title: Phylogenetic analyses of Vitis (Vitaceae) based on complete chloroplast genome sequences: effects of taxon sampling and phylogenetic methods on resolving relationships among rosids.
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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Section of Integrative Biology and Institute of Cellular and Molecular Biology, Patterson Laboratories 141, University of Texas, Austin, TX 78712, USA. jansen@mail.utexas.edu
authors.forename: Robert K
authors.initials: RK
authors.lastname: Jansen
authors.forename: Charalambos
authors.initials: C
authors.lastname: Kaittanis
authors.forename: Christopher
authors.initials: C
authors.lastname: Saski
authors.forename: Seung-Bum
authors.initials: SB
authors.lastname: Lee
authors.forename: Jeffrey
authors.initials: J
authors.lastname: Tomkins
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Alverson
authors.forename: Henry
authors.initials: H
authors.lastname: Daniell
mesh_terms: D001483:Base Sequence; D002736:Chloroplasts / Q000235:genetics*; D018742:DNA, Chloroplast / Q000235:genetics; D018076:DNA, Complementary / Q000378:metabolism; D019143:Evolution, Molecular; D020224:Expressed Sequence Tags; D017343:Genes, Plant; D018745:Genome, Plant; D019684:Magnoliopsida; D008969:Molecular Sequence Data; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D027844:Vitaceae / Q000235:genetics*
chemical_list: D018742:DNA, Chloroplast; D018076:DNA, Complementary