Unravelling the plastome complexity of Brachypodium distachyon complex

Using whole genome sequencing, we analyzed 287 Brachypodium individuals to study chloroplast genome variation. DNA was extracted and sequenced using Illumina technology. Chloroplast genomes were assembled and annotated, identifying structural differences and SSR motifs. Codon usage and genes under selection were analyzed with MEGA11, and gene expression was quantified using RNA-seq data normalized by TMM. Phylogenomic trees were constructed with IQ-TREE, and haplotype networks were visualized using NETWORK, revealing genetic diversity and evolutionary patterns in Brachypodium plastomes.