Mitochondrial DNA assessment of Phytophthora infestans isolates from potato and tomato in Ethiopia reveals unexpected diversity.
Identifieur interne : 000B78 ( Main/Exploration ); précédent : 000B77; suivant : 000B79Mitochondrial DNA assessment of Phytophthora infestans isolates from potato and tomato in Ethiopia reveals unexpected diversity.
Auteurs : Daniel Shimelash [Éthiopie] ; Temam Hussien [Éthiopie] ; Chemeda Fininsa [Éthiopie] ; Greg Forbes [République populaire de Chine] ; Jonathan Yuen [Suède]Source :
- Current genetics [ 1432-0983 ] ; 2016.
Descripteurs français
- KwdFr :
- ADN mitochondrial (MeSH), Analyse de séquence d'ADN (MeSH), Biodiversité (MeSH), Haplotypes (MeSH), Lycopersicon esculentum (microbiologie), Phylogenèse (MeSH), Phytophthora infestans (classification), Phytophthora infestans (génétique), Phytophthora infestans (isolement et purification), Polymorphisme de restriction (MeSH), Réaction de polymérisation en chaîne (MeSH), Solanum tuberosum (microbiologie), Séquence nucléotidique (MeSH), Éthiopie (MeSH).
- MESH :
- génétique : Phytophthora infestans.
- isolement et purification : Phytophthora infestans.
- microbiologie : Lycopersicon esculentum, Solanum tuberosum.
- ADN mitochondrial, Analyse de séquence d'ADN, Biodiversité, Haplotypes, Phylogenèse, Phytophthora infestans, Polymorphisme de restriction, Réaction de polymérisation en chaîne, Séquence nucléotidique, Éthiopie.
English descriptors
- KwdEn :
- Base Sequence (MeSH), Biodiversity (MeSH), DNA, Mitochondrial (MeSH), Ethiopia (MeSH), Haplotypes (MeSH), Lycopersicon esculentum (microbiology), Phylogeny (MeSH), Phytophthora infestans (classification), Phytophthora infestans (genetics), Phytophthora infestans (isolation & purification), Polymerase Chain Reaction (MeSH), Polymorphism, Restriction Fragment Length (MeSH), Sequence Analysis, DNA (MeSH), Solanum tuberosum (microbiology).
- MESH :
- chemical : DNA, Mitochondrial.
- classification : Phytophthora infestans.
- genetics : Phytophthora infestans.
- isolation & purification : Phytophthora infestans.
- microbiology : Lycopersicon esculentum, Solanum tuberosum.
- Base Sequence, Biodiversity, Ethiopia, Haplotypes, Phylogeny, Polymerase Chain Reaction, Polymorphism, Restriction Fragment Length, Sequence Analysis, DNA.
Abstract
Mitochondrial DNA (mtDNA) haplotypes were determined using restriction fragment length polymorphism (RFLP) for P. infestans sampled from 513 foliar lesions of late blight found on potato and tomato in different regions of Ethiopia. Among the four reported mitochondrial haplotypes of Phytophthora infestans, Ia, Ib and IIb were detected in 93 % of the samples analyzed but the vast majority of these were Ia. The remaining 7 % represented a previously unreported haplotype. DNA sequencing of this new haplotype also confirmed a single base nucleotide substitution that resulted in loss of EcoRI restriction site and gain of two additional MspI sites in cox1 and atp1 genes, respectively. There were 28 polymorphic sites among all nucleotide sequences including five reference isolates. Sites with alignment gaps were observed in P4 with one nucleotide deletion in 11 Ethiopian isolates. None of the reference sequence produced frame-shifts, with the exception of the 3-nucleotide deletion in the P4 region by Phytophthora andina, a feature that can be used to distinguish the new Ethiopian isolates from P. andina. While a distinguishing molecular data presented here clearly separated them from P. infestans, 7 % of the isolates that share this feature formed an important component of the late blight pathogen causing disease on Solanum tuberosum in Ethiopia. Thus, these Ethiopian isolates could represent a novel Phytophthora species reported for the first time here.
DOI: 10.1007/s00294-016-0572-8
PubMed: 26873223
Affiliations:
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xml:lang="fr">Éthiopie</country><wicri:regionArea>School of Plant Sciences, Haramaya University, P.O.Box 138, Dire Dawa</wicri:regionArea><wicri:noRegion>Dire Dawa</wicri:noRegion></affiliation></author><author><name sortKey="Hussien, Temam" sort="Hussien, Temam" uniqKey="Hussien T" first="Temam" last="Hussien">Temam Hussien</name><affiliation wicri:level="1"><nlm:affiliation>School of Plant Sciences, Haramaya University, P.O.Box 138, Dire Dawa, Ethiopia.</nlm:affiliation><country xml:lang="fr">Éthiopie</country><wicri:regionArea>School of Plant Sciences, Haramaya University, P.O.Box 138, Dire Dawa</wicri:regionArea><wicri:noRegion>Dire Dawa</wicri:noRegion></affiliation></author><author><name sortKey="Fininsa, Chemeda" sort="Fininsa, Chemeda" uniqKey="Fininsa C" first="Chemeda" last="Fininsa">Chemeda Fininsa</name><affiliation wicri:level="1"><nlm:affiliation>School of Plant Sciences, Haramaya University, P.O.Box 138, Dire Dawa, Ethiopia.</nlm:affiliation><country xml:lang="fr">Éthiopie</country><wicri:regionArea>School of Plant Sciences, Haramaya University, P.O.Box 138, Dire Dawa</wicri:regionArea><wicri:noRegion>Dire Dawa</wicri:noRegion></affiliation></author><author><name sortKey="Forbes, Greg" sort="Forbes, Greg" uniqKey="Forbes G" first="Greg" last="Forbes">Greg Forbes</name><affiliation wicri:level="1"><nlm:affiliation>CIP-China Center for Asia Pacific, Pan Pacific Plaza A12 Zhongguancun Nandajie, Beijing, 100081, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>CIP-China Center for Asia Pacific, Pan Pacific Plaza A12 Zhongguancun Nandajie, Beijing, 100081</wicri:regionArea><wicri:noRegion>100081</wicri:noRegion></affiliation></author><author><name sortKey="Yuen, Jonathan" sort="Yuen, Jonathan" uniqKey="Yuen J" first="Jonathan" last="Yuen">Jonathan Yuen</name><affiliation wicri:level="1"><nlm:affiliation>Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, 750 07, Uppsala, Sweden.</nlm:affiliation><country xml:lang="fr">Suède</country><wicri:regionArea>Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, 750 07, Uppsala</wicri:regionArea><wicri:noRegion>Uppsala</wicri:noRegion></affiliation></author></analytic><series><title level="j">Current genetics</title><idno type="eISSN">1432-0983</idno><imprint><date when="2016" type="published">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Base Sequence (MeSH)</term><term>Biodiversity (MeSH)</term><term>DNA, Mitochondrial (MeSH)</term><term>Ethiopia (MeSH)</term><term>Haplotypes (MeSH)</term><term>Lycopersicon esculentum (microbiology)</term><term>Phylogeny (MeSH)</term><term>Phytophthora infestans (classification)</term><term>Phytophthora infestans (genetics)</term><term>Phytophthora infestans (isolation & purification)</term><term>Polymerase Chain Reaction (MeSH)</term><term>Polymorphism, Restriction Fragment Length (MeSH)</term><term>Sequence Analysis, DNA (MeSH)</term><term>Solanum tuberosum (microbiology)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN mitochondrial (MeSH)</term><term>Analyse de séquence d'ADN (MeSH)</term><term>Biodiversité (MeSH)</term><term>Haplotypes (MeSH)</term><term>Lycopersicon esculentum (microbiologie)</term><term>Phylogenèse (MeSH)</term><term>Phytophthora infestans (classification)</term><term>Phytophthora infestans (génétique)</term><term>Phytophthora infestans (isolement et purification)</term><term>Polymorphisme de restriction (MeSH)</term><term>Réaction de polymérisation en chaîne (MeSH)</term><term>Solanum tuberosum (microbiologie)</term><term>Séquence nucléotidique (MeSH)</term><term>Éthiopie (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" xml:lang="en"><term>DNA, Mitochondrial</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Phytophthora infestans</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Phytophthora infestans</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Phytophthora infestans</term></keywords><keywords scheme="MESH" qualifier="isolation & purification" xml:lang="en"><term>Phytophthora infestans</term></keywords><keywords scheme="MESH" qualifier="isolement et purification" xml:lang="fr"><term>Phytophthora infestans</term></keywords><keywords scheme="MESH" qualifier="microbiologie" xml:lang="fr"><term>Lycopersicon esculentum</term><term>Solanum tuberosum</term></keywords><keywords scheme="MESH" qualifier="microbiology" xml:lang="en"><term>Lycopersicon esculentum</term><term>Solanum tuberosum</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Base Sequence</term><term>Biodiversity</term><term>Ethiopia</term><term>Haplotypes</term><term>Phylogeny</term><term>Polymerase Chain Reaction</term><term>Polymorphism, Restriction Fragment Length</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>ADN mitochondrial</term><term>Analyse de séquence d'ADN</term><term>Biodiversité</term><term>Haplotypes</term><term>Phylogenèse</term><term>Phytophthora infestans</term><term>Polymorphisme de restriction</term><term>Réaction de polymérisation en chaîne</term><term>Séquence nucléotidique</term><term>Éthiopie</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Mitochondrial DNA (mtDNA) haplotypes were determined using restriction fragment length polymorphism (RFLP) for P. infestans sampled from 513 foliar lesions of late blight found on potato and tomato in different regions of Ethiopia. Among the four reported mitochondrial haplotypes of Phytophthora infestans, Ia, Ib and IIb were detected in 93 % of the samples analyzed but the vast majority of these were Ia. The remaining 7 % represented a previously unreported haplotype. DNA sequencing of this new haplotype also confirmed a single base nucleotide substitution that resulted in loss of EcoRI restriction site and gain of two additional MspI sites in cox1 and atp1 genes, respectively. There were 28 polymorphic sites among all nucleotide sequences including five reference isolates. Sites with alignment gaps were observed in P4 with one nucleotide deletion in 11 Ethiopian isolates. None of the reference sequence produced frame-shifts, with the exception of the 3-nucleotide deletion in the P4 region by Phytophthora andina, a feature that can be used to distinguish the new Ethiopian isolates from P. andina. While a distinguishing molecular data presented here clearly separated them from P. infestans, 7 % of the isolates that share this feature formed an important component of the late blight pathogen causing disease on Solanum tuberosum in Ethiopia. Thus, these Ethiopian isolates could represent a novel Phytophthora species reported for the first time here. </div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">26873223</PMID><DateCompleted><Year>2017</Year><Month>02</Month><Day>06</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1432-0983</ISSN><JournalIssue CitedMedium="Internet"><Volume>62</Volume><Issue>3</Issue><PubDate><Year>2016</Year><Month>Aug</Month></PubDate></JournalIssue><Title>Current genetics</Title><ISOAbbreviation>Curr Genet</ISOAbbreviation></Journal><ArticleTitle>Mitochondrial DNA assessment of Phytophthora infestans isolates from potato and tomato in Ethiopia reveals unexpected diversity.</ArticleTitle><Pagination><MedlinePgn>657-67</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1007/s00294-016-0572-8</ELocationID><Abstract><AbstractText>Mitochondrial DNA (mtDNA) haplotypes were determined using restriction fragment length polymorphism (RFLP) for P. infestans sampled from 513 foliar lesions of late blight found on potato and tomato in different regions of Ethiopia. Among the four reported mitochondrial haplotypes of Phytophthora infestans, Ia, Ib and IIb were detected in 93 % of the samples analyzed but the vast majority of these were Ia. The remaining 7 % represented a previously unreported haplotype. DNA sequencing of this new haplotype also confirmed a single base nucleotide substitution that resulted in loss of EcoRI restriction site and gain of two additional MspI sites in cox1 and atp1 genes, respectively. There were 28 polymorphic sites among all nucleotide sequences including five reference isolates. Sites with alignment gaps were observed in P4 with one nucleotide deletion in 11 Ethiopian isolates. None of the reference sequence produced frame-shifts, with the exception of the 3-nucleotide deletion in the P4 region by Phytophthora andina, a feature that can be used to distinguish the new Ethiopian isolates from P. andina. While a distinguishing molecular data presented here clearly separated them from P. infestans, 7 % of the isolates that share this feature formed an important component of the late blight pathogen causing disease on Solanum tuberosum in Ethiopia. Thus, these Ethiopian isolates could represent a novel Phytophthora species reported for the first time here. </AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Shimelash</LastName><ForeName>Daniel</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>School of Plant Sciences, Haramaya University, P.O.Box 138, Dire Dawa, Ethiopia. dshamm@gmail.com.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hussien</LastName><ForeName>Temam</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>School of Plant Sciences, Haramaya University, P.O.Box 138, Dire Dawa, Ethiopia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Fininsa</LastName><ForeName>Chemeda</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>School of Plant Sciences, Haramaya University, P.O.Box 138, Dire Dawa, Ethiopia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Forbes</LastName><ForeName>Greg</ForeName><Initials>G</Initials><AffiliationInfo><Affiliation>CIP-China Center for Asia Pacific, Pan Pacific Plaza A12 Zhongguancun Nandajie, Beijing, 100081, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yuen</LastName><ForeName>Jonathan</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, 750 07, Uppsala, Sweden.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2016</Year><Month>02</Month><Day>12</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Curr Genet</MedlineTA><NlmUniqueID>8004904</NlmUniqueID><ISSNLinking>0172-8083</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D004272">DNA, Mitochondrial</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D001483" MajorTopicYN="N">Base Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D044822" MajorTopicYN="Y">Biodiversity</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D004272" MajorTopicYN="Y">DNA, Mitochondrial</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005002" MajorTopicYN="N">Ethiopia</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D006239" MajorTopicYN="N">Haplotypes</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018551" MajorTopicYN="N">Lycopersicon esculentum</DescriptorName><QualifierName UI="Q000382" MajorTopicYN="Y">microbiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="Y">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D055750" MajorTopicYN="N">Phytophthora infestans</DescriptorName><QualifierName UI="Q000145" MajorTopicYN="Y">classification</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000302" MajorTopicYN="N">isolation & purification</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D016133" MajorTopicYN="N">Polymerase Chain Reaction</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012150" MajorTopicYN="N">Polymorphism, Restriction Fragment Length</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D011198" MajorTopicYN="N">Solanum tuberosum</DescriptorName><QualifierName UI="Q000382" 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Chine</li><li>Suède</li><li>Éthiopie</li></country></list><tree><country name="Éthiopie"><noRegion><name sortKey="Shimelash, Daniel" sort="Shimelash, Daniel" uniqKey="Shimelash D" first="Daniel" last="Shimelash">Daniel Shimelash</name></noRegion><name sortKey="Fininsa, Chemeda" sort="Fininsa, Chemeda" uniqKey="Fininsa C" first="Chemeda" last="Fininsa">Chemeda Fininsa</name><name sortKey="Hussien, Temam" sort="Hussien, Temam" uniqKey="Hussien T" first="Temam" last="Hussien">Temam Hussien</name></country><country name="République populaire de Chine"><noRegion><name sortKey="Forbes, Greg" sort="Forbes, Greg" uniqKey="Forbes G" first="Greg" last="Forbes">Greg Forbes</name></noRegion></country><country name="Suède"><noRegion><name sortKey="Yuen, Jonathan" sort="Yuen, Jonathan" uniqKey="Yuen J" first="Jonathan" last="Yuen">Jonathan Yuen</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:26873223" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \
| NlmPubMed2Wicri -a PhytophthoraV1
| This area was generated with Dilib version V0.6.38. |  |