Gene discovery for the bark beetle-vectored fungal tree pathogen <it>Grosmannia clavigera</it>
<p>Abstract</p> <p>Background</p> <p><it>Grosmannia clavigera </it>is a bark beetle-vectored fungal pathogen of pines that causes wood discoloration and may kill trees by disrupting nutrient and water transport. Trees respond to attacks from beetles and asso...
| Main Authors: | , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2010-10-01
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| Series: | BMC Genomics |
| Online Access: | http://www.biomedcentral.com/1471-2164/11/536 |
| _version_ | 1811320769737654272 |
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| author | Robertson Gordon Liao Nancy Y Docking T Roderick Henderson Hannah Li Maria Wang Ye Keeling Christopher I DiGuistini Scott Hesse-Orce Uljana Holt Robert A Jones Steven JM Bohlmann Jörg Breuil Colette |
| author_facet | Robertson Gordon Liao Nancy Y Docking T Roderick Henderson Hannah Li Maria Wang Ye Keeling Christopher I DiGuistini Scott Hesse-Orce Uljana Holt Robert A Jones Steven JM Bohlmann Jörg Breuil Colette |
| author_sort | Robertson Gordon |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p><it>Grosmannia clavigera </it>is a bark beetle-vectored fungal pathogen of pines that causes wood discoloration and may kill trees by disrupting nutrient and water transport. Trees respond to attacks from beetles and associated fungi by releasing terpenoid and phenolic defense compounds. It is unclear which genes are important for <it>G. clavigera</it>'s ability to overcome antifungal pine terpenoids and phenolics.</p> <p>Results</p> <p>We constructed seven cDNA libraries from eight <it>G. clavigera </it>isolates grown under various culture conditions, and Sanger sequenced the 5' and 3' ends of 25,000 cDNA clones, resulting in 44,288 high quality ESTs. The assembled dataset of unique transcripts (unigenes) consists of 6,265 contigs and 2,459 singletons that mapped to 6,467 locations on the <it>G. clavigera </it>reference genome, representing ~70% of the predicted <it>G. clavigera </it>genes. Although only 54% of the unigenes matched characterized proteins at the NCBI database, this dataset extensively covers major metabolic pathways, cellular processes, and genes necessary for response to environmental stimuli and genetic information processing. Furthermore, we identified genes expressed in spores prior to germination, and genes involved in response to treatment with lodgepole pine phloem extract (LPPE).</p> <p>Conclusions</p> <p>We provide a comprehensively annotated EST dataset for <it>G. clavigera </it>that represents a rich resource for gene characterization in this and other ophiostomatoid fungi. Genes expressed in response to LPPE treatment are indicative of fungal oxidative stress response. We identified two clusters of potentially functionally related genes responsive to LPPE treatment. Furthermore, we report a simple method for identifying contig misassemblies in <it>de novo </it>assembled EST collections caused by gene overlap on the genome.</p> |
| first_indexed | 2024-04-13T13:05:14Z |
| format | Article |
| id | doaj.art-7dad36813cb641ffa61c8f4fa3df7dcd |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-04-13T13:05:14Z |
| publishDate | 2010-10-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-7dad36813cb641ffa61c8f4fa3df7dcd2022-12-22T02:45:47ZengBMCBMC Genomics1471-21642010-10-0111153610.1186/1471-2164-11-536Gene discovery for the bark beetle-vectored fungal tree pathogen <it>Grosmannia clavigera</it>Robertson GordonLiao Nancy YDocking T RoderickHenderson HannahLi MariaWang YeKeeling Christopher IDiGuistini ScottHesse-Orce UljanaHolt Robert AJones Steven JMBohlmann JörgBreuil Colette<p>Abstract</p> <p>Background</p> <p><it>Grosmannia clavigera </it>is a bark beetle-vectored fungal pathogen of pines that causes wood discoloration and may kill trees by disrupting nutrient and water transport. Trees respond to attacks from beetles and associated fungi by releasing terpenoid and phenolic defense compounds. It is unclear which genes are important for <it>G. clavigera</it>'s ability to overcome antifungal pine terpenoids and phenolics.</p> <p>Results</p> <p>We constructed seven cDNA libraries from eight <it>G. clavigera </it>isolates grown under various culture conditions, and Sanger sequenced the 5' and 3' ends of 25,000 cDNA clones, resulting in 44,288 high quality ESTs. The assembled dataset of unique transcripts (unigenes) consists of 6,265 contigs and 2,459 singletons that mapped to 6,467 locations on the <it>G. clavigera </it>reference genome, representing ~70% of the predicted <it>G. clavigera </it>genes. Although only 54% of the unigenes matched characterized proteins at the NCBI database, this dataset extensively covers major metabolic pathways, cellular processes, and genes necessary for response to environmental stimuli and genetic information processing. Furthermore, we identified genes expressed in spores prior to germination, and genes involved in response to treatment with lodgepole pine phloem extract (LPPE).</p> <p>Conclusions</p> <p>We provide a comprehensively annotated EST dataset for <it>G. clavigera </it>that represents a rich resource for gene characterization in this and other ophiostomatoid fungi. Genes expressed in response to LPPE treatment are indicative of fungal oxidative stress response. We identified two clusters of potentially functionally related genes responsive to LPPE treatment. Furthermore, we report a simple method for identifying contig misassemblies in <it>de novo </it>assembled EST collections caused by gene overlap on the genome.</p>http://www.biomedcentral.com/1471-2164/11/536 |
| spellingShingle | Robertson Gordon Liao Nancy Y Docking T Roderick Henderson Hannah Li Maria Wang Ye Keeling Christopher I DiGuistini Scott Hesse-Orce Uljana Holt Robert A Jones Steven JM Bohlmann Jörg Breuil Colette Gene discovery for the bark beetle-vectored fungal tree pathogen <it>Grosmannia clavigera</it> BMC Genomics |
| title | Gene discovery for the bark beetle-vectored fungal tree pathogen <it>Grosmannia clavigera</it> |
| title_full | Gene discovery for the bark beetle-vectored fungal tree pathogen <it>Grosmannia clavigera</it> |
| title_fullStr | Gene discovery for the bark beetle-vectored fungal tree pathogen <it>Grosmannia clavigera</it> |
| title_full_unstemmed | Gene discovery for the bark beetle-vectored fungal tree pathogen <it>Grosmannia clavigera</it> |
| title_short | Gene discovery for the bark beetle-vectored fungal tree pathogen <it>Grosmannia clavigera</it> |
| title_sort | gene discovery for the bark beetle vectored fungal tree pathogen it grosmannia clavigera it |
| url | http://www.biomedcentral.com/1471-2164/11/536 |
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