Transcriptome sequences resolve deep relationships of the grape family.
Previous phylogenetic studies of the grape family (Vitaceae) yielded poorly resolved deep relationships, thus impeding our understanding of the evolution of the family. Next-generation sequencing now offers access to protein coding sequences very easily, quickly and cost-effectively. To improve upon earlier work, we extracted 417 orthologous single-copy nuclear genes from the transcriptomes of 15 species of the Vitaceae, covering its phylogenetic diversity. The resulting transcriptome phylogeny provides robust support for the deep relationships, showing the phylogenetic utility of transcriptome data for plants over a time scale at least since the mid-Cretaceous. The pros and cons of transcriptome data for phylogenetic inference in plants are also evaluated.
Department of Botany, National Museum of Natural History, MRC166, Smithsonian Institution, Washington, D.C., United States of America.
Jun
J
Wen
Zhiqiang
Z
Xiong
Ze-Long
ZL
Nie
Likai
L
Mao
Yabing
Y
Zhu
Xian-Zhao
XZ
Kan
Stefanie M
SM
Ickert-Bond
Jean
J
Gerrath
Elizabeth A
EA
Zimmer
Xiao-Dong
XD
Fang
D019295:Computational Biology; D019143:Evolution, Molecular; D017343:Genes, Plant; D059014:High-Throughput Nucleotide Sequencing; D010802:Phylogeny; D059467:Transcriptome; D027843:Vitis / Q000145:classification* / Q000235:genetics*