Insight into chloroplast genome structural variation of the Mongolian endemic species Adonis mongolica (Ranunculaceae) in the Adonideae tribe

Abstract

Adonis mongolica is a threatened species that is endemic to Mongolia. It is a medicinal plant from the Adonis genus and has been used to treat heart diseases. However, the genomics and evolution of this species have not been thoroughly studied. We sequenced the first complete plastome of A. mongolica and compared it with ten Adonideae species to describe the plastome structure and infer phylogenetic relationships. The complete plastome of A. mongolica was 157,521 bp long and had a typical quadripartite structure with numerous divergent regions. The plastomes of Adonideae had relatively constant genome structures and sizes, except for those of Adonis. The plastome structure was consistent across Adonis. We identified a 44.8 kb large-scale inversion within the large single-copy region and rpl32 gene loss in the Adonis plastomes compared to other members of the Adonideae tribe. Additionally, Adonis had a smaller plastome size (156,917–157,603 bp) than the other genera within the tribe (159,666–160,940 bp), which was attributed to deletions of intergenic regions and partial and complete gene losses. These results suggested that an intramolecular mutation occurred in the ancestor of the Adonis genus. Based on the phylogenetic results, Adonis separated earlier than the other genera within the Adonideae tribe. The genome structures and divergences of specific regions in the Adonis genus were unique to the Adonideae tribe. This study provides fundamental knowledge for further genomic research in Mongolia and a better understanding of the evolutionary history of endemic plants.

Extreme Reconfiguration of Plastid Genomes in Papaveraceae: Rearrangements, Gene Loss, Pseudogenization, IR Expansion, and Repeats

“…For other closely related Ranunculales taxa, Sun et al [43] reported plastid rearrangements of Circaeasteraceae, and found an inversion of approximately 49 kb and 3.5 kb in the LSC region, with pseudogenizations or losses of the accD and ndh genes. Nevertheless, the plastomes of Eupteleaceae, Lardizabalaceae, Menispermaceae, Berberidaceae, and Ranunculaceae were generally conserved [44,45], with the exception of several genera, such as in the cases of the inversion of a 44.8 kb segment in the LSC region and loss of the rpl32 gene in Adonis [46], and the small expansion of the IR region in Mahonia and Asteropyrum [47,48].…”

The complete chloroplast genome and phylogentic results support the species position of Swertia banzragczii and Swertia marginata (Gentianaceae) in Mongolia

“…Therefore, more genomic studies are needed for reconstructing the phylogenetic relationships of Swertia . Recently, the chloroplast genome has been widely used in plant system evolution, related species identification, genetic diversity analysis, chloroplast genetic engineering, and other applications due to the development of high-throughput sequencing technology (Yang et al 2016 ; Li et al 2021 ; Fang et al 2023 ; Nyamgerel et al 2023 , 2024 ). The chloroplast genome (plastome) has a conserved structure, encodes 120–130 genes, most of which encode part of the photosynthetic apparatus of the organelle (Jensen and Leister 2014 ), and is maternally inherited (Wicke et al 2011 ).…”

The complete chloroplast genome, DNA barcoding, and taxonomic notes of Swertiabanzragczii and Swertia marginata (Gentianaceae) in Mongolia

“…The development of barcoding markers has greatly advanced our understanding of the relationships between morphologically similar species; however, it has been revealed that Swertia is strongly paraphyletic to other genera within the Gentianaceae family (Chassot et al 2001; Xi et al 2014). Recently, the chloroplast genome has been widely used in plant system evolution, related species identi cation, genetic diversity analysis, chloroplast genetic engineering, and other applications due to the development of high-throughput sequencing technology (Yang et al 2016;Li et al 2021;Fang et al 2023;Nyamgerel et al 2023). The chloroplast genome (plastome) has a conserved structure, encodes 120-130 genes, most of which encode part of the photosynthetic apparatus of the organelle (Jensen and Leister, 2014), and is maternally inherited (Wicke et al 2011).…”