Abstract
BackgroundPlastome (Plastid genome) sequences provide valuable markers for surveying evolutionary relationships and population genetics of plant species. Papilionoideae (papilionoids) has different nucleotide and structural variations in plastomes, which makes it an ideal model for genome evolution studies. Therefore, by sequencing the complete chloroplast genome of Onobrychis gaubae in this study, the characteristics and evolutionary patterns of plastome variations in IR-loss clade were compared.ResultsIn the present study, the complete plastid genome of O. gaubae, endemic to Iran, was sequenced using Illumina paired-end sequencing and was compared with previously known genomes of the IRLC species of legumes. The O. gaubae plastid genome was 122,688 bp in length and included a large single-copy (LSC) region of 81,486 bp, a small single-copy (SSC) region of 13,805 bp and one copy of the inverted repeat (IRb) of 29,100 bp. The genome encoded 110 genes, including 76 protein-coding genes, 30 transfer RNA (tRNA) genes and four ribosome RNA (rRNA) genes and possessed 83 simple sequence repeats (SSRs) and 50 repeated structures with the highest proportion in the LSC. Comparative analysis of the chloroplast genomes across IRLC revealed three hotspot genes (ycf1, ycf2, clpP) which could be used as DNA barcode regions. Moreover, seven hypervariable regions [trnL(UAA)-trnT(UGU), trnT(GGU)-trnE(UUC), ycf1, ycf2, ycf4, accD and clpP] were identified within Onobrychis, which could be used to distinguish the Onobrychis species. Phylogenetic analyses revealed that O. gaubae is closely related to Hedysarum. The complete O. gaubae genome is a valuable resource for investigating evolution of Onobrychis species and can be used to identify related species.ConclusionsOur results reveal that the plastomes of the IRLC are dynamic molecules and show multiple gene losses and inversions. The identified hypervariable regions could be used as molecular markers for resolving phylogenetic relationships and species identification and also provide new insights into plastome evolution across IRLC.
Highlights
Plastome (Plastid genome) sequences provide valuable markers for surveying evolutionary relation‐ ships and population genetics of plant species
The O. viciifolia plastome with 121,932 bp in length is very similar in gene contents, order and orientation to O. gaubae
Most of the plastid genome inversions are found in the large single-copy (LSC) region [5], while plastome inversion in the O. viciifolia is located within the Inverted repeats (IRs) region
Summary
Plastome (Plastid genome) sequences provide valuable markers for surveying evolutionary relation‐ ships and population genetics of plant species. Papilionoideae (papilionoids) has different nucleotide and structural variations in plastomes, which makes it an ideal model for genome evolution studies. By sequencing the complete chloroplast genome of Onobrychis gaubae in this study, the characteristics and evolutionary patterns of plastome variations in IR-loss clade were compared. The chloroplast genome (plastome) typically has a circular structure that ranges from 120 to 180 kb in length. In contrast to mitochondrial and nuclear genomes, the plastomes across seed plants are highly conserved with respect to gene content, structure and organization [5, 6]. Mutations including duplications, rearrangements, and losses have been reported at the genome and gene levels among some angiosperm lineages, including Asteraceae [7], Campanulaceae [8], Onagraceae [9], Fabaceae [10] and Geraniaceae [11]
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