Comparative and Evolutionary Analyses on the Complete Plastomes of Five Kalanchoe Horticultural Plants

Abstract

Many species of the genus Kalanchoe are important horticultural plants. They have evolved the Crassulacean acid metabolism (CAM) photosynthetic pathway to allow them to be better adapted to dry environments. Despite their importance, it is still debating whether Kalanchoe is monophyletic, and understanding the past diversification of this genus requires a tremendous amount of effort and work being devoted to the studies of morphological and molecular characters of this genus. However, molecular information, plastic sequence data, in particular, reported on Kalanchoe species is scarce, and this has posed a great challenge in trying to interpret the evolutionary history of this genus. In this study, plastomes of the five Kalanchoe species, including Kalanchoe daigremontiana, Kalanchoe delagoensis, Kalanchoe fedtschenkoi, Kalanchoe longiflora, and Kalanchoe pinnata, were sequenced and analyzed. The results indicate that the five plastomes are comparable in size, guanine-cytosine (GC) contents and the number of genes, which also demonstrate an insignificant difference in comparison with other species from the family Crassulaceae. About 224 simple sequence repeats (SSRs) and 144 long repeats were identified in the five plastomes, and most of these are distributed in the inverted repeat regions. In addition, highly divergent regions containing either single nucleotide polymorphism (SNP) or insertion or deletion (InDel) mutations are discovered, which could be potentially used for establishing phylogenetic relationships among members of the Kalanchoe genus in future studies. Furthermore, phylogenetic analyses suggest that Bryophyllum should be placed into one single genus as Kalanchoe. Further genomic analyses also reveal that several genes are undergone positive selection. Among them, 11 genes are involved in important cellular processes, such as cell survival, electron transfer, and may have played indispensable roles in the adaptive evolution of Kalanchoe to dry environments.

Phylogeny and diversification of genus Sanicula L. (Apiaceae): novel insights from plastid phylogenomic analyses

“…1 ). Similarly, this structure was also detected in other plastomes of angiosperm plants [ 46 – 48 ]. Although gene loss is a common evolutionary event that frequently occurs in other genera of Apiaceae, such as the ycf 15 gene was lost in genus Peucedanum [ 31 ] and the trn T-GGU gene was lost in genus Peucedanum and Kitagawia [ 31 , 35 ], it was not discovered in genus Sanicula .…”

Comparison of Magnoliaceae Plastomes: Adding Neotropical Magnolia to the Discussion

“…In the case of positive selected sites, Magnoliaceae species showed 13 genes with sites under selection; most of these are related to the photosynthetic process ( atpB , ndhD , ndhF , pbf1 , psaA , psaB , and rbcL ). Other studies have argued that positive selection in those genes could be related to differences in the photosynthetic pathways or in the habitat of each species [ 97 , 98 ].…”

Variations in genetic diversity in cultivated Pistacia chinensis

“…Moreover, the capacity to assess the mutation rate or detect variation has significantly improved. Many studies have focused on variations at the species level or above ( Liu et al., 2021 ; Ren et al., 2021 ; Tian et al., 2021 ; Xiong et al., 2021 ), however, only few studies have examined intraspecific diversity for whole plastome sequences ( Hu et al., 2022 ; Lian et al., 2022 ; Sun et al., 2022 ). Plastid markers have been used in tree population genetics but were often limited to few polymorphic sites ( Mariotti et al., 2010 ; Huang et al., 2014 ; Mohamoud et al., 2019 ).…”