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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

Distribution of the regular NBS encoding genes on the B. distachyon chromosomes. The scale is in megabases (Mb). Grey straight line connects the NBS genes present on duplicate chromosomal segments.
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fig3: Distribution of the regular NBS encoding genes on the B. distachyon chromosomes. The scale is in megabases (Mb). Grey straight line connects the NBS genes present on duplicate chromosomal segments.

Mentions: During evolution, both segmental duplication and tandem duplication have contributed to the large number of gene families in plants [37]. The gene duplications have greatly expanded the NBS gene family in both monocot and eudicot lineages. In this study, we confirmed these genome duplications by the BLAST comparison of all the predicted B. distachyon proteins against each other. A total of 49 out of the 126 regular NBS genes duplications were identified and were subsequently divided into 20 gene families. The maximum number of family members was seven, and the average number of family members was 2.45. More robust analysis of gene duplication in NBS-LRR genes was carried out by comparing recent duplications of the NBS-encoding genes in Arabidopsis, rice, and B. distachyon. Previous study showed that 472 regular R-like genes were found in rice [11]. When more stringent criteria were applied, 464 regular R-like genes in rice were identified by Yang et al. [38]. Here, the analysis of gene duplication among the three plant genomes was restricted to their regular R-like genes. The results revealed that the percentage of the multigene families (two or more members per family) in regular NBS genes of B. distachyon (38.9%) genome was significantly lower than in Arabidopsis and rice (46.6 and 53.4%, resp.) genomes (Table 3). Furthermore, the number of family members in B. distachyon (20) was lower than both of the Arabidopsis and rice (25 and 93, resp.). The average number of NBS members per multigene family was 2.45 in B. distachyon, and also lower than that of Arabidopsis (3.24) and rice (3). This analysis revealed reduced duplications in the genome and multigene families in B. distachyon. More interestingly, only two pair of NBS-LRR genes (Figure 3) was found on duplicated chromosomal segments. Thus, tandem duplication could play a major role in the expansion of NBS-encoding genes in B. distachyon.


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

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

Distribution of the regular NBS encoding genes on the B. distachyon chromosomes. The scale is in megabases (Mb). Grey straight line connects the NBS genes present on duplicate chromosomal segments.
© Copyright Policy
Related In: Results  -  Collection

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

fig3: Distribution of the regular NBS encoding genes on the B. distachyon chromosomes. The scale is in megabases (Mb). Grey straight line connects the NBS genes present on duplicate chromosomal segments.
Mentions: During evolution, both segmental duplication and tandem duplication have contributed to the large number of gene families in plants [37]. The gene duplications have greatly expanded the NBS gene family in both monocot and eudicot lineages. In this study, we confirmed these genome duplications by the BLAST comparison of all the predicted B. distachyon proteins against each other. A total of 49 out of the 126 regular NBS genes duplications were identified and were subsequently divided into 20 gene families. The maximum number of family members was seven, and the average number of family members was 2.45. More robust analysis of gene duplication in NBS-LRR genes was carried out by comparing recent duplications of the NBS-encoding genes in Arabidopsis, rice, and B. distachyon. Previous study showed that 472 regular R-like genes were found in rice [11]. When more stringent criteria were applied, 464 regular R-like genes in rice were identified by Yang et al. [38]. Here, the analysis of gene duplication among the three plant genomes was restricted to their regular R-like genes. The results revealed that the percentage of the multigene families (two or more members per family) in regular NBS genes of B. distachyon (38.9%) genome was significantly lower than in Arabidopsis and rice (46.6 and 53.4%, resp.) genomes (Table 3). Furthermore, the number of family members in B. distachyon (20) was lower than both of the Arabidopsis and rice (25 and 93, resp.). The average number of NBS members per multigene family was 2.45 in B. distachyon, and also lower than that of Arabidopsis (3.24) and rice (3). This analysis revealed reduced duplications in the genome and multigene families in B. distachyon. More interestingly, only two pair of NBS-LRR genes (Figure 3) was found on duplicated chromosomal segments. Thus, tandem duplication could play a major role in the expansion of NBS-encoding genes in B. distachyon.

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