Small homologous blocks in phytophthora genomes do not point to an ancient whole-genome duplication.
Identifieur interne : 000F81 ( Main/Exploration ); précédent : 000F80; suivant : 000F82Small homologous blocks in phytophthora genomes do not point to an ancient whole-genome duplication.
Auteurs : Jolien J E. Van Hooff [Pays-Bas] ; Berend Snel ; Michael F. SeidlSource :
- Genome biology and evolution [ 1759-6653 ] ; 2014.
Descripteurs français
- KwdFr :
- MESH :
- génétique : Phytophthora.
- pathogénicité : Phytophthora.
- Duplication de gène, Génome, Évolution biologique.
English descriptors
- KwdEn :
- MESH :
- genetics : Phytophthora.
- pathogenicity : Phytophthora.
- Biological Evolution, Gene Duplication, Genome.
Abstract
Genomes of the plant-pathogenic genus Phytophthora are characterized by small duplicated blocks consisting of two consecutive genes (2HOM blocks) and by an elevated abundance of similarly aged gene duplicates. Both properties, in particular the presence of 2HOM blocks, have been attributed to a whole-genome duplication (WGD) at the last common ancestor of Phytophthora. However, large intraspecies synteny-compelling evidence for a WGD-has not been detected. Here, we revisited the WGD hypothesis by deducing the age of 2HOM blocks. Two independent timing methods reveal that the majority of 2HOM blocks arose after divergence of the Phytophthora lineages. In addition, a large proportion of the 2HOM block copies colocalize on the same scaffold. Therefore, the presence of 2HOM blocks does not support a WGD at the last common ancestor of Phytophthora. Thus, genome evolution of Phytophthora is likely driven by alternative mechanisms, such as bursts of transposon activity.
DOI: 10.1093/gbe/evu081
PubMed: 24760277
PubMed Central: PMC4040989
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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Van Hooff</name><affiliation wicri:level="4"><nlm:affiliation>Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, The Netherlands.</nlm:affiliation><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University</wicri:regionArea><placeName><settlement type="city">Utrecht</settlement><region nuts="2">Utrecht (province)</region></placeName><orgName type="university">Université d'Utrecht</orgName></affiliation></author><author><name sortKey="Snel, Berend" sort="Snel, Berend" uniqKey="Snel B" first="Berend" last="Snel">Berend Snel</name></author><author><name sortKey="Seidl, Michael F" sort="Seidl, Michael F" uniqKey="Seidl M" first="Michael F" last="Seidl">Michael F. Seidl</name></author></analytic><series><title level="j">Genome biology and evolution</title><idno type="eISSN">1759-6653</idno><imprint><date when="2014" type="published">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Biological Evolution (MeSH)</term><term>Gene Duplication (MeSH)</term><term>Genome (MeSH)</term><term>Phytophthora (genetics)</term><term>Phytophthora (pathogenicity)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Duplication de gène (MeSH)</term><term>Génome (MeSH)</term><term>Phytophthora (génétique)</term><term>Phytophthora (pathogénicité)</term><term>Évolution biologique (MeSH)</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></keywords><keywords scheme="MESH" qualifier="pathogenicity" xml:lang="en"><term>Phytophthora</term></keywords><keywords scheme="MESH" qualifier="pathogénicité" xml:lang="fr"><term>Phytophthora</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Biological Evolution</term><term>Gene Duplication</term><term>Genome</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Duplication de gène</term><term>Génome</term><term>Évolution biologique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Genomes of the plant-pathogenic genus Phytophthora are characterized by small duplicated blocks consisting of two consecutive genes (2HOM blocks) and by an elevated abundance of similarly aged gene duplicates. Both properties, in particular the presence of 2HOM blocks, have been attributed to a whole-genome duplication (WGD) at the last common ancestor of Phytophthora. However, large intraspecies synteny-compelling evidence for a WGD-has not been detected. Here, we revisited the WGD hypothesis by deducing the age of 2HOM blocks. Two independent timing methods reveal that the majority of 2HOM blocks arose after divergence of the Phytophthora lineages. In addition, a large proportion of the 2HOM block copies colocalize on the same scaffold. Therefore, the presence of 2HOM blocks does not support a WGD at the last common ancestor of Phytophthora. Thus, genome evolution of Phytophthora is likely driven by alternative mechanisms, such as bursts of transposon activity. </div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">24760277</PMID><DateCompleted><Year>2016</Year><Month>05</Month><Day>09</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Electronic">1759-6653</ISSN><JournalIssue CitedMedium="Internet"><Volume>6</Volume><Issue>5</Issue><PubDate><Year>2014</Year><Month>May</Month></PubDate></JournalIssue><Title>Genome biology and evolution</Title><ISOAbbreviation>Genome Biol Evol</ISOAbbreviation></Journal><ArticleTitle>Small homologous blocks in phytophthora genomes do not point to an ancient whole-genome duplication.</ArticleTitle><Pagination><MedlinePgn>1079-85</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1093/gbe/evu081</ELocationID><Abstract><AbstractText>Genomes of the plant-pathogenic genus Phytophthora are characterized by small duplicated blocks consisting of two consecutive genes (2HOM blocks) and by an elevated abundance of similarly aged gene duplicates. Both properties, in particular the presence of 2HOM blocks, have been attributed to a whole-genome duplication (WGD) at the last common ancestor of Phytophthora. However, large intraspecies synteny-compelling evidence for a WGD-has not been detected. Here, we revisited the WGD hypothesis by deducing the age of 2HOM blocks. Two independent timing methods reveal that the majority of 2HOM blocks arose after divergence of the Phytophthora lineages. In addition, a large proportion of the 2HOM block copies colocalize on the same scaffold. Therefore, the presence of 2HOM blocks does not support a WGD at the last common ancestor of Phytophthora. 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1;22(21):2688-90</Citation><ArticleIdList><ArticleId IdType="pubmed">16928733</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Plant Microbe Interact. 2006 Dec;19(12):1322-8</Citation><ArticleIdList><ArticleId IdType="pubmed">17153916</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Biol Evol. 2007 Aug;24(8):1586-91</Citation><ArticleIdList><ArticleId IdType="pubmed">17483113</ArticleId></ArticleIdList></Reference><Reference><Citation>Curr Opin Genet Dev. 2007 Dec;17(6):505-12</Citation><ArticleIdList><ArticleId IdType="pubmed">18006297</ArticleId></ArticleIdList></Reference><Reference><Citation>Fungal Genet Biol. 2008 Mar;45(3):266-77</Citation><ArticleIdList><ArticleId IdType="pubmed">18039586</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Res. 2009 Feb;19(2):327-35</Citation><ArticleIdList><ArticleId IdType="pubmed">19029536</ArticleId></ArticleIdList></Reference><Reference><Citation>Nature. 2009 Sep 17;461(7262):393-8</Citation><ArticleIdList><ArticleId IdType="pubmed">19741609</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Biol. 2009;10(10):241</Citation><ArticleIdList><ArticleId IdType="pubmed">19843349</ArticleId></ArticleIdList></Reference><Reference><Citation>Gene. 2010 Apr 1;454(1-2):1-7</Citation><ArticleIdList><ArticleId IdType="pubmed">20102733</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Genomics. 2010;11:353</Citation><ArticleIdList><ArticleId IdType="pubmed">20525264</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Biol. 2010;11(7):R73</Citation><ArticleIdList><ArticleId IdType="pubmed">20626842</ArticleId></ArticleIdList></Reference><Reference><Citation>Science. 2010 Dec 10;330(6010):1549-51</Citation><ArticleIdList><ArticleId IdType="pubmed">21148394</ArticleId></ArticleIdList></Reference><Reference><Citation>Plant Physiol. 2011 Feb;155(2):628-44</Citation><ArticleIdList><ArticleId IdType="pubmed">21119047</ArticleId></ArticleIdList></Reference><Reference><Citation>PLoS One. 2011;6(12):e28150</Citation><ArticleIdList><ArticleId IdType="pubmed">22164235</ArticleId></ArticleIdList></Reference><Reference><Citation>Nature. 2011 Dec 22;480(7378):520-4</Citation><ArticleIdList><ArticleId IdType="pubmed">22089132</ArticleId></ArticleIdList></Reference><Reference><Citation>Phytopathology. 2012 Apr;102(4):348-64</Citation><ArticleIdList><ArticleId IdType="pubmed">22185336</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Biol Evol. 2012;4(3):199-211</Citation><ArticleIdList><ArticleId IdType="pubmed">22230142</ArticleId></ArticleIdList></Reference><Reference><Citation>Annu Rev Phytopathol. 2012;50:295-318</Citation><ArticleIdList><ArticleId IdType="pubmed">22920560</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Plant Microbe Interact. 2012 Oct;25(10):1350-60</Citation><ArticleIdList><ArticleId IdType="pubmed">22712506</ArticleId></ArticleIdList></Reference><Reference><Citation>PLoS Genet. 2013 Jun;9(6):e1003272</Citation><ArticleIdList><ArticleId IdType="pubmed">23785293</ArticleId></ArticleIdList></Reference><Reference><Citation>PLoS One. 2013;8(10):e75072</Citation><ArticleIdList><ArticleId IdType="pubmed">24124466</ArticleId></ArticleIdList></Reference><Reference><Citation>Science. 2013 Dec 20;342(6165):1241089</Citation><ArticleIdList><ArticleId IdType="pubmed">24357323</ArticleId></ArticleIdList></Reference><Reference><Citation>PLoS One. 2013;8(12):e85385</Citation><ArticleIdList><ArticleId IdType="pubmed">24386473</ArticleId></ArticleIdList></Reference><Reference><Citation>Science. 2000 Nov 10;290(5494):1151-5</Citation><ArticleIdList><ArticleId IdType="pubmed">11073452</ArticleId></ArticleIdList></Reference><Reference><Citation>J Comput Biol. 2000;7(3-4):429-47</Citation><ArticleIdList><ArticleId IdType="pubmed">11108472</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 2002 Apr 1;30(7):1575-84</Citation><ArticleIdList><ArticleId IdType="pubmed">11917018</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Biol Evol. 2004 Jun;21(6):1146-51</Citation><ArticleIdList><ArticleId IdType="pubmed">15014147</ArticleId></ArticleIdList></Reference><Reference><Citation>Plant Cell. 2004 Jul;16(7):1667-78</Citation><ArticleIdList><ArticleId IdType="pubmed">15208399</ArticleId></ArticleIdList></Reference><Reference><Citation>Nature. 2004 Sep 30;431(7008):569-73</Citation><ArticleIdList><ArticleId IdType="pubmed">15457261</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Rev Genet. 2004 Oct;5(10):752-63</Citation><ArticleIdList><ArticleId IdType="pubmed">15510166</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 1997 Sep 1;25(17):3389-402</Citation><ArticleIdList><ArticleId IdType="pubmed">9254694</ArticleId></ArticleIdList></Reference><Reference><Citation>J Mol Evol. 1998 Apr;46(4):409-18</Citation><ArticleIdList><ArticleId IdType="pubmed">9541535</ArticleId></ArticleIdList></Reference><Reference><Citation>Cytogenet Genome Res. 2005;110(1-4):462-7</Citation><ArticleIdList><ArticleId IdType="pubmed">16093699</ArticleId></ArticleIdList></Reference><Reference><Citation>PLoS Biol. 2005 Oct;3(10):e314</Citation><ArticleIdList><ArticleId IdType="pubmed">16128622</ArticleId></ArticleIdList></Reference><Reference><Citation>Nature. 2006 Mar 16;440(7082):341-5</Citation><ArticleIdList><ArticleId IdType="pubmed">16541074</ArticleId></ArticleIdList></Reference><Reference><Citation>Science. 2006 Sep 1;313(5791):1261-6</Citation><ArticleIdList><ArticleId IdType="pubmed">16946064</ArticleId></ArticleIdList></Reference><Reference><Citation>J Mol Evol. 2006 Oct;63(4):458-72</Citation><ArticleIdList><ArticleId IdType="pubmed">16955239</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Plant Microbe Interact. 2006 Dec;19(12):1295-301</Citation><ArticleIdList><ArticleId IdType="pubmed">17153913</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed><affiliations><list><country><li>Pays-Bas</li></country><region><li>Utrecht (province)</li></region><settlement><li>Utrecht</li></settlement><orgName><li>Université d'Utrecht</li></orgName></list><tree><noCountry><name sortKey="Seidl, Michael F" sort="Seidl, Michael F" uniqKey="Seidl M" first="Michael F" last="Seidl">Michael F. Seidl</name><name sortKey="Snel, Berend" sort="Snel, Berend" uniqKey="Snel B" first="Berend" last="Snel">Berend Snel</name></noCountry><country name="Pays-Bas"><region name="Utrecht (province)"><name sortKey="Van Hooff, Jolien J E" sort="Van Hooff, Jolien J E" uniqKey="Van Hooff J" first="Jolien J E" last="Van Hooff">Jolien J E. Van Hooff</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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