Comparative chloroplast genomes: insights into the evolution of the chloroplast genome of Camellia sinensis and the phylogeny of Camellia

Abstract

Background Chloroplast genome resources can provide useful information for the evolution of plant species. Tea plant (Camellia sinensis) is among the most economically valuable member of Camellia. Here, we determined the chloroplast genome of the first natural triploid Chinary type tea (‘Wuyi narcissus’ cultivar of Camellia sinensis var. sinensis, CWN) and conducted the genome comparison with the diploid Chinary type tea (Camellia sinensis var. sinensis, CSS) and two types of diploid Assamica type teas (Camellia sinensis var. assamica: Chinese Assamica type tea, CSA and Indian Assamica type tea, CIA). Further, the evolutionary mechanism of the chloroplast genome of Camellia sinensis and the relationships of Camellia species based on chloroplast genome were discussed. Results Comparative analysis showed the evolutionary dynamics of chloroplast genome of Camellia sinensis were the repeats and insertion-deletions (indels), and distribution of the repeats, indels and substitutions were significantly correlated. Chinese tea and Indian tea had significant differences in the structural characteristic and the codon usage of the chloroplast genome. Analysis of sequence characterized amplified region (SCAR) using sequences of the intergenic spacers (trnE/trnT) showed none of 292 different Camellia sinensis cultivars had similar sequence characteristic to triploid CWN, but the other four Camellia species did. Estimations of the divergence time showed that CIA diverged from the common ancestor of two Assamica type teas about 6.2 Mya (CI: 4.4–8.1 Mya). CSS and CSA diverged to each other about 0.8 Mya (CI: 0.4–1.5 Mya). Moreover, phylogenetic clustering was not exactly consistent with the current taxonomy of Camellia. Conclusions The repeat-induced and indel-induced mutations were two important dynamics contributed to the diversification of the chloroplast genome in Camellia sinensis, which were not mutually exclusive. Chinese tea and Indian tea might have undergone different selection pressures. Chloroplast transfer occurred during the polyploid evolution in Camellia sinensis. In addition, our results supported the three different domestication origins of Chinary type tea, Chinese Assamica type tea and Indian Assamica type tea. And, the current classification of some Camellia species might need to be further discussed.

Comparative Analysis of Codon Bias in the Chloroplast Genomes of Theaceae Species

“…In addition, the clustering results based on RSCU values were similar to the topological structure of the phylogenetic tree constructed based on chloroplast genome sequences. In the topology of the phylogenetic tree, Camellia chekiangoleosa , Camellia crapnelliana , Camellia cuspidat , Camellia granthamiana , Camellia gymnogyna , Camellia impressinervis , Camellia pitardii , Camellia ptilophylla , Camellia renshanxiangiae , Camellia yunnanensis belongs to the first clade, which has the same opinion with Li et al (2021) . And Camellia pitardii was clustered with Camellia crapnelliana , Camellia cuspidate , Camellia impressinervis , and Camellia yunnanensis , indicating that Camellia pitardii might belong to subgenus Camellia , and it means they’re very closely related, which is similar to Li et al (2021) .…”

“…In addition, there are some inconsistencies between the phylogenetic tree of this study and others’ Theaceae phylogeny. Li et al (2021) is mainly focus on the phylogeny of Camellia, Camellia renshanxiangiae and Camellia sasanqua belong to the genus Camellia . However, in cluster analysis based on RSCU values, the two species of Camellia grouped into the Stewartia-Hartia clade.…”

Comparison of Magnoliaceae Plastomes: Adding Neotropical Magnolia to the Discussion

“…Usually, diversity is smaller within species and it increases at higher taxonomic levels [ 30 , 79 ]. However, some pantropical genera, such as Aristolochia , have shown a higher nucleotide diversity, especially in intergenic regions [ 94 ].…”

“…In most plants, this strategy generally results in a much higher proportion of plastome reads compared to other regions of the genome because of the high molarity of these organelles in each cell. This strategy was effective in several plant groups [ 5 , 15 , 28 , 29 , 30 ] and has been applied in studies that use chloroplast genomes to solve evolutionary questions in different angiosperm clades [ 13 , 31 , 32 , 33 ]. Most attention has focused on sequencing crop genomes, and there is little information on wild groups.…”

Comparative Chloroplast Genomics of Seven Endangered Cypripedium Species and Phylogenetic Relationships of Orchidaceae

“…SSRs (≥ 10 bp) are small repetitive units of chloroplast DNA, together with LSRs, have played an important role in the evolution of the chloroplast genome and may contribute to the development of future molecular markers ( Zhang et al, 2016 ; Li et al, 2021 ). Interestingly, the three larger chloroplast genomes ( Cympripedium tibeticum , C. palangshanense , and C. subtropicum ; 98–154 LSRs, and 409–535 SSRs; Figure 4B and Supplementary Table 7 ) had more LSRs and SSRs than the four smaller ones ( C. debile , C. japonicum , C. calceolus , and C. formicum ; 87–114 LSRs, and 138–222 SSRs).…”