PoplarRustV1, Main, Exploration, bibRecord, 000054

Conserved loci of leaf and stem rust fungi of wheat share synteny interrupted by lineage-specific influx of repeat elements.

Identifieur interne : 000054 ( Main/Exploration ); précédent : 000053; suivant : 000055

Conserved loci of leaf and stem rust fungi of wheat share synteny interrupted by lineage-specific influx of repeat elements.

Auteurs : John P. Fellers [États-Unis] ; Bahram M. Soltani ; Myron Bruce ; Rob Linning ; Christina A. Cuomo ; Les J. Szabo ; Guus Bakkeren

Source :

BMC genomics [ 1471-2164 ] ; 2013.

RBID : pubmed:23356831

Descripteurs français

English descriptors

KwdEn :
- Amino Acid Sequence (MeSH), Basidiomycota (genetics), Basidiomycota (metabolism), Chromosomes, Artificial, Bacterial (genetics), Cloning, Molecular (MeSH), Conserved Sequence (MeSH), DNA, Fungal (MeSH), Evolution, Molecular (MeSH), Fungal Proteins (chemistry), Fungal Proteins (genetics), Fungal Proteins (metabolism), Genetic Loci (genetics), Genome, Fungal (genetics), Molecular Sequence Annotation (MeSH), Molecular Sequence Data (MeSH), Mutation (MeSH), Plant Leaves (microbiology), Plant Stems (microbiology), Repetitive Sequences, Nucleic Acid (genetics), Synteny (genetics), Triticum (microbiology).
MESH :
- chemical , chemistry : Fungal Proteins.
- chemical , genetics : Fungal Proteins.
- chemical , metabolism : Fungal Proteins.
- chemical : DNA, Fungal.
- genetics : Basidiomycota, Chromosomes, Artificial, Bacterial, Genetic Loci, Genome, Fungal, Repetitive Sequences, Nucleic Acid, Synteny.
- metabolism : Basidiomycota.
- microbiology : Plant Leaves, Plant Stems, Triticum.
- Amino Acid Sequence, Cloning, Molecular, Conserved Sequence, Evolution, Molecular, Molecular Sequence Annotation, Molecular Sequence Data, Mutation.

Abstract

BACKGROUND

Wheat leaf rust (Puccinia triticina Eriks; Pt) and stem rust fungi (P. graminis f.sp. tritici; Pgt) are significant economic pathogens having similar host ranges and life cycles, but different alternate hosts. The Pt genome, currently estimated at 135 Mb, is significantly larger than Pgt, at 88 Mb, but the reason for the expansion is unknown. Three genomic loci of Pt conserved proteins were characterized to gain insight into gene content, genome complexity and expansion.

RESULTS

A bacterial artificial chromosome (BAC) library was made from P. triticina race 1, BBBD and probed with Pt homologs of genes encoding two predicted Pgt secreted effectors and a DNA marker mapping to a region of avirulence. Three BACs, 103 Kb, 112 Kb, and 166 Kb, were sequenced, assembled, and open reading frames were identified. Orthologous genes were identified in Pgt and local conservation of gene order (microsynteny) was observed. Pairwise protein identities ranged from 26 to 99%. One Pt BAC, containing a RAD18 ortholog, shares syntenic regions with two Pgt scaffolds, which could represent both haplotypes of Pgt. Gene sequence is diverged between the species as well as within the two haplotypes. In all three BAC clones, gene order is locally conserved, however, gene shuffling has occurred relative to Pgt. These regions are further diverged by differing insertion loci of LTR-retrotransposon, Gypsy, Copia, Mutator, and Harbinger mobile elements. Uncharacterized Pt open reading frames were also found; these proteins are high in lysine and similar to multiple proteins in Pgt.

CONCLUSIONS

The three Pt loci are conserved in gene order, with a range of gene sequence divergence. Conservation of predicted haustoria expressed secreted protein genes between Pt and Pgt is extended to the more distant poplar rust, Melampsora larici-populina. The loci also reveal that genome expansion in Pt is in part due to higher occurrence of repeat-elements in this species.

DOI: 10.1186/1471-2164-14-60
PubMed: 23356831
PubMed Central: PMC3579696

Affiliations:

Links toward previous steps (curation, corpus...)

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to stream Main, to step Curation: 000053

Le document en format XML

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<term>Basidiomycota (genetics)</term>
<term>Basidiomycota (metabolism)</term>
<term>Chromosomes, Artificial, Bacterial (genetics)</term>
<term>Cloning, Molecular (MeSH)</term>
<term>Conserved Sequence (MeSH)</term>
<term>DNA, Fungal (MeSH)</term>
<term>Evolution, Molecular (MeSH)</term>
<term>Fungal Proteins (chemistry)</term>
<term>Fungal Proteins (genetics)</term>
<term>Fungal Proteins (metabolism)</term>
<term>Genetic Loci (genetics)</term>
<term>Genome, Fungal (genetics)</term>
<term>Molecular Sequence Annotation (MeSH)</term>
<term>Molecular Sequence Data (MeSH)</term>
<term>Mutation (MeSH)</term>
<term>Plant Leaves (microbiology)</term>
<term>Plant Stems (microbiology)</term>
<term>Repetitive Sequences, Nucleic Acid (genetics)</term>
<term>Synteny (genetics)</term>
<term>Triticum (microbiology)</term>
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<keywords scheme="KwdFr" xml:lang="fr"><term>ADN fongique (MeSH)</term>
<term>Annotation de séquence moléculaire (MeSH)</term>
<term>Basidiomycota (génétique)</term>
<term>Basidiomycota (métabolisme)</term>
<term>Chromosomes artificiels de bactérie (génétique)</term>
<term>Clonage moléculaire (MeSH)</term>
<term>Données de séquences moléculaires (MeSH)</term>
<term>Feuilles de plante (microbiologie)</term>
<term>Génome fongique (génétique)</term>
<term>Locus génétiques (génétique)</term>
<term>Mutation (MeSH)</term>
<term>Protéines fongiques (composition chimique)</term>
<term>Protéines fongiques (génétique)</term>
<term>Protéines fongiques (métabolisme)</term>
<term>Synténie (génétique)</term>
<term>Séquence conservée (MeSH)</term>
<term>Séquence d'acides aminés (MeSH)</term>
<term>Séquences répétées d'acides nucléiques (génétique)</term>
<term>Tiges de plante (microbiologie)</term>
<term>Triticum (microbiologie)</term>
<term>Évolution moléculaire (MeSH)</term>
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<keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Fungal Proteins</term>
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<keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Fungal Proteins</term>
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<keywords scheme="MESH" type="chemical" xml:lang="en"><term>DNA, Fungal</term>
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<term>Genetic Loci</term>
<term>Genome, Fungal</term>
<term>Repetitive Sequences, Nucleic Acid</term>
<term>Synteny</term>
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<term>Chromosomes artificiels de bactérie</term>
<term>Génome fongique</term>
<term>Locus génétiques</term>
<term>Protéines fongiques</term>
<term>Synténie</term>
<term>Séquences répétées d'acides nucléiques</term>
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<keywords scheme="MESH" qualifier="microbiologie" xml:lang="fr"><term>Feuilles de plante</term>
<term>Tiges de plante</term>
<term>Triticum</term>
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<keywords scheme="MESH" qualifier="microbiology" xml:lang="en"><term>Plant Leaves</term>
<term>Plant Stems</term>
<term>Triticum</term>
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<keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Basidiomycota</term>
<term>Protéines fongiques</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Amino Acid Sequence</term>
<term>Cloning, Molecular</term>
<term>Conserved Sequence</term>
<term>Evolution, Molecular</term>
<term>Molecular Sequence Annotation</term>
<term>Molecular Sequence Data</term>
<term>Mutation</term>
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<keywords scheme="MESH" xml:lang="fr"><term>ADN fongique</term>
<term>Annotation de séquence moléculaire</term>
<term>Clonage moléculaire</term>
<term>Données de séquences moléculaires</term>
<term>Mutation</term>
<term>Séquence conservée</term>
<term>Séquence d'acides aminés</term>
<term>Évolution moléculaire</term>
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<front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b>
</p>
<p>Wheat leaf rust (Puccinia triticina Eriks; Pt) and stem rust fungi (P. graminis f.sp. tritici; Pgt) are significant economic pathogens having similar host ranges and life cycles, but different alternate hosts. The Pt genome, currently estimated at 135 Mb, is significantly larger than Pgt, at 88 Mb, but the reason for the expansion is unknown. Three genomic loci of Pt conserved proteins were characterized to gain insight into gene content, genome complexity and expansion.</p>
</div>
<div type="abstract" xml:lang="en"><p><b>RESULTS</b>
</p>
<p>A bacterial artificial chromosome (BAC) library was made from P. triticina race 1, BBBD and probed with Pt homologs of genes encoding two predicted Pgt secreted effectors and a DNA marker mapping to a region of avirulence. Three BACs, 103 Kb, 112 Kb, and 166 Kb, were sequenced, assembled, and open reading frames were identified. Orthologous genes were identified in Pgt and local conservation of gene order (microsynteny) was observed. Pairwise protein identities ranged from 26 to 99%. One Pt BAC, containing a RAD18 ortholog, shares syntenic regions with two Pgt scaffolds, which could represent both haplotypes of Pgt. Gene sequence is diverged between the species as well as within the two haplotypes. In all three BAC clones, gene order is locally conserved, however, gene shuffling has occurred relative to Pgt. These regions are further diverged by differing insertion loci of LTR-retrotransposon, Gypsy, Copia, Mutator, and Harbinger mobile elements. Uncharacterized Pt open reading frames were also found; these proteins are high in lysine and similar to multiple proteins in Pgt.</p>
</div>
<div type="abstract" xml:lang="en"><p><b>CONCLUSIONS</b>
</p>
<p>The three Pt loci are conserved in gene order, with a range of gene sequence divergence. Conservation of predicted haustoria expressed secreted protein genes between Pt and Pgt is extended to the more distant poplar rust, Melampsora larici-populina. The loci also reveal that genome expansion in Pt is in part due to higher occurrence of repeat-elements in this species.</p>
</div>
</front>
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<Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">Wheat leaf rust (Puccinia triticina Eriks; Pt) and stem rust fungi (P. graminis f.sp. tritici; Pgt) are significant economic pathogens having similar host ranges and life cycles, but different alternate hosts. The Pt genome, currently estimated at 135 Mb, is significantly larger than Pgt, at 88 Mb, but the reason for the expansion is unknown. Three genomic loci of Pt conserved proteins were characterized to gain insight into gene content, genome complexity and expansion.</AbstractText>
<AbstractText Label="RESULTS" NlmCategory="RESULTS">A bacterial artificial chromosome (BAC) library was made from P. triticina race 1, BBBD and probed with Pt homologs of genes encoding two predicted Pgt secreted effectors and a DNA marker mapping to a region of avirulence. Three BACs, 103 Kb, 112 Kb, and 166 Kb, were sequenced, assembled, and open reading frames were identified. Orthologous genes were identified in Pgt and local conservation of gene order (microsynteny) was observed. Pairwise protein identities ranged from 26 to 99%. One Pt BAC, containing a RAD18 ortholog, shares syntenic regions with two Pgt scaffolds, which could represent both haplotypes of Pgt. Gene sequence is diverged between the species as well as within the two haplotypes. In all three BAC clones, gene order is locally conserved, however, gene shuffling has occurred relative to Pgt. These regions are further diverged by differing insertion loci of LTR-retrotransposon, Gypsy, Copia, Mutator, and Harbinger mobile elements. Uncharacterized Pt open reading frames were also found; these proteins are high in lysine and similar to multiple proteins in Pgt.</AbstractText>
<AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">The three Pt loci are conserved in gene order, with a range of gene sequence divergence. Conservation of predicted haustoria expressed secreted protein genes between Pt and Pgt is extended to the more distant poplar rust, Melampsora larici-populina. The loci also reveal that genome expansion in Pt is in part due to higher occurrence of repeat-elements in this species.</AbstractText>
</Abstract>
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<ForeName>John P</ForeName>
<Initials>JP</Initials>
<AffiliationInfo><Affiliation>USDA-ARS, Hard Winter Wheat Genetics Research Unit, Department of Plant Pathology, Manhattan, KS 66506, USA. john.fellers@ars.usda.gov</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Soltani</LastName>
<ForeName>Bahram M</ForeName>
<Initials>BM</Initials>
</Author>
<Author ValidYN="Y"><LastName>Bruce</LastName>
<ForeName>Myron</ForeName>
<Initials>M</Initials>
</Author>
<Author ValidYN="Y"><LastName>Linning</LastName>
<ForeName>Rob</ForeName>
<Initials>R</Initials>
</Author>
<Author ValidYN="Y"><LastName>Cuomo</LastName>
<ForeName>Christina A</ForeName>
<Initials>CA</Initials>
</Author>
<Author ValidYN="Y"><LastName>Szabo</LastName>
<ForeName>Les J</ForeName>
<Initials>LJ</Initials>
</Author>
<Author ValidYN="Y"><LastName>Bakkeren</LastName>
<ForeName>Guus</ForeName>
<Initials>G</Initials>
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<MeshHeading><DescriptorName UI="D009154" MajorTopicYN="N">Mutation</DescriptorName>
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Conserved loci of leaf and stem rust fungi of wheat share synteny interrupted by lineage-specific influx of repeat elements.

Conserved loci of leaf and stem rust fungi of wheat share synteny interrupted by lineage-specific influx of repeat elements.

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