Transcriptome sequences resolve deep relationships of the grape family

Abstract

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.

Figure 1. Maximum likelihood tree of Vitaceae using nucleotide sequences of 229 genes from the 15 transcriptomes of Vitaceae.

The same topology was recovered from the 417 gene data set. Bootstrap support for all nodes was 100%, and posterior probabilities in the Bayesian inference for all nodes were 1.00.

Figure 2. Unrooted tree of 15 species of Vitaceae based on nucleotide sequences of 229 genes.

The node numbers correspond to those in Table S4.

Figure 3. Average bootstrap support and the gene number in the phylogenetic analyses based on data from Table S4.

Figure 4. Divergence time estimation of Vitaceae clades using the program mcmctree in PAML and 4-fold degenerate sites.

The red dots correspond to calibration points.