In silico differential display of defense-related expressed sequence tags from sugarcane tissues infected with diazotrophic endophytes

Abstract

The expression patterns of 277 sugarcane expressed sequence tags (EST)-contigs encoding putative defense-related (DR) proteins were evaluated using the Sugarcane EST database. The DR proteins evaluated included chitinases, β-1,3-glucanases, phenylalanine ammonia-lyases, chalcone synthases, chalcone isomerases, isoflavone reductases, hydroxyproline-rich glycoproteins, proline-rich glycoproteins, peroxidases, catalases, superoxide dismutases, WRKY-like transcription factors and proteins involved in cell death control. Putative sugarcane WRKY proteins were compared and their phylogenetic relationships determined. A hierarchical clustering approach was used to identify DR ESTs with similar expression profiles in representative cDNA libraries. To identify DR ESTs differentially expressed in sugarcane tissues infected with Gluconacetobacter diazotrophicus or Herbaspirillum rubrisubalbicans, 179 putative DR EST-contigs expressed in non-infected tissues (leaves and roots) and/or infected tissues were selected and arrayed by similarity of their expression profiles. Changes in the expression levels of 124 putative DR EST-contigs, expressed in non-infected tissues, were evaluated in infected tissues. Approximately 42% of these EST-contigs showed no expression in infected tissues, whereas 15% and 3% showed more than 2-fold suppression in tissues infected with G. diazotrophicus or H. rubrisubalbicans, respectively. Approximately 14 and 8% of the DR EST-contigs evaluated showed more than 2-fold induction in tissues infected with G. diazotrophicus or H. rubrisubalbicans, respectively. The differential expression of clusters of DR genes may be important in the establishment of a compatible interaction between sugarcane and diazotrophic endophytes. It is suggested that the hierarchical clustering approach can be used on a genome-wide scale to identify genes likely involved in controlling plant-microorganism interactions.

PR gene families of citrus: their organ specific-biotic and abiotic inducible expression profiles based on ESTs approach

“…EST-contigs, expressed in non-stressed organs compared to the stressed organs, were calculated as described in Lambais (2001). Graphical representation of each data was highlighted with a color, using a color scale representing the range between suppression and induction gene expression, in relation to the counterpart control library.…”

“…A natural basis for organizing gene expression data is to group together genes with similar pat-terns of expression (Eisen et al, 1998). In plants, hierarchical clustering has been used routinely to identify genes highly expressed from rice (Ewing et al, 1999), sugarcane (Lambais, 2001), soybean (Shoemaker et al, 2002), barley (Zhang et al, 2002), wheat (Ogihara et al, 2003) and eucalypt (Domingues et al, 2005) transcriptome; and it is expected that this number will continue to increase. A combination of clustering methods with a graphical representation of the primary data, by representing each data point with a color, may quantitatively and qualitatively reflect the original experimental observations and allow an understanding of the data in a naturally intuitive manner (Eisen et al, 1998).…”

Identification and characterization of homeobox genes in Eucalyptus

“…The expression analysis used the so-called 'digital northern blot' (Carraro et al, 2001;Lambais, 2001) to represent the expression profile of the potential homeobox genes and to identify differential expression among the diverse Eucalyptus tissues/treatments used in the FORESTs project. In this approach, the frequency of reads for each EST-contig in each selected library is computed and then normalized with respect to the number of reads in the library and to the total number of reads in all libraries.…”

Isolation of a WRKY30 gene from Muscadinia rotundifolia (Michx) and validation of its function under biotic and abiotic stresses

“…Since identification of the first WRKY gene SPF1 from sweet potato (Ishiguro and Nakamura 1994), numerous WRKY genes have been identified in different plants, including parsley (Rushton et al 1996), tobacco (Hara et al 2000), sugarcane (Lambais 2001), Arabidopsis thaliana (Chen and Chen 2002), barley (Sun et al 2003), pepper (Oh et al 2006), rice (Liu et al 2007), tomato (Hofmann et al 2008), canola (Yang et al 2009), and grapevines (Marchive et al , 2013Mzid et al 2007;Guillaumie et al 2010;Liu et al 2011;Merz et al 2014). It is reported that WRKY genes have multiple functions in physiological and biochemical processes such as seed germination (Jiang and Yu 2009), root development , dormancy (Rohde and Bhalerao 2007), senescence (Ülker et al 2007), oxidative stress (Miller et al 2008), biotic stresses (Zhu et al 2012;Dang et al 2013;Guo et al 2014;Merz et al 2014), abiotic stresses (Ricachenevsky et al 2010;Rabara et al 2013;Scarpeci et al 2013;Şahin-Çevik et al 2013;Guo et al 2014), and signaling pathways of phytohormones (Li et al 2004;Rabara et al 2013;Guo et al 2014).…”