Transcriptome sequencing and phylogenomic resolution within Spalacidae (Rodentia)

Gong Hua Lin, Kun Wang, Xiao Gong Deng, Eviatar Nevo, Fang Zhao, Jian Ping Su, Song Chang Guo, Tong Zuo Zhang, Huabin Zhao

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish
Article number32
JournalBMC Genomics
Issue number1
StatePublished - 17 Jan 2014

Bibliographical note

Funding Information:
Financial support for this study was provided by the Knowledge Innovation Project of the Chinese Academy of Science (CAS) (KSCX2-EW-J-26) and the General Programs of the National Natural Science Foundation of China (Projects 31101628 and 31071915). We thank Peng Shi in Kunming Institute of Zoology, CAS for kindly sharing bamboo rat transcriptome data. HZ was supported by a start-up fund from Wuhan University.


  • Mitochondrial genome
  • Phylogenomics
  • Spalacidae
  • Subterranean rodents
  • Transcriptome

ASJC Scopus subject areas

  • Biotechnology
  • Genetics


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