Establishing the protein-protein interaction network of tomato MADS-domain proteins, investigating novel tomato mutants, and further plant genomic investigations of evolution and phylogenetics

MADS-domain proteins are important transcription factors involved in many biological processes of plants. Interactions between MADS-domain proteins are essential for their functions. In tomato (Solanum lycopersicum ), the number of MIKCc-type MADS-domain proteins identified has totaled 36, but a large-scale interaction assay is lacking. In this study, 22 tomato MADS-domain proteins were selected from six functionally important subfamilies of the MADS-box gene family, to create the first large-scale tomato protein interaction network. Compared with Arabidopsis and petunia (Petunia hybrida), protein interaction patterns in tomato displayed both conservation and divergence. The majority of proteins that can be identified as putative orthologs exhibited conserved interaction patterns and modifications were mostly found in genes underlining traits unique to tomato. JOINTLESS and RIN, characterized for their roles in abscission zone development, showed enlarged interaction networks in comparison to their Arabidopsis and petunia counterparts. Novel interactions were also found for members of the expanded subfamilies, such as those represented by AP1/FUL and AP3/PI MADS-domain proteins. Additionally, 16 proteins with the MADS-domain removed were used to assess the role of the MADS-domain in protein-protein interactions. The current work provides important knowledge for further functional and evolutionary study of the MADS-box genes in tomato.;Populus trichocarpa (poplar) is distinguished from its herbaceous counterparts Arabidopsis and rice by its woody structure, perennial life cycle, and dioecious, two-whorled flowers. Investigation of the poplar genome revealed 105 putative functional MADS-box genes and 12 pseudogenes. These numbers are comparable to those in Arabidopsis . In addition to duplications for floral organ identity genes, TM3-like, StMADS11, ANR1 and Bs clades were significantly increased. Like other gene families, the poplar MADS-box gene family has expanded through tandem gene duplication and segmental duplication events as demonstrated by two genomic regions where clustered MADS-box genes exhibited high similarities in the MADS-box domains. A survey of poplar EST sequences showed that MADS-box genes were expressed in wood and cambium tissues, which are specific to woody plants. The expression of common MADS-box genes in tree-specific tissues suggests that the novel function combinations of a set of genes similar to those in herbaceous plants may account for the development of woody characteristics in poplar.;Phylogenetic issues in the grass family Poaceae not resolved by previous multi-gene analyses can be usefully investigated by small genome-scale analyses. The complete chloroplast genome of Coix lacryma-jobi and the partial genome of Joinvillea plicata were sequenced. The latter was used as an outgroup from the family Joinvilleaceae in a phylogentic analysis with eleven species of Poaceae including Coix lacryma-jobi . The sequencing project involved amplifying regions (∼1200 bp) around the plastome generated from overlapping primers created from conserved regions of other Poaceae species. The availability of complete chloroplast genomes allows for the use of multiple-gene, insertion/deletion, and small inversion data for a deeper phylogenetic analysis here.