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Based on Complete Chloroplast Genome Sequences: Effects of Taxon Sampling and Phylogenetic Methods on Resolving Relationships Among Rosids Robert K

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Clemson University TigerPrints Publications Genetics and Biochemistry 4-2006 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 University of Texas at Austin Charalambos Kaittanis University of Central Florida Christopher Saski Clemson University, [email protected] Seung-Bum Lee University of Central Florida Jeffrey Tomkins Clemson University See next page for additional authors Follow this and additional works at: https://tigerprints.clemson.edu/gen_biochem_pubs Part of the Genetics and Genomics Commons Recommended Citation Please use publisher's recommended citation. This Article is brought to you for free and open access by the Genetics and Biochemistry at TigerPrints. It has been accepted for inclusion in Publications by an authorized administrator of TigerPrints. For more information, please contact [email protected]. Authors Robert K. Jansen, Charalambos Kaittanis, Christopher Saski, Seung-Bum Lee, Jeffrey Tomkins, Andrew Alverson, and Henry Daniell This article is available at TigerPrints: https://tigerprints.clemson.edu/gen_biochem_pubs/3 BMC Evolutionary Biology BioMed Central Research article Open Access 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 Jansen1, Charalambos Kaittanis2, Christopher Saski3, Seung- Bum Lee2, Jeffrey Tomkins3, Andrew J Alverson1 and Henry Daniell*2 Address: 1Section of Integrative Biology and Institute of Cellular and Molecular Biology, Patterson Laboratories 141, University of Texas, Austin, TX 78712, USA, 2University of Central Florida, Dept. of Molecular Biology & Microbiology, Biomolecular Science, Building #20, Orlando, FL 32816-2364, USA and 3Clemson University Genomics Institute, Clemson University, Biosystems Research Complex, 51, New Cherry Street, SC 29634, USA Email: Robert K Jansen - [email protected]; Charalambos Kaittanis - [email protected]; Christopher Saski - [email protected]; Seung-Bum Lee - [email protected]; Jeffrey Tomkins - [email protected]; Andrew J Alverson - [email protected]; Henry Daniell* - [email protected] * Corresponding author Published: 09 April 2006 Received: 09 December 2005 Accepted: 09 April 2006 BMC Evolutionary Biology 2006, 6:32 doi:10.1186/1471-2148-6-32 This article is available from: http://www.biomedcentral.com/1471-2148/6/32 © 2006 Jansen et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 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. Page 1 of 14 (page number not for citation purposes) BMC Evolutionary Biology 2006, 6:32 http://www.biomedcentral.com/1471-2148/6/32 2, 19, 26 7 9 9 16, 18 4 5, 18 t rnS-GGA 34* C trn trnL-U C F- G trnM-CAU U GA Z C A b D s A sb A trnG- b GG p - p T ps n tr CA N G r bc et C- p L yc a r rn t B t ps cc r 4 f U nT-UGU aA a ndh 3 A n s D 4 s p ndhC G d p p saI CA trnV-UAC hK rps1 - ycf4 J U C a - M tpE S c a f emA t n n M p r r -UU t -GUA B t petA E Y -GUC psb n n D r r t t n r t rpoB p et pet L poC1 G psbJ r psa p rpl33J ps sbL rps ps bF 1 b oC2 17* 8 trnW-CCE LSC rp trnP-UGG s2 A rp I rpl20 atp rps1 H atp 4 2_5en psbB clpP pF -UCU 29* d at trnR C psb G-GC 5, 16 T atpA trn psbH petB psbN psbI psbK 21* petD nS-GCU tr 1* -UUG rpoA trnQ rps11 rpl36 Vitis vinifera rps16 infA rps8 trnK-UUU rpl14 rpl16 matK rps3 trnK-UU rpl22 160,928 bp U 19 psbA rps trnH-GU rpl2 G rpl23 20, 27 8 I-CAU 3 trn rpl2 I rpl23 R trnI- b a CAU IR ycf2 A cf2 y L-CA 11**,14** 11**, 14** trn B h nd nd 6**,12**,13**, 6**,12** 13**, 7 _3e SSC 15**, 22, 23, rps s12 trnV 15**, 22, 23, rp trnL- 30, 31, 32, 33, -GAC 30, 31, 32, 33, t tr r C 35, 36 rn nI rn1 n AA 35, 36 A -G d - 6 hB UGC A tr U rp n r s R-ACG r r rps 7 r n n 2 r 1 r 4 3 2_3 N-GUU n . 5 6 5 trn rp yc en GAC1 n - n d d D s E G dhA f1 ndhF h rrn 1 h U h H rnV 5 d saC d A dh 7, 10 t C dhI n p n n 2 -G G n -U 23 trnI n 5 r . 7, 10 r tr trnA G n4 rn5 1 n 2 r r N r cf y -GUU 2 R-AC 3 G l A A s trn rp c U c trnL- 25* 2424** 7, 10, 28 Rubisco subunit 8 Photosystem protein 3, 20, 27 Cytochrome-related ATP synthase NADH dehydrogenase Ribosomal protein subunit Ribosomal RNA Plastid-encoded RNA polymerase Other Unknown function / Unnamed (ycf) Transfer RNA Intron GeneFigure map 1 of the Vitis vinifera chloroplast genome 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 tran- scribed in the clockwise direction and genes on the inside of the map are transcribed in the counterclockwise direction. Num- bers 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. Page 2 of 14 (page number not for citation purposes) BMC Evolutionary Biology 2006, 6:32 http://www.biomedcentral.com/1471-2148/6/32 ering plants. Single and multi-gene phylogenies of rosids have identified seven major clades, however, relation- ships among these clades remain unresolved [13-16]. One of these unresolved clades includes the Vitaceae, which includes grape, an important crop plant. The phylogenetic position of Vitaceae has been controversial for many years. Some previous classifications place the family within the Rhamnales in the subclass Rosidae [17]. More recent molecular phylogenies based on one to four genes provided weak support for the placement of Vitaceae sister to the Caryophylales [18], asterids [18], Saxifragales [14], Dilleniaceae [19], or to the rosids [14-16]. Thus, the phy- logenetic relationship of the grape family to core eudicots remains unresolved. In this article, we report on the complete sequence of the chloroplast genome of grape (Vitis vinifera, Vitaceae). In addition to describing the organization of the chloroplast HistogrambpplastFigure long genome with2 showing a sequence the number identity of≥ 90%repeated in the sequences grape chloro- ≥ 30 genome, we present results of phylogenetic analyses of Histogram showing the number of repeated sequences ≥ 30 DNA sequences for 61 genes from grape and 26 other bp long with a sequence identity ≥ 90% in the grape chloro- angiosperm chloroplast genomes, including eight other plast genome. members of the rosid clade.
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