Climate-influenced boreotropical survival and rampant introgressions explain the thriving of New World grapes in the north temperate zone.

The north temperate region was characterized by a warm climate and a rich thermophilic flora before the Eocene, but early diversifications of the temperate biome under global climate change and biome shift remain uncertain. Moreover, it is becoming clear that hybridization/introgression is an important driving force of speciation in plant diversity. Here, we applied analyses from biogeography and phylogenetic networks to account for both introgression and incomplete lineage sorting based on genomic data from the New World Vitis, a charismatic component of the temperate North American flora with known and suspected gene flow among species. Biogeographic inference and fossil evidence suggest that the grapes were widely distributed from North America to Europe during the Paleocene to the Eocene, followed by widespread extinction and survival of relicts in the tropical New World. During the climate warming in the early Miocene, a Vitis ancestor migrated northward from the refugia with subsequent diversification in the North American region. We found strong evidence for widespread incongruence and reticulate evolution among nuclear genes within both recent and ancient lineages of the New World Vitis. Furthermore, the organellar genomes showed strong conflicts with the inferred species tree from the nuclear genomes. Our phylogenomic analyses provided an important assessment of the wide occurrence of reticulate introgression in the New World Vitis, which potentially represents one of the most important mechanisms for the diversification of Vitis species in temperate North America and even the entire temperate Northern Hemisphere. The scenario we report here may be a common model of temperate diversification of flowering plants adapted to the global climate cooling and fluctuation in the Neogene.

Comparative Chloroplast Genome Analyses of the Winter-Blooming Eastern Asian Endemic Genus Chimonanthus (Calycanthaceae) With Implications For Its Phylogeny and Diversification.

Chimonanthus of Calycanthaceae is a small endemic genus in China, with unusual winter-blooming sweet flowers widely cultivated for ornamentals and medicinal uses. The evolution of Chimonanthus plastomes and its phylogenetic relationships remain unresolved due to limited availability of genetic resources. Here, we report fully assembled and annotated chloroplast genomes of five Chimonanthus species. The chloroplast genomes of the genus (size range 153,010 - 153,299 bp) reveal high similarities in gene content, gene order, GC content, codon usage, amino acid frequency, simple sequence repeats, oligonucleotide repeats, synonymous and non-synonymous substitutions, and transition and transversion substitutions. Signatures of positive selection are detected in atpF and rpoB genes in C. campanulatus. The correlations among substitutions, InDels, and oligonucleotide repeats reveal weak to strong correlations in distantly related species at the intergeneric levels, and very weak to weak correlations among closely related Chimonanthus species. Chloroplast genomes are used to reconstruct a well-resolved phylogenetic tree, which supports the monophyly of Chimonanthus. Within Chimonanthus, C. praecox and C. campanulatus form one clade, while C. grammatus, C. salicifolius, C. zhejiangensis, and C. nitens constitute another clade. Chimonanthus nitens appears paraphyletic and is closely related to C. salicifolius and C. zhejiangensis, suggesting the need to reevaluate the species delimitation of C. nitens. Chimonanthus and Calycanthus diverged in mid-Oligocene; the radiation of extant Chimonanthus species was dated to the mid-Miocene, while C. grammatus diverged from other Chimonanthus species in the late Miocene. C. salicifolius, C. nitens (a), and C. zhejiangensis are inferred to have diverged in the Pleistocene of the Quaternary period, suggesting recent speciation of a relict lineage in the subtropical forest regions in eastern China. This study provides important insights into the chloroplast genome features and evolutionary history of Chimonanthus and family Calycanthaceae.

Vitisshizishanensis, a new species of the grape genus from Hubei province, China.

Vitisshizishanensis (Vitaceae), a new species from Hubei, China, is described and illustrated. It is morphologically similar to V.flexuosa and V.bryoniifolia, but differs in leaf lobing and pubescence. It can be easily distinguished from the two species based on its glabrous or with very sparse arachnoid tomentum on the abaxial mature leaf surface, and its unlobed to 3-7 lobed leaves. A detailed description, along with photographs for the new species, and a table for morphological comparisons with similar Vitis species, are also provided.

Phylogenomic relationships and character evolution of the grape family (Vitaceae).

The grape family consists of 16 genera and ca. 950 species. It is best known for the economically important fruit crop - the grape Vitis vinifera. The deep phylogenetic relationships and character evolution of the grape family have attracted the attention of researchers in recent years. We herein reconstruct the phylogenomic relationships within Vitaceae using nuclear and plastid genes based on the Hyb-Seq approach and test the newly proposed classification system of the family. The five tribes of the grape family, including Ampelopsideae, Cayratieae, Cisseae, Parthenocisseae, and Viteae, are each robustly supported by both nuclear and chloroplast genomic data and the backbone relationships are congruent with previous reports. The cupular floral disc (raised above and free from ovary at the upper part) is an ancestral state of Vitaceae, with the inconspicuous floral disc as derived in the tribe Parthenocisseae, and the state of adnate to the ovary as derived in the tribe Viteae. The 5-merous floral pattern was inferred to be the ancestral in Vitaceae, with the 4-merous flowers evolved at least two times in the family. The compound dichasial cyme (cymose with two secondary axes) is ancestral in Vitaceae and the thyrse inflorescence (a combination of racemose and cymose branching) in tribe Viteae is derived. The ribbon-like trichome only evolved once in Vitaceae, as a synapomorphy for the tribe Viteae.

Expression of the subgroup IIIf bHLH transcription factor CpbHLH1 from Chimonanthus praecox (L.) in transgenic model plants inhibits anthocyanin accumulation.

KEY MESSAGE: Overexpression of CpbHLH1 in Arabidopsis and tobacco resulted in a dramatic decrease in anthocyanin accumulation by repressing the expression of late biosynthesis genes in the flavonoid biosynthesis pathway. Many basic helix-loop-helix (bHLH) transcription factors (TFs) of subgroup IIIf have been characterized as anthocyanin-associated activators in higher plants, but information regarding bHLH TFs that inhibit anthocyanin accumulation remains scarce. In this study, the subgroup IIIf bHLH TF CpbHLH1 from Chimonanthus praecox (L.) was identified as a negative regulator of anthocyanin accumulation. Our results showed that overexpression of CpbHLH1 in model plant species, Arabidopsis and tobacco, resulted in a dramatic decrease in anthocyanin content, whereas the content of proanthocyanidin was little affected. Quantitative RT-PCR (qRT-PCR) assays of the structural genes in the flavonoid biosynthesis pathway revealed that CpbHLH1 inhibits anthocyanin accumulation mainly through repressing the expression of late biosynthesis genes (LBGs). Interactions between CpbHLH1 protein and AtPAP1/NtAN2 protein were detected via yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays. This is the first bHLH repressor of anthocyanin biosynthesis identified in dicotyledons. These results can help us better understand the anthocyanin regulatory network in plants and may provide insights into the diverse functions of bHLH proteins.

Testing morphological trait evolution and assessing species delimitations in the grape genus using a phylogenomic framework.

The grape genus (Vitis L.) is of great agronomic importance and represents an economically valuable resource. Researchers have explored the phylogenetic relationships of subgenus Vitis for decades. However, the evolutionary patterns of many morphological characters of subgenus Vitis have not yet been explored in the context of a robust phylogenetic framework. Within the East Asian clade, V. bryoniifolia and its closely related taxa form the V. bryoniifolia clade, which is taxonomically complex. The phylogenetic relationships and species delimitation within this clade remain poorly resolved, due to the limited sampling in prior studies. We tested morphological trait evolution based on ancestral character state reconstruction using a phylogenomic framework. With 89 accessions from the East Asian subgenus Vitis sampled, a robust phylogenetic relationship of the V. bryoniifolia clade is reconstructed using the restriction-site associated DNA sequencing (RAD-seq) data, which support the monophyly of most taxa of the V. bryoniifolia clade. Ancestral character state reconstructions suggest that the weak climbing ability and simplified tendrils of Vitis each evolved multiple times. This study provides a reliable phylogenomic framework for the V. bryoniifolia clade. Coupled with morphological analyses, we discuss the taxonomic status of some taxa in the V. bryoniifolia clade and untangle a taxonomic dilemma in the grape genus.

Phylogenomics, biogeography, and adaptive radiation of grapes.

The application of whole-genome resequencing based on next-generation sequencing technologies provides an unprecedented opportunity for researchers to resolve long-standing evolutionary problems. Taxa belonging to the grape genus (Vitis L.) represent important genetic resources for the improvement of cultivated grapes. However, it has been challenging to resolve the deep phylogenetic relationships within Vitis, limiting the current understanding of the evolutionary history of Vitis and preventing the use of valuable wild grape resources. In this study, we obtained whole-genome sequence data from 41 accessions representing most taxa within subgenus Vitis and aligned these sequences to the Vitis vinifera L. reference genome. We reconstructed deep phylogenetic relationships within subgenus Vitis based on 2068 single-copy orthologous genes, which led to a robust topology with bootstrap support values of 100% for almost all branches. Three main clades are recovered within subgenus Vitis reflecting their continental distribution through North America, Europe, and East Asia, respectively. Our results suggest that the most possible migration route of the East Asian Vitis is from northeastern Asia southward to South Asia and Southeast Asia. The East Asian Vitis seems to have experienced adaptive radiation during the Miocene. This study provides novel insights into the diversification history of the grape genus Vitis.

Morphology, Structure, and Ontogeny of Trichomes of the Grape Genus (Vitis, Vitaceae).

Trichomes are widely distributed on surfaces of different organs in the grape genus Vitis and are of taxonomic utility. To explore the morphology, structure and ontogeny of Vitis trichomes, we investigated the diversity and distribution of trichomes in 34 species of Vitis. Two main types of trichomes in Vitis are documented: non-glandular and glandular. Within non-glandular trichomes, ribbon and simple trichomes are found on different vegetative plant organs. The morphology and ontogeny of these types of trichomes are further examined with light microscopy and scanning electron microscopy. The ultrastructure of the glandular trichomes is explored with transmission electron microscopy. The ribbon trichomes are twisted, greatly elongated and unicellular, and this trichome type may be a morphological synapomorphy of Vitis and its closest tropical relative Ampelocissus and Pterisanthes in Vitaceae. The simple trichomes are documented in most species sampled in the genus. The glandular trichomes are multicellular, non-vascularized and composed of both epidermis and subjacent layers. We show that prickles occurring along the stems and petioles of Vitis davidii are modified glandular trichomes. We observed that glandular trichomes of V. romanetii secrete mucilage and volatile substances which trap insectes on the glands. Transmission electron microscopy indicates that metabolic products accumulate in vacuoles, the cytoplasm and intercellular spaces. We infer that glandular trichomes and young prickles are involved in the secretion of these metabolic products and the intercellular spaces may be the places of temporary storage of these secretions.

Phylogeny of the Ampelocissus-Vitis clade in Vitaceae supports the New World origin of the grape genus.

The grapes and the close allies in Vitaceae are of great agronomic and economic importance. Our previous studies showed that the grape genus Vitis was closely related to three tropical genera, which formed the Ampelocissus-Vitis clade (including Vitis, Ampelocissus, Nothocissus and Pterisanthes). Yet the phylogenetic relationships of the four genera within this clade remain poorly resolved. Furthermore, the geographic origin of Vitis is still controversial, because the sampling of the close relatives of Vitis was too limited in the previous studies. This study reconstructs the phylogenetic relationships within the clade, and hypothesizes the origin of Vitis in a broader phylogenetic framework, using five plastid and two nuclear markers. The Ampelocissus-Vitis clade is supported to be composed of five main lineages. Vitis includes two described subgenera each as a monophyletic group. Ampelocissus is paraphyletic. The New World Ampelocissus does not form a clade and shows a complex phylogenetic relationship, with A. acapulcensis and A. javalensis forming a clade, and A. erdvendbergiana sister to Vitis. The majority of the Asian Ampelocissus species form a clade, within which Pterisanthes is nested. Pterisanthes is polyphyletic, suggesting that the lamellate inflorescence characteristic of the genus represents convergence. Nothocissus is sister to the clade of Asian Ampelocissus and Pterisanthes. The African Ampelocissus forms a clade with several Asian species. Based on the Bayesian dating and both the RASP and Lagrange analyses, Vitis is inferred to have originated in the New World during the late Eocene (39.4Ma, 95% HPD: 32.6-48.6Ma), then migrated to Eurasia in the late Eocene (37.3Ma, 95% HPD: 30.9-45.1Ma). The North Atlantic land bridges (NALB) are hypothesized to be the most plausible route for the Vitis migration from the New World to Eurasia, while intercontinental long distance dispersal (LDD) cannot be eliminated as a likely mechanism.

Molecular phylogeny of Cissus L. of Vitaceae (the grape family) and evolution of its pantropical intercontinental disjunctions.

Pantropical intercontinental disjunct distribution is a major biogeographic pattern in plants, and has been explained mainly by boreotropical migration via the North Atlantic land bridges (NALB) and transoceanic long-distance dispersal (LDD), and sometimes by vicariance. However, well-resolved phylogenies of pantropical clades are still relatively few. Cissus is the largest genus of the grape family Vitaceae and shows a pantropical intercontinental disjunction with its 300 species distributed in all major tropical regions. This study constructed the phylogenetic relationships and biogeographic diversification history of Cissus, employing five plastid markers (rps16, trnL-F, atpB-rbcL, trnH-psbA and trnC-petN). The results confirmed that Cissus polyphyletic, consisting of three main clades: the core Cissus, the Cissus striata complex, and the Australian-Neotropical disjunct Cissus antarctica -C. trianae clade. The latter two clades need to be removed from Cissus to maintain the monophyly of the genus. The core Cissus is inferred to have originated in Africa and is estimated to have diverged from its relatives in Vitaceae in the late Cretaceous. It diversified in Africa into several main lineages in the late Paleocene to the early Eocene, colonized Asia at least three times in the Miocene, and the Neotropics in the middle Eocene. The NALB seems the most plausible route for the core Cissus migration from Africa to the Neotropics in the middle Eocene. Three African-Asian and two Neotropical-Australian disjunctions in Cissus s.l. are estimated to have originated in the Miocene and may be best explained by LDD.