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Genome-partitioning strategy, plastid and nuclear phylogenomic discordance, and its evolutionary implications of Clematis (Ranunculaceae)
Clematis is one of the largest genera of Ranunculaceae with many phylogenetic problems left to be resolved. Clematis species have considerable genome size of more than 7 Gbp, and there was no whole-genome reference sequence published in this genus. This raises difficulties in acquiring nuclear genom...
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Frontiers Media S.A.
2022
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9703796/ https://www.ncbi.nlm.nih.gov/pubmed/36452086 http://dx.doi.org/10.3389/fpls.2022.1059379 |
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author | Xiao, Jiamin Lyu, Rudan He, Jian Li, Mingyang Ji, Jiaxin Cheng, Jin Xie, Lei |
author_facet | Xiao, Jiamin Lyu, Rudan He, Jian Li, Mingyang Ji, Jiaxin Cheng, Jin Xie, Lei |
author_sort | Xiao, Jiamin |
collection | PubMed |
description | Clematis is one of the largest genera of Ranunculaceae with many phylogenetic problems left to be resolved. Clematis species have considerable genome size of more than 7 Gbp, and there was no whole-genome reference sequence published in this genus. This raises difficulties in acquiring nuclear genome data for its phylogenetic analysis. Previous studies based on Sanger sequencing data, plastid genome data, and nrDNA sequences did not well resolve the phylogeny of Clematis. In this study, we used genome skimming and transcriptome data to assemble the plastid genome sequences, nuclear single nucleotide polymorphisms (SNPs) datasets, and single-copy nuclear orthologous genes (SCOGs) to reconstruct the phylogenetic backbone of Clematis, and test effectiveness of these genome partitioning methods. We also further analyzed the discordance among nuclear gene trees and between plastid and nuclear phylogenies. The results showed that the SCOGs datasets, assembled from transcriptome method, well resolved the phylogenetic backbone of Clematis. The nuclear SNPs datasets from genome skimming method can also produce similar results with the SCOGs data. In contrast to the plastid phylogeny, the phylogeny resolved by nuclear genome data is more robust and better corresponds to morphological characters. Our results suggested that rapid species radiation may have generated high level of incomplete lineage sorting, which was the major cause of nuclear gene discordance. Our simulation also showed that there may have been frequent interspecific hybridization events, which led to some of the cyto-nuclear discordances in Clematis. This study not only provides the first robust phylogenetic backbone of Clematis based on nuclear genome data, but also provides suggestions of genome partitioning strategies for the phylogenomic study of other plant taxa. |
format | Online Article Text |
id | pubmed-9703796 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-97037962022-11-29 Genome-partitioning strategy, plastid and nuclear phylogenomic discordance, and its evolutionary implications of Clematis (Ranunculaceae) Xiao, Jiamin Lyu, Rudan He, Jian Li, Mingyang Ji, Jiaxin Cheng, Jin Xie, Lei Front Plant Sci Plant Science Clematis is one of the largest genera of Ranunculaceae with many phylogenetic problems left to be resolved. Clematis species have considerable genome size of more than 7 Gbp, and there was no whole-genome reference sequence published in this genus. This raises difficulties in acquiring nuclear genome data for its phylogenetic analysis. Previous studies based on Sanger sequencing data, plastid genome data, and nrDNA sequences did not well resolve the phylogeny of Clematis. In this study, we used genome skimming and transcriptome data to assemble the plastid genome sequences, nuclear single nucleotide polymorphisms (SNPs) datasets, and single-copy nuclear orthologous genes (SCOGs) to reconstruct the phylogenetic backbone of Clematis, and test effectiveness of these genome partitioning methods. We also further analyzed the discordance among nuclear gene trees and between plastid and nuclear phylogenies. The results showed that the SCOGs datasets, assembled from transcriptome method, well resolved the phylogenetic backbone of Clematis. The nuclear SNPs datasets from genome skimming method can also produce similar results with the SCOGs data. In contrast to the plastid phylogeny, the phylogeny resolved by nuclear genome data is more robust and better corresponds to morphological characters. Our results suggested that rapid species radiation may have generated high level of incomplete lineage sorting, which was the major cause of nuclear gene discordance. Our simulation also showed that there may have been frequent interspecific hybridization events, which led to some of the cyto-nuclear discordances in Clematis. This study not only provides the first robust phylogenetic backbone of Clematis based on nuclear genome data, but also provides suggestions of genome partitioning strategies for the phylogenomic study of other plant taxa. Frontiers Media S.A. 2022-11-14 /pmc/articles/PMC9703796/ /pubmed/36452086 http://dx.doi.org/10.3389/fpls.2022.1059379 Text en Copyright © 2022 Xiao, Lyu, He, Li, Ji, Cheng and Xie https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Plant Science Xiao, Jiamin Lyu, Rudan He, Jian Li, Mingyang Ji, Jiaxin Cheng, Jin Xie, Lei Genome-partitioning strategy, plastid and nuclear phylogenomic discordance, and its evolutionary implications of Clematis (Ranunculaceae) |
title | Genome-partitioning strategy, plastid and nuclear phylogenomic discordance, and its evolutionary implications of Clematis (Ranunculaceae) |
title_full | Genome-partitioning strategy, plastid and nuclear phylogenomic discordance, and its evolutionary implications of Clematis (Ranunculaceae) |
title_fullStr | Genome-partitioning strategy, plastid and nuclear phylogenomic discordance, and its evolutionary implications of Clematis (Ranunculaceae) |
title_full_unstemmed | Genome-partitioning strategy, plastid and nuclear phylogenomic discordance, and its evolutionary implications of Clematis (Ranunculaceae) |
title_short | Genome-partitioning strategy, plastid and nuclear phylogenomic discordance, and its evolutionary implications of Clematis (Ranunculaceae) |
title_sort | genome-partitioning strategy, plastid and nuclear phylogenomic discordance, and its evolutionary implications of clematis (ranunculaceae) |
topic | Plant Science |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9703796/ https://www.ncbi.nlm.nih.gov/pubmed/36452086 http://dx.doi.org/10.3389/fpls.2022.1059379 |
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