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
{"title":"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","authors":"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","doi":"10.1016/j.gpb.2022.05.008","DOIUrl":null,"url":null,"abstract":"<div><p><strong>Sika deer</strong> are known to prefer <strong>oak leaves</strong>, 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 <em>UGT</em> and <em>CYP</em> gene families are functionally involved in the adaptation of sika deer to high-tannin food, especially the expansion of the <em>UGT</em> family 2 subfamily B of <em>UGT</em> 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.</p></div>","PeriodicalId":12528,"journal":{"name":"Genomics, Proteomics & Bioinformatics","volume":"21 1","pages":"Pages 203-215"},"PeriodicalIF":11.5000,"publicationDate":"2023-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10372904/pdf/","citationCount":"0","resultStr":"{\"title\":\"The First High-quality Reference Genome of Sika Deer Provides Insights into High-tannin Adaptation\",\"authors\":\"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\",\"doi\":\"10.1016/j.gpb.2022.05.008\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><p><strong>Sika deer</strong> are known to prefer <strong>oak leaves</strong>, 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 <em>UGT</em> and <em>CYP</em> gene families are functionally involved in the adaptation of sika deer to high-tannin food, especially the expansion of the <em>UGT</em> family 2 subfamily B of <em>UGT</em> 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.</p></div>\",\"PeriodicalId\":12528,\"journal\":{\"name\":\"Genomics, Proteomics & Bioinformatics\",\"volume\":\"21 1\",\"pages\":\"Pages 203-215\"},\"PeriodicalIF\":11.5000,\"publicationDate\":\"2023-02-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10372904/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Genomics, Proteomics & Bioinformatics\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S1672022922000754\",\"RegionNum\":2,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"GENETICS & HEREDITY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Genomics, Proteomics & Bioinformatics","FirstCategoryId":"99","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S1672022922000754","RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"GENETICS & HEREDITY","Score":null,"Total":0}
The First High-quality Reference Genome of Sika Deer Provides Insights into High-tannin Adaptation
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.
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.