爱尔兰都柏林大学Emma C. Teeling、德国马克斯普朗克研究所Eugene W. Myers和Michael Hiller以及荷兰马克斯·普朗克心理语言学研究所Sonja C. Vernes团队合作取得新进展。六个参考质量的基因组揭示了蝙蝠适应性进化。2020年7月22日，《自然》发表了这一成果。
他们结合了长片段测序技术和最新的脚手架协议，生成了六个蝙蝠物种（Rhinolophus ferrumequinum，Rousettus aegyptiacus，Phyllostomus discolor，Myotis myotis，Pipistrellus kuhlii和Molossus molossus）的参考质量基因组。他们将“从基因组比对推断直系同源物工具”（TOGA）软件中的基因预测与从头和同源性基因预测以及短时和长时转录组相结合，以生成高度完整的基因注释。
为了解蝙蝠在Laurasiatheria中的系统发生位置，他们将几种系统发生方法应用于基因组直系同源的蛋白质编码和非编码区域的综合集，并确定了Scorotifera中蝙蝠的基础起源。他们的全基因组筛选，揭示了蝙蝠祖先分支中与听力相关的基因的阳性选择，这表明喉头回声定位是该进化枝的祖先特征。
他们发现免疫相关基因（包括促炎性NF-κB调节因子）的选择和缺失以及抗病毒APOBEC3基因的扩展，突出了可能有助于蝙蝠异常免疫的分子机制。多种病毒的基因组整合提供了蝙蝠对病毒感染的历史耐受性的基因组记录。
最后，他们发现和实验验证了microRNA中的蝙蝠特异性变异，它可能调控蝙蝠特异性基因表达程序。他们的参考质量蝙蝠基因组提供了发现和验证蝙蝠适应性基因组基础所需的资源，并激发了与人类健康和疾病直接相关的新研究途径。
据介绍，蝙蝠具有非凡的适应能力，包括飞行、回声定位、超长寿命和独特的免疫力。高质量的基因组对于理解这些特征的分子基础和进化至关重要。
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
Nature：《自然》，创刊于1869年。隶属于施普林格·自然出版集团，最新IF：69.504
官方网址：http://www.nature.com/
投稿链接：http://www.nature.com/authors/submit_manuscript.html
本期文章：《自然》：Online/在线发表
