ARS | Publication request: Do potatoes and tomatoes have a single evolutionary history, and what proportion of the genome supports this history

Submitted to: BMC Evolutionary Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: August 7, 2009
Publication Date: August 7, 2009
Citation: Rodriguez, F., Tanksley, S., Wu, F., Spooner, D.M. 2009. Do potatoes and tomatoes have a single evolutionary history, and what proportion of the genome supports this history. BMC Evolutionary Biology. 9:191.

Interpretive Summary: Molecular systematics is science of using DNA methods to investigate the two main questions posed by plant taxonomists: 1) what is a species, and 2) how are these species interrelated. As the field has developed, many additional types of DNA regions have been explored for their use in molecular systematics. Recently, a new class of DNA characters, technically called COSII genes have been developed. This is a major advance in that COSII development has shown many additional DNA regions to be used to address what is a species and how are these species interrelated. This study is one of the first uses of this technique, and they are applied to address taxonomic questions in wild species of tomatoes and potatoes, two very closely related groups of species. The results show much greater “taxonomic resolution” in these major crop plants than prior methods. That is, the method shows much better statistical power to address these questions. The results are important not only to know that interrelationships of these crops better, but they point the way to other researchers in other crops to use these methods.

Technical Abstract: A paucity of validated nuclear orthologs for phylogenetic studies has resulted in a situation where most molecular taxonomic studies rely heavily on a few plastid and/or ribosomal genes. Phylogenies reconstructed with only one or a few independently inherited loci may be unresolved or incongruent due to taxon and gene sampling, horizontal gene transfer, or differential selection and lineage sorting at individual loci. I examined the utility of conserved orthologous sequences (COS markers) to elucidate the phylogenetic relationships among a total of 29 diploid Solanum species in the sister clades tomato (13 species), and potato (9), with successively farther outgroups to include section Etuberosum (2), section Juglandifolium (2), section Lycopersicoides (2), S. dulcamara; and Datura inoxia. I screened 40 COS markers with intron content over 60% and located in different chromosomes; selected a subset of 24 out of them by the presence of single band amplification of size mostly between 600 and 1200; sequenced 19 of these, and performed phylogenetic analyses of the concatenated dataset. Results are entirely in concordance with prior analyses of GBSSI sequence data, but with a significant increase in