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Ecol Evol. 2015 Sep;5(17):3800-7. doi: 10.1002/ece3.1642. Epub 2015 Aug 20.

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

Author information

1
State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry Beijing, 100091, China.
2
Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen Shenzhen 518114, China.
3
Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen Shenzhen 518114, China ; The Center for Biotechnology and BioMedicine, Graduate School at Shenzhen, Tsinghua University Shenzhen 518055, China ; College of Forestry, South China Agricultural University Guangzhou 510642, China.

Abstract

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.

KEYWORDS:

Orchidaceae; RNA sequences; phylogeny; single-copy orthologous genes

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