Insight from newly sequenced chloroplast genome challenges the primitive position of Corydalis temulifolia (Papaveraceae)

Abstract

Corydalis temulifolia has been considered to be one of the primitive species of Corydalis; however, some recent works based on DNA markers revealed instead that Corydalis adunca rather C. temulifolia is in the basal clade within the Corydalis lineage. Both views are in conflict over concerns of species representing the primitive member of Corydalis. In this study, the chloroplast genome of C. temulifolia has been sequenced and compared with previously published chloroplast genome of C. adunca. With the sequences obtained, genomic phylogenetic analyses have been carried out. Although sharing the quadripartite structure of C. adunca, the complete chloroplast genome of C. temulifolia has particular features with respect to its genome size, gene order, gene content, and nucleotide substitution rates. For instance, we found the complete chloroplast genome of C. temulifolia has SSC region of 341 bp, which is markedly different in size than that of C. adunca (9,531 bp). C. temulifolia was determined as a species with large-scale rearrangements, consisting of the relocation of segment (~5 kb, trnV-UAC-rbcL) in the LSC region, the inversion of segment (~14 kb, ndhB-trnR-ACG) in the IR region and a large size (>10 kb) of IR expansion in IRs/SSC junction. Significantly, of the four large-scale rearrangements the relocation of the segment (trnV-UAC-rbcL) was absent from C. adunca but other two rearrangements were shared by C. adunca. In the latter, the segment (trnV-UAC-rbcL) resided in the conserved location and has not occurred rearrangement, suggesting that C. adunca was most likely represent a relatively early divergence species in Corydalis that compared to C. temulifolia. Further, we noticed that there was no change to the gene order of rps16 and rrn16 in C. temulifolia relative to C. adunca, and unlike C. adunca that seven out of ndh genes reside as pseudogenes, 11 ndh genes are all present in C. temulifolia. In addition, C. temulifolia has not only more dispersed repeats but slightly more tandem repeats and simple sequence repeats than C. adunca. The selection pressure estimation of protein-coding genes (psaI and rps7) in C. temulifolia were under positive selection, and it is different from four genes (psaI, rpl23, rpl36 and rps7) in C. adunca. Phylogenetic analysis based on the plastid genome revealed C. adunca to be the basal clade within the Corydalis lineage in the present sampling, suggesting that C. temulifolia is most likely not representative of the primitive members of Corydalis. This might indicate that the importance of morphological characters such as stigma may be in part misinterpreted, when being used to make inference about the evolutionary status of the Corydalis species. The results emphasise the need to consider both morphological and molecular evidence when determining not only the systematic position of species but also character evolution.