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      Coffee and tomato share common gene repertoires as revealed by deep sequencing of seed and cherry transcripts

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          Abstract

          An EST database has been generated for coffee based on sequences from approximately 47,000 cDNA clones derived from five different stages/tissues, with a special focus on developing seeds. When computationally assembled, these sequences correspond to 13,175 unigenes, which were analyzed with respect to functional annotation, expression profile and evolution. Compared with Arabidopsis, the coffee unigenes encode a higher proportion of proteins related to protein modification/turnover and metabolism—an observation that may explain the high diversity of metabolites found in coffee and related species. Several gene families were found to be either expanded or unique to coffee when compared with Arabidopsis. A high proportion of these families encode proteins assigned to functions related to disease resistance. Such families may have expanded and evolved rapidly under the intense pathogen pressure experienced by a tropical, perennial species like coffee. Finally, the coffee gene repertoire was compared with that of Arabidopsis and Solanaceous species (e.g. tomato). Unlike Arabidopsis, tomato has a nearly perfect gene-for-gene match with coffee. These results are consistent with the facts that coffee and tomato have a similar genome size, chromosome karyotype (tomato, n=12; coffee n=11) and chromosome architecture. Moreover, both belong to the Asterid I clade of dicot plant families. Thus, the biology of coffee (family Rubiacaeae) and tomato (family Solanaceae) may be united into one common network of shared discoveries, resources and information.

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          Most cited references32

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          Phylogenetics of Seed Plants: An Analysis of Nucleotide Sequences from the Plastid Gene rbcL

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            TRANSPARENT TESTA GLABRA2, a trichome and seed coat development gene of Arabidopsis, encodes a WRKY transcription factor.

            Mutants of a new gene, TRANSPARENT TESTA GLABRA2 (TTG2), show disruptions to trichome development and to tannin and mucilage production in the seed coat. The gene was tagged by the endogenous transposon Tag1 and shown to encode a WRKY transcription factor. It is the first member of this large, plant-specific family known to control morphogenesis. The functions of all other WRKY genes revealed to date involve responses to pathogen attack, mechanical stress, and senescence. TTG2 is strongly expressed in trichomes throughout their development, in the endothelium of developing seeds (in which tannin is later generated) and subsequently in other layers of the seed coat, and in the atrichoblasts of developing roots. TTG2 acts downstream of the trichome initiation genes TTG1 and GLABROUS1, although trichome expression of TTG2 continues to occur if they are inactivated. Later, TTG2 shares functions with GLABRA2 in controlling trichome outgrowth. In the seed coat, TTG2 expression requires TTG1 function in the production of tannin. Finally, TTG2 also may be involved in specifying atrichoblasts in roots redundantly with other gene(s) but independently of TTG1 and GLABRA2.
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              Clusters of resistance genes in plants evolve by divergent selection and a birth-and-death process.

              Classical genetic and molecular data show that genes determining disease resistance in plants are frequently clustered in the genome. Genes for resistance (R genes) to diverse pathogens cloned from several species encode proteins that have motifs in common. These motifs indicate that R genes are part of signal-transduction systems. Most of these R genes encode a leucine-rich repeat (LRR) region. Sequences encoding putative solvent-exposed residues in this region are hypervariable and have elevated ratios of nonsynonymous to synonymous substitutions; this suggests that they have evolved to detect variation in pathogen-derived ligands. Generation of new resistance specificities previously had been thought to involve frequent unequal crossing-over and gene conversions. However, comparisons between resistance haplotypes reveal that orthologs are more similar than paralogs implying a low rate of sequence homogenization from unequal crossing-over and gene conversion. We propose a new model adapted and expanded from one proposed for the evolution of vertebrate major histocompatibility complex and immunoglobulin gene families. Our model emphasizes divergent selection acting on arrays of solvent-exposed residues in the LRR resulting in evolution of individual R genes within a haplotype. Intergenic unequal crossing-over and gene conversions are important but are not the primary mechanisms generating variation.
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                Author and article information

                Contributors
                +1-607-2556683 , sdt4@cornell.edu
                Journal
                Theor Appl Genet
                TAG. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik
                Springer-Verlag (Berlin/Heidelberg )
                0040-5752
                1432-2242
                5 November 2005
                December 2005
                : 112
                : 1
                : 114-130
                Affiliations
                [1 ]Department of Plant Breeding and Genetics, Department of Plant Biology, Cornell University, Ithaca, NY 14853 USA
                [2 ]Nestlé Research Center, Tours, 101, Avenue Gustave Eiffel, 49716, 37097 Tours Cedex 2, France
                Author notes

                Communicated by R. Hagemann

                Article
                112
                10.1007/s00122-005-0112-2
                1544375
                16273343
                70b2dbb6-88a4-4404-bfbe-22ac9805970b
                © Springer-Verlag 2005
                History
                : 23 June 2005
                : 10 September 2005
                Categories
                Original Paper
                Custom metadata
                © Springer-Verlag 2005

                Genetics
                solanaceae,seed development,coffea canephora,rubiaceae,comparative genomics
                Genetics
                solanaceae, seed development, coffea canephora, rubiaceae, comparative genomics

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