RESEARCH ARTICLE

nri Background chloroplast evolution can also potentially layout the basis Hu et al. BMC Genomics (2015) 16:306 DOI 10.1186/s12864-015-1498-0large inverted repeat regions (IRA and IRB) separated by38010 S Michele all’Adige (TN), Italy Full list of author information is available at the end of the articleChloroplast genomes, hereafter referred to as plastomes, have been widely used as models for elucidating the pat-terns of genetic variation in space and time, ranging from colonization to speciation and phylogeny, encompassing both micro- and macro-evolutionary events across all line-ages of plants [1]. Understanding the phyletic patterns of of species discrimination [2], as indicated by the fact that the core DNA barcode chosen for plants is composed by the two plastomic regions rbcL and matK [3]. In fact, the presence of a high number of plastomes per cell, ease of amplification across the angiosperm phylogeny, and good content in terms of phylogenetic information explain the popularity of these and other plastidial markers for both species identification and phylogenetic reconstruction. The organization of the plastome is remarkably conserved in higher plants, and it is characterized by two usuall