Chloroplast genome characteristics and phylogeny of the sinodielsia clade (apiaceae: apioideae)

Abstract

Background The Sinodielsia clade of the subfamily Apioideae (Apiacieae) was established in 2008, and it is composed of 37 species from 17 genera. Its circumscription is still poorly delimited and unstable, and interspecific relationships in the clade lack comprehensive analysis. Chloroplast (cp.) genomes provide valuable and informative data sources for evolutionary biology and have been widely used in studies on plant phylogeny. To infer the phylogenetic history of the Sinodielsia clade, we assembled complete cp. genomes of 39 species and then performed phylogenetic analysis based on these cp. genome sequence data combined with 66 published cp. genomes from 16 genera relative to the Sinodielsia clade. Results These 39 newly assembled genomes had a typical quadripartite structure with two inverted repeat regions (IRs: 17,599–31,486 bp) separated by a large single-copy region (LSC: 82,048–94,046 bp) and a small single-copy region (SSC: 16,343–17,917 bp). The phylogenetic analysis showed that 19 species were clustered into the Sinodielsia clade, and they were divided into two subclades. Six mutation hotspot regions were detected from the whole cp. genomes among the Sinodielsia clade, namely, rbcL–accD, ycf4–cemA, petA–psbJ, ycf1–ndhF, ndhF–rpl32 and ycf1, and it was found that ndhF–rpl32 and ycf1 were highly variable in the 105 sampled cp. genomes. Conclusion The Sinodielsia clade was subdivided into two subclades relevant to geographical distributions, except for cultivated and introduced species. Six mutation hotspot regions, especially ndhF–rpl32 and ycf1, could be used as potential DNA markers in the identification and phylogenetic analyses of the Sinodielsia clade and Apioideae. Our study provided new insights into the phylogeny of the Sinodielsia clade and valuable information on cp. genome evolution in Apioideae.

Complete chloroplast genomes and phylogenetic relationships of Pedicularis chinensis and Pedicularis kansuensis

“…Therefore, the ycf1 gene and three non-coding regions of trnV - UAC , ndhJ - trnV and ycf4 - cemA in the SSC region have universal reference value for the development of DNA barcoding or play a role in the future identification of Pedicularis plants. Among them, the high mutation of ycf4 - cemA has been proved and widely used in the study of geographical pedigree 45 . In conclusion, more chloroplast genome data will promote the classification of Pedicularis plants.…”

Plastome evolution in the genus Sium (Apiaceae, Oenantheae) inferred from phylogenomic and comparative analyses

“…Plastomes can provide valuable information for taxonomy and phylogeny, and have proven to be a powerful tool for exploring phylogenetic relationships [ 15 , 16 ]. It have been applied to the comparative analysis and phylogenetic reconstruction of Apiaceae, in which the genome structure was characterized and some contentious phylogenetic relationships have been resolved [ 17 – 24 ]. Furthermore, highly divergent regions and simple sequence repeats (SSRs) obtained from plastome sequences can be used as efficient molecular markers for species delimitation, as well as population genetics [ 25 ].…”