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Title

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

Other TitlesPan-plastome and phylogenomics of Brachypodium: flowering time signatures, introgression and recombination in recently diverged ecotypes
AuthorsSancho, Rubén; Cantalapiedra, Carlos P.; López-Alvarez, Diana; Gordon, Sean P.; Vogel, John P.; Catalán, Pilar; Contreras-Moreira, Bruno
KeywordsBrachypodium distachyon
B. stacei
B. hybridum
comparative cpDNA genomics
grass phylogenomics
intraspecific genealogy
nested dating analysis
plastid introgression and recombination
Issue DateDec-2017
PublisherJohn Wiley & Sons
CitationSancho R, Cantalapiedra CP, López-Alvarez D, Gordon SP, Vogel JP, Catalán P, Contreras-Moreira B. Pan-plastome and phylogenomics of Brachypodium: flowering time signatures, introgression and recombination in recently diverged ecotypes. New Phytologist, doi:10.1111/nph.14926 (2017)
AbstractFew 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.
Description99 pags.- Tabls.- Figs. This is the pre-peer reviewed version of the article doi 10.1111/nph.14926 which has been published in final form at http://onlinelibrary.wiley.com/doi/10.1111/nph.14926/abstract This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.
Publisher version (URL)http://dx.doi.org/10.1111/nph.14926
URIhttp://hdl.handle.net/10261/158372
ISSN0028-646X
E-ISSN1469-8137
Appears in Collections:(EEAD) Artículos
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