Phylogenetic analysis of the grape family (Vitaceae) based on the noncoding plastid trnC-petN, trnH-psbA, and trnL-F sequences

Abstract

The phylogeny of Vitaceae was reconstructed sampling 114 accessions of Vitaceae and the outgroup Leea of Leeaceae, using three noncoding plastid markers: trnC-petN, trnH-psbA, and trnL-F. Six 5-merous genera including Parthenocissus, Yua, Ampelocissus, Vitis, Nothocissus, and Pterisanthes form a well-supported clade. Ampelopsis, Rhoicissus, and the Cissus striata complex form a clade sister to the clade containing all the other taxa of Vitaceae. The core Cissus clade is resolved to be sister to the Cayratia-Tetrastigma-Cyphostemma clade, forming a clade of taxa with 4-merous flowers. The Parthenocissus-Yua clade is sister to the Ampelocissus-Vitis-Nothocissus-Pterisanthes clade. The Old World Cissus is paraphyletic, with the New World core Cissus nested within it. The intercontinental disjunction between Africa and Asia may have evolved at least twice in Cissus. Cayratia is paraphyletic with four Asian species sampled grouping with Tetrastigma and the African species forming another clade.

Chloroplast diversity indicates two independent maternal lineages in cultivated grapevine (Vitis vinifera L. subsp. vinifera)

“…This deletion was absent in the investigated Vitis species and in other Vitis species investigated in previous studies (Ren et al 2011). This region tends to contain relatively large deletions (Shaw et al 2005), and the deletions are more than twice as rare in angiosperms as nucleotide substitutions (Shaw et al 2007).…”

“…1). The markers comprised trnH-psbA, trnL-trnF, trnC-petN (Ren et al 2011), ccmp5, ccmp3, ccmp10 (Arroyo-García et al 2002), ccSSR-23, ccSSR-9 (Arroyo-García et al 2006, VVCP14789, VVCP28926, VVCP50403, VVCP13285, VVCP32585, VVCP67629, VVCP69871, VVCP121638, and VVCP123308 (Péros et al 2011). Those markers were predicted to be UCMs that potentially amplify only one fragment solely from the plastome.…”

“…Based on the in silico predictions we chose four UCMs for detailed investigation: one that was used successfully in Vitis (trnC-petN) (Ren et al 2011;Liu et al 2013) and three hypervariable cpSSR markers that were specifically designed for Vitis (VVCP14789 [atpF-atpH], VVCP28926 [rpoB-trnC], and VVCP50403 [trnT-trnL]) (Péros et al 2011). …”

“…1). We examined whether 17 markers (Péros et al 2011;Ren et al 2011) were located in a unique chloroplast segment (Fig. 1).…”

Synopsis of Nekemias Raf., a segregate genus from Ampelopsis Michx. (Vitaceae) disjunct between eastern/southeastern Asia and eastern North America, with ten new combinations

“…(Vitaceae) is one of the 15 recognized genera in Vitaceae with about 25 species (Suessenguth 1953; Chen et al 2007; Wen 2007; Wen et al 2013a). The genus was shown to be paraphyletic by recent phylogenetic analyses based on plastid (Soejima and Wen 2006; Ren et al 2011; Nie et al 2012) and nuclear GAI1 (Wen et al 2007) analyses. The plastid data (Soejima and Wen 2006; Ren et al 2011; Nie et al 2012) supported that the African Rhoicissus and the South American Cissus striata complex formed a clade with the simple or palmately leaved Ampelopsis (sect.…”