10.5061/DRYAD.D15V3
Zhang, Ning
Smithsonian Institution
Wen, Jun
Smithsonian Institution
Zimmer, Elizabeth A.
Smithsonian Institution
Data from: Congruent deep relationships in the grape family (Vitaceae)
based on sequences of chloroplast genomes and mitochondrial genes via
genome skimming
Dryad
dataset
2016
genome skimming
Next-generation sequencing
Grapes
2016-11-30T00:00:00Z
2016-11-30T00:00:00Z
en
https://doi.org/10.1371/journal.pone.0144701
10342122 bytes
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CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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
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 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.
174_coding_noncoding_genes174 regions including 79 coding genes and 95
non-coding regions79genes_concatenated79 coding genes56genes-less-9056
coding genes with the sequence identity less than
90%16mitogenes-modified16 mitochondrial genes26genes-less-8526 coding
genes with the sequence identity less than 85%10genes_less_8010 coding
genes with sequence identity less than
80%concatenated_non_coding_95genes95 non-coding regions