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

Sancho, Rubén; Cantalapiedra, Carlos P.; López-Alvarez, Diana; Gordon, Sean P.; Vogel, John P.; Catalán, Pilar; Contreras-Moreira, Bruno

doi:10.1111/nph.14926

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

Journal Article · 05 December 2017 · New Phytologist

DOI:https://doi.org/10.1111/nph.14926· OSTI ID:1529113

Sancho, Rubén ^[1]; Cantalapiedra, Carlos P. ^[2]; López-Alvarez, Diana ^[3]; Gordon, Sean P. ^[4]; Vogel, John P. ^[5]; Catalán, Pilar ^[1]; Contreras-Moreira, Bruno ^[6]

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
Department of Genetics and Plant Breeding, Estación Experimental de Aula Dei-Consejo Superior de Investigaciones Científicas, Zaragoza Spain
Department of Agricultural and Environmental Sciences, High Polytechnic School of Huesca, University of Zaragoza, Huesca Spain
DOE Joint Genome Institute, Walnut Creek CA 94598 USA
DOE Joint Genome Institute, Walnut Creek CA 94598 USA; Department of Plant and Microbial Biology, University of California, Berkeley CA 94720 USA
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

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.

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC)

Sponsoring Organization:: USDOE Office of Science (SC)

DOE Contract Number:: AC02-05CH11231

OSTI ID:: 1529113

Journal Information:: New Phytologist, Vol. 218, Issue 4; ISSN 0028-646X

Country of Publication:: United States

Language:: English

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