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

Abstract

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

CLC Number:

S825.2

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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A Comparative Study on Chromosome-level Genomes of Sika Deer and Red Deer

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