Research Comparative plastome genomics and phylogenomics of Brachypodium: flowering time signatures, introgression and recombination in recently diverged ecotypes Ruben Sancho1,2, Carlos P. Cantalapiedra3, Diana Lopez-Alvarez 1, Sean P. Gordon4, John P. Vogel4,5, Pilar Catalan1,2 and Bruno Contreras-Moreira2,3,6 1Department of Agricultural and Environmental Sciences, High Polytechnic School of Huesca, University of Zaragoza, Huesca, Spain; 2Grupo de Bioquımica, Biofısica y Biologıa Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Saragossa, Spain; 3Department of Genetics and Plant Breeding, Estacion Experimental de Aula Dei-Consejo Superior de Investigaciones Cientıficas, Zaragoza, Spain; 4DOE Joint Genome Institute, Walnut Creek, CA 94598, USA; 5Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA; 6Fundacion ARAID, Zaragoza, Spain Summary Authors for correspondence: Few pan-genomic studies have been conducted in plants, and none of them have focused Pilar Catalan on the intraspecific diversity and evolution of their plastid genomes. Tel: +34 974232465 We address this issue in Brachypodium distachyon and its close relatives B. stacei and Email:
[email protected] B. hybridum, for which a large genomic data set has been compiled. We analyze inter- and Bruno Contreras-Moreira intraspecific plastid comparative genomics and phylogenomic relationships within a family- Tel: +34 976716089 wide framework. Email:
[email protected] Major indel differences were detected between Brachypodium plastomes. Within Received: 10 October 2016 B. distachyon, we detected two main lineages, a mostly Extremely Delayed Flowering (EDF+) Accepted: 3 March 2017 clade and a mostly Spanish (S+) – Turkish (T+) clade, plus nine chloroplast capture and two plastid DNA (ptDNA) introgression and micro-recombination events.