ArticlePloS one2015
Congruent Deep Relationships in the Grape Family (Vitaceae) Based on Sequences of Chloroplast Genomes and Mitochondrial Genes via Genome Skimming.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- Chromosome-level phylogenomics and genome evolution of the grape family.Nature plants · 2026Article
- Complete assembly of Onobrychis viciifolia mitochondrial genome reveals evolutionary dynamics.Planta · 2026Article
- Extensive genome-wide phylogenetic discordance is due to incomplete lineage sorting in the rapidly radiated East Asian genus Nekemias (Vitaceae).Annals of botany · 2025Article
- Deep genome skimming reveals the hybrid origin ofPlant diversity · 2024Article
- Plastid genome data provide new insights into the dynamic evolution of the tribe Ampelopsideae (Vitaceae).BMC genomics · 2024Article
- Comparative and phylogenetic analyses of plastid genomes of the medicinally important genusFrontiers in plant science · 2024Article
- Whole mitochondrial and chloroplast genome sequencing of Tunisian date palm cultivars: diversity and evolutionary relationships.BMC genomics · 2023Article
- Molecular phylogeny and inflorescence evolution ofPlant diversity · 2023Article
- Detecting signals of adaptive evolution in grape plastomes with a focus on the Cretaceous-Palaeogene (K/Pg) transition.Annals of botany · 2022Article
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- Seed Geometry in the Vitaceae.Plants (Basel, Switzerland) · 2021Review
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- On the Species Delimitation of theFrontiers in plant science · 2021Article
- Dates and rates in grape's plastomes: evolution in slow motion.Current genetics · 2020Article
- Nuclear and Chloroplast Sequences Resolve the Enigmatic Origin of the Concord Grape.Frontiers in plant science · 2020Article
- Complete Chloroplast Genomes ofPlants (Basel, Switzerland) · 2019Article
- Understanding the phyllosphere microbiome assemblage in grape species (Vitaceae) with amplicon sequence data structures.Scientific reports · 2019Article
- Does the EnigmaticFrontiers in plant science · 2019Article
- Article
Corrections and comments
- Erratum issued
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Vitaceae is well-known for having one of the most economically important fruits, i.e., the grape (Vitis vinifera). The deep phylogeny of the grape family was not resolved until a recent phylogenomic analysis of 417 nuclear genes from transcriptome data. However, it has been reported extensively that topologies based on nuclear and organellar genes may be incongruent due to differences in their evolutionary histories. Therefore, it is important to reconstruct a backbone phylogeny of the grape family using plastomes and mitochondrial genes. In this study,next-generation sequencing data sets of 27 species were obtained using genome skimming with total DNAs from silica-gel preserved tissue samples on an Illumina NextSeq 500 instrument [corrected]. Plastomes were assembled using the combination of de novo and reference genome (of V. vinifera) methods. Sixteen mitochondrial genes were also obtained via genome skimming using the reference genome of V. vinifera. Extensive phylogenetic analyses were performed using maximum likelihood and Bayesian methods. The topology based on either plastome data or mitochondrial genes is congruent with the one using hundreds of nuclear genes, indicating that the grape family did not exhibit significant reticulation at the deep level. The results showcase the power of genome skimming in capturing extensive phylogenetic data: especially from chloroplast and mitochondrial DNAs.
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