PhytophthoraV1, Main, Exploration, bibRecord, 000472

Insights into evolving global populations of Phytophthora infestans via new complementary mtDNA haplotype markers and nuclear SSRs.

Identifieur interne : 000472 ( Main/Exploration ); précédent : 000471; suivant : 000473

Insights into evolving global populations of Phytophthora infestans via new complementary mtDNA haplotype markers and nuclear SSRs.

Auteurs : Frank N. Martin [États-Unis] ; Yonghong Zhang [États-Unis] ; David E L. Cooke [Royaume-Uni] ; Mike D. Coffey [États-Unis] ; Niklaus J. Grünwald [États-Unis] ; William E. Fry [États-Unis]

Source :

PloS one [ 1932-6203 ] ; 2019.

RBID : pubmed:30601865

Descripteurs français

KwdFr :
- ADN mitochondrial (génétique), Analyse en composantes principales (MeSH), Génome mitochondrial (MeSH), Géographie (MeSH), Haplotypes (génétique), Locus génétiques (MeSH), Marqueurs génétiques (MeSH), Noyau de la cellule (génétique), Phylogenèse (MeSH), Phytophthora infestans (génétique), Phytophthora infestans (isolement et purification), Répétitions microsatellites (génétique), Variation génétique (MeSH), Évolution moléculaire (MeSH).
MESH :
- génétique : ADN mitochondrial, Haplotypes, Noyau de la cellule, Phytophthora infestans, Répétitions microsatellites.
- isolement et purification : Phytophthora infestans.
- Analyse en composantes principales, Génome mitochondrial, Géographie, Locus génétiques, Marqueurs génétiques, Phylogenèse, Variation génétique, Évolution moléculaire.

English descriptors

KwdEn :
- Cell Nucleus (genetics), DNA, Mitochondrial (genetics), Evolution, Molecular (MeSH), Genetic Loci (MeSH), Genetic Markers (MeSH), Genetic Variation (MeSH), Genome, Mitochondrial (MeSH), Geography (MeSH), Haplotypes (genetics), Microsatellite Repeats (genetics), Phylogeny (MeSH), Phytophthora infestans (genetics), Phytophthora infestans (isolation & purification), Principal Component Analysis (MeSH).
MESH :
- chemical , genetics : DNA, Mitochondrial.
- genetics : Cell Nucleus, Haplotypes, Microsatellite Repeats, Phytophthora infestans.
- isolation & purification : Phytophthora infestans.
- Evolution, Molecular, Genetic Loci, Genetic Markers, Genetic Variation, Genome, Mitochondrial, Geography, Phylogeny, Principal Component Analysis.

Abstract

In many parts of the world the damaging potato late blight pathogen, Phytophthora infestans, is spread as a succession of clonal lineages. The discrimination of genetic diversity within such evolving populations provides insights into the processes generating novel lineages and the pathways and drivers of pathogen evolution and dissemination at local and global scales. This knowledge, in turn, helps optimise management practices. Here we combine two key methods for dissecting mitochondrial and nuclear diversity and resolve intra and inter-lineage diversity of over 100 P. infestans isolates representative of key clonal lineages found globally. A novel set of PCR primers that amplify five target regions are provided for mitochondrial DNA sequence analysis. These five loci increased the number of mtDNA haplotypes resolved from four with the PCR RFLP method to 37 (17, 6, 8 and 4 for Ia, Ib, IIa, and IIb haplotypes, respectively, plus 2 Herb-1 haplotypes). As with the PCR RFLP method, two main lineages, I and II were defined. Group I contained 25 mtDNA haplotypes that grouped broadly according to the Ia and Ib types and resolved several sub-clades amongst the global sample. Group II comprised two distinct clusters with four haplotypes corresponding to the RFLP type IIb and eight haplotypes resolved within type IIa. The 12-plex SSR assay revealed 90 multilocus genotypes providing accurate discrimination of dominant clonal lineages and other genetically diverse isolates. Some association of genetic diversity and geographic region of contemporary isolates was observed; US and Mexican isolates formed a loose grouping, distinct from isolates from Europe, South America and other regions. Diversity within clonal lineages was observed that varied according to the age of the clone. In combination, these fine-scale nuclear and maternally inherited mitochondrial markers enabled a greater level of discrimination among isolates than previously available and provided complementary perspectives on evolutionary questions relating to the diversity, phylogeography and the origins and spread of clonal lineages of P. infestans.

DOI: 10.1371/journal.pone.0208606
PubMed: 30601865
PubMed Central: PMC6314598

Affiliations:

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

to stream Main, to step Corpus: 000584
to stream Main, to step Curation: 000584

Le document en format XML

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<front><div type="abstract" xml:lang="en">In many parts of the world the damaging potato late blight pathogen, Phytophthora infestans, is spread as a succession of clonal lineages. The discrimination of genetic diversity within such evolving populations provides insights into the processes generating novel lineages and the pathways and drivers of pathogen evolution and dissemination at local and global scales. This knowledge, in turn, helps optimise management practices. Here we combine two key methods for dissecting mitochondrial and nuclear diversity and resolve intra and inter-lineage diversity of over 100 P. infestans isolates representative of key clonal lineages found globally. A novel set of PCR primers that amplify five target regions are provided for mitochondrial DNA sequence analysis. These five loci increased the number of mtDNA haplotypes resolved from four with the PCR RFLP method to 37 (17, 6, 8 and 4 for Ia, Ib, IIa, and IIb haplotypes, respectively, plus 2 Herb-1 haplotypes). As with the PCR RFLP method, two main lineages, I and II were defined. Group I contained 25 mtDNA haplotypes that grouped broadly according to the Ia and Ib types and resolved several sub-clades amongst the global sample. Group II comprised two distinct clusters with four haplotypes corresponding to the RFLP type IIb and eight haplotypes resolved within type IIa. The 12-plex SSR assay revealed 90 multilocus genotypes providing accurate discrimination of dominant clonal lineages and other genetically diverse isolates. Some association of genetic diversity and geographic region of contemporary isolates was observed; US and Mexican isolates formed a loose grouping, distinct from isolates from Europe, South America and other regions. Diversity within clonal lineages was observed that varied according to the age of the clone. In combination, these fine-scale nuclear and maternally inherited mitochondrial markers enabled a greater level of discrimination among isolates than previously available and provided complementary perspectives on evolutionary questions relating to the diversity, phylogeography and the origins and spread of clonal lineages of P. infestans.</div>
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<Abstract><AbstractText>In many parts of the world the damaging potato late blight pathogen, Phytophthora infestans, is spread as a succession of clonal lineages. The discrimination of genetic diversity within such evolving populations provides insights into the processes generating novel lineages and the pathways and drivers of pathogen evolution and dissemination at local and global scales. This knowledge, in turn, helps optimise management practices. Here we combine two key methods for dissecting mitochondrial and nuclear diversity and resolve intra and inter-lineage diversity of over 100 P. infestans isolates representative of key clonal lineages found globally. A novel set of PCR primers that amplify five target regions are provided for mitochondrial DNA sequence analysis. These five loci increased the number of mtDNA haplotypes resolved from four with the PCR RFLP method to 37 (17, 6, 8 and 4 for Ia, Ib, IIa, and IIb haplotypes, respectively, plus 2 Herb-1 haplotypes). As with the PCR RFLP method, two main lineages, I and II were defined. Group I contained 25 mtDNA haplotypes that grouped broadly according to the Ia and Ib types and resolved several sub-clades amongst the global sample. Group II comprised two distinct clusters with four haplotypes corresponding to the RFLP type IIb and eight haplotypes resolved within type IIa. The 12-plex SSR assay revealed 90 multilocus genotypes providing accurate discrimination of dominant clonal lineages and other genetically diverse isolates. Some association of genetic diversity and geographic region of contemporary isolates was observed; US and Mexican isolates formed a loose grouping, distinct from isolates from Europe, South America and other regions. Diversity within clonal lineages was observed that varied according to the age of the clone. In combination, these fine-scale nuclear and maternally inherited mitochondrial markers enabled a greater level of discrimination among isolates than previously available and provided complementary perspectives on evolutionary questions relating to the diversity, phylogeography and the origins and spread of clonal lineages of P. infestans.</AbstractText>
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Insights into evolving global populations of Phytophthora infestans via new complementary mtDNA haplotype markers and nuclear SSRs.

Insights into evolving global populations of Phytophthora infestans via new complementary mtDNA haplotype markers and nuclear SSRs.

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