The complete chloroplast genome of Onobrychis gaubae (Fabaceae - Papilionoideae): comparative analysis with related IR-lacking clade species

Background and Aim: Fabaceae (legumes) are the third largest family of angiosperms which have experienced a remarkable number of plastome rearrangements. The remarkable loss of the one of the plastid IR in the inverted repeat lacking clade (IRLC), a largest legume lineage, is an example of genome variation in papilionoids. This clade comprises ۵۲ genera and ca ۴۰۰۰ species divided into seven tribes. The existence of a diversity of changes in the organization and gene content of IRLC plastome have made it as an excellent model for genome evolution studies. High-throughput sequencing of chloroplast genomes has been used to gain insight into the evolutionary relationships of plant species. To date chloroplast genomes are available for members of all tribes of IRLC except tribe Hedysareae. In this study, we sequenced and analyzed the complete chloroplast genome of Onobrychis gaubae Bornm. ,as a member of tribe Hedysareae, using the next generation DNA sequencing technology and compared it with previously known genomes of the IRLC within Papilionoideae.Methods: The plastome of O. gaubae was reconstructed using Illumina next-generation sequencing. Its structure, repetitive sequences, gene content and sequence divergence were compared with those of other IRLC plastomes.Results: The genome is a circular structure of ۱۲۳,۶۴۵ bases and it lacks one copy of the inverted repeat. Gene prediction revealed ۱۱۰ unique genes, including ۷۶ protein-coding, ۳۰ tRNA, and four rRNA genes. The overall GC content of O. gaubae plastid genome is ۳۵.۱%.The plastome is characterized by loss of the rps۱۶ gene, intron of rps۱۲, and the first intron of clpP.Conclusion: The structural characteristics in chloroplast genome among IRLC species revealed that gene coding regions were more conserved than the noncoding regions, and IR was more conserved than LSC and SSC regions. Additionally, it was also observed that some intergenic spacers regions and some genes (such as ycf۱ and ycf۲) varied greatly. Some of these regions had also the highest level of nucleotide diversity. Comparative genomic analyses demonstrated the dynamic nature of the IRLC chloroplast genomes, which showed occurrence of numerous hypermutation loci and frequent gene losses and consequently elucidated the complex evolutionary history of chloroplast genomes.

Keywords:

Chloroplast genome , Onobrychis gaubae , IRLC