Transcriptome sequencing and phylogenomic resolution within Spalacidae (Rodentia).
Transcriptome sequencing and phylogenomic resolution within Spalacidae (Rodentia).
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Spalacidae（啮齿动物）的转录组测序和系统发育解析
DOI：
10.1186/1471-2164-15-32
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发表时间：
2014-01-17
期刊：
影响因子：
4.4
通讯作者：
Zhao H
中科院分区：
文献类型：
--
作者：
Lin GH;Wang K;Deng XG;Nevo E;Zhao F;Su JP;Guo SC;Zhang TZ;Zhao H
研究背景地下哺乳动物因其高度特化的地下生活特征而引起进化生物学家的极大兴趣。由于形态特征的趋同性和分子证据的不一致性，使得鼠科中三个亚科Myospalacinae、Spalacinae和Rhizomyinae之间的系统发育关系尚未得到解决。在这里，我们进行novotranscriptome测序的四个RNA-seq文库制备的大脑和肝脏组织的高原鼢鼠（Eospalax baileyi）和白竹鼠（Rhizomys pruinosus），并分析了转录组序列一起公布的转录组的中东盲鼹鼠（Spalax galili）。我们的特点的两个spalacids的转录组组件，并恢复的三个亚科的同源性使用一个pseudogenomic approach.ResultsApproximately 50.3万清洁读取从鼢鼠和140.8万清洁读取从竹鼠产生的Illumina配对末端RNA-seq技术。将所有干净的读段组装成138，872个（鼢鼠）和157，167个（竹鼠）单基因，这些单基因由公共数据库注释：Swiss-prot、Trembl、NCBI非冗余蛋白（NR）、NCBI核苷酸序列（NT）、基因本体（GO）、Orthopathy Group簇（COG）和京都基因和基因组百科全书（KEGG）。在三种spalacids和小鼠中总共鉴定了5，116个核直向同源基因，小鼠用作外群。系统发育分析显示，中华鼢鼠和竹鼠之间的姐妹群关系，这是支持大多数的基因树推断从个人的orthopathic基因，建议亚科Myospalacinae更密切相关的亚科Rhizomyinae。相同的拓扑结构被恢复从串联序列的5,116个核基因，四倍简并位点的5,116个核基因和串联序列的13个蛋白质编码mitochondrial gene.ConclusionsThis是转录组测序的首次报告，在鼢鼠和竹鼠，代表了一个宝贵的资源，为未来的研究在地下哺乳动物的比较基因组学。系统基因组分析提供了一个决定性的解决家庭Spalacidae内的三个亚科的相互关系，并强调了快速辐射的生命树的进化历史解剖的能力。
BackgroundSubterranean mammals have been of great interest for evolutionary biologists because of their highly specialized traits for the life underground. Owing to the convergence of morphological traits and the incongruence of molecular evidence, the phylogenetic relationships among three subfamilies Myospalacinae (zokors), Spalacinae (blind mole rats) and Rhizomyinae (bamboo rats) within the family Spalacidae remain unresolved. Here, we performedde novotranscriptome sequencing of four RNA-seq libraries prepared from brain and liver tissues of a plateau zokor (Eospalax baileyi) and a hoary bamboo rat (Rhizomys pruinosus), and analyzed the transcriptome sequences alongside a published transcriptome of the Middle East blind mole rat (Spalax galili). We characterize the transcriptome assemblies of the two spalacids, and recover the phylogeny of the three subfamilies using a phylogenomic approach.ResultsApproximately 50.3 million clean reads from the zokor and 140.8 million clean reads from the bamboo ratwere generated by Illumina paired-end RNA-seq technology. All clean reads were assembled into 138,872 (the zokor) and 157,167 (the bamboo rat) unigenes, which were annotated by the public databases: the Swiss-prot, Trembl, NCBI non-redundant protein (NR), NCBI nucleotide sequence (NT), Gene Ontology (GO), Cluster of Orthologous Groups (COG), and Kyoto Encyclopedia of Genes and Genomes (KEGG). A total of 5,116 nuclear orthologous genes were identified in the three spalacids and mouse, which was used as an outgroup. Phylogenetic analysis revealed a sister group relationship between the zokor and the bamboo rat, which is supported by the majority of gene trees inferred from individual orthologous genes, suggesting subfamily Myospalacinae is more closely related to subfamily Rhizomyinae. The same topology was recovered from concatenated sequences of 5,116 nuclear genes, fourfold degenerate sites of the 5,116 nuclear genes and concatenated sequences of 13 protein coding mitochondrial genes.ConclusionsThis is the first report of transcriptome sequencing in zokors and bamboo rats, representing a valuable resource for future studies of comparative genomics in subterranean mammals. Phylogenomic analysis provides a conclusive resolution of interrelationships of the three subfamilies within the family Spalacidae, and highlights the power of phylogenomic approach to dissect the evolutionary history of rapid radiations in the tree of life.
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影响因子：
4.1
作者：
Norris, RW;Zhou, KY;Honeycutt, RL
通讯作者：
Honeycutt, RL
影响因子：
3.7
作者：
Ranwez V;Harispe S;Delsuc F;Douzery EJ
通讯作者：
Douzery EJ
影响因子：
3.7
作者：
Malik A;Korol A;Hübner S;Hernandez AG;Thimmapuram J;Ali S;Glaser F;Paz A;Avivi A;Band M
通讯作者：
Band M
影响因子：
14.9
作者：
Lee Y;Tsai J;Sunkara S;Karamycheva S;Pertea G;Sultana R;Antonescu V;Chan A;Cheung F;Quackenbush J
通讯作者：
Quackenbush J
DOI：
10.1073/pnas.0409137102
发表时间：
2005-07-26
影响因子：
11.1
作者：
Löytynoja, A;Goldman, N
通讯作者：
Goldman, N