Six reference-quality genomes reveal evolution of bat adaptations.
Six reference-quality genomes reveal evolution of bat adaptations.
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DOI：
10.1038/s41586-020-2486-3
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发表时间：
2020-07
期刊：
影响因子：
64.8
通讯作者：
Teeling EC
中科院分区：
文献类型：
--
作者：
Jebb D;Huang Z;Pippel M;Hughes GM;Lavrichenko K;Devanna P;Winkler S;Jermiin LS;Skirmuntt EC;Katzourakis A;Burkitt-Gray L;Ray DA;Sullivan KAM;Roscito JG;Kirilenko BM;Dávalos LM;Corthals AP;Power ML;Jones G;Ransome RD;Dechmann DKN;Locatelli AG;Puechmaille SJ;Fedrigo O;Jarvis ED;Hiller M;Vernes SC;Myers EW;Teeling EC
蝙蝠具有非凡的适应能力，包括飞行、回声定位、极长的寿命和独特的免疫力。高质量的基因组对于理解这些性状的分子基础和进化至关重要。在这里，我们结合了长读测序和最先进的支架协议，以产生，据我们所知，第一个参考质量的基因组的六个蝙蝠物种（菊头蝠ferrumequinum，Rousettus aegyptiacus，Phyllostomus discolor，Myotis myotis，Pipistrellus kuhlii和Molossus molossus）。我们将来自我们的“从基因组比对推断直系同源物的工具”（TOGA）软件的基因预测与从头和同源基因预测以及短读和长读转录组学相结合，以生成高度完整的基因注释。为了解决蝙蝠的系统发育位置内Laurasiatheria，我们采用了几种系统发育方法，全面的正交蛋白质编码和非编码区的基因组，并确定了一个基本的起源蝙蝠内Scrotifera。我们的全基因组筛选揭示了蝙蝠祖先分支中听觉相关基因的正选择，这表明喉部回声定位是这一分支的祖先特征。我们发现了免疫相关基因（包括促炎性NF-κB调节因子）的选择和丢失以及抗病毒APOBEC 3基因的扩增，这突出了可能有助于蝙蝠特殊免疫力的分子机制。不同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，我们发现并实验验证了蝙蝠特异性的microRNA变异，这可能会调节蝙蝠特异性的基因表达程序。我们的参考质量蝙蝠基因组提供了发现和验证蝙蝠适应的基因组基础所需的资源，并刺激了与人类健康和疾病直接相关的新研究途径。六种蝙蝠的参考质量基因组揭示了翼手目的系统发育位置，并提供了深入了解这一分支的独特适应性的遗传基础。
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 protocols 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 disease. Reference-quality genomes for six bat species shed light on the phylogenetic position of Chiroptera, and provide insight into the genetic underpinnings of the unique adaptations of this clade.
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影响因子：
5.3
作者：
Devanna P;van de Vorst M;Pfundt R;Gilissen C;Vernes SC
通讯作者：
Vernes SC
影响因子：
7
作者：
Barker BR;Taxman DJ;Ting JP
通讯作者：
Ting JP
DOI：
10.1093/bioinformatics/bts565
发表时间：
2012-12-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Fu L;Niu B;Zhu Z;Wu S;Li W
通讯作者：
Li W
影响因子：
11
作者：
Devanna P;Chen XS;Ho J;Gajewski D;Smith SD;Gialluisi A;Francks C;Fisher SE;Newbury DF;Vernes SC
通讯作者：
Vernes SC
DOI：
10.1073/pnas.1315419110
发表时间：
2013-12-10
影响因子：
11.1
作者：
Hayward, Alexander;Grabherr, Manfred;Jern, Patric
通讯作者：
Jern, Patric