The First High-quality Reference Genome of Sika Deer Provides Insights into High-tannin Adaptation

IF 11.5 2区 生物学 Q1 GENETICS & HEREDITY
Xiumei Xing , Cheng Ai , Tianjiao Wang , Yang Li , Huitao Liu , Pengfei Hu , Guiwu Wang , Huamiao Liu , Hongliang Wang , Ranran Zhang , Junjun Zheng , Xiaobo Wang , Lei Wang , Yuxiao Chang , Qian Qian , Jinghua Yu , Lixin Tang , Shigang Wu , Xiujuan Shao , Alun Li , Fuhe Yang
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Abstract

Sika deer are known to prefer oak leaves, which are rich in tannins and toxic to most mammals; however, the genetic mechanisms underlying their unique ability to adapt to living in the jungle are still unclear. In identifying the mechanism responsible for the tolerance of a highly toxic diet, we have made a major advancement by explaining the genome of sika deer. We generated the first high-quality, chromosome-level genome assembly of sika deer and measured the correlation between tannin intake and RNA expression in 15 tissues through 180 experiments. Comparative genome analyses showed that the UGT and CYP gene families are functionally involved in the adaptation of sika deer to high-tannin food, especially the expansion of the UGT family 2 subfamily B of UGT genes. The first chromosome-level assembly and genetic characterization of the tolerance to a highly toxic diet suggest that the sika deer genome may serve as an essential resource for understanding evolutionary events and tannin adaptation. Our study provides a paradigm of comparative expressive genomics that can be applied to the study of unique biological features in non-model animals.

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梅花鹿的第一个高质量参考基因组为高单宁适应提供了见解
众所周知,梅花鹿喜欢橡树叶,橡树叶富含单宁,对大多数哺乳动物有毒;然而,它们适应丛林生活的独特能力的遗传机制尚不清楚。在确定对高毒性饮食耐受的机制方面,我们通过解释梅花鹿的基因组取得了重大进展。我们产生了第一个高质量的梅花鹿染色体水平基因组组装,并通过180个实验测量了15个组织中单宁摄入量与RNA表达之间的相关性。比较基因组分析表明,UGT和CYP基因家族在功能上参与了梅花鹿对高单宁食物的适应,特别是UGT基因的UGT家族2亚家族B的扩展。第一个染色体水平的组装和对高毒性饮食耐受性的遗传特征表明,梅花鹿基因组可能是了解进化事件和单宁适应的重要资源。我们的研究提供了一种比较表达基因组学的范式,可用于研究非模型动物的独特生物学特征。
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来源期刊
Genomics, Proteomics & Bioinformatics
Genomics, Proteomics & Bioinformatics Biochemistry, Genetics and Molecular Biology-Biochemistry
CiteScore
14.30
自引率
4.20%
发文量
844
审稿时长
61 days
期刊介绍: Genomics, Proteomics and Bioinformatics (GPB) is the official journal of the Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation and Genetics Society of China. It aims to disseminate new developments in the field of omics and bioinformatics, publish high-quality discoveries quickly, and promote open access and online publication. GPB welcomes submissions in all areas of life science, biology, and biomedicine, with a focus on large data acquisition, analysis, and curation. Manuscripts covering omics and related bioinformatics topics are particularly encouraged. GPB is indexed/abstracted by PubMed/MEDLINE, PubMed Central, Scopus, BIOSIS Previews, Chemical Abstracts, CSCD, among others.
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