研究揭示蝙蝠適應性進化
作者：
小柯機器人發布時間：2020/7/24 16:52:37
愛爾蘭都柏林大學Emma C. Teeling、德國馬克斯普朗克研究所Eugene W. Myers和Michael Hiller以及荷蘭馬克斯·普朗克心理語言學研究所Sonja C. Vernes團隊合作取得新進展。六個參考質量的基因組揭示了蝙蝠適應性進化。2020年7月22日，《自然》發表了這一成果。
他們結合了長片段測序技術和最新的腳手架協議，生成了六個蝙蝠物種（Rhinolophus ferrumequinum，Rousettus aegyptiacus，Phyllostomus discolor，Myotis myotis，Pipistrellus kuhlii和Molossus molossus）的參考質量基因組。他們將「從基因組比對推斷直系同源物工具」（TOGA）軟體中的基因預測與從頭和同源性基因預測以及短時和長時轉錄組相結合，以生成高度完整的基因注釋。
為了解蝙蝠在Laurasiatheria中的系統發生位置，他們將幾種系統發生方法應用於基因組直系同源的蛋白質編碼和非編碼區域的綜合集，並確定了Scorotifera中蝙蝠的基礎起源。他們的全基因組篩選，揭示了蝙蝠祖先分支中與聽力相關的基因的陽性選擇，這表明喉頭回聲定位是該進化枝的祖先特徵。
他們發現免疫相關基因（包括促炎性NF-κB調節因子）的選擇和缺失以及抗病毒APOBEC3基因的擴展，突出了可能有助於蝙蝠異常免疫的分子機制。多種病毒的基因組整合提供了蝙蝠對病毒感染的歷史耐受性的基因組記錄。
最後，他們發現和實驗驗證了microRNA中的蝙蝠特異性變異，它可能調控蝙蝠特異性基因表達程序。他們的參考質量蝙蝠基因組提供了發現和驗證蝙蝠適應性基因組基礎所需的資源，並激發了與人類健康和疾病直接相關的新研究途徑。
據介紹，蝙蝠具有非凡的適應能力，包括飛行、回聲定位、超長壽命和獨特的免疫力。高質量的基因組對於理解這些特徵的分子基礎和進化至關重要。
附：英文原文
Title: Six reference-quality genomes reveal evolution of bat adaptations
Author: David Jebb, Zixia Huang, Martin Pippel, Graham M. Hughes, Ksenia Lavrichenko, Paolo Devanna, Sylke Winkler, Lars S. Jermiin, Emilia C. Skirmuntt, Aris Katzourakis, Lucy Burkitt-Gray, David A. Ray, Kevin A. M. Sullivan, Juliana G. Roscito, Bogdan M. Kirilenko, Liliana M. Dvalos, Angelique P. Corthals, Megan L. Power, Gareth Jones, Roger D. Ransome, Dina K. N. Dechmann, Andrea G. Locatelli, Sbastien J. Puechmaille, Olivier Fedrigo, Erich D. Jarvis, Michael Hiller, Sonja C. Vernes, Eugene W. Myers, Emma C. Teeling
Issue&Volume: 2020-07-22
Abstract: Bats possess extraordinary adaptations, including flight, echolocation, extreme longevity and unique immunity. High-quality genomes are crucial for understanding the molecular basis and evolution of these traits. Here we incorporated long-read sequencing and state-of-the-art scaffolding protocols1 to generate, to our knowledge, the first reference-quality genomes of six bat species (Rhinolophus ferrumequinum, Rousettus aegyptiacus, Phyllostomus discolor, Myotis myotis, Pipistrellus kuhlii and Molossus molossus). We integrated gene projections from our 『Tool to infer Orthologs from Genome Alignments』 (TOGA) software with de novo and homology gene predictions as well as short- and long-read transcriptomics to generate highly complete gene annotations. To resolve the phylogenetic position of bats within Laurasiatheria, we applied several phylogenetic methods to comprehensive sets of orthologous protein-coding and noncoding regions of the genome, and identified a basal origin for bats within Scrotifera. Our genome-wide screens revealed positive selection on hearing-related genes in the ancestral branch of bats, which is indicative of laryngeal echolocation being an ancestral trait in this clade. We found selection and loss of immunity-related genes (including pro-inflammatory NF-κB regulators) and expansions of anti-viral APOBEC3 genes, which highlights molecular mechanisms that may contribute to the exceptional immunity of bats. Genomic integrations of diverse viruses provide a genomic record of historical tolerance to viral infection in bats. Finally, we found and experimentally validated bat-specific variation in microRNAs, which may regulate bat-specific gene-expression programs. Our reference-quality bat genomes provide the resources required to uncover and validate the genomic basis of adaptations of bats, and stimulate new avenues of research that are directly relevant to human health and disease1.
DOI: 10.1038/s41586-020-2486-3
Source: https://www.nature.com/articles/s41586-020-2486-3