Abstract
Nucleotide binding site leucine-rich repeats (NBS-LRR) disease resistance proteins play an important role in plant defense against pathogen attack. A number of recent studies have been carried out to identify and characterize NBS-LRR gene families in many important plant species. In this study, we identified NBS-LRR gene family comprising of 1015 NBS-LRRs using highly stringent computational methods. These NBS-LRRs were characterized on the basis of conserved protein motifs, gene duplication events, chromosomal locations, phylogenetic relationships and digital gene expression analysis. Surprisingly, equal distribution of Toll/interleukin-1 receptor (TIR) and coiled coil (CC) (1∶1) was detected in apple while the unequal distribution was reported in majority of all other known plant genome studies. Prediction of gene duplication events intriguingly revealed that not only tandem duplication but also segmental duplication may equally be responsible for the expansion of the apple NBS-LRR gene family. Gene expression profiling using expressed sequence tags database of apple and quantitative real-time PCR (qRT-PCR) revealed the expression of these genes in wide range of tissues and disease conditions, respectively. Taken together, this study will provide a blueprint for future efforts towards improvement of disease resistance in apple.
Highlights
The battle between plants and pathogens is continued from ancient times
The nucleotide binding site (NBS) domain was defined as a region of,300 amino acids containing several motifs arranged in specific order and is responsible for binding and hydrolysis of ATP and GTP during plant disease resistance whereas leucine rich repeats (LRR) motif is responsible for recognition of pathogen derived virulence factors in plant nucleotide binding sites and leucine rich repeats (NBS-LRR) proteins [6,7,8]
We have followed two methods that were earlier proposed for the identification of NBS-LRRs
Summary
The battle between plants and pathogens is continued from ancient times. plants have evolved sophisticated mechanisms to identify and produce specific defense response against wide range of pathogens, including fungi, bacteria and insects [1]. The NBS-LRR genes are the members of the STAND (Signal Transduction ATPase with Numerous Domains) family of NTPases and comprise the largest disease resistance gene family in plants [5] These NBSLRR genes encode proteins with amino-terminal variable domain, a central nucleotide binding site (NBS) and carboxy-terminal leucine rich repeats (LRR) domain [6]. The first class is termed as TIR-NBS-LRR (TNL) comprise of proteins containing the Toll/Interleukin-1 (TIR) receptor domain and the second is non-TIR-NBS-LRR (non-TNL) proteins that lack the TIR domain [1,6] In addition to their structural divergence, these two classes differ in their downstream signaling pathways, possess functional divergence between them. It was observed that TNL and CNL class form distinct clades [4,6,8]
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