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Phylogenetic Analyses of Vitis (Vitaceae) Based on Complete Chloroplast Genome Sequences: Effects of Taxon Sampling and Phylogenetic Methods on Resolving Relationships Among Rosids

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Phylogenetic Analyses of Vitis (Vitaceae) Based on Complete Chloroplast Genome Sequences: Effects of Taxon Sampling and Phylogenetic Methods on Resolving Relationships Among Rosids

Robert K Jansen et al. BMC Evol Biol.

Abstract

Background: The Vitaceae (grape) is an economically important family of angiosperms whose phylogenetic placement is currently unresolved. Recent phylogenetic analyses based on one to several genes have suggested several alternative placements of this family, including sister to Caryophyllales, asterids, Saxifragales, Dilleniaceae or to rest of rosids, though support for these different results has been weak. There has been a recent interest in using complete chloroplast genome sequences for resolving phylogenetic relationships among angiosperms. These studies have clarified relationships among several major lineages but they have also emphasized the importance of taxon sampling and the effects of different phylogenetic methods for obtaining accurate phylogenies. We sequenced the complete chloroplast genome of Vitis vinifera and used these data to assess relationships among 27 angiosperms, including nine taxa of rosids.

Results: The Vitis vinifera chloroplast genome is 160,928 bp in length, including a pair of inverted repeats of 26,358 bp that are separated by small and large single copy regions of 19,065 bp and 89,147 bp, respectively. The gene content and order of Vitis is identical to many other unrearranged angiosperm chloroplast genomes, including tobacco. Phylogenetic analyses using maximum parsimony and maximum likelihood were performed on DNA sequences of 61 protein-coding genes for two datasets with 28 or 29 taxa, including eight or nine taxa from four of the seven currently recognized major clades of rosids. Parsimony and likelihood phylogenies of both data sets provide strong support for the placement of Vitaceae as sister to the remaining rosids. However, the position of the Myrtales and support for the monophyly of the eurosid I clade differs between the two data sets and the two methods of analysis. In parsimony analyses, the inclusion of Gossypium is necessary to obtain trees that support the monophyly of the eurosid I clade. However, maximum likelihood analyses place Cucumis as sister to the Myrtales and therefore do not support the monophyly of the eurosid I clade.

Conclusion: Phylogenies based on DNA sequences from complete chloroplast genome sequences provide strong support for the position of the Vitaceae as the earliest diverging lineage of rosids. Our phylogenetic analyses support recent assertions that inadequate taxon sampling and incorrect model specification for concatenated multi-gene data sets can mislead phylogenetic inferences when using whole chloroplast genomes for phylogeny reconstruction.

Figures

Figure 1
Figure 1
Gene map of the Vitis vinifera chloroplast genome. The thick lines indicate the extent of the inverted repeats (IRa and IRb), which separate the genome into small (SSC) and large (LSC) single copy regions. Genes on the outside of the map are transcribed in the clockwise direction and genes on the inside of the map are transcribed in the counterclockwise direction. Numbers on the outside of map indicate location of repeats in Table 1. Repeats indicated by * (palindrome) and ** (tandem) are only shown once since they occur in the same location.
Figure 2
Figure 2
Histogram showing the number of repeated sequences ≥ 30 bp long with a sequence identity ≥ 90% in the grape chloroplast genome.
Figure 3
Figure 3
Phylogenetic tree of 28-taxon data set based on 61 chloroplast protein-coding genes using maximum parsimony (MP) and maximum likelihood (ML). (A) The MP tree has a length of 49,511, a consistency index of 0.47 (excluding uninformative characters) and a retention index of 0.62. (B) The ML tree has a ML value of – lnL = 289638.676. Numbers above and below nodes are bootstrap support values ≥ 50%. Ordinal and higher level group names follow APG II [94]. Taxa in red are members of eurosid I and Vitis is indicated in blue. Thicker lines in tree indicate members of Eudicots.
Figure 4
Figure 4
Phylogenetic trees of 29-taxon data set (including Gossypium) based on 61 chloroplast protein-coding genes using maximum parsimony (MP) and maximum likelihood (MP). (A) The MP tree has a length of 51,056, a consistency index of 0.46 (excluding uninformative characters) and a retention index of 0.61. (B) The ML tree has a ML value of – lnL = 296670.545. Numbers at nodes indicate bootstrap support ≥ 50%. Arrows indicate taxa that have lost the rpl22 gene. Ordinal and higher level group names follow APG II [94]. Taxa in red are members of eurosid I and Vitis is indicated in blue. Thicker lines in tree indicate members of Eudicots.

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