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

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 (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. 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.

Comparative chloroplast genome analysis of Ficus (Moraceae): Insight into adaptive evolution and mutational hotspot regions

“…Our results indicated that chloroplast genes clpP , rbcL , and ccsA were subjected to positive selection, indicating that they may have contributed to environmental adaptation in Ficus . The clpP gene, which encodes clpP protease, is also positively selected in several angiosperm lineages, such as Paphiopedilum (Orchidaceae) ( Guo et al, 2021 ), Acacia (Fabaceae) ( Dugas et al, 2015 ), and Bupleurum (Apiaceae) ( Huang et al, 2021b ), and shows hypervariability in Amaryllidaceae and Papilionoideae ( Liu et al, 2022 ; Moghaddam et al, 2022 ), suggesting it may have accelerated substitution rates in many angiosperms. Functional studies have also indicated that clpP protease degrades or restores damaged proteins ( Wicke et al, 2011 ), and is important for changes in plant development in response to stress ( Erixon and Oxelman, 2008 ).…”

Complete Chloroplast Genome of the Inverted Repeat-Lacking Species Vicia bungei and Development of Polymorphic Simple Sequence Repeat Markers

“…Instead, the gene is either transferred to the nuclear genome, or its function is replaced by a nuclear gene ( Wang et al, 2018 ). Recent sequencing and analyses of some IRLC plastomes ( Kim et al, 2005 ; Li et al, 2018 ; Moghaddam et al, 2022 ) have revealed important evolutionary patterns in this clade, including loss of the genes rpl22 and rps16 , the deletion of one intron of clpP ( Jansen et al, 2008 ; Li et al, 2020 ), multiple sequence inversions ( Schwarz et al, 2015 ; Williams et al, 2015 ), and gene transfers to the nucleus ( Moghaddam and Kazempour-Osaloo, 2020 ; Wu et al, 2021 ). Vicia bungei plastome lacked one intron of clpP , which was consistent with the finding of Jansen et al (2008) and confirmed the parallel loss of this clpP intron in V. bungei and in members of the papilionoid IRLC.…”

“…Some Fabaceae plastomes have been highly rearranged owing to multiple rounds of translocations and/or inversions. As a result, the plastomes of the IRLC have undergone considerable diversification in both gene order and gene/intron content ( Wang et al, 2018 ; Li et al, 2020 ; Xin and Yang, 2020 ; Moghaddam et al, 2022 ).…”

Full-length chloroplast genome of Dongxiang wild rice reveals small single-copy region switching

“…seed plants) exhibit a higher degree of conservation with respect to their gene content, structure and organization (Asaf et al, 2017). Most cpDNAs encode about 80 protein-coding genes that are primarily involved in photosynthesis and other biochemical processes, along with 4 rRNA and 30 tRNA genes (Moghaddam et al, 2022). A plant cpDNA typically has a circular structure and includes a large single-copy region (LSC), a small single-copy region (SSC) and two inverted repeats (denoted as IR1 and IR2) separating the LSC and SSC.…”