Transcriptome analysis of Neotyphodium and Epichloe grass endophytes

S Felitti; K Shields; M Ramsperger; P Tian; T Sawbridge; T Webster; E Logan; T Erwin; J Forster; D Edwards; G Spangenberg

doi:10.1016/j.fgb.2006.01.013

Transcriptome analysis of Neotyphodium and Epichloe grass endophytes

S Felitti, K Shields, M Ramsperger, P Tian, T Sawbridge, T Webster, E Logan, T Erwin, J Forster, D Edwards, G Spangenberg

Research output: Contribution to journal › Article › peer-review

32 Citations (Scopus)

Abstract

Large-scale gene discovery has been performed for the grass fungal endophytes Neotyphodium coenophialum, Neotyphodium lolii, and Epichloe festucae. The resulting sequences have been annotated by comparison with public DNA and protein sequence databases and using intermediate gene ontology annotation tools. Endophyte sequences have also been analysed for the presence of simple sequence repeat and single nucleotide polymorphism molecular genetic markers. Sequences and annotation are maintained within a MySQL database that may be queried using a custom web interface. Two cDNA-based microarrays have been generated from this genome resource, They permit the interrogation of 3806 Neotyphodium genes (Nchip (TM) rnicroarray), and 4195 Neotyphodium and 920 Epichloe genes (EndoChip (TM) microarray), respectively. These microarrays provide tools for high-throughput transcriptome analysis, including genome-specific gene expression studies, profiling of novel endophyte genes, and investigation of the host grass-symbiont interaction. Comparative transcriptome analysis in Neotyphodium and Epichloe was performed. (c) 2006 Elsevier Inc. All rights reserved.

Original language	English
Pages (from-to)	465-475
Number of pages	11
Journal	Fungal Genetics and Biology
Volume	43
Issue number	7
DOIs	https://doi.org/10.1016/j.fgb.2006.01.013
Publication status	Published - Jul 2006
Externally published	Yes

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10.1016/j.fgb.2006.01.013

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title = "Transcriptome analysis of Neotyphodium and Epichloe grass endophytes",

abstract = "Large-scale gene discovery has been performed for the grass fungal endophytes Neotyphodium coenophialum, Neotyphodium lolii, and Epichloe festucae. The resulting sequences have been annotated by comparison with public DNA and protein sequence databases and using intermediate gene ontology annotation tools. Endophyte sequences have also been analysed for the presence of simple sequence repeat and single nucleotide polymorphism molecular genetic markers. Sequences and annotation are maintained within a MySQL database that may be queried using a custom web interface. Two cDNA-based microarrays have been generated from this genome resource, They permit the interrogation of 3806 Neotyphodium genes (Nchip (TM) rnicroarray), and 4195 Neotyphodium and 920 Epichloe genes (EndoChip (TM) microarray), respectively. These microarrays provide tools for high-throughput transcriptome analysis, including genome-specific gene expression studies, profiling of novel endophyte genes, and investigation of the host grass-symbiont interaction. Comparative transcriptome analysis in Neotyphodium and Epichloe was performed. (c) 2006 Elsevier Inc. All rights reserved.",

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author = "S Felitti and K Shields and M Ramsperger and P Tian and T Sawbridge and T Webster and E Logan and T Erwin and J Forster and D Edwards and G Spangenberg",

year = "2006",

month = jul,

doi = "10.1016/j.fgb.2006.01.013",

language = "English",

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AU - Felitti, S

AU - Shields, K

AU - Ramsperger, M

AU - Tian, P

AU - Sawbridge, T

AU - Webster, T

AU - Logan, E

AU - Erwin, T

AU - Forster, J

AU - Edwards, D

AU - Spangenberg, G

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N2 - Large-scale gene discovery has been performed for the grass fungal endophytes Neotyphodium coenophialum, Neotyphodium lolii, and Epichloe festucae. The resulting sequences have been annotated by comparison with public DNA and protein sequence databases and using intermediate gene ontology annotation tools. Endophyte sequences have also been analysed for the presence of simple sequence repeat and single nucleotide polymorphism molecular genetic markers. Sequences and annotation are maintained within a MySQL database that may be queried using a custom web interface. Two cDNA-based microarrays have been generated from this genome resource, They permit the interrogation of 3806 Neotyphodium genes (Nchip (TM) rnicroarray), and 4195 Neotyphodium and 920 Epichloe genes (EndoChip (TM) microarray), respectively. These microarrays provide tools for high-throughput transcriptome analysis, including genome-specific gene expression studies, profiling of novel endophyte genes, and investigation of the host grass-symbiont interaction. Comparative transcriptome analysis in Neotyphodium and Epichloe was performed. (c) 2006 Elsevier Inc. All rights reserved.

AB - Large-scale gene discovery has been performed for the grass fungal endophytes Neotyphodium coenophialum, Neotyphodium lolii, and Epichloe festucae. The resulting sequences have been annotated by comparison with public DNA and protein sequence databases and using intermediate gene ontology annotation tools. Endophyte sequences have also been analysed for the presence of simple sequence repeat and single nucleotide polymorphism molecular genetic markers. Sequences and annotation are maintained within a MySQL database that may be queried using a custom web interface. Two cDNA-based microarrays have been generated from this genome resource, They permit the interrogation of 3806 Neotyphodium genes (Nchip (TM) rnicroarray), and 4195 Neotyphodium and 920 Epichloe genes (EndoChip (TM) microarray), respectively. These microarrays provide tools for high-throughput transcriptome analysis, including genome-specific gene expression studies, profiling of novel endophyte genes, and investigation of the host grass-symbiont interaction. Comparative transcriptome analysis in Neotyphodium and Epichloe was performed. (c) 2006 Elsevier Inc. All rights reserved.

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KW - Epichloe

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KW - expressed sequence tag

KW - annotation

KW - gene ontology

KW - simple sequence repeat

KW - single nucleotide polymorphism

KW - microarrays

KW - transcriptome analysis

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KW - NEUROSPORA-CRASSA

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DO - 10.1016/j.fgb.2006.01.013

M3 - Article

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SP - 465

EP - 475

JO - Fungal Genetics and Biology

JF - Fungal Genetics and Biology

IS - 7

ER -

Transcriptome analysis of Neotyphodium and Epichloe grass endophytes

Abstract

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