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

Mahtab Moghaddam; Atsushi Ohta; Motoki Shimizu; Ryohei Terauchi; Shahrokh Kazempour-Osaloo

doi:10.1186/s12870-022-03465-4

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

BMC Plant Biol. 2022 Feb 19;22(1):75. doi: 10.1186/s12870-022-03465-4.

Authors

Mahtab Moghaddam¹, Atsushi Ohta², Motoki Shimizu³, Ryohei Terauchi^{2

3}, Shahrokh Kazempour-Osaloo⁴

Affiliations

¹ Department of Plant Biology, Faculty of Biological Sciences, Tarbiat Modares University, 14115-154, Tehran, Iran. mahtabmoghaddam@modares.ac.ir.
² Graduate School of Agriculture, Kyoto University, Kyoto, 617-0001, Japan.
³ Iwate Biotechnology Research Center, Kitakami, Iwate, 024-0003, Japan.
⁴ Department of Plant Biology, Faculty of Biological Sciences, Tarbiat Modares University, 14115-154, Tehran, Iran. skosaloo@modares.ac.ir.

Abstract

Background: Plastome (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.

Results: In 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 (IR_b) 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.

Conclusions: Our 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.

Keywords: Hypervariable region; IRLC; Onobrychis; Phylogenetic relationship; Plastome.

Publication types

Comparative Study

MeSH terms

Codon Usage
Fabaceae / genetics*
Genome, Chloroplast*
Genome, Plant
High-Throughput Nucleotide Sequencing
Iran
Phylogeny*
Repetitive Sequences, Nucleic Acid
Selection, Genetic