Evolution of non-specific lipid transfer protein (nsLTP) genes in the Poaceae family: their duplication and diversity

Abstract

Previously, the genes encoding non-specific lipid transfer proteins (nsLTPs) of the Poaceae family appear to evidence different genomic distribution and somewhat different shares of EST clones, which is suggestive of independent duplication(s) followed by functional diversity. To further evaluate the evolutionary fate of the Poaceae nsLTP genes, we have identified Ka/Ks values, conserved, mutated or lost cis-regulatory elements, responses to several elicitors, genome-wide expression profiles, and nsLTP gene-coexpression networks of both (or either) wheat and rice. The Ka/Ks values within each group and between groups appeared to be similar, but not identical, in both species. The conserved cis-regulatory elements, e.g. the RY repeat (CATGCA) element related to ABA regulation in group A, might be reflected in some degree of long-term conservation in transcriptional regulation post-dating speciation. In group A, wheat nsLTP genes, with the exception of TaLTP4, evidenced responses similar to those of plant elicitors; however, the rice nsLTP genes evidenced differences in expression profiles, even though the genes of both species have undergone purifying selection, thereby suggesting their independent functional diversity. The expression profiles of rice nsLTP genes with a microarray dataset of 155 gene expression omnibus sample (GSM) plates suggest that subfunctionalization is not the sole mechanism inherent to the evolutionary history of nsLTP genes but may, rather, function in concert with other mechanism(s). As inferred by the nsLTP gene-coexpression networks, the functional diversity of nsLTP genes appears not to be randomized, but rather to be specialized in the direction of specific biological processes over evolutionary time.

Expression diversity and evolutionary dynamics of rice duplicate genes

“…In order to evaluate the expression patterns of the duplicate genes, a set of 155 gene expression omnibus samples (GSM) of the AVymetrix GeneChip rice genome array (accession no. GPL2025) were downloaded from the GEO database at NCBI, as described elsewhere (Jang et al 2008). AVymetrix GeneChip probe IDs matched to the rice genes were retrieved via the rice multi-platform microarray search of the NSF rice oligo nucleotide array project (http://www.…”

“…In particular, the advent and rapid growth of public microarray databases, e.g., the gene expression omnibus (GEO) of the National Center for Biotechnology Information (NCBI), enables us to simultaneously monitor the expression levels of thousands of genes over a range of biological issues, thereby further providing some clues on the entirety of the genome's networks (Barrett et al 2007;Edgar et al 2002). Previously, we described the evolutionary dynamics of a rice gene family via in silico analysis using a microarray dataset of 155 gene expression omnibus sample (GSM) plates (Jang et al 2008). In an eVort to evaluate the diversity and evolutionary dynamics of the rice duplicate genes formed by whole genome duplication events, as well as segmental duplication events, we have employed a rice microarray dataset and bioinformatics tools, further dividing the non-and divergent duplicate genes.…”

Identification of wheat non-specific lipid transfer proteins involved in chilling tolerance

“…The sequences of the TaLTP promoters were previously identified elsewhere (Jang et al 2008). The promoter of TaLTPIb.1 (-723 to ?3) was amplified from the genomic DNA of the wheat cultivar, Sumai 3, and cloned into the pMD-19 vector (Takara, Japan) with the HindIII restriction enzyme site at the 5 0 end and the BamHI restriction enzyme site at the 3 0 end.…”

Plant lipid transfer proteins: Evolution, expression and function

“…The nsLTPs have been found in many different land plants, including Arabidopsis, rice, wheat, pine, peach and corn Boutrot et al, 2008;Jang et al, 2008;Kirubakaran et al, 2008;Kovaleva et al, 2009). The protein family is very large, with more than 150 members in wheat, 49 in Arabidopsis and 52 in rice (Boutrot et al, 2008).…”