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Genome Wide Analysis of Nucleotide-Binding Site Disease Resistance Genes in Brachypodium distachyon.

Tan S, Wu S - Comp. Funct. Genomics (2012)

Bottom Line: EST hits and full-length cDNA sequences (from Brachypodium database) of 126 R-like candidates supported their existence.Based on the occurrence of conserved protein motifs such as coiled-coil (CC), NBS, leucine-rich repeat (LRR), these regular NBS-LRR genes were classified into four subgroups: CC-NBS-LRR, NBS-LRR, CC-NBS, and X-NBS.Further expression analysis of the regular NBS-encoding genes in Brachypodium database revealed that these genes are expressed in a wide range of libraries, including those constructed from various developmental stages, tissue types, and drought challenged or nonchallenged tissue.

View Article: PubMed Central - PubMed

Affiliation: Services Computing Technology and System Laboratory, Cluster and Grid Computing Laboratory, School of Computer Science and Technology, Huazhong University of Science & Technology (HUST), Luoyu Road 1037, Wuhan 430074, China.

ABSTRACT
Nucleotide-binding site (NBS) disease resistance genes play an important role in defending plants from a variety of pathogens and insect pests. Many R-genes have been identified in various plant species. However, little is known about the NBS-encoding genes in Brachypodium distachyon. In this study, using computational analysis of the B. distachyon genome, we identified 126 regular NBS-encoding genes and characterized them on the bases of structural diversity, conserved protein motifs, chromosomal locations, gene duplications, promoter region, and phylogenetic relationships. EST hits and full-length cDNA sequences (from Brachypodium database) of 126 R-like candidates supported their existence. Based on the occurrence of conserved protein motifs such as coiled-coil (CC), NBS, leucine-rich repeat (LRR), these regular NBS-LRR genes were classified into four subgroups: CC-NBS-LRR, NBS-LRR, CC-NBS, and X-NBS. Further expression analysis of the regular NBS-encoding genes in Brachypodium database revealed that these genes are expressed in a wide range of libraries, including those constructed from various developmental stages, tissue types, and drought challenged or nonchallenged tissue.

No MeSH data available.


Related in: MedlinePlus

Examples of summarized and aligned MEME motifs for different domains of CNL proteins. All proteins were displayed in the Supplementary Material (Supplementary File 4 available online at doi:10.1155/2012/418208).
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fig2: Examples of summarized and aligned MEME motifs for different domains of CNL proteins. All proteins were displayed in the Supplementary Material (Supplementary File 4 available online at doi:10.1155/2012/418208).

Mentions: To investigate whether the N-terminal region in regular NBS genes shared motifs, and to examine whether the CC and non-CC gene groups also shared motifs the genes and gene groups were analyzed together using the program MEME. And, as expected, 20 putative conserved motifs were found (Figure 2; Supplemental File 4) among them. The detailed motif sequences were shown in Table 2.


Genome Wide Analysis of Nucleotide-Binding Site Disease Resistance Genes in Brachypodium distachyon.

Tan S, Wu S - Comp. Funct. Genomics (2012)

Examples of summarized and aligned MEME motifs for different domains of CNL proteins. All proteins were displayed in the Supplementary Material (Supplementary File 4 available online at doi:10.1155/2012/418208).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3368180&req=5

fig2: Examples of summarized and aligned MEME motifs for different domains of CNL proteins. All proteins were displayed in the Supplementary Material (Supplementary File 4 available online at doi:10.1155/2012/418208).
Mentions: To investigate whether the N-terminal region in regular NBS genes shared motifs, and to examine whether the CC and non-CC gene groups also shared motifs the genes and gene groups were analyzed together using the program MEME. And, as expected, 20 putative conserved motifs were found (Figure 2; Supplemental File 4) among them. The detailed motif sequences were shown in Table 2.

Bottom Line: EST hits and full-length cDNA sequences (from Brachypodium database) of 126 R-like candidates supported their existence.Based on the occurrence of conserved protein motifs such as coiled-coil (CC), NBS, leucine-rich repeat (LRR), these regular NBS-LRR genes were classified into four subgroups: CC-NBS-LRR, NBS-LRR, CC-NBS, and X-NBS.Further expression analysis of the regular NBS-encoding genes in Brachypodium database revealed that these genes are expressed in a wide range of libraries, including those constructed from various developmental stages, tissue types, and drought challenged or nonchallenged tissue.

View Article: PubMed Central - PubMed

Affiliation: Services Computing Technology and System Laboratory, Cluster and Grid Computing Laboratory, School of Computer Science and Technology, Huazhong University of Science & Technology (HUST), Luoyu Road 1037, Wuhan 430074, China.

ABSTRACT
Nucleotide-binding site (NBS) disease resistance genes play an important role in defending plants from a variety of pathogens and insect pests. Many R-genes have been identified in various plant species. However, little is known about the NBS-encoding genes in Brachypodium distachyon. In this study, using computational analysis of the B. distachyon genome, we identified 126 regular NBS-encoding genes and characterized them on the bases of structural diversity, conserved protein motifs, chromosomal locations, gene duplications, promoter region, and phylogenetic relationships. EST hits and full-length cDNA sequences (from Brachypodium database) of 126 R-like candidates supported their existence. Based on the occurrence of conserved protein motifs such as coiled-coil (CC), NBS, leucine-rich repeat (LRR), these regular NBS-LRR genes were classified into four subgroups: CC-NBS-LRR, NBS-LRR, CC-NBS, and X-NBS. Further expression analysis of the regular NBS-encoding genes in Brachypodium database revealed that these genes are expressed in a wide range of libraries, including those constructed from various developmental stages, tissue types, and drought challenged or nonchallenged tissue.

No MeSH data available.


Related in: MedlinePlus