Resolving interspecific relationships within evolutionarily young lineages using RNA-seq data: An example from Pedicularis section Cyathophora (Orobanchaceae)
Phylogenomics has shown great potential in resolving evolutionary relationships at different taxonomical levels. However, it remains controversial whether all orthologous genes under different selective pressures can be concatenated for phylogenomic reconstruction. Here we used sect. Cyathophora of...
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Online Access: | http://ir.ibcas.ac.cn/handle/2S10CLM1/22130 https://doi.org/10.1038/srep42328 |
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ftchiacadscibcas:oai:ir.ibcas.ac.cn:2S10CLM1/22130 2023-05-15T15:13:47+02:00 Resolving interspecific relationships within evolutionarily young lineages using RNA-seq data: An example from Pedicularis section Cyathophora (Orobanchaceae) Wang, Hong-Juan Li, Wei-Tao Liu, Ya-Nan Yang, Fu-Sheng Wang, Xiao-Quan 2017 http://ir.ibcas.ac.cn/handle/2S10CLM1/22130 https://doi.org/10.1038/srep42328 英语 eng ACADEMIC PRESS INC ELSEVIER SCIENCE MOLECULAR PHYLOGENETICS AND EVOLUTION http://ir.ibcas.ac.cn/handle/2S10CLM1/22130 doi:10.1038/srep42328 cn.org.cspace.api.content.CopyrightPolicy@2507d767 Non-neutral gene Phylogenomics Phylogeny Recent radiation Selective pressure Transcriptome Science & Technology - Other Topics COPY NUCLEAR GENES PHYLOGENETIC ANALYSES TRANSCRIPTOME ANALYSIS FLORAL DIVERSITY SNP DISCOVERY GENOMIC DATA RADSEQ DATA RADIATION GENERATION ORIGIN Article 期刊论文 2017 ftchiacadscibcas https://doi.org/10.1038/srep42328 2022-06-12T18:14:25Z Phylogenomics has shown great potential in resolving evolutionary relationships at different taxonomical levels. However, it remains controversial whether all orthologous genes under different selective pressures can be concatenated for phylogenomic reconstruction. Here we used sect. Cyathophora of Pedicularis, one of the most species-rich genera of angiosperms in the alpine and arctic regions of the Northern Hemisphere, as a model to investigate the efficiency of RNA-seq in resolving relationships of closely related congeneric species. Flower transcriptomes were sequenced for all species of sect. Cyathophora and two outgroup species. Forty-one highly conserved single-/low-copy nuclear genes and 1553 orthologous groups (OGs) were identified and concatenated into five datasets based on gene copy numbers and Ka/Ks values to reconstruct the phylogeny of section Cyathophora. We also tested how many genes minimally can resolve the interspecific relationships, and reconstructed the evolutionary history of some floral characters in sect. Cyathophora. The results showed that the five different datasets consistently resolved the interspecific relationships of sect. Cyathophora, and the interspecific relationships can be robustly reconstructed with maximal support when >= 20 single-/low-copy nuclear genes or 25 OGs are used. Our study suggests that all OGs under different selective pressures can be concatenated for phylogenomic reconstruction, and provides a successful and efficient use of RNA-seq in reconstructing interspecific relationships of a non-model plant group with recent radiations. (C) 2016 Elsevier Inc. All rights reserved. Article in Journal/Newspaper Arctic Institute of Botany: IBCAS OpenIR (Chinese Academy Of Sciences) Arctic Scientific Reports 7 1 |
institution |
Open Polar |
collection |
Institute of Botany: IBCAS OpenIR (Chinese Academy Of Sciences) |
op_collection_id |
ftchiacadscibcas |
language |
English |
topic |
Non-neutral gene Phylogenomics Phylogeny Recent radiation Selective pressure Transcriptome Science & Technology - Other Topics COPY NUCLEAR GENES PHYLOGENETIC ANALYSES TRANSCRIPTOME ANALYSIS FLORAL DIVERSITY SNP DISCOVERY GENOMIC DATA RADSEQ DATA RADIATION GENERATION ORIGIN |
spellingShingle |
Non-neutral gene Phylogenomics Phylogeny Recent radiation Selective pressure Transcriptome Science & Technology - Other Topics COPY NUCLEAR GENES PHYLOGENETIC ANALYSES TRANSCRIPTOME ANALYSIS FLORAL DIVERSITY SNP DISCOVERY GENOMIC DATA RADSEQ DATA RADIATION GENERATION ORIGIN Wang, Hong-Juan Li, Wei-Tao Liu, Ya-Nan Yang, Fu-Sheng Wang, Xiao-Quan Resolving interspecific relationships within evolutionarily young lineages using RNA-seq data: An example from Pedicularis section Cyathophora (Orobanchaceae) |
topic_facet |
Non-neutral gene Phylogenomics Phylogeny Recent radiation Selective pressure Transcriptome Science & Technology - Other Topics COPY NUCLEAR GENES PHYLOGENETIC ANALYSES TRANSCRIPTOME ANALYSIS FLORAL DIVERSITY SNP DISCOVERY GENOMIC DATA RADSEQ DATA RADIATION GENERATION ORIGIN |
description |
Phylogenomics has shown great potential in resolving evolutionary relationships at different taxonomical levels. However, it remains controversial whether all orthologous genes under different selective pressures can be concatenated for phylogenomic reconstruction. Here we used sect. Cyathophora of Pedicularis, one of the most species-rich genera of angiosperms in the alpine and arctic regions of the Northern Hemisphere, as a model to investigate the efficiency of RNA-seq in resolving relationships of closely related congeneric species. Flower transcriptomes were sequenced for all species of sect. Cyathophora and two outgroup species. Forty-one highly conserved single-/low-copy nuclear genes and 1553 orthologous groups (OGs) were identified and concatenated into five datasets based on gene copy numbers and Ka/Ks values to reconstruct the phylogeny of section Cyathophora. We also tested how many genes minimally can resolve the interspecific relationships, and reconstructed the evolutionary history of some floral characters in sect. Cyathophora. The results showed that the five different datasets consistently resolved the interspecific relationships of sect. Cyathophora, and the interspecific relationships can be robustly reconstructed with maximal support when >= 20 single-/low-copy nuclear genes or 25 OGs are used. Our study suggests that all OGs under different selective pressures can be concatenated for phylogenomic reconstruction, and provides a successful and efficient use of RNA-seq in reconstructing interspecific relationships of a non-model plant group with recent radiations. (C) 2016 Elsevier Inc. All rights reserved. |
format |
Article in Journal/Newspaper |
author |
Wang, Hong-Juan Li, Wei-Tao Liu, Ya-Nan Yang, Fu-Sheng Wang, Xiao-Quan |
author_facet |
Wang, Hong-Juan Li, Wei-Tao Liu, Ya-Nan Yang, Fu-Sheng Wang, Xiao-Quan |
author_sort |
Wang, Hong-Juan |
title |
Resolving interspecific relationships within evolutionarily young lineages using RNA-seq data: An example from Pedicularis section Cyathophora (Orobanchaceae) |
title_short |
Resolving interspecific relationships within evolutionarily young lineages using RNA-seq data: An example from Pedicularis section Cyathophora (Orobanchaceae) |
title_full |
Resolving interspecific relationships within evolutionarily young lineages using RNA-seq data: An example from Pedicularis section Cyathophora (Orobanchaceae) |
title_fullStr |
Resolving interspecific relationships within evolutionarily young lineages using RNA-seq data: An example from Pedicularis section Cyathophora (Orobanchaceae) |
title_full_unstemmed |
Resolving interspecific relationships within evolutionarily young lineages using RNA-seq data: An example from Pedicularis section Cyathophora (Orobanchaceae) |
title_sort |
resolving interspecific relationships within evolutionarily young lineages using rna-seq data: an example from pedicularis section cyathophora (orobanchaceae) |
publisher |
ACADEMIC PRESS INC ELSEVIER SCIENCE |
publishDate |
2017 |
url |
http://ir.ibcas.ac.cn/handle/2S10CLM1/22130 https://doi.org/10.1038/srep42328 |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic |
genre_facet |
Arctic |
op_relation |
MOLECULAR PHYLOGENETICS AND EVOLUTION http://ir.ibcas.ac.cn/handle/2S10CLM1/22130 doi:10.1038/srep42328 |
op_rights |
cn.org.cspace.api.content.CopyrightPolicy@2507d767 |
op_doi |
https://doi.org/10.1038/srep42328 |
container_title |
Scientific Reports |
container_volume |
7 |
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1 |
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1766344301249298432 |