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Title: Comparative plastome genomics and phylogenomics of Brachypodium : flowering time signatures, introgression and recombination in recently diverged ecotypes

Abstract

Few pan-genomic studies have been conducted in plants, and none of them have focused on the intraspecific diversity and evolution of their plastid genomes. We address this issue in Brachypodium distachyon and its close relatives B. stacei and B. hybridum, for which a large genomic data set has been compiled. We analyze inter- and intraspecific plastid comparative genomics and phylogenomic relationships within a family-wide framework. Major indel differences were detected between Brachypodium plastomes. Within B. distachyon, we detected two main lineages, a mostly Extremely Delayed Flowering (EDF+) clade and a mostly Spanish (S+) – Turkish (T+) clade, plus nine chloroplast capture and two plastid DNA (ptDNA) introgression and micro-recombination events. Early Oligocene (30.9 million yr ago (Ma)) and Late Miocene (10.1 Ma) divergence times were inferred for the respective stem and crown nodes of Brachypodium and a very recent Mid-Pleistocene(0.9 Ma) time for the B. distachyon split. Flowering time variation is a main factor driving rapid intraspecific divergence in B. distachyon, although it is counterbalanced by repeated introgression between previously isolated lineages. Swapping of plastomes between the three different genomic groups, EDF+,T+, S+, probably resulted from random backcrossing followed by stabilization through selection pressure.

Authors:
 [1];  [2];  [3];  [4];  [5];  [1];  [6]
  1. Department of Agricultural and Environmental Sciences, High Polytechnic School of Huesca, University of Zaragoza, Huesca Spain; Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Saragossa Spain
  2. Department of Genetics and Plant Breeding, Estación Experimental de Aula Dei-Consejo Superior de Investigaciones Científicas, Zaragoza Spain
  3. Department of Agricultural and Environmental Sciences, High Polytechnic School of Huesca, University of Zaragoza, Huesca Spain
  4. DOE Joint Genome Institute, Walnut Creek CA 94598 USA
  5. DOE Joint Genome Institute, Walnut Creek CA 94598 USA; Department of Plant and Microbial Biology, University of California, Berkeley CA 94720 USA
  6. Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Saragossa Spain; Department of Genetics and Plant Breeding, Estación Experimental de Aula Dei-Consejo Superior de Investigaciones Científicas, Zaragoza Spain; Fundación ARAID, Zaragoza Spain
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory-National Energy Research Scientific Computing Center (NERSC)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1529113
DOE Contract Number:  
AC02-05CH11231
Resource Type:
Journal Article
Journal Name:
New Phytologist
Additional Journal Information:
Journal Volume: 218; Journal Issue: 4; Journal ID: ISSN 0028-646X
Country of Publication:
United States
Language:
English

Citation Formats

Sancho, Rubén, Cantalapiedra, Carlos P., López-Alvarez, Diana, Gordon, Sean P., Vogel, John P., Catalán, Pilar, and Contreras-Moreira, Bruno. Comparative plastome genomics and phylogenomics of Brachypodium : flowering time signatures, introgression and recombination in recently diverged ecotypes. United States: N. p., 2017. Web. doi:10.1111/nph.14926.
Sancho, Rubén, Cantalapiedra, Carlos P., López-Alvarez, Diana, Gordon, Sean P., Vogel, John P., Catalán, Pilar, & Contreras-Moreira, Bruno. Comparative plastome genomics and phylogenomics of Brachypodium : flowering time signatures, introgression and recombination in recently diverged ecotypes. United States. https://doi.org/10.1111/nph.14926
Sancho, Rubén, Cantalapiedra, Carlos P., López-Alvarez, Diana, Gordon, Sean P., Vogel, John P., Catalán, Pilar, and Contreras-Moreira, Bruno. Tue . "Comparative plastome genomics and phylogenomics of Brachypodium : flowering time signatures, introgression and recombination in recently diverged ecotypes". United States. https://doi.org/10.1111/nph.14926.
@article{osti_1529113,
title = {Comparative plastome genomics and phylogenomics of Brachypodium : flowering time signatures, introgression and recombination in recently diverged ecotypes},
author = {Sancho, Rubén and Cantalapiedra, Carlos P. and López-Alvarez, Diana and Gordon, Sean P. and Vogel, John P. and Catalán, Pilar and Contreras-Moreira, Bruno},
abstractNote = {Few pan-genomic studies have been conducted in plants, and none of them have focused on the intraspecific diversity and evolution of their plastid genomes. We address this issue in Brachypodium distachyon and its close relatives B. stacei and B. hybridum, for which a large genomic data set has been compiled. We analyze inter- and intraspecific plastid comparative genomics and phylogenomic relationships within a family-wide framework. Major indel differences were detected between Brachypodium plastomes. Within B. distachyon, we detected two main lineages, a mostly Extremely Delayed Flowering (EDF+) clade and a mostly Spanish (S+) – Turkish (T+) clade, plus nine chloroplast capture and two plastid DNA (ptDNA) introgression and micro-recombination events. Early Oligocene (30.9 million yr ago (Ma)) and Late Miocene (10.1 Ma) divergence times were inferred for the respective stem and crown nodes of Brachypodium and a very recent Mid-Pleistocene(0.9 Ma) time for the B. distachyon split. Flowering time variation is a main factor driving rapid intraspecific divergence in B. distachyon, although it is counterbalanced by repeated introgression between previously isolated lineages. Swapping of plastomes between the three different genomic groups, EDF+,T+, S+, probably resulted from random backcrossing followed by stabilization through selection pressure.},
doi = {10.1111/nph.14926},
url = {https://www.osti.gov/biblio/1529113}, journal = {New Phytologist},
issn = {0028-646X},
number = 4,
volume = 218,
place = {United States},
year = {2017},
month = {12}
}

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