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

Persistent Link:
http://hdl.handle.net/10150/610397
Title:
Deep and comparative analysis of the mycelium and appressorium transcriptomes of Magnaporthe grisea using MPSS, RL-SAGE, and oligoarray methods
Author:
Gowda, Malali; Venu, R. C.; Raghupathy, Mohan; Nobuta, Kan; Li, Huameng; Wing, Rod; Stahlberg, Eric; Couglan, Sean; Haudenschild, Christian; Dean, Ralph; Nahm, Baek-Hie; Meyers, Blake; Wang, Guo-Liang
Affiliation:
Department of Plant Pathology, Ohio State University, Columbus, OH 43210, USA; Department of Plant and Soil Sciences, University of Delaware, DE 19711, USA; Arizona Genomics Institute, Department of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA; Ohio Supercomputer Center, The Ohio State University, Columbus, OH 43210, USA; Agilent Technologies Inc, Little Falls Site, 2850 Centerville Road, Delaware 19711, USA; Solexa, Inc. 25861 Industrial Blvd, Hayward, CA, 94545, USA; Fungal Genomics Laboratory, Department of Plant Pathology, North Carolina State University, Raleigh, NC 27606, USA; Department of Biological Science, Myongji University, Kyonggido, 449728, Korea
Issue Date:
2006
Publisher:
BioMed Central
Citation:
BMC Genomics 2006, 7:310 doi:10.1186/1471-2164-7-310
Journal:
BMC Genomics
Rights:
© 2006 Gowda et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0)
Collection Information:
This item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.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.
EISSN:
1471-2164
DOI:
10.1186/1471-2164-7-310
Version:
Final published version
Additional Links:
http://www.biomedcentral.com/1471-2164/7/310

Full metadata record

DC FieldValue Language
dc.contributor.authorGowda, Malalien
dc.contributor.authorVenu, R. C.en
dc.contributor.authorRaghupathy, Mohanen
dc.contributor.authorNobuta, Kanen
dc.contributor.authorLi, Huamengen
dc.contributor.authorWing, Roden
dc.contributor.authorStahlberg, Ericen
dc.contributor.authorCouglan, Seanen
dc.contributor.authorHaudenschild, Christianen
dc.contributor.authorDean, Ralphen
dc.contributor.authorNahm, Baek-Hieen
dc.contributor.authorMeyers, Blakeen
dc.contributor.authorWang, Guo-Liangen
dc.date.accessioned2016-05-20T09:05:54Z-
dc.date.available2016-05-20T09:05:54Z-
dc.date.issued2006en
dc.identifier.citationBMC Genomics 2006, 7:310 doi:10.1186/1471-2164-7-310en
dc.identifier.doi10.1186/1471-2164-7-310en
dc.identifier.urihttp://hdl.handle.net/10150/610397-
dc.description.abstractBACKGROUND: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.en
dc.language.isoenen
dc.publisherBioMed Centralen
dc.relation.urlhttp://www.biomedcentral.com/1471-2164/7/310en
dc.rights© 2006 Gowda et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0)en
dc.titleDeep and comparative analysis of the mycelium and appressorium transcriptomes of Magnaporthe grisea using MPSS, RL-SAGE, and oligoarray methodsen
dc.typeArticleen
dc.identifier.eissn1471-2164en
dc.contributor.departmentDepartment of Plant Pathology, Ohio State University, Columbus, OH 43210, USAen
dc.contributor.departmentDepartment of Plant and Soil Sciences, University of Delaware, DE 19711, USAen
dc.contributor.departmentArizona Genomics Institute, Department of Plant Sciences, University of Arizona, Tucson, AZ 85721, USAen
dc.contributor.departmentOhio Supercomputer Center, The Ohio State University, Columbus, OH 43210, USAen
dc.contributor.departmentAgilent Technologies Inc, Little Falls Site, 2850 Centerville Road, Delaware 19711, USAen
dc.contributor.departmentSolexa, Inc. 25861 Industrial Blvd, Hayward, CA, 94545, USAen
dc.contributor.departmentFungal Genomics Laboratory, Department of Plant Pathology, North Carolina State University, Raleigh, NC 27606, USAen
dc.contributor.departmentDepartment of Biological Science, Myongji University, Kyonggido, 449728, Koreaen
dc.identifier.journalBMC Genomicsen
dc.description.collectioninformationThis item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.en
dc.eprint.versionFinal published versionen
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