Complete Chloroplast Genome of Cercis chuniana (Fabaceae) with Structural and Genetic Comparison to Six Species in Caesalpinioideae

Abstract

The subfamily Caesalpinioideae of the Fabaceae has long been recognized as non-monophyletic due to its controversial phylogenetic relationships. Cercis chuniana, endemic to China, is a representative species of Cercis L. placed within Caesalpinioideae in the older sense. Here, we report the whole chloroplast (cp) genome of C. chuniana and compare it to six other species from the Caesalpinioideae. Comparative analyses of gene synteny and simple sequence repeats (SSRs), as well as estimation of nucleotide diversity, the relative ratios of synonymous and nonsynonymous substitutions (dn/ds), and Kimura 2-parameter (K2P) interspecific genetic distances, were all conducted. The whole cp genome of C. chuniana was found to be 158,433 bp long with a total of 114 genes, 81 of which code for proteins. Nucleotide substitutions and length variation are present, particularly at the boundaries among large single copy (LSC), inverted repeat (IR) and small single copy (SSC) regions. Nucleotide diversity among all species was estimated to be 0.03, the average dn/ds ratio 0.3177, and the average K2P value 0.0372. Ninety-one SSRs were identified in C. chuniana, with the highest proportion in the LSC region. Ninety-seven species from the old Caesalpinioideae were selected for phylogenetic reconstruction, the analysis of which strongly supports the monophyly of Cercidoideae based on the new classification of the Fabaceae. Our study provides genomic information for further phylogenetic reconstruction and biogeographic inference of Cercis and other legume species.

Complete chloroplast genome of Jasminum sambac L. (Oleaceae)

“…In this study, the most abundant SSR units were mononucleotides and the majority of SSRs had a high AT content located in the IGS, consistent with other previous reports (Ni et al 2016;Chen et al 2018). Moreover, it was found that the main SSRs (60.17% in SP and 59.83% in DP) were located in the LSC region, which is also in concordance with other studies (Wang et al 2017;Dong et al 2018;Liu et al 2018). Therefore, it can be speculated that cp genomes of different land species were enriched for A/T and were mostly located in the LSC region.…”

“…SSRs are highly polymorphic and widely developed as valuable molecular markers for population genetics (Zhang et al 2012;Hu et al 2015). SSRs of the cp genome were determined to be rich in A/T and rare in tandem G or C repeats (Choi et al 2016;Hong et al 2017;Liu et al 2018). For example, mononucleotide SSRs were the most abundant SSRs in C. quinoa and C. Album, and A/T were their major motifs (Hong et al 2017).…”

Complete Chloroplast Genome Sequence of Chinese Lacquer Tree (Toxicodendron vernicifluum, Anacardiaceae) and Its Phylogenetic Significance

“…We compared the complete cp genome structure of T. vernicifluum with five species from different genera in Anacardiaceae. Our results indicated that the six Anacardiaceae cp genomes were relatively conserved (Figure 4), which is consistent with the slow rates of sequence and structural evolution of plant plastomes [78,80,81]. However, the synteny analysis still detected a large inversed segment (16,910 bp in length) in the LSC region of M. indica.…”

Evolution and Function of the Chloroplast. Current Investigations and Perspectives

“…Mainly focussed on phylogenetic comparisons of medicinal plant families, articles on Aristolochia [ 5 ], Forsythia [ 6 ], Eucommia [ 7 ], and the Stemonaceae family [ 8 ] report and analyse the complete sequences of the corresponding chloroplast DNA. Similar approaches on other economically important plants have been reported in articles on genera Catha [ 9 ], Primula [ 10 ], Caragana [ 11 ], Genciana [ 12 ], and Quercus [ 13 ], and on the families of Balsaminaceae [ 14 ], Meliaceae [ 15 ], Orchidaceae [ 16 ], and Fabaceae [ 17 ]. The chloroplast DNA sequence and the analysis of the species of plant branches, that are still poorly investigated have been reported in articles on the Antarctic Bryophyte Sanionia uncinate [ 18 ], on Ailanthus altissima [ 19 ], and on genus Urophysa [ 20 ].…”