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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

Phylogenetic tree derived from 126 regular NBS encoding genes in B. distachyon. Chromosomal origin of each gene is indicated in the sixth character (Bradi4, etc.) of each sequence name. Bootstrap values for important basal clades are indicated in black beside the branch. Different color patternings indicate different gene clusters or superclusters. The genes belonging to duplicated chromosomal segments were indicated with their gene names in blue. Columns on the right side show orthologs, domain configurations, numbers of EST, and predicted regulatory elements (Supplemental File 1).
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fig4: Phylogenetic tree derived from 126 regular NBS encoding genes in B. distachyon. Chromosomal origin of each gene is indicated in the sixth character (Bradi4, etc.) of each sequence name. Bootstrap values for important basal clades are indicated in black beside the branch. Different color patternings indicate different gene clusters or superclusters. The genes belonging to duplicated chromosomal segments were indicated with their gene names in blue. Columns on the right side show orthologs, domain configurations, numbers of EST, and predicted regulatory elements (Supplemental File 1).

Mentions: The phylogenetic relationships, among the regular NBS genes and the evolutionary history of this gene family were inferred by constructing a combined phylogenetic tree with the aligned regular R-like protein sequences. For the size of the inferred tree image was too large, we divided it into two parts (Figures 4(a) and 4(b)) on the basis of the clades constructed from B. distachyon R-like genes. Figure 4 showed phylogenies, including chromosome of origin (by sequence name), gene relatedness, gene ortholog in A. thaliana and rice, evolutionary rate, approximate expression levels, and the regulatory element counts (Right). The phylogenetic tree also showed the gene clusters of B. distachyon with labels before the gene name in different color patterning. For example, the majority of members in the largest gene supercluster on chromosome 4 (by green circle patterning) happened to cluster together in the phylogenetic tree. However, the rest of gene clusters was not the case. Figure 4 also revealed the genes due to chromosomal duplicate with their name in blue. For example, Bradi4g09957.1 m and Bradi3g61040.1 are from different chromosome, and they had 88.48% identification between their aminoacid sequences, which showed that these genes were possibly originated from genomic duplication and subsequent divergence under the selective pressure of pathogens. In addition, we found that 111 of these 126 R-like genes from different chromosomes are the orthologs of A. thaliana from the same chromosome 3, which showed that the 111 R-like genes from B. distachyon and the chromosome 3 of A. thaliana may have evolved from a common ancestral gene via speciation. However, it was not the case in rice. Even the members from the same gene family of B. distachyon had high similarity in protein sequences, their orthologs in rice were still from different chromosomes. That may be the reason that A. thaliana and Poaceae split far before the separation of B. distachyon and rice.


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

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

Phylogenetic tree derived from 126 regular NBS encoding genes in B. distachyon. Chromosomal origin of each gene is indicated in the sixth character (Bradi4, etc.) of each sequence name. Bootstrap values for important basal clades are indicated in black beside the branch. Different color patternings indicate different gene clusters or superclusters. The genes belonging to duplicated chromosomal segments were indicated with their gene names in blue. Columns on the right side show orthologs, domain configurations, numbers of EST, and predicted regulatory elements (Supplemental File 1).
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3368180&req=5

fig4: Phylogenetic tree derived from 126 regular NBS encoding genes in B. distachyon. Chromosomal origin of each gene is indicated in the sixth character (Bradi4, etc.) of each sequence name. Bootstrap values for important basal clades are indicated in black beside the branch. Different color patternings indicate different gene clusters or superclusters. The genes belonging to duplicated chromosomal segments were indicated with their gene names in blue. Columns on the right side show orthologs, domain configurations, numbers of EST, and predicted regulatory elements (Supplemental File 1).
Mentions: The phylogenetic relationships, among the regular NBS genes and the evolutionary history of this gene family were inferred by constructing a combined phylogenetic tree with the aligned regular R-like protein sequences. For the size of the inferred tree image was too large, we divided it into two parts (Figures 4(a) and 4(b)) on the basis of the clades constructed from B. distachyon R-like genes. Figure 4 showed phylogenies, including chromosome of origin (by sequence name), gene relatedness, gene ortholog in A. thaliana and rice, evolutionary rate, approximate expression levels, and the regulatory element counts (Right). The phylogenetic tree also showed the gene clusters of B. distachyon with labels before the gene name in different color patterning. For example, the majority of members in the largest gene supercluster on chromosome 4 (by green circle patterning) happened to cluster together in the phylogenetic tree. However, the rest of gene clusters was not the case. Figure 4 also revealed the genes due to chromosomal duplicate with their name in blue. For example, Bradi4g09957.1 m and Bradi3g61040.1 are from different chromosome, and they had 88.48% identification between their aminoacid sequences, which showed that these genes were possibly originated from genomic duplication and subsequent divergence under the selective pressure of pathogens. In addition, we found that 111 of these 126 R-like genes from different chromosomes are the orthologs of A. thaliana from the same chromosome 3, which showed that the 111 R-like genes from B. distachyon and the chromosome 3 of A. thaliana may have evolved from a common ancestral gene via speciation. However, it was not the case in rice. Even the members from the same gene family of B. distachyon had high similarity in protein sequences, their orthologs in rice were still from different chromosomes. That may be the reason that A. thaliana and Poaceae split far before the separation of B. distachyon and rice.

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