Patterns of diversifying selection in the phytotoxin-like scr74 gene family of Phytophthora infestans.
Identifieur interne : 000301 ( Main/Exploration ); précédent : 000300; suivant : 000302Patterns of diversifying selection in the phytotoxin-like scr74 gene family of Phytophthora infestans.
Auteurs : Zhenyu Liu [États-Unis] ; Jorunn I B. Bos ; Miles Armstrong ; Stephen C. Whisson ; Luis Da Cunha ; Trudy Torto-Alalibo ; Joe Win ; Anna O. Avrova ; Frank Wright ; Paul R J. Birch ; Sophien KamounSource :
- Molecular biology and evolution [ 0737-4038 ] ; 2005.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : Algal Proteins.
- genetics : Phytophthora.
- Amino Acid Sequence, Molecular Sequence Data, Point Mutation, Polymorphism, Single Nucleotide, Selection, Genetic.
Abstract
Phytophthora infestans, the organism responsible for the Irish famine, causes late blight, a re-emerging disease of potato and tomato. Little is known about the molecular evolution of P. infestans genes. To identify candidate effector genes (virulence or avirulence genes) that may have co-evolved with the host, we mined expressed sequence tag (EST) data from infection stages of P. infestans for secreted and potentially polymorphic genes. This led to the identification of scr74, a gene that encodes a predicted 74-amino acid secreted cysteine-rich protein with similarity to the Phytophthora cactorum phytotoxin PcF. The expression of scr74 was upregulated approximately 60-fold 2 to 4 days after inoculation of tomato and was also significantly induced during early stages of colonization of potato. The scr74 gene was found to belong to a highly polymorphic gene family within P. infestans with 21 different sequences identified. Using the approximate and maximum likelihood (ML) methods, we found that diversifying selection likely caused the extensive polymorphism observed within the scr74 gene family. Pairwise comparisons of 17 scr74 sequences revealed elevated ratios of nonsynonymous to synonymous nucleotide-substitution rates, particularly in the mature region of the proteins. Using ML, all 21 polymorphic amino acid sites were identified to be under diversifying selection. Of these 21 amino acids, 19 are located in the mature protein region, suggesting that selection may have acted on the functional portions of the proteins. Further investigation of gene copy number and organization revealed that the scr74 gene family comprises at least three copies located in a region of no more than 300 kb of the P. infestans genome. We found evidence that recombination contributed to sequence divergence within at least one gene locus. These results led us to propose an evolutionary model that involves gene duplication and recombination, followed by functional divergence of scr74 genes. This study provides support for using diversifying selection as a criterion for identifying candidate effector genes from sequence databases.
DOI: 10.1093/molbev/msi049
PubMed: 15548752
Affiliations:
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Avrova</name></author><author><name sortKey="Wright, Frank" sort="Wright, Frank" uniqKey="Wright F" first="Frank" last="Wright">Frank Wright</name></author><author><name sortKey="Birch, Paul R J" sort="Birch, Paul R J" uniqKey="Birch P" first="Paul R J" last="Birch">Paul R J. Birch</name></author><author><name sortKey="Kamoun, Sophien" sort="Kamoun, Sophien" uniqKey="Kamoun S" first="Sophien" last="Kamoun">Sophien Kamoun</name></author></analytic><series><title level="j">Molecular biology and evolution</title><idno type="ISSN">0737-4038</idno><imprint><date when="2005" type="published">2005</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algal Proteins (genetics)</term><term>Amino Acid Sequence (MeSH)</term><term>Molecular Sequence Data (MeSH)</term><term>Phytophthora (genetics)</term><term>Point Mutation (MeSH)</term><term>Polymorphism, Single Nucleotide (MeSH)</term><term>Selection, Genetic (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Données de séquences moléculaires (MeSH)</term><term>Mutation ponctuelle (MeSH)</term><term>Phytophthora (génétique)</term><term>Polymorphisme de nucléotide simple (MeSH)</term><term>Protéines d'algue (génétique)</term><term>Sélection génétique (MeSH)</term><term>Séquence d'acides aminés (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Algal Proteins</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Phytophthora</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Phytophthora</term><term>Protéines d'algue</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Amino Acid Sequence</term><term>Molecular Sequence Data</term><term>Point Mutation</term><term>Polymorphism, Single Nucleotide</term><term>Selection, Genetic</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Données de séquences moléculaires</term><term>Mutation ponctuelle</term><term>Polymorphisme de nucléotide simple</term><term>Sélection génétique</term><term>Séquence d'acides aminés</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Phytophthora infestans, the organism responsible for the Irish famine, causes late blight, a re-emerging disease of potato and tomato. Little is known about the molecular evolution of P. infestans genes. To identify candidate effector genes (virulence or avirulence genes) that may have co-evolved with the host, we mined expressed sequence tag (EST) data from infection stages of P. infestans for secreted and potentially polymorphic genes. This led to the identification of scr74, a gene that encodes a predicted 74-amino acid secreted cysteine-rich protein with similarity to the Phytophthora cactorum phytotoxin PcF. The expression of scr74 was upregulated approximately 60-fold 2 to 4 days after inoculation of tomato and was also significantly induced during early stages of colonization of potato. The scr74 gene was found to belong to a highly polymorphic gene family within P. infestans with 21 different sequences identified. Using the approximate and maximum likelihood (ML) methods, we found that diversifying selection likely caused the extensive polymorphism observed within the scr74 gene family. Pairwise comparisons of 17 scr74 sequences revealed elevated ratios of nonsynonymous to synonymous nucleotide-substitution rates, particularly in the mature region of the proteins. Using ML, all 21 polymorphic amino acid sites were identified to be under diversifying selection. Of these 21 amino acids, 19 are located in the mature protein region, suggesting that selection may have acted on the functional portions of the proteins. Further investigation of gene copy number and organization revealed that the scr74 gene family comprises at least three copies located in a region of no more than 300 kb of the P. infestans genome. We found evidence that recombination contributed to sequence divergence within at least one gene locus. These results led us to propose an evolutionary model that involves gene duplication and recombination, followed by functional divergence of scr74 genes. This study provides support for using diversifying selection as a criterion for identifying candidate effector genes from sequence databases.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">15548752</PMID><DateCompleted><Year>2005</Year><Month>09</Month><Day>01</Day></DateCompleted><DateRevised><Year>2009</Year><Month>11</Month><Day>19</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">0737-4038</ISSN><JournalIssue CitedMedium="Print"><Volume>22</Volume><Issue>3</Issue><PubDate><Year>2005</Year><Month>Mar</Month></PubDate></JournalIssue><Title>Molecular biology and evolution</Title><ISOAbbreviation>Mol Biol Evol</ISOAbbreviation></Journal><ArticleTitle>Patterns of diversifying selection in the phytotoxin-like scr74 gene family of Phytophthora infestans.</ArticleTitle><Pagination><MedlinePgn>659-72</MedlinePgn></Pagination><Abstract><AbstractText>Phytophthora infestans, the organism responsible for the Irish famine, causes late blight, a re-emerging disease of potato and tomato. Little is known about the molecular evolution of P. infestans genes. To identify candidate effector genes (virulence or avirulence genes) that may have co-evolved with the host, we mined expressed sequence tag (EST) data from infection stages of P. infestans for secreted and potentially polymorphic genes. This led to the identification of scr74, a gene that encodes a predicted 74-amino acid secreted cysteine-rich protein with similarity to the Phytophthora cactorum phytotoxin PcF. The expression of scr74 was upregulated approximately 60-fold 2 to 4 days after inoculation of tomato and was also significantly induced during early stages of colonization of potato. The scr74 gene was found to belong to a highly polymorphic gene family within P. infestans with 21 different sequences identified. Using the approximate and maximum likelihood (ML) methods, we found that diversifying selection likely caused the extensive polymorphism observed within the scr74 gene family. Pairwise comparisons of 17 scr74 sequences revealed elevated ratios of nonsynonymous to synonymous nucleotide-substitution rates, particularly in the mature region of the proteins. Using ML, all 21 polymorphic amino acid sites were identified to be under diversifying selection. Of these 21 amino acids, 19 are located in the mature protein region, suggesting that selection may have acted on the functional portions of the proteins. Further investigation of gene copy number and organization revealed that the scr74 gene family comprises at least three copies located in a region of no more than 300 kb of the P. infestans genome. We found evidence that recombination contributed to sequence divergence within at least one gene locus. These results led us to propose an evolutionary model that involves gene duplication and recombination, followed by functional divergence of scr74 genes. This study provides support for using diversifying selection as a criterion for identifying candidate effector genes from sequence databases.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Liu</LastName><ForeName>Zhenyu</ForeName><Initials>Z</Initials><AffiliationInfo><Affiliation>Department of Plant Pathology, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster, Ohio, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Bos</LastName><ForeName>Jorunn I B</ForeName><Initials>JI</Initials></Author><Author ValidYN="Y"><LastName>Armstrong</LastName><ForeName>Miles</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Whisson</LastName><ForeName>Stephen C</ForeName><Initials>SC</Initials></Author><Author ValidYN="Y"><LastName>da Cunha</LastName><ForeName>Luis</ForeName><Initials>L</Initials></Author><Author ValidYN="Y"><LastName>Torto-Alalibo</LastName><ForeName>Trudy</ForeName><Initials>T</Initials></Author><Author ValidYN="Y"><LastName>Win</LastName><ForeName>Joe</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>Avrova</LastName><ForeName>Anna O</ForeName><Initials>AO</Initials></Author><Author ValidYN="Y"><LastName>Wright</LastName><ForeName>Frank</ForeName><Initials>F</Initials></Author><Author ValidYN="Y"><LastName>Birch</LastName><ForeName>Paul R J</ForeName><Initials>PR</Initials></Author><Author ValidYN="Y"><LastName>Kamoun</LastName><ForeName>Sophien</ForeName><Initials>S</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType><PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2004</Year><Month>11</Month><Day>17</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Mol Biol Evol</MedlineTA><NlmUniqueID>8501455</NlmUniqueID><ISSNLinking>0737-4038</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D020418">Algal Proteins</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><CommentsCorrectionsList><CommentsCorrections RefType="ErratumIn"><RefSource>Mol Biol Evol. 2005 Apr;22(4):1159</RefSource></CommentsCorrections></CommentsCorrectionsList><MeshHeadingList><MeshHeading><DescriptorName UI="D020418" MajorTopicYN="N">Algal Proteins</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D000595" MajorTopicYN="N">Amino Acid Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008969" MajorTopicYN="N">Molecular Sequence Data</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010838" MajorTopicYN="N">Phytophthora</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017354" MajorTopicYN="Y">Point Mutation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020641" MajorTopicYN="Y">Polymorphism, Single Nucleotide</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012641" MajorTopicYN="Y">Selection, Genetic</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2004</Year><Month>11</Month><Day>19</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2005</Year><Month>9</Month><Day>2</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2004</Year><Month>11</Month><Day>19</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">15548752</ArticleId><ArticleId IdType="pii">msi049</ArticleId><ArticleId IdType="doi">10.1093/molbev/msi049</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>États-Unis</li></country><region><li>Ohio</li></region></list><tree><noCountry><name sortKey="Armstrong, Miles" sort="Armstrong, Miles" uniqKey="Armstrong M" first="Miles" last="Armstrong">Miles Armstrong</name><name sortKey="Avrova, Anna O" sort="Avrova, Anna O" uniqKey="Avrova A" first="Anna O" last="Avrova">Anna O. Avrova</name><name sortKey="Birch, Paul R J" sort="Birch, Paul R J" uniqKey="Birch P" first="Paul R J" last="Birch">Paul R J. Birch</name><name sortKey="Bos, Jorunn I B" sort="Bos, Jorunn I B" uniqKey="Bos J" first="Jorunn I B" last="Bos">Jorunn I B. Bos</name><name sortKey="Da Cunha, Luis" sort="Da Cunha, Luis" uniqKey="Da Cunha L" first="Luis" last="Da Cunha">Luis Da Cunha</name><name sortKey="Kamoun, Sophien" sort="Kamoun, Sophien" uniqKey="Kamoun S" first="Sophien" last="Kamoun">Sophien Kamoun</name><name sortKey="Torto Alalibo, Trudy" sort="Torto Alalibo, Trudy" uniqKey="Torto Alalibo T" first="Trudy" last="Torto-Alalibo">Trudy Torto-Alalibo</name><name sortKey="Whisson, Stephen C" sort="Whisson, Stephen C" uniqKey="Whisson S" first="Stephen C" last="Whisson">Stephen C. Whisson</name><name sortKey="Win, Joe" sort="Win, Joe" uniqKey="Win J" first="Joe" last="Win">Joe Win</name><name sortKey="Wright, Frank" sort="Wright, Frank" uniqKey="Wright F" first="Frank" last="Wright">Frank Wright</name></noCountry><country name="États-Unis"><region name="Ohio"><name sortKey="Liu, Zhenyu" sort="Liu, Zhenyu" uniqKey="Liu Z" first="Zhenyu" last="Liu">Zhenyu Liu</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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