000171657 001__ 171657 000171657 005__ 20260527123126.0 000171657 0247_ $$2doi$$a10.1186/s12870-026-08570-2 000171657 0248_ $$2sideral$$a149393 000171657 037__ $$aART-2026-149393 000171657 041__ $$aeng 000171657 100__ $$aCampos, Miguel 000171657 245__ $$aPlastome evolution in annual Brachypodium species reveals widespread heteroplasmy and chloroplast capture, lineage-specific codon usage bias, and low positive selection 000171657 260__ $$c2026 000171657 5060_ $$aAccess copy available to the general public$$fUnrestricted 000171657 5203_ $$aBackground Comparative genomics and plastome phylogenomics have advanced significantly in recent years, highlighting the diversity, possible admixture, and non-neutral evolution of the predominantly considered non-recombinant chloroplast genomes in angiosperms. The grass genus Brachypodium serves as a powerful model for studying evolutionary processes in monocots. Results We analyzed 287 plastomes across the native circum-Mediterranean range of the three annual Brachypodium species (B. distachyon, B. stacei, B. hybridum), focusing on their structural variation, selection patterns and phylogenomic relationships. Our analyses confirmed the differentiation of the S and D plastomes, inherited respectively from the diploid progenitor species B. stacei and B. distachyon. We identified novel structural rearrangements and indels, and unique repeat motifs, along with widespread heteroplasmy, particularly in ancestral B. hybridum-D plastotypes. SNP diversity varied among plastotypes, reflecting population dynamics and evolutionary histories, with B. hybridum-D plastotypes showing the highest normalized diversity and B. hybridum-S the lowest. Positive selection was detected in 29 plastid genes by Tajima’s neutrality test, and in nine genes by site and branch-site evolutionary models, including matK, ndhF, rbcL, and rpoC2. Phylogenomic analyses revealed well-supported clades corresponding to the S and D plastome lineages, with frequent chloroplast capture events and long-distance dispersals shaping their evolutionary trajectories. Conclusions These findings highlight the evolutionary complexity of the Brachypodium panplastome, emphasizing the roles of heteroplasmy, structural variation, and adaptive evolution in shaping plastome diversity in this group of model grasses. While the ancestral plastomes of B. hybridum-D show evidence of heteroplasmy caused by introgressive hybridization and recombination, most of the heteroplasmic patterns in the other plastome groups can be attributed to somatic mutations. The topological congruence of phylogenies based on neutrally evolving whole plastome sequences and the majority of the plastid encoding gene sequences, including positively selected genes like ndhF, underscores the robustness of plastome-based phylogenies even under selective pressures. Together, these results shed new light on the evolutionary complexity of plastid genomes in a model polyploid system, demonstrating the interplay of structural divergence, heteroplasmy, hybridization, and selection in shaping plastome diversity. Our work thus provides a valuable comparative framework for future evolutionary, ecological, and functional genomic studies in Brachypodium and other grasses. 000171657 536__ $$9info:eu-repo/grantAgreement/ES/DGA-FSE/A01-23R$$9info:eu-repo/grantAgreement/ES/MICINN/PID2019-108195GB-I00$$9info:eu-repo/grantAgreement/ES/MICINN/PID2022-140074NB-I00 000171657 540__ $$9info:eu-repo/semantics/openAccess$$aby-nc-nd$$uhttps://creativecommons.org/licenses/by-nc-nd/4.0/deed.es 000171657 655_4 $$ainfo:eu-repo/semantics/article$$vinfo:eu-repo/semantics/publishedVersion 000171657 700__ $$aVogel, John P. 000171657 700__ $$0(orcid)0000-0002-8731-1009$$aPérez-Collazos, Ernesto$$uUniversidad de Zaragoza 000171657 700__ $$0(orcid)0000-0001-7793-5259$$aCatalán, Pilar$$uUniversidad de Zaragoza 000171657 7102_ $$15011$$2063$$aUniversidad de Zaragoza$$bDpto. CC.Agrar.y Medio Natural$$cÁrea Botánica 000171657 773__ $$g26, 788 (2026), [24 pp.]$$pBMC PLANT BIOLOGY$$tBMC PLANT BIOLOGY$$x1471-2229 000171657 8564_ $$s4179754$$uhttps://zaguan.unizar.es/record/171657/files/texto_completo.pdf$$yVersión publicada 000171657 8564_ $$s2336592$$uhttps://zaguan.unizar.es/record/171657/files/texto_completo.jpg?subformat=icon$$xicon$$yVersión publicada 000171657 909CO $$ooai:zaguan.unizar.es:171657$$particulos$$pdriver 000171657 951__ $$a2026-05-27-11:25:55 000171657 980__ $$aARTICLE