Genome-wide identification of NBS resistance genes in Populus trichocarpa

Abstract

As the largest class of disease resistance R genes, the genes encoding nucleotide binding site and leucine-rich repeat proteins ("NBS-LRR genes") play a critical role in defending plants from a multitude of pathogens and pests. The diversity of NBS-LRR genes was examined in the Populus trichocarpa draft genome sequence. The NBS class of genes in this perennial tree is large and diverse, comprised of approximately 400 genes, at least twice the complement of Arabidopsis. The NBS family can be divided into multiple subfamilies with distinct domain organizations. It includes 119 Coiled-Coil-NBS-LRR genes, 64 TIR-NBS-LRR genes, 34 BED-finger-NBS-LRR, and both truncated and unusual NBS- and NBS-LRR-containing genes. The transcripts of only 34 NBS-LRR genes were detected in rust-infected and non-infected leaves using a whole-genome oligoarray. None showed an altered expression two days post inoculation.

Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement

“…A diverse set of 1,120 protein sequences from the highly conserved NBS domain was built from a panel of cloned legume NBS sequences (B.D.R., unpublished data), as well as published NBS domains from Mt1.0 and Poplar 43,44 . These sequences were used as a TBLASTN query against CaGA v1.0 to identify all NBS genomic regions.…”

The obscure events contributing to the evolution of an incipient sex chromosome in Populus: a retrospective working hypothesis

“…Moreover, with a large root system maintaining water and P. deltoides Female 1,991.7 (145.6) 100.9 (13.9) 31.6 (4.2) 13.8 (1.6) 37.5 (6.0) 10.7 (3.8) 32.3 (6.7) P. nigra As determined by gas chromatography-mass spectrometry; retention time and key m/z are shown at the column headings; mean and SEM () of two male to six female replicate buds are shown within rows nutrient uptake and functioning to facilitate interannual store of carbon over multiple decades, the selective pressure to develop symbiotic interactions with soil microflora may be as strong as to develop pathogenic resistances. As an illustration, various loci controlling variation for both symbiosis levels and resistance have been identified in Populus (Zhang et al 2001;Yin et al 2004b;Jorge et al 2005;Tagu et al 2005;Kohler et al 2008;Duplessis et al 2009;Labbé et al 2011). Plants, in general, and Populus, in particular, have a variety of disease resistance genes (R) encoding proteins involved in the detection of pathogens and herbivores.…”

“…NBS-LRR genes are known to trigger protease inhibitor activity; control protease, chitinase, and kinase production; and regulate salicylic acid, jasmonic acid, ethylene, and nitric oxide signaling (Duplessis et al 2009;Sánchez-Rodríguez et al 2009;McHale et al 2006;Meyers et al 1999Meyers et al , 2003McDowell and Wolffenden 2003). In Populus, 37 NBS-LRR genes are found in the peritelomeric region of chromosomes XIX and represents nearly 10 % of all NBS-LRR found throughout the rest of the genome (Tuskan et al 2006;Kohler et al 2008, Fig. 1).…”

“…In addition, the peritelomeric end of chromosome XIX contains the largest cluster of the nucleotide-binding siteleucine-rich repeat (NBS-LRR) class of disease resistance genes in the entire Populus genome (Tuskan et al 2006;Kohler et al 2008). NBS-LRR genes function in the detection of pathogen occurrence and convey disease resistance signaling to activate gene expression.…”

“…A number of the identified miRNA are predicted to target the NBS-LRR disease resistance genes within the peritelomeric region of chromosome XIX. Furthermore, the NBS-LRR genes have been significantly expanded in Populus relative to Arabidopsis (Kohler et al 2008;Meyers et al 2003).…”