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Transcriptome sequencing and phylogenomic resolution within Spalacidae (Rodentia).
Gong-Hua Lin, Kun Wang, Xiao-Gong Deng
1Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China. zhangtz@nwipb.cas.cn.
BMC Genomics
|January 21, 2014
Summary
Phylogenomic analysis reveals zokors (Myospalacinae) are closely related to bamboo rats (Rhizomyinae), resolving evolutionary relationships within Spalacidae. This study provides crucial data for understanding subterranean mammal evolution.
Area of Science:
- Evolutionary Biology
- Genomics
- Mammalogy
Background:
- Subterranean mammals exhibit specialized traits, making them key subjects for evolutionary studies.
- Phylogenetic relationships among Spalacidae subfamilies (zokors, blind mole rats, bamboo rats) are unclear due to conflicting morphological and molecular data.
- Previous studies lacked comprehensive genomic data for resolving these relationships.
Purpose of the Study:
- To resolve the phylogenetic relationships among the three subfamilies within the family Spalacidae.
- To characterize the transcriptomes of zokors (Myospalacinae) and bamboo rats (Rhizomyinae).
- To utilize phylogenomic approaches for understanding the evolutionary history of subterranean mammals.
Main Methods:
- De novo transcriptome sequencing of brain and liver tissues from plateau zokor (Eospalax baileyi) and hoary bamboo rat (Rhizomys pruinosus).
- Analysis of RNA-seq data alongside a published transcriptome of the Middle East blind mole rat (Spalax galili).
- Phylogenomic analysis using 5,116 nuclear orthologous genes and mitochondrial genes, with mouse as an outgroup.
Main Results:
- Generated millions of clean reads, assembled into hundreds of thousands of unigenes for both species.
- Identified 5,116 nuclear orthologous genes across the three spalacids and mouse.
- Phylogenetic analysis consistently showed a sister group relationship between zokors and bamboo rats, indicating Myospalacinae is closely related to Rhizomyinae.
Conclusions:
- This study presents the first transcriptome data for zokors and bamboo rats, a valuable resource for comparative genomics.
- Phylogenomic analysis definitively resolves the interrelationships of the Spalacidae subfamilies.
- The findings underscore the effectiveness of phylogenomics in deciphering rapid evolutionary radiations.
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