Open Access Research article

Transcriptome sequencing and phylogenomic resolution within Spalacidae (Rodentia)

Gong-Hua Lin1, Kun Wang2, Xiao-Gong Deng13, Eviatar Nevo4, Fang Zhao1, Jian-Ping Su1, Song-Chang Guo1, Tong-Zuo Zhang1* and Huabin Zhao5*

Author Affiliations

1 Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China

2 State Key Laboratory of Grassland Agro-ecosystem, College of Life Science, Lanzhou University, Lanzhou, China

3 Graduate University of the Chinese Academy of Sciences, Beijing 100049, China

4 Institute of Evolution, University of Haifa, Mount Carmel, Haifa 31905, Israel

5 Department of Zoology, College of Life Sciences, Wuhan University, Wuhan 430072, China

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BMC Genomics 2014, 15:32  doi:10.1186/1471-2164-15-32

Published: 17 January 2014

Abstract

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.

Keywords:
Spalacidae; Phylogenomics; Transcriptome; Mitochondrial genome; Subterranean rodents