MBE Advance Access published online on October 14, 2008
Molecular Biology and Evolution, doi:10.1093/molbev/msn226
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Research Article |
mtDNA of Vitis vinifera and the issue of rampant horizontal gene transfer
IASMA Research Center, Via E. Mach 1, 38010 San Michele all'Adige (TN), Italy
Agricultural Faculty, Via Celoria 26, University of Milan, 20133 Milan Italy
Correspondence and requests for materials should be addressed to: Dr. Vadim Goremykin, e-mail: Vadim.Goremykin{at}iasma.it
Received for publication April 21, 2008. Revision received June 28, 2008. Revision received August 27, 2008. Revision received October 4, 2008. Accepted for publication October 4, 2008.
The mitochondrial genome of grape (Vitis vinifera), the largest organelle genome sequenced so far, is presented. The genome is 773,279 nucleotides long and has the highest coding capacity among known angiosperm mtDNAs. The proportion of promiscuous DNA of plastid origin in the genome is also the largest ever reported for an angiosperm mtDNA, both in absolute and relative terms. 42.4% of chloroplast genome of Vitis has been incorporated into its mitochondrial genome. In order to test if horizontal gene transfer (HGT) has also contributed to the gene content of the grape mtDNA, we built phylogenetic trees with the coding sequences of mitochondrial genes of grape and their homologs from plant mitochondrial genomes. Many incongruent gene tree topologies were obtained. However, the extent of incongruence between these gene trees is not significantly greater than that observed among optimal trees for chloroplast genes, the common ancestry of which has never been in doubt. In both cases, we attribute this incongruence to artifacts of tree reconstruction, insufficient numbers of characters and gene paralogy. This findings leads us to question the recent phylogenetic interpretation of Bergthorsson et al (2003, 2004) and Richardson and Palmer (2007) that rampant HGT into the mtDNA of Amborella best explains phylogenetic incongruence between mitochondrial and chloroplast gene trees for angiosperms. The only evidence for HGT into the Vitis mtDNA found involves fragments of two coding sequences stemming from two closteroviruses that cause the leafroll disease of this plant. We also report that analysis of sequences shared by both chloroplast and mitochondrial genomes provide evidence for a previously unknown gene transfer route from the mitochondrion to the chloroplast.
Key Words: grape mtDNA • horizontal gene transfer • molecular evolution