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Complete Plastome Sequences from Glycine syndetika and Six Additional Perennial Wild Relatives of Soybean

Organelle sequences have a long history of utility in phylogenetic analyses. Chloroplast sequences when combined with nuclear data can help resolve relationships among flowering plant genera, and within genera incongruence can point to reticulate evolution. Plastome sequences are becoming plentiful...

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Autores principales: Sherman-Broyles, Sue, Bombarely, Aureliano, Grimwood, Jane, Schmutz, Jeremy, Doyle, Jeff
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Genetics Society of America 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4199708/
https://www.ncbi.nlm.nih.gov/pubmed/25155272
http://dx.doi.org/10.1534/g3.114.012690
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author Sherman-Broyles, Sue
Bombarely, Aureliano
Grimwood, Jane
Schmutz, Jeremy
Doyle, Jeff
author_facet Sherman-Broyles, Sue
Bombarely, Aureliano
Grimwood, Jane
Schmutz, Jeremy
Doyle, Jeff
author_sort Sherman-Broyles, Sue
collection PubMed
description Organelle sequences have a long history of utility in phylogenetic analyses. Chloroplast sequences when combined with nuclear data can help resolve relationships among flowering plant genera, and within genera incongruence can point to reticulate evolution. Plastome sequences are becoming plentiful because they are increasingly easier to obtain. Complete plastome sequences allow us to detect rare rearrangements and test the tempo of sequence evolution. Chloroplast sequences are generally considered a nuisance to be kept to a minimum in bacterial artificial chromosome libraries. Here, we sequenced two bacterial artificial chromosomes per species to generate complete plastome sequences from seven species. The plastome sequences from Glycine syndetika and six other perennial Glycine species are similar in arrangement and gene content to the previously published soybean plastome. Repetitive sequences were detected in high frequencies as in soybean, but further analysis showed that repeat sequence numbers are inflated. Previous chloroplast-based phylogenetic trees for perennial Glycine were incongruent with nuclear gene–based phylogenetic trees. We tested whether the hypothesis of introgression was supported by the complete plastomes. Alignment of complete plastome sequences and Bayesian analysis allowed us to date putative hybridization events supporting the hypothesis of introgression and chloroplast “capture.”
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spelling pubmed-41997082014-10-20 Complete Plastome Sequences from Glycine syndetika and Six Additional Perennial Wild Relatives of Soybean Sherman-Broyles, Sue Bombarely, Aureliano Grimwood, Jane Schmutz, Jeremy Doyle, Jeff G3 (Bethesda) Investigations Organelle sequences have a long history of utility in phylogenetic analyses. Chloroplast sequences when combined with nuclear data can help resolve relationships among flowering plant genera, and within genera incongruence can point to reticulate evolution. Plastome sequences are becoming plentiful because they are increasingly easier to obtain. Complete plastome sequences allow us to detect rare rearrangements and test the tempo of sequence evolution. Chloroplast sequences are generally considered a nuisance to be kept to a minimum in bacterial artificial chromosome libraries. Here, we sequenced two bacterial artificial chromosomes per species to generate complete plastome sequences from seven species. The plastome sequences from Glycine syndetika and six other perennial Glycine species are similar in arrangement and gene content to the previously published soybean plastome. Repetitive sequences were detected in high frequencies as in soybean, but further analysis showed that repeat sequence numbers are inflated. Previous chloroplast-based phylogenetic trees for perennial Glycine were incongruent with nuclear gene–based phylogenetic trees. We tested whether the hypothesis of introgression was supported by the complete plastomes. Alignment of complete plastome sequences and Bayesian analysis allowed us to date putative hybridization events supporting the hypothesis of introgression and chloroplast “capture.” Genetics Society of America 2014-08-25 /pmc/articles/PMC4199708/ /pubmed/25155272 http://dx.doi.org/10.1534/g3.114.012690 Text en Copyright © 2014 Sherman-Broyles et al. http://creativecommons.org/licenses/by/3.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution Unported License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Investigations
Sherman-Broyles, Sue
Bombarely, Aureliano
Grimwood, Jane
Schmutz, Jeremy
Doyle, Jeff
Complete Plastome Sequences from Glycine syndetika and Six Additional Perennial Wild Relatives of Soybean
title Complete Plastome Sequences from Glycine syndetika and Six Additional Perennial Wild Relatives of Soybean
title_full Complete Plastome Sequences from Glycine syndetika and Six Additional Perennial Wild Relatives of Soybean
title_fullStr Complete Plastome Sequences from Glycine syndetika and Six Additional Perennial Wild Relatives of Soybean
title_full_unstemmed Complete Plastome Sequences from Glycine syndetika and Six Additional Perennial Wild Relatives of Soybean
title_short Complete Plastome Sequences from Glycine syndetika and Six Additional Perennial Wild Relatives of Soybean
title_sort complete plastome sequences from glycine syndetika and six additional perennial wild relatives of soybean
topic Investigations
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4199708/
https://www.ncbi.nlm.nih.gov/pubmed/25155272
http://dx.doi.org/10.1534/g3.114.012690
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