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Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi

BACKGROUND: Rust fungi are biotrophic basidiomycete plant pathogens that cause major diseases on plants and trees world-wide, affecting agriculture and forestry. Their biotrophic nature precludes many established molecular genetic manipulations and lines of research. The generation of genomic resour...

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Autores principales: Xu, Junhuan, Linning, Rob, Fellers, John, Dickinson, Matthew, Zhu, Wenhan, Antonov, Ivan, Joly, David L, Donaldson, Michael E, Eilam, Tamar, Anikster, Yehoshua, Banks, Travis, Munro, Sarah, Mayo, Michael, Wynhoven, Brian, Ali, Johar, Moore, Richard, McCallum, Brent, Borodovsky, Mark, Saville, Barry, Bakkeren, Guus
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3074555/
https://www.ncbi.nlm.nih.gov/pubmed/21435244
http://dx.doi.org/10.1186/1471-2164-12-161
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author Xu, Junhuan
Linning, Rob
Fellers, John
Dickinson, Matthew
Zhu, Wenhan
Antonov, Ivan
Joly, David L
Donaldson, Michael E
Eilam, Tamar
Anikster, Yehoshua
Banks, Travis
Munro, Sarah
Mayo, Michael
Wynhoven, Brian
Ali, Johar
Moore, Richard
McCallum, Brent
Borodovsky, Mark
Saville, Barry
Bakkeren, Guus
author_facet Xu, Junhuan
Linning, Rob
Fellers, John
Dickinson, Matthew
Zhu, Wenhan
Antonov, Ivan
Joly, David L
Donaldson, Michael E
Eilam, Tamar
Anikster, Yehoshua
Banks, Travis
Munro, Sarah
Mayo, Michael
Wynhoven, Brian
Ali, Johar
Moore, Richard
McCallum, Brent
Borodovsky, Mark
Saville, Barry
Bakkeren, Guus
author_sort Xu, Junhuan
collection PubMed
description BACKGROUND: Rust fungi are biotrophic basidiomycete plant pathogens that cause major diseases on plants and trees world-wide, affecting agriculture and forestry. Their biotrophic nature precludes many established molecular genetic manipulations and lines of research. The generation of genomic resources for these microbes is leading to novel insights into biology such as interactions with the hosts and guiding directions for breakthrough research in plant pathology. RESULTS: To support gene discovery and gene model verification in the genome of the wheat leaf rust fungus, Puccinia triticina (Pt), we have generated Expressed Sequence Tags (ESTs) by sampling several life cycle stages. We focused on several spore stages and isolated haustorial structures from infected wheat, generating 17,684 ESTs. We produced sequences from both the sexual (pycniospores, aeciospores and teliospores) and asexual (germinated urediniospores) stages of the life cycle. From pycniospores and aeciospores, produced by infecting the alternate host, meadow rue (Thalictrum speciosissimum), 4,869 and 1,292 reads were generated, respectively. We generated 3,703 ESTs from teliospores produced on the senescent primary wheat host. Finally, we generated 6,817 reads from haustoria isolated from infected wheat as well as 1,003 sequences from germinated urediniospores. Along with 25,558 previously generated ESTs, we compiled a database of 13,328 non-redundant sequences (4,506 singlets and 8,822 contigs). Fungal genes were predicted using the EST version of the self-training GeneMarkS algorithm. To refine the EST database, we compared EST sequences by BLASTN to a set of 454 pyrosequencing-generated contigs and Sanger BAC-end sequences derived both from the Pt genome, and to ESTs and genome reads from wheat. A collection of 6,308 fungal genes was identified and compared to sequences of the cereal rusts, Puccinia graminis f. sp. tritici (Pgt) and stripe rust, P. striiformis f. sp. tritici (Pst), and poplar leaf rust Melampsora species, and the corn smut fungus, Ustilago maydis (Um). While extensive homologies were found, many genes appeared novel and species-specific; over 40% of genes did not match any known sequence in existing databases. Focusing on spore stages, direct comparison to Um identified potential functional homologs, possibly allowing heterologous functional analysis in that model fungus. Many potentially secreted protein genes were identified by similarity searches against genes and proteins of Pgt and Melampsora spp., revealing apparent orthologs. CONCLUSIONS: The current set of Pt unigenes contributes to gene discovery in this major cereal pathogen and will be invaluable for gene model verification in the genome sequence.
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spelling pubmed-30745552011-04-13 Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi Xu, Junhuan Linning, Rob Fellers, John Dickinson, Matthew Zhu, Wenhan Antonov, Ivan Joly, David L Donaldson, Michael E Eilam, Tamar Anikster, Yehoshua Banks, Travis Munro, Sarah Mayo, Michael Wynhoven, Brian Ali, Johar Moore, Richard McCallum, Brent Borodovsky, Mark Saville, Barry Bakkeren, Guus BMC Genomics Research Article BACKGROUND: Rust fungi are biotrophic basidiomycete plant pathogens that cause major diseases on plants and trees world-wide, affecting agriculture and forestry. Their biotrophic nature precludes many established molecular genetic manipulations and lines of research. The generation of genomic resources for these microbes is leading to novel insights into biology such as interactions with the hosts and guiding directions for breakthrough research in plant pathology. RESULTS: To support gene discovery and gene model verification in the genome of the wheat leaf rust fungus, Puccinia triticina (Pt), we have generated Expressed Sequence Tags (ESTs) by sampling several life cycle stages. We focused on several spore stages and isolated haustorial structures from infected wheat, generating 17,684 ESTs. We produced sequences from both the sexual (pycniospores, aeciospores and teliospores) and asexual (germinated urediniospores) stages of the life cycle. From pycniospores and aeciospores, produced by infecting the alternate host, meadow rue (Thalictrum speciosissimum), 4,869 and 1,292 reads were generated, respectively. We generated 3,703 ESTs from teliospores produced on the senescent primary wheat host. Finally, we generated 6,817 reads from haustoria isolated from infected wheat as well as 1,003 sequences from germinated urediniospores. Along with 25,558 previously generated ESTs, we compiled a database of 13,328 non-redundant sequences (4,506 singlets and 8,822 contigs). Fungal genes were predicted using the EST version of the self-training GeneMarkS algorithm. To refine the EST database, we compared EST sequences by BLASTN to a set of 454 pyrosequencing-generated contigs and Sanger BAC-end sequences derived both from the Pt genome, and to ESTs and genome reads from wheat. A collection of 6,308 fungal genes was identified and compared to sequences of the cereal rusts, Puccinia graminis f. sp. tritici (Pgt) and stripe rust, P. striiformis f. sp. tritici (Pst), and poplar leaf rust Melampsora species, and the corn smut fungus, Ustilago maydis (Um). While extensive homologies were found, many genes appeared novel and species-specific; over 40% of genes did not match any known sequence in existing databases. Focusing on spore stages, direct comparison to Um identified potential functional homologs, possibly allowing heterologous functional analysis in that model fungus. Many potentially secreted protein genes were identified by similarity searches against genes and proteins of Pgt and Melampsora spp., revealing apparent orthologs. CONCLUSIONS: The current set of Pt unigenes contributes to gene discovery in this major cereal pathogen and will be invaluable for gene model verification in the genome sequence. BioMed Central 2011-03-24 /pmc/articles/PMC3074555/ /pubmed/21435244 http://dx.doi.org/10.1186/1471-2164-12-161 Text en Copyright ©2011 Xu et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Xu, Junhuan
Linning, Rob
Fellers, John
Dickinson, Matthew
Zhu, Wenhan
Antonov, Ivan
Joly, David L
Donaldson, Michael E
Eilam, Tamar
Anikster, Yehoshua
Banks, Travis
Munro, Sarah
Mayo, Michael
Wynhoven, Brian
Ali, Johar
Moore, Richard
McCallum, Brent
Borodovsky, Mark
Saville, Barry
Bakkeren, Guus
Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi
title Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi
title_full Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi
title_fullStr Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi
title_full_unstemmed Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi
title_short Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi
title_sort gene discovery in est sequences from the wheat leaf rust fungus puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3074555/
https://www.ncbi.nlm.nih.gov/pubmed/21435244
http://dx.doi.org/10.1186/1471-2164-12-161
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