Natural Genetic Diversity in Tomato Flavor Genes

Fruit flavor is defined as the perception of the food by the olfactory and gustatory systems, and is one of the main determinants of fruit quality. Tomato flavor is largely determined by the balance of sugars, acids and volatile compounds. Several genes controlling the levels of these metabolites in tomato fruit have been cloned, including LIN5, ALMT9, AAT1, CXE1, and LoxC. The aim of this study was to identify any association of these genes with trait variation and to describe the genetic diversity at these loci in the red-fruited tomato clade comprised of the wild ancestor Solanum pimpinellifolium, the semi-domesticated species Solanum lycopersicum cerasiforme and early domesticated Solanum lycopersicum. High genetic diversity was observed at these five loci, including novel haplotypes that could be incorporated into breeding programs to improve fruit quality of modern tomatoes. Using newly available high-quality genome assemblies, we assayed each gene for potential functional causative polymorphisms and resolved a duplication at the LoxC locus found in several wild and semi-domesticated accessions which caused lower accumulation of lipid derived volatiles. In addition, we explored gene expression of the five genes in nine phylogenetically diverse tomato accessions. In general, the expression patterns of these genes increased during fruit ripening but diverged between accessions without clear relationship between expression and metabolite levels

Data from: Reticulate evolution in Elatine L. (Elatinaceae), a predominantly autogamous genus of aquatic plants

The study of hybridization in aquatic plants is complicated by rarity of flower production, absence of roots, and asexuality. Elatine is a cosmopolitan genus of aquatic flowering plants with about 25 species worldwide. Historically, there has been little concern regarding hybridization in the genus due to the prevalence of autogamy (i.e. self-pollination), which potentially limits xenogamous pollen transfer among the species. Two morphologically complex species (Elatine hexandra and E. americana) are the only known polyploids in the genus. In previous phylogenetic analyses, both species resolved incongruently in gene trees obtained from nuclear (ITS) versus plastid (matK/trnK and rbcL) regions. Suspecting that the phylogenetic incongruence might be a consequence of past hybridization events, we tested that hypothesis by conducting an additional phylogenetic analysis of Elatine, which incorporated sequences from a low copy nuclear gene (phyC). Elatine hexandra and E. americana were the only Elatine species exhibiting intraspecific polymorphic sites, i.e. heterozygosity, in phyC. Allele specific amplification enabled us to resolve these polymorphisms for inclusion in a phylogenetic analysis along with the monomorphic phyC sequences within species obtained for the remaining Elatine species. The phyC tree confirmed that both polyploids probably are allopolyploids, in a pattern consistent with the placement of the putative parental taxa in previous phylogenetic analyses of ITS, matK/trnK, and rbcL sequence data. The distributions of E. americana and E. hexandra, along with their potential parental species, are consistent with the proposed hybrid origins for the polyploids and provide additional clues on their geographic regions of origin

HRazifard_cpDNA_11APR16

Chloroplast DNA (cpDNA) sequence alignment including matK/trnK and rbc

HRazifard_ITS_11APR16

Internal Transcribed Spacer (ITS) sequence alignmen

HRazifard_phyC_11APR16

Phytochrome C (phyC) sequence alignmen

Data from: Evidence for the transfer of Elatine rotundifolia to Linderniaceae

Elatine rotundifolia was described in 2008 from Ecuador as a new species because of its unique morphology and geographical distribution. However, an examination of type material for E. rotundifolia suggested to us initially that this taxon had been assigned incorrectly to Elatine, despite some superficial similarity to that genus. This possibility was investigated using morphological and molecular data. We found that E. rotundifolia differed from other members of Elatine by several vegetative and reproductive features, which indicated a distant alliance closer to Linderniaceae (Lamiids; Asterids) rather than Elatinaceae (Fabids; Superrosids). We then conducted a phylogenetic analysis of DNA sequences from the internal transcribed spacer region, which included isotype material of E. rotundifolia, as well as various representatives of Elatinaceae, Linderniaceae, and other angiosperm clades. The molecular data resolved E. rotundifolia among several accessions of Micranthemum (Linderniaceae) in a position quite remote phylogenetically from accessions of Bergia and Elatine (Elatinaceae). From these results, we conclude that the name E. rotundifolia refers to a taxon that was misplaced in Elatine, and represents instead a member of Micranthemum (Linderniaceae), and possibly is synonymous with the aquatic species M. umbrosum

ITS alignment

aligned ITS sequences from Elatine and Bergia specie

matK alignment

aligned matK sequences from Elatine and Bergia specie

HamidRazifard_ITSforDryad_17DEC15

nexus file for the DNA sequences used in this stud