New insights into the evolutionary characteristic between the New World and Old World Lupinus species using complete chloroplast genomes

Abstract

Lupinus is one of the most geographically widespread genera. It can be divided into New World and Old World Lupinus species according to the geographical distribution of its members. However, there are relatively few studies on their genetic differences, especially regarding the taxonomy and geographical evolutionary history of New World species. Here, we conducted comparative, phylogenetic, and evolution analysis between one New World and five Old World Lupinus species based on their complete chloroplast genomes. Compared with the Old World species, the chloroplast genome of L. westianus in the New World was more variable, showing the deletion of the pseudogene ycf1 and two rps12 gene introns, the 20 kb inversion, the higher number of repeated sequences, the larger genome size, and the lower GC content. Phylogenetic analysis indicated that the genetic relationship between the New World species L. westianus and the Old World species L. albus was closer than to the rest. Evolutionary analysis confirmed that the matK and ycf1 genes were under positive selection, and rpoA, accD, and rpoC2 genes have site-specific selection in L. westianus, which might be related to adaptive evolution. Therefore, our finding would provide genetic information for the evolutionary history and taxonomy of Lupinus species.

Complete chloroplast genome of Lens lamottei reveals intraspecies variation among with Lens culinaris

“…Flip-flop recombination is a plausible theory to explain the existence of structural heteroplasmy and has been reported previously 35 , 36 . Gene loss, changes in the intergenic region, and expansion, or contraction of the IR region are all variables that affect genome size 37 . The cp genome of L. lamottei (122.8 kb) of the Fabaceae family has a similar size to that of the close wild relative L. ervoides 20 , the cultivated form L. culinaris , and other Fabaceae species such as O. arctobia 38 .…”

“…Among these mononucleotides, the most common SSR motif found in the L. lamottei cp genome is the A/T motif. The common consensus is that plastid SSRs are mostly composed of A/T repeats, with G/C repeats considered as rare 37 . Similar results were found in the wild chickpea species belonging to Fabaceae family and in the L. ervoides cp genome 20 , 50 , 51 .…”

Comparative Analyses of Plastomes of Four Anubias (Araceae) Taxa, Tropical Aquatic Plants Endemic to Africa

“…The ccsA gene is required for the biogenesis of c-type cytochromes at the step of heme attachment, and its function is linked to electron transfer in respiration and photosynthesis [ 61 , 62 ]. The matK gene has been reported to be under positive selection in some aquatic or hygrophilous plants (e.g., Oryza , Lupinus L.) [ 59 , 63 ]. This gene encodes an intron maturase that is involved in the splicing of group II RNA transcriptional introns, and its function is linked to plastid translation and photosynthesis [ 64 , 65 , 66 ].…”