Exploring evolution characteristic between cultivated tea and its wild relatives using complete chloroplast genomes

Abstract

<jats:title>Abstract</jats:title> <jats:p><jats:bold>Background: </jats:bold>The cultivated tea is one of the most important economic and ecological trees distributing worldwide. The cultivated tea suffered from long-term targeted selection of traits and overexploitation of habitats by human beings, which may change the genetic structure. Chloroplast is an organelle with a conserved cyclic structure, and can help us better understand the evolutionary relationship of <jats:italic>Camellia</jats:italic> plants.<jats:bold>Results:</jats:bold> The study conducted comparative analysis and evolution analysis between cultivated tea and wild tea, and detected the evolution characteristic in cultivated tea. Chloroplast genome sizes of cultivated tea were slightly different, ranged from 157,025 bp to 157,085 bp. These cultivated species were more conservative than wild species, in terms of the genome length, genes number, genes arrangement and GC contents. However, the IRs length of cultivated species was about 20 bp shorter than that of <jats:italic>C. sinensis </jats:italic>var. sisnensis. We also found that the nucleotide diversity of 14 sequences in cultivated tea was higher than that of wild tea. These results provided the evidence on the variation of chloroplast genomes of cultivated tea. Detail analysis on the chloroplast genome variation and evolution of cultivated tea showed that 67 SNPs and 46 indels and 16 protein coding genes had nucleotide substitutions. The most comment variation gene was <jats:italic>ycf1</jats:italic>. It has the largest number of nucleotide substitutions. At the same time, in<jats:italic> ycf1</jats:italic>, five amino acid sites were exhibiting site-specific selection, and a 9 bp sequence insertion was found in the <jats:italic>C. sinensis</jats:italic> cultivar. Anhua. The phylogenetic tree constructed by<jats:italic> ycf1</jats:italic> sequence shows that two cultivated tea were not completely clustered, and the evolutionary relationship between <jats:italic>C. sinensis</jats:italic> var. sisnensis and <jats:italic>C. sinensis</jats:italic> cultivar. Longjing is closer than that of <jats:italic>C. sinensis</jats:italic> cultivar. Anhua.<jats:bold>Conclusions:</jats:bold> The cultivated species were more conservative than wild species in terms of architecture and linear sequence order. The variation of chloroplast genome of cultivated tea was mainly manifested in the nucleotide polymorphism of some sequences. The <jats:italic>ycf1</jats:italic> gene played an important role in the adaptive evolution of cultivated tea. These results provided evidence regarding the influence of human activities on tea.</jats:p>