文献类型：期刊文献

英文题名：Mining from transcriptomes: 315 single-copy orthologous genes concatenated for the phylogenetic analyses of Orchidaceae

作者：Deng, Hua[1] Zhang, Guo-Qiang[2,3] Lin, Min[2,3] Wang, Yan[1] Liu, Zhong-Jian[2,3,4,5]

通信作者：Wang, Y[1]

机构：[1]Chinese Acad Forestry, Res Inst Forestry, State Key Lab Tree Genet & Breeding, Key Lab Tree Breeding & Cultivat State Forestry A, Beijing 100091, Peoples R China;[2]Natl Orchid Conservat Ctr China, Shenzhen Key Lab Orchid Conservat & Utilizat, Shenzhen 518114, Peoples R China;[3]Orchid Conservat & Res Ctr Shenzhen, Shenzhen 518114, Peoples R China;[4]Tsinghua Univ, Grad Sch Shenzhen, Ctr Biotechnol & BioMed, Shenzhen 518057, Peoples R China;[5]South China Agr Univ, Coll Forestry, Guangzhou 510642, Guangdong, Peoples R China

年份：2015

卷号：5

期号：17

起止页码：3800-3807

外文期刊名：ECOLOGY AND EVOLUTION

收录：;Scopus(收录号：2-s2.0-84941178301);WOS:【SCI-EXPANDED(收录号:WOS:000361010200023)】；

基金：This study was supported by the Innovation Fund for Forestry Technology of Guangdong (No. 2011KJCX009).

语种：英文

外文关键词：Orchidaceae; phylogeny; RNA sequences; single-copy orthologous genes

摘要：Phylogenetic relationships are hotspots for orchid studies with controversial standpoints. Traditionally, the phylogenies of orchids are based on morphology and subjective factors. Although more reliable than classic phylogenic analyses, the current methods are based on a few gene markers and PCR amplification, which are labor intensive and cannot identify the placement of some species with degenerated plastid genomes. Therefore, a more efficient, labor-saving and reliable method is needed for phylogenic analysis. Here, we present a method of orchid phylogeny construction using transcriptomes. Ten representative species covering five subfamilies of Orchidaceae were selected, and 315 single-copy orthologous genes extracted from the transcriptomes of these organisms were applied to reconstruct a more robust phylogeny of orchids. This approach provided a rapid and reliable method of phylogeny construction for Orchidaceae, one of the most diversified family of angiosperms. We also showed the rigorous systematic position of holomycotrophic species, which has previously been difficult to determine because of the degenerated plastid genome. We concluded that the method presented in this study is more efficient and reliable than methods based on a few gene markers for phylogenic analyses, especially for the holomycotrophic species or those whose DNA sequences have been difficult to amplify. Meanwhile, a total of 315 single-copy orthologous genes of orchids are offered and more informative loci could be used in the future orchid phylogenetic studies.