DOI: 10.5061/dryad.gs135
title: Data from: Transcriptome sequencing and phylogenomic resolution within Spalacidae (Rodentia)

description: Background: Subterranean mammals have been of great interest for
 evolutionary biologists because of their highly specialized traits for the
 life underground, however, the scarcity of genomic information limits our
 better understanding of their evolutionary history. Owing to the
 convergence of morphological traits and the incongruence of molecular
 data, 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 rat were 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 combined sequences of concatenated
 sequences of 5,116 nuclear genes (5,541,534 bp in length), fourfold
 degenerate sites of the 5,116 nuclear genes (715,762 bp) and concatenated
 sequences of 13 protein coding mitochondrial genes (11,307 bp). In this
 topology, notably, the branch leading to subfamilies Myospalacinae and
 Rhizomyinae is remarkably short, indicative of a burst of speciation
 within the family Spalacidae. Conclusions: This is the first report of
 transcriptome data 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.
description: tree files and sequence
 alignmentsThe
 tree_and_alignment.zip includes two folds, the treefile and the alignment.
 The fole "treefile" contains all trees reconstructed from the
 corresponding alignments in the "alignment" fold. For details
 please see the readme.txt file. All files can be opened by text editor
 such as Editplus or other free editor programs. Also, the tree files can
 be viewed by FigTree, and the alignments can be viewed by
 MEGA.tree_and_alignment.zip