Generation of a wheat leaf rust, Puccinia triticina, EST database from stage‐specific cDNA libraries
Identifieur interne : 000C20 ( Istex/Curation ); précédent : 000C19; suivant : 000C21Generation of a wheat leaf rust, Puccinia triticina, EST database from stage‐specific cDNA libraries
Auteurs : Guanggan Hu [Canada] ; Rob Linning [Canada] ; Brent Mccallum [Canada] ; Travis Banks [Canada] ; Sylvie Cloutier [Canada] ; Yaron Butterfield [Canada] ; Jerry Liu [Canada] ; Robert Kirkpatrick [Canada] ; Jeff Stott [Canada] ; George Yang [Canada] ; Duane Smailus [Canada] ; Steven Jones [Canada] ; Marco Marra [Canada] ; Jacqueline Schein [Canada] ; Guus Bakkeren [Canada]Source :
- Molecular Plant Pathology [ 1464-6722 ] ; 2007-07.
English descriptors
- Teeft :
- Academic press, Alternate host, Annotation, Appressorium, Appressorium stage, Bean rust, Biol, Biosynthesis, Biotrophic, Blackwell, Blackwell publishing, Cdna, Cdna libraries, Cdna library, Cdna library construction, Cdna molecules, Cereal rusts, Cereal sequences, Certain stages, Clone, Conservative criteria, Contigs, Database, Defence, Early stages, Est, Experimental procedures, Fabae, Fems, Fems microbiol, Fungal, Fungal development, Fungal genet, Fungal origin, Fungal sequences, Fungi, Fungus, Gene, Gene discovery, Gene expression, Genet, Genome, Genomic, Genomic sequences, Genomics, Germinated, Germinated urediniospores, Germinating, Germinating urediniospores, Germination, Graminis, Grisea, Hahn, Haustorial, Haustorial stage, Haustorium, Homologue, Homologues, Incompatible, Incompatible interaction, Interactive, Interactive libraries, Invitrogen, Jakupovic, Leaf rust, Lett, Likely wheat, Magnaporthe grisea, Maydis, Mendgen, Metabolism, Microbiol, Molecular plant pathology, Mrna, Natl acad, Normalization, Ornithine, Other stages, Pathogen, Pathogenicity, Pathol, Plant pathol, Plant pathology, Plant tissues, Primer, Public databases, Puccinia, Puccinia graminis, Puccinia recondita, Puccinia triticina, Putative, Quality sequences, Rust, Rust fungi, Rust genes, Sequence tags, Sequencing, Several stages, Similarity searches, Singlet, Software, Spore, Spore germination, Staple, Stratagene, Supplementary table, Szabo, Thara, Transient expression, Tritici, Triticina, Triticina ests, Unigene, Unigenes, Unpublished data, Urediniospore, Urediniospores, Uromyces, Uromyces fabae, Various levels, Various stages, Voegele, Wheat, Wheat genes, Wheat leaf rust, Zhang.
Abstract
Thirteen cDNA libraries constructed from small amounts of leaf rust mRNA using optimized methods served as the source for the generation of 25 558 high‐quality DNA sequence reads. Five life‐cycle stages were sampled: resting urediniospores, urediniospores germinated over water or plant extract, compatible, interactive stages during appressorium or haustorium formation just before sporulation, and an incompatible interaction. mRNA populations were subjected to treatments such as full‐length cDNA production, subtractive and normalizing hybridizations, and size selection methods combined with PCR amplification. Pathogen and host sequences from interactive libraries were differentiated in silico using cereal and fungal sequences, codon usage analyses, and by means of a partial prototype cDNA microarray hybridized with genomic DNAs. This yielded a non‐redundant unigene set of 9760 putative fungal sequences consisting of 6616 singlets and 3144 contigs, representing 4.7 Mbp. At an E‐value 10−5, 3670 unigenes (38%) matched sequences in various databases and collections but only 694 unigenes (7%) were similar to genes with known functions. In total, 296 unigenes were identified as most probably wheat and ten as rRNA sequences. Annotation rates were low for germinated urediniospores (4%) and appressoria (2%). Gene sets obtained from the various life‐cycle stages appear to be remarkably different, suggesting drastic reprogramming of the transcriptome during these major differentiation processes. Redundancy within contigs yielded information about possible expression levels of certain genes among stages. Many sequences were similar to genes from other rusts such as Uromyces and Melampsora species; some of these genes have been implicated in pathogenicity and virulence.
Url:
DOI: 10.1111/j.1364-3703.2007.00406.x
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Linning</name><affiliation wicri:level="1"><mods:affiliation>Pacific Agri‐Food Research Centre, Agriculture and Agri‐Food Canada, Highway 97, Summerland, BC, V0H 1Z0, Canada</mods:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Pacific Agri‐Food Research Centre, Agriculture and Agri‐Food Canada, Highway 97, Summerland, BC, V0H 1Z0</wicri:regionArea></affiliation></author><author><name sortKey="Mccallum, Brent" sort="Mccallum, Brent" uniqKey="Mccallum B" first="Brent" last="Mccallum">Brent Mccallum</name><affiliation wicri:level="1"><mods:affiliation>Cereal Research Centre, Agriculture and Agri‐Food Canada, 195 Dafoe Road., Winnipeg, MB, R3T 2M9, Canada</mods:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Cereal Research Centre, Agriculture and Agri‐Food Canada, 195 Dafoe Road., Winnipeg, MB, R3T 2M9</wicri:regionArea></affiliation></author><author><name sortKey="Banks, Travis" sort="Banks, Travis" uniqKey="Banks T" first="Travis" last="Banks">Travis Banks</name><affiliation wicri:level="1"><mods:affiliation>Cereal Research Centre, Agriculture and Agri‐Food Canada, 195 Dafoe Road., Winnipeg, MB, R3T 2M9, Canada</mods:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Cereal Research Centre, Agriculture and Agri‐Food Canada, 195 Dafoe Road., Winnipeg, MB, R3T 2M9</wicri:regionArea></affiliation></author><author><name sortKey="Cloutier, Sylvie" sort="Cloutier, Sylvie" uniqKey="Cloutier S" first="Sylvie" last="Cloutier">Sylvie Cloutier</name><affiliation wicri:level="1"><mods:affiliation>Cereal Research Centre, Agriculture and Agri‐Food Canada, 195 Dafoe Road., Winnipeg, MB, R3T 2M9, Canada</mods:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Cereal Research Centre, Agriculture and Agri‐Food Canada, 195 Dafoe Road., Winnipeg, MB, R3T 2M9</wicri:regionArea></affiliation></author><author><name sortKey="Butterfield, Yaron" sort="Butterfield, Yaron" uniqKey="Butterfield Y" first="Yaron" last="Butterfield">Yaron Butterfield</name><affiliation wicri:level="1"><mods:affiliation>Michael Smith Genome Sciences Centre, 600 W 10th Avenue, Vancouver, BC, V5Z 4E6, Canada</mods:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Michael Smith Genome Sciences Centre, 600 W 10th Avenue, Vancouver, BC, V5Z 4E6</wicri:regionArea></affiliation></author><author><name sortKey="Liu, Jerry" sort="Liu, Jerry" uniqKey="Liu J" first="Jerry" last="Liu">Jerry Liu</name><affiliation wicri:level="1"><mods:affiliation>Michael Smith Genome Sciences Centre, 600 W 10th Avenue, Vancouver, BC, V5Z 4E6, Canada</mods:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Michael Smith Genome Sciences Centre, 600 W 10th Avenue, Vancouver, BC, V5Z 4E6</wicri:regionArea></affiliation></author><author><name sortKey="Kirkpatrick, Robert" sort="Kirkpatrick, Robert" uniqKey="Kirkpatrick R" first="Robert" last="Kirkpatrick">Robert Kirkpatrick</name><affiliation wicri:level="1"><mods:affiliation>Michael Smith Genome Sciences Centre, 600 W 10th Avenue, Vancouver, BC, V5Z 4E6, Canada</mods:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Michael Smith Genome Sciences Centre, 600 W 10th Avenue, Vancouver, BC, V5Z 4E6</wicri:regionArea></affiliation></author><author><name sortKey="Stott, Jeff" sort="Stott, Jeff" uniqKey="Stott J" first="Jeff" last="Stott">Jeff Stott</name><affiliation wicri:level="1"><mods:affiliation>Michael Smith Genome Sciences Centre, 600 W 10th Avenue, Vancouver, BC, V5Z 4E6, Canada</mods:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Michael Smith Genome Sciences Centre, 600 W 10th Avenue, Vancouver, BC, V5Z 4E6</wicri:regionArea></affiliation></author><author><name sortKey="Yang, George" sort="Yang, George" uniqKey="Yang G" first="George" last="Yang">George Yang</name><affiliation wicri:level="1"><mods:affiliation>Michael Smith Genome Sciences Centre, 600 W 10th Avenue, Vancouver, BC, V5Z 4E6, Canada</mods:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Michael Smith Genome Sciences Centre, 600 W 10th Avenue, Vancouver, BC, V5Z 4E6</wicri:regionArea></affiliation></author><author><name sortKey="Smailus, Duane" sort="Smailus, Duane" uniqKey="Smailus D" first="Duane" last="Smailus">Duane Smailus</name><affiliation wicri:level="1"><mods:affiliation>Michael Smith Genome Sciences Centre, 600 W 10th Avenue, Vancouver, BC, V5Z 4E6, Canada</mods:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Michael Smith Genome Sciences Centre, 600 W 10th Avenue, Vancouver, BC, V5Z 4E6</wicri:regionArea></affiliation></author><author><name sortKey="Jones, Steven" sort="Jones, Steven" uniqKey="Jones S" first="Steven" last="Jones">Steven Jones</name><affiliation wicri:level="1"><mods:affiliation>Michael Smith Genome Sciences Centre, 600 W 10th Avenue, Vancouver, BC, V5Z 4E6, Canada</mods:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Michael Smith Genome Sciences Centre, 600 W 10th Avenue, Vancouver, BC, V5Z 4E6</wicri:regionArea></affiliation></author><author><name sortKey="Marra, Marco" sort="Marra, Marco" uniqKey="Marra M" first="Marco" last="Marra">Marco Marra</name><affiliation wicri:level="1"><mods:affiliation>Michael Smith Genome Sciences Centre, 600 W 10th Avenue, Vancouver, BC, V5Z 4E6, Canada</mods:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Michael Smith Genome Sciences Centre, 600 W 10th Avenue, Vancouver, BC, V5Z 4E6</wicri:regionArea></affiliation></author><author><name sortKey="Schein, Jacqueline" sort="Schein, Jacqueline" uniqKey="Schein J" first="Jacqueline" last="Schein">Jacqueline Schein</name><affiliation wicri:level="1"><mods:affiliation>Michael Smith Genome Sciences Centre, 600 W 10th Avenue, Vancouver, BC, V5Z 4E6, Canada</mods:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Michael Smith Genome Sciences Centre, 600 W 10th Avenue, Vancouver, BC, V5Z 4E6</wicri:regionArea></affiliation></author><author><name sortKey="Bakkeren, Guus" sort="Bakkeren, Guus" uniqKey="Bakkeren G" first="Guus" last="Bakkeren">Guus Bakkeren</name><affiliation wicri:level="1"><mods:affiliation>Pacific Agri‐Food Research Centre, Agriculture and Agri‐Food Canada, Highway 97, Summerland, BC, V0H 1Z0, Canada</mods:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Pacific Agri‐Food Research Centre, Agriculture and Agri‐Food Canada, Highway 97, Summerland, BC, V0H 1Z0</wicri:regionArea></affiliation><affiliation wicri:level="1"><mods:affiliation>E-mail: BakkerenG@agr.gc.ca</mods:affiliation><country wicri:rule="url">Canada</country></affiliation></author></analytic><monogr></monogr><series><title level="j" type="main">Molecular Plant Pathology</title><title level="j" type="alt">MOLECULAR PLANT PATHOLOGY</title><idno type="ISSN">1464-6722</idno><idno type="eISSN">1364-3703</idno><imprint><biblScope unit="vol">8</biblScope><biblScope unit="issue">4</biblScope><biblScope unit="page" from="451">451</biblScope><biblScope unit="page" to="467">467</biblScope><biblScope unit="page-count">17</biblScope><publisher>Blackwell Publishing Ltd</publisher><pubPlace>Oxford, UK</pubPlace><date type="published" when="2007-07">2007-07</date></imprint><idno type="ISSN">1464-6722</idno></series></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">1464-6722</idno></seriesStmt></fileDesc><profileDesc><textClass><keywords scheme="Teeft" xml:lang="en"><term>Academic press</term><term>Alternate host</term><term>Annotation</term><term>Appressorium</term><term>Appressorium stage</term><term>Bean rust</term><term>Biol</term><term>Biosynthesis</term><term>Biotrophic</term><term>Blackwell</term><term>Blackwell publishing</term><term>Cdna</term><term>Cdna libraries</term><term>Cdna library</term><term>Cdna library construction</term><term>Cdna molecules</term><term>Cereal rusts</term><term>Cereal sequences</term><term>Certain stages</term><term>Clone</term><term>Conservative criteria</term><term>Contigs</term><term>Database</term><term>Defence</term><term>Early stages</term><term>Est</term><term>Experimental procedures</term><term>Fabae</term><term>Fems</term><term>Fems microbiol</term><term>Fungal</term><term>Fungal development</term><term>Fungal genet</term><term>Fungal origin</term><term>Fungal sequences</term><term>Fungi</term><term>Fungus</term><term>Gene</term><term>Gene discovery</term><term>Gene expression</term><term>Genet</term><term>Genome</term><term>Genomic</term><term>Genomic sequences</term><term>Genomics</term><term>Germinated</term><term>Germinated urediniospores</term><term>Germinating</term><term>Germinating urediniospores</term><term>Germination</term><term>Graminis</term><term>Grisea</term><term>Hahn</term><term>Haustorial</term><term>Haustorial stage</term><term>Haustorium</term><term>Homologue</term><term>Homologues</term><term>Incompatible</term><term>Incompatible interaction</term><term>Interactive</term><term>Interactive libraries</term><term>Invitrogen</term><term>Jakupovic</term><term>Leaf rust</term><term>Lett</term><term>Likely wheat</term><term>Magnaporthe grisea</term><term>Maydis</term><term>Mendgen</term><term>Metabolism</term><term>Microbiol</term><term>Molecular plant pathology</term><term>Mrna</term><term>Natl acad</term><term>Normalization</term><term>Ornithine</term><term>Other stages</term><term>Pathogen</term><term>Pathogenicity</term><term>Pathol</term><term>Plant pathol</term><term>Plant pathology</term><term>Plant tissues</term><term>Primer</term><term>Public databases</term><term>Puccinia</term><term>Puccinia graminis</term><term>Puccinia recondita</term><term>Puccinia triticina</term><term>Putative</term><term>Quality sequences</term><term>Rust</term><term>Rust fungi</term><term>Rust genes</term><term>Sequence tags</term><term>Sequencing</term><term>Several stages</term><term>Similarity searches</term><term>Singlet</term><term>Software</term><term>Spore</term><term>Spore germination</term><term>Staple</term><term>Stratagene</term><term>Supplementary table</term><term>Szabo</term><term>Thara</term><term>Transient expression</term><term>Tritici</term><term>Triticina</term><term>Triticina ests</term><term>Unigene</term><term>Unigenes</term><term>Unpublished data</term><term>Urediniospore</term><term>Urediniospores</term><term>Uromyces</term><term>Uromyces fabae</term><term>Various levels</term><term>Various stages</term><term>Voegele</term><term>Wheat</term><term>Wheat genes</term><term>Wheat leaf rust</term><term>Zhang</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Thirteen cDNA libraries constructed from small amounts of leaf rust mRNA using optimized methods served as the source for the generation of 25 558 high‐quality DNA sequence reads. Five life‐cycle stages were sampled: resting urediniospores, urediniospores germinated over water or plant extract, compatible, interactive stages during appressorium or haustorium formation just before sporulation, and an incompatible interaction. mRNA populations were subjected to treatments such as full‐length cDNA production, subtractive and normalizing hybridizations, and size selection methods combined with PCR amplification. Pathogen and host sequences from interactive libraries were differentiated in silico using cereal and fungal sequences, codon usage analyses, and by means of a partial prototype cDNA microarray hybridized with genomic DNAs. This yielded a non‐redundant unigene set of 9760 putative fungal sequences consisting of 6616 singlets and 3144 contigs, representing 4.7 Mbp. At an E‐value 10−5, 3670 unigenes (38%) matched sequences in various databases and collections but only 694 unigenes (7%) were similar to genes with known functions. In total, 296 unigenes were identified as most probably wheat and ten as rRNA sequences. Annotation rates were low for germinated urediniospores (4%) and appressoria (2%). Gene sets obtained from the various life‐cycle stages appear to be remarkably different, suggesting drastic reprogramming of the transcriptome during these major differentiation processes. Redundancy within contigs yielded information about possible expression levels of certain genes among stages. Many sequences were similar to genes from other rusts such as Uromyces and Melampsora species; some of these genes have been implicated in pathogenicity and virulence.</div></front></TEI></record>Pour manipuler ce document sous Unix (Dilib)
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