅花鹿与欧洲马鹿染色体水平基因组的比较研究[J]. 畜牧兽医学报, 2021, 52(2): 376-388.

TANG Lixin, WANG Tianjiao, LIU Huamiao, ZHANG Ranran, XING Xiumei. A Comparative Study on Chromosome-level Genomes of Sika Deer and Red Deer[J]. Acta Veterinaria et Zootechnica Sinica, 2021, 52(2): 376-388.

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