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Deep and comparative analysis of the mycelium and appressorium transcriptomes of Magnaporthe grisea using MPSS, RL-SAGE, and oligoarray methods.

Gowda M, Venu RC, Raghupathy MB, Nobuta K, Li H, Wing R, Stahlberg E, Couglan S, Haudenschild CD, Dean R, Nahm BH, Meyers BC, Wang GL - BMC Genomics (2006)

Bottom Line: The comprehensive and deep transcriptome analysis by MPSS and RL-SAGE methods identified many novel sense and antisense transcripts in the M. grisea genome at two important growth stages.The differentially expressed transcripts that were identified, especially those specifically expressed in appressoria, represent a genomic resource useful for gaining a better understanding of the molecular basis of M. grisea pathogenicity.Further analysis of the novel antisense transcripts will provide new insights into the regulation and function of these genes in fungal growth, development and pathogenesis in the host plants.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Plant Pathology, Ohio State University, Columbus, OH 43210, USA. mgowda@ncsu.edu <mgowda@ncsu.edu>

ABSTRACT

Background: Rice blast, caused by the fungal pathogen Magnaporthe grisea, is a devastating disease causing tremendous yield loss in rice production. The public availability of the complete genome sequence of M. grisea provides ample opportunities to understand the molecular mechanism of its pathogenesis on rice plants at the transcriptome level. To identify all the expressed genes encoded in the fungal genome, we have analyzed the mycelium and appressorium transcriptomes using massively parallel signature sequencing (MPSS), robust-long serial analysis of gene expression (RL-SAGE) and oligoarray methods.

Results: The MPSS analyses identified 12,531 and 12,927 distinct significant tags from mycelia and appressoria, respectively, while the RL-SAGE analysis identified 16,580 distinct significant tags from the mycelial library. When matching these 12,531 mycelial and 12,927 appressorial significant tags to the annotated CDS, 500 bp upstream and 500 bp downstream of CDS, 6,735 unique genes in mycelia and 7,686 unique genes in appressoria were identified. A total of 7,135 mycelium-specific and 7,531 appressorium-specific significant MPSS tags were identified, which correspond to 2,088 and 1,784 annotated genes, respectively, when matching to the same set of reference sequences. Nearly 85% of the significant MPSS tags from mycelia and appressoria and 65% of the significant tags from the RL-SAGE mycelium library matched to the M. grisea genome. MPSS and RL-SAGE methods supported the expression of more than 9,000 genes, representing over 80% of the predicted genes in M. grisea. About 40% of the MPSS tags and 55% of the RL-SAGE tags represent novel transcripts since they had no matches in the existing M. grisea EST collections. Over 19% of the annotated genes were found to produce both sense and antisense tags in the protein-coding region. The oligoarray analysis identified the expression of 3,793 mycelium-specific and 4,652 appressorium-specific genes. A total of 2,430 mycelial genes and 1,886 appressorial genes were identified by both MPSS and oligoarray.

Conclusion: The comprehensive and deep transcriptome analysis by MPSS and RL-SAGE methods identified many novel sense and antisense transcripts in the M. grisea genome at two important growth stages. The differentially expressed transcripts that were identified, especially those specifically expressed in appressoria, represent a genomic resource useful for gaining a better understanding of the molecular basis of M. grisea pathogenicity. Further analysis of the novel antisense transcripts will provide new insights into the regulation and function of these genes in fungal growth, development and pathogenesis in the host plants.

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Location of MPSS and RL-SAGE tags on upstream (0.5 kb), coding sequence (CDS) and downstream (0.5 kb) regions of annotated genes of M. grisea. The sense and antisense tags locations are shown on the predicted transcription units of the M. grisea genes. The percentage of tags are shown within the parenthesis.
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Figure 1: Location of MPSS and RL-SAGE tags on upstream (0.5 kb), coding sequence (CDS) and downstream (0.5 kb) regions of annotated genes of M. grisea. The sense and antisense tags locations are shown on the predicted transcription units of the M. grisea genes. The percentage of tags are shown within the parenthesis.

Mentions: Numerous antisense tags were identified in this study that matched M. grisea annotated genes in an antisense orientation. A total of 3,747 significant antisense tags (1,825 from the coding region, 1,452 from the 500 bp downstream regions, and 470 from the 500 bp upstream regions) corresponding to 2,958 genes from the mycelial library and 2,849 significant antisense tags (653 from the coding region, 1,879 from the 500 bp downstream regions, and 317 from the 500 bp upstream regions) corresponding to 2,629 genes from the appressorial library were identified. Of which, 1,586 and 1,257 genes were mycelium and appressorium-specific, respectively. Among them, 1,372 antisense genes were commonly expressed in both appressoria and mycelia. Total antisense tags from significant and non-significant tags are shown in Figure 1. Only fewer significant antisense tags (653 tags) were identified in the appressorium library as compared to the mycelial library (1,825 tags). Interestingly, we observed antisense transcripts for some of the well-known genes that are involved in appressorium formation and pathogenesis such as hydrophobin (MPG1), and calmodulin [see Additional File 3]. When the tags only matching the antisense sequences and having a single hit to the annotated genes were chosen, 232 genes in appressoria and 274 genes in mycelia were identified as antisense transcripts. The antisense tags and their frequency are listed in Additional File 4.


Deep and comparative analysis of the mycelium and appressorium transcriptomes of Magnaporthe grisea using MPSS, RL-SAGE, and oligoarray methods.

Gowda M, Venu RC, Raghupathy MB, Nobuta K, Li H, Wing R, Stahlberg E, Couglan S, Haudenschild CD, Dean R, Nahm BH, Meyers BC, Wang GL - BMC Genomics (2006)

Location of MPSS and RL-SAGE tags on upstream (0.5 kb), coding sequence (CDS) and downstream (0.5 kb) regions of annotated genes of M. grisea. The sense and antisense tags locations are shown on the predicted transcription units of the M. grisea genes. The percentage of tags are shown within the parenthesis.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1764740&req=5

Figure 1: Location of MPSS and RL-SAGE tags on upstream (0.5 kb), coding sequence (CDS) and downstream (0.5 kb) regions of annotated genes of M. grisea. The sense and antisense tags locations are shown on the predicted transcription units of the M. grisea genes. The percentage of tags are shown within the parenthesis.
Mentions: Numerous antisense tags were identified in this study that matched M. grisea annotated genes in an antisense orientation. A total of 3,747 significant antisense tags (1,825 from the coding region, 1,452 from the 500 bp downstream regions, and 470 from the 500 bp upstream regions) corresponding to 2,958 genes from the mycelial library and 2,849 significant antisense tags (653 from the coding region, 1,879 from the 500 bp downstream regions, and 317 from the 500 bp upstream regions) corresponding to 2,629 genes from the appressorial library were identified. Of which, 1,586 and 1,257 genes were mycelium and appressorium-specific, respectively. Among them, 1,372 antisense genes were commonly expressed in both appressoria and mycelia. Total antisense tags from significant and non-significant tags are shown in Figure 1. Only fewer significant antisense tags (653 tags) were identified in the appressorium library as compared to the mycelial library (1,825 tags). Interestingly, we observed antisense transcripts for some of the well-known genes that are involved in appressorium formation and pathogenesis such as hydrophobin (MPG1), and calmodulin [see Additional File 3]. When the tags only matching the antisense sequences and having a single hit to the annotated genes were chosen, 232 genes in appressoria and 274 genes in mycelia were identified as antisense transcripts. The antisense tags and their frequency are listed in Additional File 4.

Bottom Line: The comprehensive and deep transcriptome analysis by MPSS and RL-SAGE methods identified many novel sense and antisense transcripts in the M. grisea genome at two important growth stages.The differentially expressed transcripts that were identified, especially those specifically expressed in appressoria, represent a genomic resource useful for gaining a better understanding of the molecular basis of M. grisea pathogenicity.Further analysis of the novel antisense transcripts will provide new insights into the regulation and function of these genes in fungal growth, development and pathogenesis in the host plants.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Plant Pathology, Ohio State University, Columbus, OH 43210, USA. mgowda@ncsu.edu <mgowda@ncsu.edu>

ABSTRACT

Background: Rice blast, caused by the fungal pathogen Magnaporthe grisea, is a devastating disease causing tremendous yield loss in rice production. The public availability of the complete genome sequence of M. grisea provides ample opportunities to understand the molecular mechanism of its pathogenesis on rice plants at the transcriptome level. To identify all the expressed genes encoded in the fungal genome, we have analyzed the mycelium and appressorium transcriptomes using massively parallel signature sequencing (MPSS), robust-long serial analysis of gene expression (RL-SAGE) and oligoarray methods.

Results: The MPSS analyses identified 12,531 and 12,927 distinct significant tags from mycelia and appressoria, respectively, while the RL-SAGE analysis identified 16,580 distinct significant tags from the mycelial library. When matching these 12,531 mycelial and 12,927 appressorial significant tags to the annotated CDS, 500 bp upstream and 500 bp downstream of CDS, 6,735 unique genes in mycelia and 7,686 unique genes in appressoria were identified. A total of 7,135 mycelium-specific and 7,531 appressorium-specific significant MPSS tags were identified, which correspond to 2,088 and 1,784 annotated genes, respectively, when matching to the same set of reference sequences. Nearly 85% of the significant MPSS tags from mycelia and appressoria and 65% of the significant tags from the RL-SAGE mycelium library matched to the M. grisea genome. MPSS and RL-SAGE methods supported the expression of more than 9,000 genes, representing over 80% of the predicted genes in M. grisea. About 40% of the MPSS tags and 55% of the RL-SAGE tags represent novel transcripts since they had no matches in the existing M. grisea EST collections. Over 19% of the annotated genes were found to produce both sense and antisense tags in the protein-coding region. The oligoarray analysis identified the expression of 3,793 mycelium-specific and 4,652 appressorium-specific genes. A total of 2,430 mycelial genes and 1,886 appressorial genes were identified by both MPSS and oligoarray.

Conclusion: The comprehensive and deep transcriptome analysis by MPSS and RL-SAGE methods identified many novel sense and antisense transcripts in the M. grisea genome at two important growth stages. The differentially expressed transcripts that were identified, especially those specifically expressed in appressoria, represent a genomic resource useful for gaining a better understanding of the molecular basis of M. grisea pathogenicity. Further analysis of the novel antisense transcripts will provide new insights into the regulation and function of these genes in fungal growth, development and pathogenesis in the host plants.

Show MeSH
Related in: MedlinePlus