Knowledge Management System of Northwest Institute of Plateau Biology, CAS
| Transcriptome sequencing and phylogenomic resolution within Spalacidae (Rodentia) | |
| Lin, Gong-Hua1; Wang, Kun2; Deng, Xiao-Gong1,3; Nevo, Eviatar4; Zhao, Fang1; Su, Jian-Ping1; Guo, Song-Chang1; Zhang, Tong-Zuo1; Zhao, Huabin5 | |
| 2014-01-17 | |
| 发表期刊 | BMC GENOMICS
 |
| ISSN | 1471-2164 |
| 卷号 | 15 |
| 文章类型 | Article |
| 摘要 | Background: Subterranean 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 performed de novo transcriptome 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. Results: Approximately 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. Conclusions: This 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.; Background: Subterranean 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 performed de novo transcriptome 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. |
| 关键词 | Spalacidae Phylogenomics Transcriptome Mitochondrial Genome Subterranean Rodents |
| WOS标题词 | Science & Technology ; Life Sciences & Biomedicine |
| 关键词[WOS] | MAXIMUM-LIKELIHOOD ; MUROID RODENTS ; MOLECULAR PHYLOGENY ; NUCLEOTIDE-SEQUENCES ; NUCLEAR GENE ; ORTHOLOGS ; DIVERGENCE ; POSITION ; MAMMALS ; GENOMES |
| 收录类别 | SCI |
| 语种 | 英语 |
| WOS研究方向 | Biotechnology & Applied Microbiology ; Genetics & Heredity |
| WOS类目 | Biotechnology & Applied Microbiology ; Genetics & Heredity |
| WOS记录号 | WOS:000330063000002 |
| 引用统计 | |
| 文献类型 | 期刊论文 |
| 条目标识符 | http://210.75.249.4/handle/363003/4262 |
| 专题 | 中国科学院西北高原生物研究所 |
| 作者单位 | 1.Chinese Acad Sci, Northwest Inst Plateau Biol, Key Lab Adaptat & Evolut Plateau Biota, Xining 810008, Peoples R China 2.Lanzhou Univ, Coll Life Sci, State Key Lab Grassland Agro Ecosyst, Lanzhou 730000, Peoples R China 3.Chinese Acad Sci, Grad Univ, Beijing 100049, Peoples R China 4.Univ Haifa, Inst Evolut, IL-31905 Haifa, Israel 5.Wuhan Univ, Coll Life Sci, Dept Zool, Wuhan 430072, Peoples R China |
| 推荐引用方式 GB/T 7714 | Lin, Gong-Hua,Wang, Kun,Deng, Xiao-Gong,et al. Transcriptome sequencing and phylogenomic resolution within Spalacidae (Rodentia)[J]. BMC GENOMICS,2014,15. |
| APA | Lin, Gong-Hua.,Wang, Kun.,Deng, Xiao-Gong.,Nevo, Eviatar.,Zhao, Fang.,...&Zhao, Huabin.(2014).Transcriptome sequencing and phylogenomic resolution within Spalacidae (Rodentia).BMC GENOMICS,15. |
| MLA | Lin, Gong-Hua,et al."Transcriptome sequencing and phylogenomic resolution within Spalacidae (Rodentia)".BMC GENOMICS 15(2014). |
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