Comparative Analysis of Chloroplast Genomes within Saxifraga (Saxifragaceae) Takes Insights into Their Genomic Evolution and Adaption to the High-Elevation Environment

Abstract

Saxifraga species are widely distributed in alpine and arctic regions in the Northern hemisphere. Highly morphological diversity within this genus brings great difficulties for species identification, and their typical highland living properties make it interesting how they adapt to the extreme environment. Here, we newly generated the chloroplast (cp) genomes of two Saxifraga species and compared them with another five Saxifraga cp genomes to understand the characteristics of cp genomes and their potential roles in highland adaptation. The genome size, structure, gene content, GC content, and codon usage pattern were found to be highly similar. Cp genomes ranged from 146,549 bp to 151,066 bp in length, most of which comprised 130 predicted genes. Yet, due to the expansion of IR regions, the second copy of rps19 in Saxifraga stolonifera was uniquely kept. Through sequence divergence analysis, we identified seven hypervariable regions and detected some signatures of regularity associated with genetic distance. We also identified 52 to 89 SSRs and some long repeats among seven Saxifraga species. Both ML and BI phylogenetic analyses confirmed that seven Saxifraga species formed a monophyletic clade in the Saxifragaceae family, and their intragenus relationship was also well supported. Additionally, the ndhI and ycf1 genes were considered under positive selection in species inhabiting relatively high altitudes. Given the conditions of intense light and low CO2 concentration in the highland, the products of these two genes might participate in the adaptation to the extreme environment.

Characteristics of the complete chloroplast genome of Saxifragaceae species Bergenia purpurascens (Hook. f. et Thoms.) Engl

“…The following sequences were used: B. purpurascens OR004350 (this study), OK012000 (Chen et al. 2022 ), B. scopulosa NC036061 (Bai et al. 2017 ), Heuchera richardsonii R.Br.…”

“… 2017 ; Chen et al. 2022 ). Our results provide fundamental information for comparative chloroplast genomics and further phylogenetic studies of Bergenia .…”

The complete chloroplast genome of Meconopsis torquata (Papaveraceae), a traditional Tibetan medicine

“…This characteristic may be closely related to its evolutionary adaptation to high-altitude environments, reflecting the impact of specific environments on genomic adaptive changes (Chen et al. 2022 ).…”

Chloroplast genome data of five Amygdalus species: Clarifying genome structure and phylogenetic relationships

“…Chloroplasts (cp) are semi-autonomous organelles with a conserved, maternally inherited genome separate from the rest of the plant. The genome size of terrestrial plants cp varies from 100 to 200 kb and generally contains 110–130 genes, which are mainly composed of genes involved in photosynthesis, transcription, and translation [11] . Most higher-plant cp genomes form a quadripartite structure, containing one pair of inverted repeats (IR), a small single-copy (SSC) region, and a large single-copy (LSC) region separated by IRs [12] .…”