- Comparative chloroplast genomes: insights into the evolution of the chloroplast. - Here, we determined the chloroplast genome of the first natural triploid Chinary type tea. - 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. - Estimations of the divergence time showed that CIA diverged from the common ancestor of two Assamica type teas about 6.2 Mya (CI Mya). - 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. - Full list of author information is available at the end of the article Li et al. - So far, the cp genome of the polyploid tea plant has not been reported, and the pos- sible effects of polyploidization on the cp genome of tea plant need to be further explored.. - In this study, we generated the complete cp genome of the first natural triploid tea plant (‘Wuyi narcissus’ culti- var of C. - sinensis) which belong to asexual propagation cultivar and was recognized as one of the national quality tea varieties by China National Crop Variety Examination Committee in 1985 (GS13009–. - Then, we presented the detailed sequence and structural variations of the cp genome among the four representative tea plants, including ‘Wuyi narcissus’. - Further- more, the phylogenetic analysis and the divergence time estimation based on complete cp genomes were con- ducted to explore the evolutionary relationship between Chinary type tea, Chinese Assamica type tea and Indian Assamica type tea, and to further improve our under- standing of the taxonomic classification of Camellia.. - deposited in the NCBI GenBank (SRA: SRR12002624, Accession numbers: MT612435).. - The ycf1 was located in the. - Dashed area in the inner circle indicated the GC content of the chloroplast genome. - Li et al. - boundary regions between IR/SSC, leading to incomplete duplication of the gene within IRs. - Mutations of the. - base replacement or deletion may cause changes in the length of the coding gene sequence, leading to changes in the coding and non-coding regions. - To further observe the potential contraction and ex- pansion of IR regions, the gene variation at the IR/SSC and IR/LSC boundary regions of the four plastomes was compared (Fig. - The ndhF gene in all four cp genomes was located in the SSC region. - The number of the three re- peated types was consistent in CSS and CWN, as follows:. - Only one repeat was in the intron regions (ndhA) (Supplementary Tab. - Most of the indels events occurred in IGS regions (70. - Correlations were highly significant in the pairwise com- parisons between the three types of mutations: “repeats. - 3 Sliding window analysis of the complete chloroplast genomes of four tea species. - X-axis: position of the window midpoint, Y-axis:. - 5 The comparison of the LSC, IR and SSC border regions among the four chloroplast genomes. - ENc plots analysis showed only a few points lie near the curve, however, most of the genes with lower ENc values than expected values lay below the curve (Fig. - 9), suggest- ing the codon usage bias of the cp genome was slightly af- fected by the mutation pressure, but selection and other factors play an important role. - The distributions of codon usage in four cp genomes showed that RSCU values of the 37 codons were identical in the three Chinese teas, but dif- ferent from those in Indian tea (Table 4).. - Excluding seven non-Camellia species, the sequence variation of the 37 Camellia species associated with the six datasets (Complete cp genome, LSC, SSC, IR, PCGs, and non-PCGs) showed different percentage variation (Supplementary Tab. - b Number of simple sequence repeats (SSRs) in the four chloroplast genomes by Venn diagram. - c Location of the all SSRs from four species. - The support values of nodes increased significantly with the increasing of the sequence length in the differ- ent data partitions. - Genetic variation and mutational dynamics of the chloroplast genome in tea plant. - The four cp genomes of the tea plants showed a high de- gree of conservation in genome structure, gene content, gene order, intron number, and also GC content. - a Number of the three repeat types. - b Number of repeat sequences in the four chloroplast genomes by Venn diagram. - c Number of the repeats by different length. - 8 Analyses of the Indel sequences in four chloroplast genomes. - a Number of the Indel types by length. - b Location of the all indels from four species. - d Number of indel sequences in the four chloroplast genomes by Venn diagram. - Correlations were significant in the pairwise com- parisons between the three types of mutations:. - It also implied that if the distribution of the repeat or indel sequences had been identified, the mutational hotspot regions and the appropriate sequences for genetic analysis could be predicted based on their location.. - the four cp genomes, the IR regions of CIA were the smallest, and the more sequence deletions were found in SC/IR regions of CIA, suggesting that deletions might cause the contraction of the IR region. - RSCU values of the 37 codons were identical in all three Chinese teas (Blue background), but different in Indian tea (Yellow background). - The position of the primers was indicated by the arrow. - (2) Chinese teas and In- dian tea exhibited the distinct repeat patterns, Indian tea possessed high level of species-specific long repeats, with 18, while three Chinese teas only possessed 0–2, and most of the long repeats in three Chinese teas were shared (Fig. - Similarly, the indel patterns also exhib- ited obviously different between Chinese teas and Indian tea, Indian tea possessed 49 species-specific indels pat- terns, accounting for 49% of the total number of indel loci, while only 5–16 indels were specific to each of the three Chinese teas (Fig. - (3) In particular, the analysis showed that selection played an important role in the codon usage of cp genome in all four species (Figs. - However, 37 codons of the three Chinese teas had the identical RSCU value, accounting for 57.8% of the codons, all of which were different from that of In- dian tea (Table 4). - However, SCAR analysis using a 335 bp deletion of the intergenic spacers (trnE/trnT) in 292 cultivars of C. - sinensis showed that none of the cultivars had this sequence deletion like trip- loid CWN (Fig. - 13 Phylogeny of Camellia inferred from maximum likelihood analysis of the complete chloroplast genome dataset. - sinen- sis, that was, the progenitor of the triploid CWN (C. - sinen- sis) itself captured the cp genome of another Camellia species when hybridization occurred where the ranges of the species overlap.. - The controversy over the domestication origin of the tea plant has existed for a long time. - 13) of Camellia did not agree with any of the current trad- itional classification methods used recently in Camellia taxonomy, such as: C. - In our phylogenetic analysis of the data partitions of cp genome, the sequence variations in the six datasets showed different percentage variation (Supplementary Tab. - datasets generated mostly similar topological structures, there were still some individual species showing different locations in the six trees, and the support values of nodes increased significantly with the increasing of the sequence length (Fig. - While the analyses of the complete cp genomes pro- vided a feasible way to clarify relationships [59], it might still be insufficient to fully resolve all phylogenetic rela- tionships [60, 61]. - In this study, we had found that the repeats and indels were two most important evolutionary dynamics con- tributed to the diversification of the cp genome, which were not mutually exclusive. - Chinese tea and Indian tea exhibited significantly differences in the structural char- acteristic and the codon usage of the cp genome, sug- gesting they might have undergone different selection pressures. - Yongcong Hong (Wuyi University) and deposited in the Wuyi University herbarium.. - To estimate the quality and coverage of the assembled genome [72], we mapped all Illumina and. - an SSR of the compound formation).. - According to Ibrar et al.′s method [40], the correla- tions were analyzed in the pairwise comparisons be- tween the three types of mutations: substitutions and indels, repeats and indels, and repeats and substitutions.. - The slope of the plot regression is zero which indicates that there is no effect on directional mutation pressure (complete selection constraint). - A sequence part of the chloroplast trnE/trnT intergenic spacer, where a 335 bp long deletion was observed in trip- loid CWN by comparing with another three tea species, was used to SCAR analysis. - Screening of the distribution of the similar deletion in the trnE/trnT intergenic spacer was conducted by PCR amplification of the respective chloroplast region in 292 individuals covering the majority of C. - A set of the primers (trnE: 5′- TCCTGAACCACTAGACGATG-3′. - trnT: 5′-ATGGCG TTACTCTACCACTG-3′) were designed in conserved re- gions on either side of the 335 bp long deletion region by comparing cp genome sequences.. - Non- parametric bootstrapping test was implemented in the. - were assigned to constrain the age of the Panax. - Yu et al. - Based on the results of Yu et al., the divergence times of Polyspora species/Camellia species Mya) were assigned to constrain the stem of Camellia family. - SCAR analysis was conducted by PCR amplification of the respective chloroplast region in 292 different cultivars of Camellia sinensis. - PCR amplification to screen the distribution of a 335 bp deletion of the intergenic spacers (trnE/trnT) in 292 different cultivars of Camellia sinensis. - The meaning of the figures and symbols was consistent with Fig. - The mean- ing of the figures and symbols was consistent with Fig. - List of genes in the cp genome. - Distribution of the different and the shared SSRs in four Camellia chloroplast genomes. - Primers used for assembly and junction verification of the chloroplast genome.. - All complete chloroplast genomes adopted in this study, including the three reference chloroplast genomes, were available in NCBI database, and the accession numbers of the complete chloroplast genomes of each species were listed in the Supplementary Tab. - The evolution of the plastid chromosome in land plants: gene content, gene order, gene function. - Possible loss of the chloroplast genome in the parasitic flowering plant Rafflesia lagascae (Rafflesiaceae).. - Gene losses and partial deletion of small single copy regions of the chloroplast genomes of two hemiparasitic Taxillus species. - The complete nucleotide sequence of the hornwort (Anthoceros formosae) chloroplast genome: insight into the earliest land plants. - The chloroplast genome of the hexaploid Spartina maritima (Poaceae, Chloridoideae): comparative analyses and molecular dating. - A comparative analysis of the Lactuca and Helianthus (Asteraceae) plastid genomes: identification of divergent regions and categorization of shared repeats. - Expansion and contraction of the chloroplast inverted repeat in Apiaceae subfamily Apioideae [J]. - Chloroplast DNA variation within and among genera of the Heuchera group (Saxifragaceae): evidence for chloroplast transfer and Paraphyly [J]. - Preliminary investigations on the genetic relationships and origin of domestication of the tea plant (Camellia sinensis (L. - Monograph of the genus camellia. - Genome-wide characterization of the biggest grass, bamboo, based on 10,608 putative full-length cDNA sequences. - Database resources of the National Center for Biotechnology Information Nucleic Acids Res. - Insights into the historical assembly of East Asian subtropical evergreen broadleaved forests revealed by the temporal history of the tea family [J]
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