Vitis, Linnaeus, 1753

Mu, Xian-Yun, Shen, Xue-Li, Wu, Yuan-Mi, Zhu, Yi-Xuan, Dong, Shu-Bin, Xia, Xiao-Fei, Lin, Qin- Wen, Fan, Pei-Ge, Liu, Yu-Lin & Zhang, Zhi-Xiang, 2018, Plastid phylogenomic study of grape species and its implications for evolutionary study and conservation of Vitis, Phytotaxa 364 (1), pp. 71-80 : 75

Phylogeny of Vitis

Advances in the molecular phylogeny of Vitis has been limited by extensive reticulation and low genetic variation. Although Vitis has been split into three clades that mirror the species’ continental distribution pattern, these main clades are paraphyletic, each consisting of several polytomies ( Tröndle et al., 2010; Zecca et al., 2012). Although the two subgenera classification system is supported by analysis with more molecular markers, the origin of Vitis and delimitation of modern grape species are questionable ( Zecca et al., 2012). Furthermore, the divergence time of Vitis and main clades within the genus are conflicting because of different fossil calibration schemes ( Liu et al., 2016; Wan et al., 2013; Zecca et al., 2012). The poor resolution of the molecular trees hinders our further understanding of the classification and evolution of Vitis .

In this study, well resolved molecular trees were generated, and the tree generated from LSC ( Fig. 3 ) was better resolved than that of the complete chloroplast genome ( Fig. S1 ) and the nine hyper-variable regions ( Fig. S2 ). Within subg. Vitis , two strongly supported monophyletic clades were presented which mirrored their distribution pattern (purple clade represent species from North America, and blue clade represent species from Eurasia). The Eurasia clade was consisted by two strongly supported monophyletic clade, the Europe clade (yellow branch) and the Asia clade (green branch). Two samples of V. amurensis nested together, and V. baihuashanensis is resolved as closest sister of them ( Fig. 3 ). Molecular trees generated from SSC and IR were poorly resolved. Based on the molecular tree, the identity of another V. amurensis deposited in Genbank ( V. amurensis USDA in Fig. 3 , accession number: LC318487) might be a misidentification. The molecular tree presented in this study is basically the same as the phylogenetic inference that focusing at Norther America Vitis species based on high-throughput sequencing method ( Klein et al., 2018), which further implies the great potential of chloroplast genome sequences and nine markers suggested here for Vitis phylogeny.

Figures

FIGURE 1. Gene map of the four Vitis chloroplast genomes.

FIGURE 2. Sliding window analysis of the complete chloroplast genome of 13 Vitis taxa (window length: 600 bp, step size: 50 bp). X- axis: position of the midpoint of a window, Y-axis: nucleotide diversity of each window.

FIGURE 3. Phylogenetic tree of Vitis based on large single copy region inferred from maximum likelihood (ML) analysis based on IQ- TREE website. Purple branches represent species from North America, yellow branch represent species from Europe, and green branches represent species from Asia. Value of ultrafast bootstrap approximation are indicated on the branches.