Evolution of secondary metabolites from an ecological and molecular phylogenetic perspective.

A phylogenetic analysis of 589 plastid rbcL gene sequences representing nearly all eudicot families (a total of 308 families; seven photosynthetic and four parasitic families are missing) was performed, and bootstrap re-sampling was used to assess support for clades. Based on these data, the ordinal classification of eudicots is revised following the previous classification of angiosperms by the Angiosperm Phylogeny Group (APG). Putative additional orders are discussed (e.g. Dilleniales, Escalloniales, Vitales), and several additional families are assigned to orders for future updates of the APG classification. The use of rbcL alone in such a large matrix was found to be practical in discovering and providing bootstrap support for most orders. Combination of these data with other matrices for the rest of the angiosperms should provide the framework for a complete phylogeny to be used in macro-evolutionary studies.

/pdf/phylogeny-of-the-eudicots-a-nearly-complete-familial-4j50biz534.pdf

Phylogeny of the eudicots : a nearly complete familial analysis based on rbcL gene sequences

A phylogeny of Solanaceae is presented based on the chloroplast DNA regions ndhF and trnLF. With 89 genera and 190 species included, this represents a nearly comprehensive genus-level sampling and provides a framework phylogeny for the entire family that helps integrate many previously-published phylogenetic studies within Solanaceae. The four genera comprising the family Goetzeaceae and the monotypic families Duckeodendraceae, Nolanaceae, and Sclerophylaceae, often recognized in traditional classifications, are shown to be included in Solanaceae. The current results corroborate previous studies that identify a monophyletic subfamily Solanoideae and the more inclusive "x = 12" clade, which includes Nicotiana and the Australian tribe Anthocercideae. These results also provide greater resolution among lineages within Solanoideae, confirming Jaltomata as sister to Solanum and identifying a clade comprised primarily of tribes Capsiceae (Capsicum and Lycianthes) and Physaleae. Stronger evidence also is provided for the inclusion of Capsicum within a paraphyletic Lycianthes. Solanaceae are a predominantly New World group, with several lineages represented on other continents. Apart from events within Solanum (for which sampling in this study is inadequate for biogeographic interpretations) the Old World representatives of Solanaceae can be accounted for by eight or nine dispersal events.

http://depts.washington.edu/phylo/OlmsteadPubs/Olmstead_et_al_2008.pdf

A molecular phylogeny of the Solanaceae

The cultivated tomato, Lycopersicon esculentum, is the second most consumed vegetable worldwide and a well-studied crop species in terms of genetics, genomics, and breeding. It is one of the earliest crop plants for which a genetic linkage map was constructed, and currently there are several molecular maps based on crosses between the cultivated and various wild species of tomato. The high-density molecular map, developed based on an L. esculentum x L. pennellii cross, includes more than 2200 markers with an average marker distance of less than 1 cM and an average of 750 kbp per cM. Different types of molecular markers such as RFLPs, AFLPs, SSRs, CAPS, RGAs, ESTs, and COSs have been developed and mapped onto the 12 tomato chromosomes. Markers have been used extensively for identification and mapping of genes and QTLs for many biologically and agriculturally important traits and occasionally for germplasm screening, fingerprinting, and marker-assisted breeding. The utility of MAS in tomato breeding has been restricted largely due to limited marker polymorphism within the cultivated species and economical reasons. Also, when used, MAS has been employed mainly for improving simply-inherited traits and not much for improving complex traits. The latter has been due to unavailability of reliable PCR-based markers and problems with linkage drag. Efforts are being made to develop high-throughput markers with greater resolution, including SNPs. The expanding tomato EST database, which currently includes approximately 214 000 sequences, the new microarray DNA chips, and the ongoing sequencing project are expected to aid development of more practical markers. Several BAC libraries have been developed that facilitate map-based cloning of genes and QTLs. Sequencing of the euchromatic portions of the tomato genome is paving the way for comparative and functional analysis of important genes and QTLs.

/pdf/genome-mapping-and-molecular-breeding-of-tomato-1t1npjizx4.pdf

Genome Mapping and Molecular Breeding of Tomato

The Solanaceae contains many species of agricultural importance. Several of these are cultivated for their fruits, such as the tomato, the pepper and the aubergine. The family is very diverse in fruit type with capsules, drupes, pyrenes, berries, and several sorts of dehiscent non-capsular fruits occurring in the 90+ genera. In this paper, recent work on fruit type evolution in angiosperms is reviewed in relation to dispersal agents and habitat ecology. Defining fruit types in the Solanaceae in a simple five state system, then mapping them onto a previously published molecular phylogeny based on chloroplast DNA allows discussion of the evolution of these fruit types in a phylogenetic framework. Capsules are plesiomorphic in the family, and although berries are a synapomorphy (shared derived character) for a large clade including the genus Solanum (tomatoes and aubergines), they have arisen several times in the family as a whole. Problems with homology of drupes and pyrenes are discussed, and areas for future investigation of fruit structure homology identified. The distribution of fruit types in the large and diverse genus Solanum is also discussed in the light of monophyletic groups identified using chloroplast gene sequences. This variety is related to recent advances in the understanding of the molecular biology of fruit development. Finally, several key areas of future comparative, phylogenetic investigation into fruit type evolution in the family are highlighted.

/pdf/tobacco-to-tomatoes-a-phylogenetic-perspective-on-fruit-3jkn87wu5h.pdf

Tobacco to tomatoes: a phylogenetic perspective on fruit diversity in the Solanaceae.

A phylogenetic analysis of the Solanaceae based on chloroplast DNA variation is presented. Restriction site maps were determined for 79 species (52 genera) for 11 restriction enzymes. Sequences of two chloroplast genes, rbch and ndhF, were determined for 30 and 36 species respectively, including six genera not sampled in the restriction site survey. The results are presented as three separate analyses examining relationships at different hierarchical levels. The resulting cladograms provide the basis for a provisional new infrafamilial classification. This classification includes seven subfamilies, three of which are further subdivided into tribes, two of which are further subdivided into subtribes. This classification is compared to the contemporary classification of A. Hunziker, G. Barboza, L. Bernadello & A.A. Cocucci (in prep.).

http://depts.washington.edu/phylo/OlmsteadPubs/Solanaceae_IV.pdf

D. Palmer

Papers

Phylogeny and provisional classification of the Solanaceae based on chloroplast DNA