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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

Manual modification of six gene models. Exons are drawn approximately to scale as shading boxes; connecting thin lines indicate the positions of introns, which are also drawn to scale.
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fig1: Manual modification of six gene models. Exons are drawn approximately to scale as shading boxes; connecting thin lines indicate the positions of introns, which are also drawn to scale.

Mentions: Availability of the complete B. distachyon genome sequences has made it possible for the first time to identify all the NBS-encoding genes in this plant species. From the first two steps of filters, a total of 239 NBS-encoding genes were identified in the B. distachyon (Supplemental File 1 and Supplemental File 2). 6 gene models were improved through manual modification, which were indicated with an “m” beside the gene name (Figure 1). For each revised gene model, the number of introns, exons and their positions on the genome were determined by BLASTN search using a local database containing the complete B. distachyon genome sequences of each chromosome (Supplemental File 3). Among of the six gene models, the sequence of Bradi4g09957.1 m matched perfectly with the accession number ACF22730.1 of GenBank and was thought to have a wrong terminal exon. Bradi4g44560.1, Bradi1g00227.1, and Bradi1g01397.1 were predicted as those which lacked specific motifs or contained large deletions compared with conventional NBS-RR genes even though they had apparently intact ORFs. For example, Bradi1g00227.1 lacked a C-terminal of the predicted protein as a result of a deletion at the 3′end of the gene. Bradi4g10037.1 was thought as the gene fusion of Bradi4g10037.1m1 and Bradi4g10037.1 m2. Through searching the B. distachyon EST database, we found that all the revised gene models were supported by EST evidence.


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

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

Manual modification of six gene models. Exons are drawn approximately to scale as shading boxes; connecting thin lines indicate the positions of introns, which are also drawn to scale.
© Copyright Policy
Related In: Results  -  Collection

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

fig1: Manual modification of six gene models. Exons are drawn approximately to scale as shading boxes; connecting thin lines indicate the positions of introns, which are also drawn to scale.
Mentions: Availability of the complete B. distachyon genome sequences has made it possible for the first time to identify all the NBS-encoding genes in this plant species. From the first two steps of filters, a total of 239 NBS-encoding genes were identified in the B. distachyon (Supplemental File 1 and Supplemental File 2). 6 gene models were improved through manual modification, which were indicated with an “m” beside the gene name (Figure 1). For each revised gene model, the number of introns, exons and their positions on the genome were determined by BLASTN search using a local database containing the complete B. distachyon genome sequences of each chromosome (Supplemental File 3). Among of the six gene models, the sequence of Bradi4g09957.1 m matched perfectly with the accession number ACF22730.1 of GenBank and was thought to have a wrong terminal exon. Bradi4g44560.1, Bradi1g00227.1, and Bradi1g01397.1 were predicted as those which lacked specific motifs or contained large deletions compared with conventional NBS-RR genes even though they had apparently intact ORFs. For example, Bradi1g00227.1 lacked a C-terminal of the predicted protein as a result of a deletion at the 3′end of the gene. Bradi4g10037.1 was thought as the gene fusion of Bradi4g10037.1m1 and Bradi4g10037.1 m2. Through searching the B. distachyon EST database, we found that all the revised gene models were supported by EST evidence.

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