Abstract
BackgroundCultivated tea is one of the most important economic and ecological trees distributed worldwide. Cultivated tea suffer from long-term targeted selection of traits and overexploitation of habitats by human beings, which may have changed its genetic structure. The chloroplast is an organelle with a conserved cyclic genomic structure, and it can help us better understand the evolutionary relationship of Camellia plants.ResultsWe conducted comparative and evolutionary analyses on cultivated tea and wild tea, and we detected the evolutionary characteristics of cultivated tea. The chloroplast genome sizes of cultivated tea were slightly different, ranging from 157,025 to 157,100 bp. In addition, the cultivated species were more conserved than the wild species, in terms of the genome length, gene number, gene arrangement and GC content. However, comparing Camellia sinensis var. sinensis and Camellia sinensis var. assamica with their cultivars, the IR length variation was approximately 20 bp and 30 bp, respectively. The nucleotide diversity of 14 sequences in cultivated tea was higher than that in wild tea. Detailed analysis on the genomic variation and evolution of Camellia sinensis var. sinensis cultivars revealed 67 single nucleotide polymorphisms (SNPs), 46 insertions/deletions (indels), and 16 protein coding genes with nucleotide substitutions, while Camellia sinensis var. assamica cultivars revealed 4 indels. In cultivated tea, the most variable gene was ycf1. The largest number of nucleotide substitutions, five amino acids exhibited site-specific selection, and a 9 bp sequence insertion were found in the Camellia sinensis var. sinensis cultivars. In addition, phylogenetic relationship in the ycf1 tree suggested that the ycf1 gene has diverged in cultivated tea. Because C. sinensis var. sinensis and its cultivated species were not tightly clustered.ConclusionsThe cultivated species were more conserved than the wild species in terms of architecture and linear sequence order. The variation of the chloroplast genome in cultivated tea was mainly manifested in the nucleotide polymorphisms and sequence insertions. These results provided evidence regarding the influence of human activities on tea.
Highlights
Cultivated tea is one of the most important economic and ecological trees distributed worldwide
The differences in the GC content of the Protein-coding regions (CDS), intron and Intergeneric regions (IGS) in the Chinese cultivated type and Assam cultivated type were approximately 0.01–0.03%, and 0–0.02%, respectively, but we found that the differences of the CDS, intron and IGS in the wild type were 0.02–1.05%
At the genomic level, the cultivated species were more conserved than the wild species
Summary
Cultivated tea is one of the most important economic and ecological trees distributed worldwide. Cultivated tea suffer from long-term targeted selection of traits and overexploitation of habitats by human beings, which may have changed its genetic structure. Numerous plant species have been taken from their habitats and introduced into cultivation—that is, into various human-made systems [1]. The cultivation process has played an important role in human history and cultivated environments often present strong ecological contrasts with wild environments [2]. Wild species are exposed to natural selection that. Alterations in vegetation phenology, growth and reproductive traits occur because the plants are subjected to different levels of stress and distinctive selection pressures [3]. The inadequate genetic information prevents us from fully understanding the spreading process of cultivated plants. We need to compare the genetic differences between cultivated species and wild species in order to use these species more effectively
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