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Spatio-temporal expression patterns of Arabidopsis thaliana and Medicago truncatula defensin-like genes

Samac, Deborah A
PloS one 2013 v.8 no.3 pp. 1
Arabidopsis thaliana, Medicago truncatula, algorithms, gene expression, genes, genetic markers, inflorescences, messenger RNA, microarray technology, mutants, polypeptides, proteins, root nodules, seeds, transcription (genetics)
Plant genomes typically contain several hundred defensin-like (DEFL) genes that encode short proteins resembling defensins, which are antimicrobial polypeptides. Little is known about the expression patterns of DEFL genes because most were recently discovered and many are not well represented on standard microarray chips. To make a comparative analysis of DEFL gene expression in two model species, we designed a custom Affymetrix chip for transcript profiling of nearly all DEFL genes from Arabidopsis thaliana and Medicago truncatula, as well as additional genes for data normalization. We examined three normalization algorithms and found that the Stable-Based Quantile (SBQ) approach is the preferred normalization approach for the custom chip. The DEFL gene chip analysis provided evidence for the transcription of many of the recently identified DEFL genes that previously lacked gene expression data. DEFL gene expression patterns appear highly condition-specific and differ strikingly between Arabidopsis and Medicago. DEFL gene expression in Arabidopsis was most pronounced in inflorescences, whereas DEFL genes in Medicago were expressed primarily in nitrogen-fixing nodules. Both species contain a subset of DEFL genes specifically expressed in seeds. A few DEFL genes and classical defensins were significantly induced in pathogen-infected tissues of Arabidopsis and Medicago. Using plant and bacterial mutants with defects in defense signaling and co-expression analysis with three marker genes for early defense signaling and jasmonic acid-mediated host response, we were able to identify a few DEFL genes that may be associated with putative defense responses.