Identification, comparative and phylogenetic analysis of eight Vitis species based on the chloroplast genome revealed their contribution to heat tolerance in grapevines

The chloroplast genome plays an important role in exploring the origin and evolution of grapes. In this study, the chloroplast genomes of eight grape germplasms were analyzed. The results show that the sequence arrangement was highly conserved and has a typical annular quadripartite structure. At the same time, GC content, gene sequence, repeat type and codon bias pattern are highly conserved. Whereas, 19 mutation hotspot regions were identified by the comparative analysis, including 9 protein-coding genes (atpF, rpoC2, rps18, psbC, atpB, rbcL, rps20, ycf1 and ycf15) and 10 non-coding regions (trnK - rps16, rps16 - trnQ, trnE - trnT, psbZ - trnG, ndhC - trnV, accD - psaI, ycf2 - trnL, ndhF - rpl32, ccsA - ndhD, trnL - ycf2). Most of these highly variable genes were involved in the physiological process of photosynthesis. Further examination of photosynthetic fluorescence showed an obvious difference among those species under high-temperature conditions. In addition, maximum likelihood (ML) evolutionary trees depend on the chloroplast genome and CDS sequences suggest that heat tolerance may be related to the phylogeny of grapevine. In the future, the highly variable sequences and SSR loci were also identified by the chloroplast genome comparison, and those results may be used for the DNA molecular marker in taxonomic studies and contribute to the heat stress resistance breeding of grapevine.