[Molecular authentication of Sailonggu and its resource distribution in Qinghai-Tibet Plateau].

To provide accurate information on geographic distribution of crude drug Sailonggu in the plateau, we identified zokor species (Eospalax spp.) in Qinghai-Tibet Plateau using molecular methods. Based on the mitochondrial cytochrome B (cytb) gene sequences, we then extracted haplotypes from these sequences and reconstructed phylogenetic trees for the haplotypes using both maximum likelihood (ML) and Bayesian inference (BI) methods. Based on the trees, the species of each sample were determined. Five hundred and three samples from 35 populations were sequenced and their whole cytb sequences (1140 bp) were obtained. From these sequences 150 haplotypes were detected, in which, 126 were Eospalax baileyi, 20 were E. cansus, and 4 were E. smithi of the 35 populations, 28 were E. baileyi type, 5 were E. cansus type, and the remaining 2 were mixed of E. baileyi + E. cansus (DT2) and E. baileyi + E. smithi (ZN3). The results showed that, the regions around the Qinghai lake and near the upper stream of Yellow River started at Guide could be viewed as the producing area of authentic Sailonggu, and also, the cytb gene is a powerful molecular marker to determine the species of zokors as well as for the authentication of geographic distribution of Sailonggu.

Transcriptome sequencing and phylogenomic resolution within Spalacidae (Rodentia).

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.