Genome analysis and avirulence gene cloning using a high-density RADseq linkage map of the flax rust fungus, Melampsora lini
Identifieur interne : 000731 ( Ncbi/Checkpoint ); précédent : 000730; suivant : 000732Genome analysis and avirulence gene cloning using a high-density RADseq linkage map of the flax rust fungus, Melampsora lini
Auteurs : Claire Anderson ; Muhammad Adil Khan ; Ann-Maree Catanzariti ; Cameron A. Jack ; Adnane Nemri [Allemagne] ; Gregory J. Lawrence ; Narayana M. Upadhyaya ; Adrienne R. Hardham ; Jeffrey G. Ellis ; Peter N. Dodds ; David A. JonesSource :
- BMC Genomics [ 1471-2164 ] ; 2016.
Descripteurs français
- KwdFr :
- Basidiomycota (génétique), Basidiomycota (pathogénicité), Biologie informatique (méthodes), Cartographie chromosomique (MeSH), Fréquence d'allèle (MeSH), Génome fongique (MeSH), Génomique (méthodes), Locus génétiques (MeSH), Mutation (MeSH), Perte d'hétérozygotie (MeSH), Phénotype (MeSH), Polymorphisme de nucléotide simple (MeSH), Recombinaison génétique (MeSH), Séquence d'acides aminés (MeSH), Séquençage nucléotidique à haut débit (MeSH), Virulence (génétique).
- MESH :
- génétique : Basidiomycota, Virulence.
- méthodes : Biologie informatique, Génomique.
- pathogénicité : Basidiomycota.
- Cartographie chromosomique, Fréquence d'allèle, Génome fongique, Locus génétiques, Mutation, Perte d'hétérozygotie, Phénotype, Polymorphisme de nucléotide simple, Recombinaison génétique, Séquence d'acides aminés, Séquençage nucléotidique à haut débit.
English descriptors
- KwdEn :
- Amino Acid Sequence (MeSH), Basidiomycota (genetics), Basidiomycota (pathogenicity), Chromosome Mapping (MeSH), Computational Biology (methods), Gene Frequency (MeSH), Genetic Loci (MeSH), Genome, Fungal (MeSH), Genomics (methods), High-Throughput Nucleotide Sequencing (MeSH), Loss of Heterozygosity (MeSH), Mutation (MeSH), Phenotype (MeSH), Polymorphism, Single Nucleotide (MeSH), Recombination, Genetic (MeSH), Virulence (genetics).
- MESH :
- genetics : Basidiomycota, Virulence.
- methods : Computational Biology, Genomics.
- pathogenicity : Basidiomycota.
- Amino Acid Sequence, Chromosome Mapping, Gene Frequency, Genetic Loci, Genome, Fungal, High-Throughput Nucleotide Sequencing, Loss of Heterozygosity, Mutation, Phenotype, Polymorphism, Single Nucleotide, Recombination, Genetic.
Abstract
Rust fungi are an important group of plant pathogens that cause devastating losses in agricultural, silvicultural and natural ecosystems. Plants can be protected from rust disease by resistance genes encoding receptors that trigger a highly effective defence response upon recognition of specific pathogen avirulence proteins. Identifying avirulence genes is crucial for understanding how virulence evolves in the field.
To facilitate avirulence gene cloning in the flax rust fungus,
The
The online version of this article (doi:10.1186/s12864-016-3011-9) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/s12864-016-3011-9
PubMed: 27550217
PubMed Central: 4994203
Affiliations:
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PMC:4994203Le document en format XML
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Jack</name><affiliation><nlm:aff id="Aff2">ANU Bioinformatics Consulting Unit, The John Curtin School of Medical Research, The Australian National University, 131 Garran Road, Acton, ACT 2601 Australia</nlm:aff><wicri:noCountry code="subfield">ACT 2601 Australia</wicri:noCountry></affiliation></author><author><name sortKey="Nemri, Adnane" sort="Nemri, Adnane" uniqKey="Nemri A" first="Adnane" last="Nemri">Adnane Nemri</name><affiliation><nlm:aff id="Aff3">CSIRO Agriculture, GPO Box 1600, Canberra, ACT 2601 Australia</nlm:aff><wicri:noCountry code="subfield">ACT 2601 Australia</wicri:noCountry></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff5">Current address: KWS SAAT SE, Grimsehlstraße 31, Einbeck, 37574 Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Current address: KWS SAAT SE, Grimsehlstraße 31, Einbeck</wicri:regionArea><wicri:noRegion>Einbeck</wicri:noRegion><wicri:noRegion>Einbeck</wicri:noRegion><wicri:noRegion>Einbeck</wicri:noRegion></affiliation></author><author><name sortKey="Lawrence, Gregory J" sort="Lawrence, Gregory J" uniqKey="Lawrence G" first="Gregory J." last="Lawrence">Gregory J. Lawrence</name><affiliation><nlm:aff id="Aff3">CSIRO Agriculture, GPO Box 1600, Canberra, ACT 2601 Australia</nlm:aff><wicri:noCountry code="subfield">ACT 2601 Australia</wicri:noCountry></affiliation></author><author><name sortKey="Upadhyaya, Narayana M" sort="Upadhyaya, Narayana M" uniqKey="Upadhyaya N" first="Narayana M." last="Upadhyaya">Narayana M. Upadhyaya</name><affiliation><nlm:aff id="Aff3">CSIRO Agriculture, GPO Box 1600, Canberra, ACT 2601 Australia</nlm:aff><wicri:noCountry code="subfield">ACT 2601 Australia</wicri:noCountry></affiliation></author><author><name sortKey="Hardham, Adrienne R" sort="Hardham, Adrienne R" uniqKey="Hardham A" first="Adrienne R." last="Hardham">Adrienne R. Hardham</name><affiliation><nlm:aff id="Aff1">Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton, ACT 2601 Australia</nlm:aff><wicri:noCountry code="subfield">ACT 2601 Australia</wicri:noCountry></affiliation></author><author><name sortKey="Ellis, Jeffrey G" sort="Ellis, Jeffrey G" uniqKey="Ellis J" first="Jeffrey G." last="Ellis">Jeffrey G. Ellis</name><affiliation><nlm:aff id="Aff3">CSIRO Agriculture, GPO Box 1600, Canberra, ACT 2601 Australia</nlm:aff><wicri:noCountry code="subfield">ACT 2601 Australia</wicri:noCountry></affiliation></author><author><name sortKey="Dodds, Peter N" sort="Dodds, Peter N" uniqKey="Dodds P" first="Peter N." last="Dodds">Peter N. Dodds</name><affiliation><nlm:aff id="Aff3">CSIRO Agriculture, GPO Box 1600, Canberra, ACT 2601 Australia</nlm:aff><wicri:noCountry code="subfield">ACT 2601 Australia</wicri:noCountry></affiliation></author><author><name sortKey="Jones, David A" sort="Jones, David A" uniqKey="Jones D" first="David A." last="Jones">David A. Jones</name><affiliation><nlm:aff id="Aff1">Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton, ACT 2601 Australia</nlm:aff><wicri:noCountry code="subfield">ACT 2601 Australia</wicri:noCountry></affiliation></author></analytic><series><title level="j">BMC Genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2016">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Amino Acid Sequence (MeSH)</term><term>Basidiomycota (genetics)</term><term>Basidiomycota (pathogenicity)</term><term>Chromosome Mapping (MeSH)</term><term>Computational Biology (methods)</term><term>Gene Frequency (MeSH)</term><term>Genetic Loci (MeSH)</term><term>Genome, Fungal (MeSH)</term><term>Genomics (methods)</term><term>High-Throughput Nucleotide Sequencing (MeSH)</term><term>Loss of Heterozygosity (MeSH)</term><term>Mutation (MeSH)</term><term>Phenotype (MeSH)</term><term>Polymorphism, Single Nucleotide (MeSH)</term><term>Recombination, Genetic (MeSH)</term><term>Virulence (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Basidiomycota (génétique)</term><term>Basidiomycota (pathogénicité)</term><term>Biologie informatique (méthodes)</term><term>Cartographie chromosomique (MeSH)</term><term>Fréquence d'allèle (MeSH)</term><term>Génome fongique (MeSH)</term><term>Génomique (méthodes)</term><term>Locus génétiques (MeSH)</term><term>Mutation (MeSH)</term><term>Perte d'hétérozygotie (MeSH)</term><term>Phénotype (MeSH)</term><term>Polymorphisme de nucléotide simple (MeSH)</term><term>Recombinaison génétique (MeSH)</term><term>Séquence d'acides aminés (MeSH)</term><term>Séquençage nucléotidique à haut débit (MeSH)</term><term>Virulence (génétique)</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Basidiomycota</term><term>Virulence</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Basidiomycota</term><term>Virulence</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Computational Biology</term><term>Genomics</term></keywords><keywords scheme="MESH" qualifier="méthodes" xml:lang="fr"><term>Biologie informatique</term><term>Génomique</term></keywords><keywords scheme="MESH" qualifier="pathogenicity" xml:lang="en"><term>Basidiomycota</term></keywords><keywords scheme="MESH" qualifier="pathogénicité" xml:lang="fr"><term>Basidiomycota</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Amino Acid Sequence</term><term>Chromosome Mapping</term><term>Gene Frequency</term><term>Genetic Loci</term><term>Genome, Fungal</term><term>High-Throughput Nucleotide Sequencing</term><term>Loss of Heterozygosity</term><term>Mutation</term><term>Phenotype</term><term>Polymorphism, Single Nucleotide</term><term>Recombination, Genetic</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Cartographie chromosomique</term><term>Fréquence d'allèle</term><term>Génome fongique</term><term>Locus génétiques</term><term>Mutation</term><term>Perte d'hétérozygotie</term><term>Phénotype</term><term>Polymorphisme de nucléotide simple</term><term>Recombinaison génétique</term><term>Séquence d'acides aminés</term><term>Séquençage nucléotidique à haut débit</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Rust fungi are an important group of plant pathogens that cause devastating losses in agricultural, silvicultural and natural ecosystems. Plants can be protected from rust disease by resistance genes encoding receptors that trigger a highly effective defence response upon recognition of specific pathogen avirulence proteins. Identifying avirulence genes is crucial for understanding how virulence evolves in the field.</p></sec><sec><title>Results</title><p>To facilitate avirulence gene cloning in the flax rust fungus, <italic>Melampsora lini</italic>, we constructed a high-density genetic linkage map using single nucleotide polymorphisms detected in restriction site-associated DNA sequencing (RADseq) data. The map comprises 13,412 RADseq markers in 27 linkage groups that together span 5860 cM and contain 2756 recombination bins. The marker sequences were used to anchor 68.9 % of the <italic>M. lini</italic> genome assembly onto the genetic map. The map and anchored assembly were then used to: 1) show that <italic>M. lini</italic> has a high overall meiotic recombination rate, but recombination distribution is uneven and large coldspots exist; 2) show that substantial genome rearrangements have occurred in spontaneous loss-of-avirulence mutants; and 3) identify the <italic>AvrL2</italic> and <italic>AvrM14</italic> avirulence genes by map-based cloning. <italic>AvrM14</italic> is a dual-specificity avirulence gene that encodes a predicted nudix hydrolase. <italic>AvrL2</italic> is located in the region of the <italic>M. lini</italic> genome with the lowest recombination rate and encodes a small, highly-charged proline-rich protein.</p></sec><sec><title>Conclusions</title><p>The <italic>M. lini</italic> high-density linkage map has greatly advanced our understanding of virulence mechanisms in this pathogen by providing novel insights into genome variability and enabling identification of two new avirulence genes.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/s12864-016-3011-9) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Singh, Rp" uniqKey="Singh R">RP Singh</name></author><author><name sortKey="Hodson, Dp" uniqKey="Hodson D">DP Hodson</name></author><author><name sortKey="Huerta Espino, J" uniqKey="Huerta Espino J">J Huerta-Espino</name></author><author><name sortKey="Jin, Y" uniqKey="Jin Y">Y Jin</name></author><author><name sortKey="Bhavani, S" uniqKey="Bhavani S">S Bhavani</name></author><author><name sortKey="Njau, P" uniqKey="Njau P">P Njau</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wellings, Cr" uniqKey="Wellings C">CR Wellings</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Avelino, J" uniqKey="Avelino 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Peter N" sort="Dodds, Peter N" uniqKey="Dodds P" first="Peter N." last="Dodds">Peter N. Dodds</name><name sortKey="Ellis, Jeffrey G" sort="Ellis, Jeffrey G" uniqKey="Ellis J" first="Jeffrey G." last="Ellis">Jeffrey G. Ellis</name><name sortKey="Hardham, Adrienne R" sort="Hardham, Adrienne R" uniqKey="Hardham A" first="Adrienne R." last="Hardham">Adrienne R. Hardham</name><name sortKey="Jack, Cameron A" sort="Jack, Cameron A" uniqKey="Jack C" first="Cameron A." last="Jack">Cameron A. Jack</name><name sortKey="Jones, David A" sort="Jones, David A" uniqKey="Jones D" first="David A." last="Jones">David A. Jones</name><name sortKey="Khan, Muhammad Adil" sort="Khan, Muhammad Adil" uniqKey="Khan M" first="Muhammad Adil" last="Khan">Muhammad Adil Khan</name><name sortKey="Lawrence, Gregory J" sort="Lawrence, Gregory J" uniqKey="Lawrence G" first="Gregory J." last="Lawrence">Gregory J. Lawrence</name><name sortKey="Upadhyaya, Narayana M" sort="Upadhyaya, Narayana M" uniqKey="Upadhyaya N" first="Narayana M." last="Upadhyaya">Narayana M. Upadhyaya</name></noCountry><country name="Allemagne"><noRegion><name sortKey="Nemri, Adnane" sort="Nemri, Adnane" uniqKey="Nemri A" first="Adnane" last="Nemri">Adnane Nemri</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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