The complete chloroplast genome provides insight into the polymorphism and adaptive evolution of Garcinia paucinervis

Abstract

Garcinia paucinervis is an evergreen tree with high medicinal value. Due to its vulnerable reproductive capacity coupled with excessive logging by humans, G. paucinervis has become an endangered species. In order to protect this species effectively, we drew the complete chloroplast genome of G. paucinervis and performed a series of comparative analyses on G. paucinervis and its neighbouring species. The chloroplast genome size of G. paucinervis is 157702 bp. In the chloroplast genome, we identified 130 genes, 56 RNA editing sites in the protein-coding genes, as well as 241 simple sequence repeats (SSRs) and 49 complex repetitive sequences. Comparative analysis identified some high divergent sequences in the intergenic spacers, which can be used as candidate markers for phylogenetic study. From an adaptive evolution point of view, a branch-site model analysis identified positively selected sites in 5 genes, most of which are involved in ribosome biogenesis, protein synthesis and other developmental processes. The detected codon substitutions may be associated with the evolution of G. paucinervis to adapt to the extreme habitat in karst. In addition, the result of the phylogenetic analysis supports the previous phylogenomic studies of taxa within the rosids clade. The ML tree revealed that G. mangostana was a sister to G. gummi-gutta, and they formed a diverging lineage to G. paucinervis in Garcinia. The above information is of great significance for us to understand the evolution of G. paucinervis chloroplast and lays the foundations for future studies in species conservation.

Plastomes of Garcinia mangostana L. and comparative analysis with other Garcinia species

“…We detected two mis-annotations of genes ( infA and rpl32 ) in G. pedunculata 19 and one mis-annotation of infA in G. anomala 49 . The infA is usually located between rpl36 and rps8 , whereas rpl32 is usually located between ndhF and trnL-UAG 50 .…”

“…In this study, we assembled and analyzed the complete mangosteen plastomes of Manggis and Mesta. Furthermore, we performed a comprehensive comparison of all available Garcinia plastomes from GenBank and provided an update to a previous comparative analysis 19 . The current comparative study elucidates the structural differences in plastomes for evolutionary inference of the Garcinia genus.…”

Genome skimming approach reveals the gene arrangements in the chloroplast genomes of the highly endangered Crocus L. species: Crocus istanbulensis (B.Mathew) Rukšāns

“…Because psbK is directly involved in PSII, the positive selection observed in the psbK gene of various plants such as Echinacanthus Nees. [ 69 ], Robinia L. [ 70 ], Debregeasia Gaudich [ 71 ], Monsteroideae (Araceae) [ 72 ] and Garcinia paucinervis Chun & F.C.How [ 73 ] are important for plant adaptation to harsh environmental conditions. A significant positive selection signature was also detected in ccsA gene, which encodes a component of cytochrome c synthase complex for cytochrome c biogenesis [ 74 ] and has been reported to play a role in the adaptation of species to environmental conditions [ 75 – 77 ].…”

Complete Chloroplast Genomes Provide Insights Into Evolution and Phylogeny of Campylotropis (Fabaceae)

“…As expected, the ω values for most genes, especially photosynthesis genes, were less than 1, either in Campylotropis or in background branches ( Figure 5 ). The two genes under significant positive selection in Campylotropis : atpF and rps19 (ω f > 1; p < 0.05) were also found under positive selection in other species, e.g., atpF in two deciduous Quercus species ( Yin et al, 2018 ), and rps19 in Garcinia paucinervis ( Wang et al, 2021 ). As indicated in Yin et al (2018) , atpF gene is highly divergent between deciduous and evergreen sclerophyllous oaks since the former loses its leaves in cold and drought seasons.…”