| 1. Genome-wide analysis of NBS-LRR-encoding genes in indica rice(Oryza sativa L.)By BLAST(Basic Local Alignment Search Tool) and HMM(Hidden Markov Model) analysis, we screen 549 genes encoding resistance proteins, similar to the NBS-LRR(nucleotide binding site and leucine-rich repeats), from total 47077 predictive genes in indica rice cv9311genome. 258 (47%) genes contain the full NBS region (from P-loop to MHD motif) and LRR domain in their sequences, and 157 (61%)genes own one CC motif, and 12 genes had two CC respectively, which consist of 20-50 amino acid residues in the upstream of NBS domain. The major conserved regions gather on NBS region, such as five main motifs P-loop, kinase2, RNBS-B, GLPL and MHD, in the two consensus sequences covered in NBS-LRR gene of rice and CNL of Arabidopsis. As high a conservative sequence as 90% in N terminus, which is named as motifl (ELRELAYDAEDVIDEFxYx), can be detected in both the CNL and n-CNL gene families of rice, but cannot be in CNL family of Arabidopsis. Most of NBS domains of rice genes span -300 amino acids with an extreme type of 1048 amino acids. In NBS region, we identify numerous conserved motifs, some of which showed high conservation, such as motif9 motif7, motif10 motif1 motif8 motif6, except five major motifs mentioned above.The majority amino acid residue in each motifs shows a considerable degree of conservation, except the second and the fifth that in P-loop (GMGGLGKTT). The second in GLPL and first amino acid residue in MHD also showed lower conservation. LRR distributed in all the C terminal sequences, but most were located at -80 amino acids after the MHD domain. The LRR domain ranges from 2 to 33 with a mean of 10.5 LRRs. By MEME, we identified 12 major patterns of LRRs with 10-24 amino acids residues, of which most LRR motifs shared the L(XX)n pattern, that is two leucines (L) were separated by random amino acid. We also found several special domains in few genes, eight NBS-LRR genes of them having two full NBS domains. Introns scatter in about 85% NBS-LRR gene sequences of rice, and show their diversity in splicing sites, about 40% of them being at the beginning of the kinase2. By analyzing sequence diversity and relationships in NBS domains (i.e. from the 10 amino acids N terminal to first Gly in the P-loop motif to ~30 amino acids after MHD motif)of NBS-LRR genes between rice and other species, we have constructed two phylogenetic trees based on the genes encoding protein sequences of about 30 amino acids. The trees are composed of 88 groups at any values when bootstrap used to define the groups exceeds 75%. Expect Rpl of maize and RPMl oi Arabidopsis results single clade respectively, seven known rice NBS-LRR genes dispersed on the different clades in the trees, indicating that higher sequence similarity between these genes. What interesting was that in cluster formed by four TIR-NBS-LRR genes included Atlg33560, a gene of CNL family member of Arabidopsis, suggesting that they might be arise from the same ancient. This may be generated by biology to detect the presence of pathogens and induce corresponding recognition and defense responses in the long evolution.2. Comparison of synonymous codon usage of NBS-LRR gene family in rice and ArabidopsisWe investigated variation in codon usage of NBS-LRR gene in completely sequenced genomes of rice and Arabidopsis families both within and between genomes using a universal multivariate analysis program-CodonW. In 59 synonymous codons we detected, 25 optimal codons of rice and 16 optimal codons of Arabidopsis were identified. NBS-LRR genes of rice had a specific codon usage bias that differed from which of Arabidopsis. The patterns of synonymous codon usage of two NBS-LRR families had a tendency with their whole genome, which reflected their specific behavior within the genome. The each member of two NBS-LRR gene families shared different bias in codon usage and also presented differences within each NBS-LRR genes. The most strongly biased codons of rice NBS-LRR genes were mainl...
|
PDF Full Text Request