Specific bioinformatic analyses were carried out in peach and olive, starting with the ab initio identification of genes responsible for flower differentiation (‘ABCDE’ genes). The peach MADS-box genes involved in this process, already identified and partially characterized, were used to validate the bioinformatic approach herein adopted using the recent release of the genome. A double experimental approach including Hidden Markov Models and Blast was set up by exploiting all available genes with function validated not only in model plants but also in crop species. Since the genome sequence of olive is not available, a 454 collection recently generated from flower buds at different developmental stages was used as a target database. In peach, the list of candidates was implemented with further members, such as four AP2- and two AP3-like genes, with a putative ‘A’ and ‘B’ function, respectively. In olive, a higher number of candidates was identified compared to peach, probably due both to the larger size and the polyploid origin of its genome, as well as to the presence of different alleles of the same gene (being most loci heterozygous in olive and homozygous in peach). Phylogenetic analyses pointed out homogeneous clusters in which candidates of the same class group together with proteins already characterized in model species (i.e. Arabidopsis and Antirrhinum). Expression analyses of candidates are currently in progress in order to assess the organ specificity and the timing of expression.

Comparative genomics for identifying flower organ identity genes in peach and olive.

BARCACCIA, GIANNI;BOTTON, ALESSANDRO;GALLA, GIULIO;
2012

Abstract

Specific bioinformatic analyses were carried out in peach and olive, starting with the ab initio identification of genes responsible for flower differentiation (‘ABCDE’ genes). The peach MADS-box genes involved in this process, already identified and partially characterized, were used to validate the bioinformatic approach herein adopted using the recent release of the genome. A double experimental approach including Hidden Markov Models and Blast was set up by exploiting all available genes with function validated not only in model plants but also in crop species. Since the genome sequence of olive is not available, a 454 collection recently generated from flower buds at different developmental stages was used as a target database. In peach, the list of candidates was implemented with further members, such as four AP2- and two AP3-like genes, with a putative ‘A’ and ‘B’ function, respectively. In olive, a higher number of candidates was identified compared to peach, probably due both to the larger size and the polyploid origin of its genome, as well as to the presence of different alleles of the same gene (being most loci heterozygous in olive and homozygous in peach). Phylogenetic analyses pointed out homogeneous clusters in which candidates of the same class group together with proteins already characterized in model species (i.e. Arabidopsis and Antirrhinum). Expression analyses of candidates are currently in progress in order to assess the organ specificity and the timing of expression.
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11577/2480012
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