The reference genome and transcriptome of the limestone langur, Trachypithecus leucocephalus, reveal expansion of genes related to alkali tolerance
-
Published:2021-04-08
Issue:1
Volume:19
Page:
-
ISSN:1741-7007
-
Container-title:BMC Biology
-
language:en
-
Short-container-title:BMC Biol
Author:
Que Tengcheng,Wang Huifeng,Yang Weifei,Wu Jianbao,Hou Chenyang,Pei Surui,Wu Qunying,Li Liu Ming,Wei Shilu,Xie Xing,Huang Hongli,Chen Panyu,Huang Yiming,Wu Aiqiong,He Meihong,Nong Dengpan,Wei Xiao,Wu Junyi,Nong Ru,Huang Ning,Zhou Qingniao,Lin Yaowang,Lu Tingxi,Wei Yongjie,Li Shousheng,Yao Jianglong,Zhong Yanli,Qin Huayong,Tan Luohao,Li Yingjiao,Li Weidong,Liu Tao,Liu Sanyang,Yu Yongyi,Qiu Hong,Jiang Yonghua,Li Youcheng,Liu Zhijin,Huang Cheng Ming,Hu Yanling
Abstract
Abstract
Background
Trachypithecus leucocephalus, the white-headed langur, is a critically endangered primate that is endemic to the karst mountains in the southern Guangxi province of China. Studying the genomic and transcriptomic mechanisms underlying its local adaptation could help explain its persistence within a highly specialized ecological niche.
Results
In this study, we used PacBio sequencing and optical assembly and Hi-C analysis to create a high-quality de novo assembly of the T. leucocephalus genome. Annotation and functional enrichment revealed many genes involved in metabolism, transport, and homeostasis, and almost all of the positively selected genes were related to mineral ion binding. The transcriptomes of 12 tissues from three T. leucocephalus individuals showed that the great majority of genes involved in mineral absorption and calcium signaling were expressed, and their gene families were significantly expanded. For example, FTH1 primarily functions in iron storage and had 20 expanded copies.
Conclusions
These results increase our understanding of the evolution of alkali tolerance and other traits necessary for the persistence of T. leucocephalus within an ecologically unique limestone karst environment.
Funder
National Natural Science Foundation of China Guangxi Forestry Department Foundation Guangxi Medical University Training Program for Distinguished Young Scholars by the National Natural Science Foundation of China
Publisher
Springer Science and Business Media LLC
Subject
Cell Biology,Developmental Biology,Plant Science,General Agricultural and Biological Sciences,General Biochemistry, Genetics and Molecular Biology,Physiology,Ecology, Evolution, Behavior and Systematics,Structural Biology,Biotechnology
Reference72 articles.
1. Pinheiro HT, Bernardi G, Simon T, Joyeux JC, Macieira RM, Gasparini JL, Rocha C, Rocha LA. Island biogeography of marine organisms. Nature. 2017;549(7670):82–5. https://doi.org/10.1038/nature23680. 2. Palesch D, Bosinger SE, Tharp GK, Vanderford TH, Paiardini M, Chahroudi A, Johnson ZP, Kirchhoff F, Hahn BH, Norgren RB, Patel NB, Sodora DL, Dawoud RA, Stewart CB, Seepo SM, Harris RA, Liu Y, Raveendran M, Han Y, English A, Thomas GWC, Hahn MW, Pipes L, Mason CE, Muzny DM, Gibbs RA, Sauter D, Worley K, Rogers J, Silvestri G. Sooty mangabey genome sequence provides insight into AIDS resistance in a natural SIV host. Nature. 2018;553(7686):77–80. https://doi.org/10.1038/nature25140. 3. Pavlovich SS, Lovett SP, Koroleva G, Guito JC, Arnold CE, Nagle ER, Kulcsar K, Lee A, Thibaud-Nissen F, Hume AJ, Mühlberger E, Uebelhoer LS, Towner JS, Rabadan R, Sanchez-Lockhart M, Kepler TB, Palacios G. The Egyptian Rousette genome reveals unexpected features of bat antiviral immunity. Cell. 2018;173(5):1098–110 e1018. https://doi.org/10.1016/j.cell.2018.03.070. 4. Suryamohan K, Krishnankutty SP, Guillory J, Jevit M, Schroder MS, Wu M, Kuriakose B, Mathew OK, Perumal RC, Koludarov I, et al. The Indian cobra reference genome and transcriptome enables comprehensive identification of venom toxins. Nat Genet. 2020;52(1):106–17. https://doi.org/10.1038/s41588-019-0559-8. 5. Clements R, Sodhi NS, Schilthuizen M, Ng PKL. Limestone karsts of southeast Asia: Imperiled arks of biodiversity. Bioscience. 2006;56(9):733–42. https://doi.org/10.1641/0006-3568(2006)56[733:Lkosai]2.0.Co;2.
Cited by
4 articles.
订阅此论文施引文献
订阅此论文施引文献,注册后可以免费订阅5篇论文的施引文献,订阅后可以查看论文全部施引文献
|
|