Extensive reorganization of the chloroplast genome of : A comparative analysis of their organization and evolution with other plastomes.

Introduction: The chloroplast (cp) is an autonomous plant organelle with an individual genome that encodes essential cellular functions. The genome architecture and gene content of the cp is highly conserved in angiosperms. The plastome of belongs to the Papaveraceae family, and the genome is comprised of unusual rearrangements and gene content. Thus far, no extensive comparative studies have been carried out to understand the evolution of chloroplast genomes.

Methods: Therefore, the cp genome was sequenced, and wide-scale comparative studies were conducted using publicly available twenty plastomes.

Results: Comparative analyses showed that an extensive genome rearrangement and IR expansion occurred, and these events evolved independently in the species. By contrast, the plastomes of its closely related subfamily Papaveroideae and other Ranunculales taxa are highly conserved. On the other hand, the synapomorphy characteristics of both and the gene loss events happened in the common ancestor of the and sub-clade of the lineage, respectively. The -sub clade species ( lost) are distributed predominantly in the Qinghai-Tibetan plateau (QTP) region. The phylogenetic analysis and divergence time estimation were also employed for the species.

Discussion: The divergence time of the gene in the sub-clade species (44.31 - 15.71 mya) coincides very well with the uplift of the Qinghai-Tibet Plateau in Oligocene and Miocene periods, and maybe during this period, it has probably triggered the radiation of the species.

Conclusion: To the best of the authors' knowledge, this is the first large-scale comparative study of plastomes and their evolution. The present study may provide insights into the plastome architecture and the molecular evolution of species.