RESEARCH ARTICLE Congruent Deep Relationships in the Grape Family (Vitaceae) Based on Sequences of

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 incon-gruent due to differences in their evolutionary histories. Therefore, it is important to recon-struct 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 HiSeq 2500 instrument. 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 hun-dreds 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 exten-sive phylogenetic data: especially from chloroplast and mitochondrial DNAs