Differential Locus Expansion Distinguishes Toxoplasmatinae Species and Closely Related Strains of Toxoplasma gondii
Identifieur interne : 000F71 ( Ncbi/Merge ); précédent : 000F70; suivant : 000F72Differential Locus Expansion Distinguishes Toxoplasmatinae Species and Closely Related Strains of Toxoplasma gondii
Auteurs : Yaw Adomako-Ankomah ; Gregory M. Wier ; Adair L. Borges ; Hannah E. Wand ; Jon P. BoyleSource :
- mBio [ 2150-7511 ] ; 2014.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : DNA, Protozoan.
- genetics : Sarcocystidae.
- Comparative Genomic Hybridization, Computational Biology, Gene Duplication, Genetic Loci, Genetic Variation, Synteny.
Abstract
Url:
DOI: 10.1128/mBio.01003-13
PubMed: 24496792
PubMed Central: 3950507
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Differential Locus Expansion Distinguishes <italic>Toxoplasmatinae</italic> Species and Closely Related Strains of <italic>Toxoplasma gondii</italic></title><author><name sortKey="Adomako Ankomah, Yaw" sort="Adomako Ankomah, Yaw" uniqKey="Adomako Ankomah Y" first="Yaw" last="Adomako-Ankomah">Yaw Adomako-Ankomah</name></author><author><name sortKey="Wier, Gregory M" sort="Wier, Gregory M" uniqKey="Wier G" first="Gregory M." last="Wier">Gregory M. Wier</name></author><author><name sortKey="Borges, Adair L" sort="Borges, Adair L" uniqKey="Borges A" first="Adair L." last="Borges">Adair L. Borges</name></author><author><name sortKey="Wand, Hannah E" sort="Wand, Hannah E" uniqKey="Wand H" first="Hannah E." last="Wand">Hannah E. Wand</name></author><author><name sortKey="Boyle, Jon P" sort="Boyle, Jon P" uniqKey="Boyle J" first="Jon P." last="Boyle">Jon P. Boyle</name></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">24496792</idno><idno type="pmc">3950507</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3950507</idno><idno type="RBID">PMC:3950507</idno><idno type="doi">10.1128/mBio.01003-13</idno><date when="2014">2014</date><idno type="wicri:Area/Pmc/Corpus">001E29</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">001E29</idno><idno type="wicri:Area/Pmc/Curation">001E04</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">001E04</idno><idno type="wicri:Area/Pmc/Checkpoint">001617</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">001617</idno><idno type="wicri:source">PubMed</idno><idno type="wicri:Area/PubMed/Corpus">003C55</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">003C55</idno><idno type="wicri:Area/PubMed/Curation">003C28</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">003C28</idno><idno type="wicri:Area/PubMed/Checkpoint">003C28</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">003C28</idno><idno type="wicri:Area/Ncbi/Merge">000F71</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Differential Locus Expansion Distinguishes <italic>Toxoplasmatinae</italic> Species and Closely Related Strains of <italic>Toxoplasma gondii</italic></title><author><name sortKey="Adomako Ankomah, Yaw" sort="Adomako Ankomah, Yaw" uniqKey="Adomako Ankomah Y" first="Yaw" last="Adomako-Ankomah">Yaw Adomako-Ankomah</name></author><author><name sortKey="Wier, Gregory M" sort="Wier, Gregory M" uniqKey="Wier G" first="Gregory M." last="Wier">Gregory M. Wier</name></author><author><name sortKey="Borges, Adair L" sort="Borges, Adair L" uniqKey="Borges A" first="Adair L." last="Borges">Adair L. Borges</name></author><author><name sortKey="Wand, Hannah E" sort="Wand, Hannah E" uniqKey="Wand H" first="Hannah E." last="Wand">Hannah E. Wand</name></author><author><name sortKey="Boyle, Jon P" sort="Boyle, Jon P" uniqKey="Boyle J" first="Jon P." last="Boyle">Jon P. Boyle</name></author></analytic><series><title level="j">mBio</title><idno type="eISSN">2150-7511</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Comparative Genomic Hybridization</term><term>Computational Biology</term><term>DNA, Protozoan (genetics)</term><term>Gene Duplication</term><term>Genetic Loci</term><term>Genetic Variation</term><term>Sarcocystidae (genetics)</term><term>Synteny</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN des protozoaires (génétique)</term><term>Biologie informatique</term><term>Duplication de gène</term><term>Hybridation génomique comparative</term><term>Locus génétiques</term><term>Sarcocystidae (génétique)</term><term>Synténie</term><term>Variation génétique</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA, Protozoan</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Sarcocystidae</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ADN des protozoaires</term><term>Sarcocystidae</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Comparative Genomic Hybridization</term><term>Computational Biology</term><term>Gene Duplication</term><term>Genetic Loci</term><term>Genetic Variation</term><term>Synteny</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Biologie informatique</term><term>Duplication de gène</term><term>Hybridation génomique comparative</term><term>Locus génétiques</term><term>Synténie</term><term>Variation génétique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><title>ABSTRACT</title><p><italic>Toxoplasma gondii</italic> is a human obligate intracellular parasite that has infected over 20% of the world population and has a vast intermediate host range compared to those of its nearest relatives <italic>Neospora caninum</italic> and <italic>Hammondia hammondi</italic>. While these 3 species have highly syntenic genomes (80 to 99%), in this study we examined and compared species-specific structural variations, specifically at loci that have undergone local (i.e., tandem) duplication and expansion. To do so, we used genomic sequence coverage analysis to identify and curate <italic>T. gondii</italic> and <italic>N. caninum</italic> loci that have undergone duplication and expansion (expanded loci [ELs]). The 53 <italic>T. gondii</italic> ELs are significantly enriched for genes with predicted signal sequences and single-exon genes and genes that are developmentally regulated at the transcriptional level. We validated 24 <italic>T. gondii</italic> ELs using comparative genomic hybridization; these data suggested significant copy number variation at these loci. High-molecular-weight Southern blotting for 3 <italic>T. gondii</italic> ELs revealed that copy number varies across <italic>T. gondii</italic> lineages and also between members of the same clonal lineage. Using similar methods, we identified 64 <italic>N. caninum</italic> ELs which were significantly enriched genes belonging to the SAG-related surface (SRS) antigen family. Moreover, there is significantly less overlap (30%) between the expanded gene sets in <italic>T. gondii</italic> and <italic>N. caninum</italic> than would be predicted by overall genomic synteny (81%). Consistent with this finding, only 59% of queried <italic>T. gondii</italic> ELs are similarly duplicated/expanded in <italic>H. hammondi</italic> despite over 99% genomic synteny between these species.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Lelu, M" uniqKey="Lelu M">M Lélu</name></author><author><name sortKey="Villena, I" uniqKey="Villena I">I Villena</name></author><author><name sortKey="Darde, Ml" uniqKey="Darde M">ML Dardé</name></author><author><name sortKey="Aubert, D" uniqKey="Aubert D">D Aubert</name></author><author><name sortKey="Geers, R" uniqKey="Geers R">R Geers</name></author><author><name sortKey="Dupuis, E" uniqKey="Dupuis E">E Dupuis</name></author><author><name sortKey="Marnef, F" uniqKey="Marnef F">F Marnef</name></author><author><name sortKey="Poulle, Ml" uniqKey="Poulle M">ML Poulle</name></author><author><name sortKey="Gotteland, C" uniqKey="Gotteland C">C Gotteland</name></author><author><name 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xml:lang="en">Differential Locus Expansion Distinguishes <italic>Toxoplasmatinae</italic> Species and Closely Related Strains of <italic>Toxoplasma gondii</italic></title><author><name sortKey="Adomako Ankomah, Yaw" sort="Adomako Ankomah, Yaw" uniqKey="Adomako Ankomah Y" first="Yaw" last="Adomako-Ankomah">Yaw Adomako-Ankomah</name></author><author><name sortKey="Wier, Gregory M" sort="Wier, Gregory M" uniqKey="Wier G" first="Gregory M." last="Wier">Gregory M. Wier</name></author><author><name sortKey="Borges, Adair L" sort="Borges, Adair L" uniqKey="Borges A" first="Adair L." last="Borges">Adair L. Borges</name></author><author><name sortKey="Wand, Hannah E" sort="Wand, Hannah E" uniqKey="Wand H" first="Hannah E." last="Wand">Hannah E. Wand</name></author><author><name sortKey="Boyle, Jon P" sort="Boyle, Jon P" uniqKey="Boyle J" first="Jon P." last="Boyle">Jon P. Boyle</name></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">24496792</idno><idno type="pmc">3950507</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3950507</idno><idno type="RBID">PMC:3950507</idno><idno type="doi">10.1128/mBio.01003-13</idno><date when="2014">2014</date><idno type="wicri:Area/Pmc/Corpus">001E29</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">001E29</idno><idno type="wicri:Area/Pmc/Curation">001E04</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">001E04</idno><idno type="wicri:Area/Pmc/Checkpoint">001617</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">001617</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Differential Locus Expansion Distinguishes <italic>Toxoplasmatinae</italic> Species and Closely Related Strains of <italic>Toxoplasma gondii</italic></title><author><name sortKey="Adomako Ankomah, Yaw" sort="Adomako Ankomah, Yaw" uniqKey="Adomako Ankomah Y" first="Yaw" last="Adomako-Ankomah">Yaw Adomako-Ankomah</name></author><author><name sortKey="Wier, Gregory M" sort="Wier, Gregory M" uniqKey="Wier G" first="Gregory M." last="Wier">Gregory M. Wier</name></author><author><name sortKey="Borges, Adair L" sort="Borges, Adair L" uniqKey="Borges A" first="Adair L." last="Borges">Adair L. Borges</name></author><author><name sortKey="Wand, Hannah E" sort="Wand, Hannah E" uniqKey="Wand H" first="Hannah E." last="Wand">Hannah E. Wand</name></author><author><name sortKey="Boyle, Jon P" sort="Boyle, Jon P" uniqKey="Boyle J" first="Jon P." last="Boyle">Jon P. Boyle</name></author></analytic><series><title level="j">mBio</title><idno type="eISSN">2150-7511</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><title>ABSTRACT</title><p><italic>Toxoplasma gondii</italic> is a human obligate intracellular parasite that has infected over 20% of the world population and has a vast intermediate host range compared to those of its nearest relatives <italic>Neospora caninum</italic> and <italic>Hammondia hammondi</italic>. While these 3 species have highly syntenic genomes (80 to 99%), in this study we examined and compared species-specific structural variations, specifically at loci that have undergone local (i.e., tandem) duplication and expansion. To do so, we used genomic sequence coverage analysis to identify and curate <italic>T. gondii</italic> and <italic>N. caninum</italic> loci that have undergone duplication and expansion (expanded loci [ELs]). The 53 <italic>T. gondii</italic> ELs are significantly enriched for genes with predicted signal sequences and single-exon genes and genes that are developmentally regulated at the transcriptional level. We validated 24 <italic>T. gondii</italic> ELs using comparative genomic hybridization; these data suggested significant copy number variation at these loci. High-molecular-weight Southern blotting for 3 <italic>T. gondii</italic> ELs revealed that copy number varies across <italic>T. gondii</italic> lineages and also between members of the same clonal lineage. Using similar methods, we identified 64 <italic>N. caninum</italic> ELs which were significantly enriched genes belonging to the SAG-related surface (SRS) antigen family. Moreover, there is significantly less overlap (30%) between the expanded gene sets in <italic>T. gondii</italic> and <italic>N. caninum</italic> than would be predicted by overall genomic synteny (81%). Consistent with this finding, only 59% of queried <italic>T. gondii</italic> ELs are similarly duplicated/expanded in <italic>H. hammondi</italic> despite over 99% genomic synteny between these species.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Lelu, M" uniqKey="Lelu M">M Lélu</name></author><author><name sortKey="Villena, I" uniqKey="Villena I">I Villena</name></author><author><name sortKey="Darde, Ml" uniqKey="Darde M">ML Dardé</name></author><author><name sortKey="Aubert, D" uniqKey="Aubert D">D Aubert</name></author><author><name sortKey="Geers, R" uniqKey="Geers R">R Geers</name></author><author><name sortKey="Dupuis, E" uniqKey="Dupuis E">E Dupuis</name></author><author><name sortKey="Marnef, F" uniqKey="Marnef F">F Marnef</name></author><author><name sortKey="Poulle, Ml" uniqKey="Poulle M">ML Poulle</name></author><author><name sortKey="Gotteland, C" uniqKey="Gotteland C">C Gotteland</name></author><author><name 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xml:lang="en">Differential locus expansion distinguishes Toxoplasmatinae species and closely related strains of Toxoplasma gondii.</title><author><name sortKey="Adomako Ankomah, Yaw" sort="Adomako Ankomah, Yaw" uniqKey="Adomako Ankomah Y" first="Yaw" last="Adomako-Ankomah">Yaw Adomako-Ankomah</name><affiliation wicri:level="4"><nlm:affiliation>Dietrich School of Arts and Sciences, University of Pittsburgh, Department of Biological Sciences, Pittsburgh, Pennsylvania, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Dietrich School of Arts and Sciences, University of Pittsburgh, Department of Biological Sciences, Pittsburgh, Pennsylvania</wicri:regionArea><placeName><region type="state">Pennsylvanie</region><settlement type="city">Pittsburgh</settlement></placeName><orgName type="university">Université de Pittsburgh</orgName></affiliation></author><author><name sortKey="Wier, Gregory M" sort="Wier, Gregory M" uniqKey="Wier G" first="Gregory M" last="Wier">Gregory M. Wier</name></author><author><name sortKey="Borges, Adair L" sort="Borges, Adair L" uniqKey="Borges A" first="Adair L" last="Borges">Adair L. Borges</name></author><author><name sortKey="Wand, Hannah E" sort="Wand, Hannah E" uniqKey="Wand H" first="Hannah E" last="Wand">Hannah E. Wand</name></author><author><name sortKey="Boyle, Jon P" sort="Boyle, Jon P" uniqKey="Boyle J" first="Jon P" last="Boyle">Jon P. Boyle</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2014">2014</date><idno type="RBID">pubmed:24496792</idno><idno type="pmid">24496792</idno><idno type="doi">10.1128/mBio.01003-13</idno><idno type="wicri:Area/PubMed/Corpus">003C55</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">003C55</idno><idno type="wicri:Area/PubMed/Curation">003C28</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">003C28</idno><idno type="wicri:Area/PubMed/Checkpoint">003C28</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">003C28</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Differential locus expansion distinguishes Toxoplasmatinae species and closely related strains of Toxoplasma gondii.</title><author><name sortKey="Adomako Ankomah, Yaw" sort="Adomako Ankomah, Yaw" uniqKey="Adomako Ankomah Y" first="Yaw" last="Adomako-Ankomah">Yaw Adomako-Ankomah</name><affiliation wicri:level="4"><nlm:affiliation>Dietrich School of Arts and Sciences, University of Pittsburgh, Department of Biological Sciences, Pittsburgh, Pennsylvania, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Dietrich School of Arts and Sciences, University of Pittsburgh, Department of Biological Sciences, Pittsburgh, Pennsylvania</wicri:regionArea><placeName><region type="state">Pennsylvanie</region><settlement type="city">Pittsburgh</settlement></placeName><orgName type="university">Université de Pittsburgh</orgName></affiliation></author><author><name sortKey="Wier, Gregory M" sort="Wier, Gregory M" uniqKey="Wier G" first="Gregory M" last="Wier">Gregory M. Wier</name></author><author><name sortKey="Borges, Adair L" sort="Borges, Adair L" uniqKey="Borges A" first="Adair L" last="Borges">Adair L. Borges</name></author><author><name sortKey="Wand, Hannah E" sort="Wand, Hannah E" uniqKey="Wand H" first="Hannah E" last="Wand">Hannah E. Wand</name></author><author><name sortKey="Boyle, Jon P" sort="Boyle, Jon P" uniqKey="Boyle J" first="Jon P" last="Boyle">Jon P. Boyle</name></author></analytic><series><title level="j">mBio</title><idno type="eISSN">2150-7511</idno><imprint><date when="2014" type="published">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Comparative Genomic Hybridization</term><term>Computational Biology</term><term>DNA, Protozoan (genetics)</term><term>Gene Duplication</term><term>Genetic Loci</term><term>Genetic Variation</term><term>Sarcocystidae (genetics)</term><term>Synteny</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN des protozoaires (génétique)</term><term>Biologie informatique</term><term>Duplication de gène</term><term>Hybridation génomique comparative</term><term>Locus génétiques</term><term>Sarcocystidae (génétique)</term><term>Synténie</term><term>Variation génétique</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA, Protozoan</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Sarcocystidae</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ADN des protozoaires</term><term>Sarcocystidae</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Comparative Genomic Hybridization</term><term>Computational Biology</term><term>Gene Duplication</term><term>Genetic Loci</term><term>Genetic Variation</term><term>Synteny</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Biologie informatique</term><term>Duplication de gène</term><term>Hybridation génomique comparative</term><term>Locus génétiques</term><term>Synténie</term><term>Variation génétique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Toxoplasma gondii is a human obligate intracellular parasite that has infected over 20% of the world population and has a vast intermediate host range compared to those of its nearest relatives Neospora caninum and Hammondia hammondi. While these 3 species have highly syntenic genomes (80 to 99%), in this study we examined and compared species-specific structural variations, specifically at loci that have undergone local (i.e., tandem) duplication and expansion. To do so, we used genomic sequence coverage analysis to identify and curate T. gondii and N. caninum loci that have undergone duplication and expansion (expanded loci [ELs]). The 53 T. gondii ELs are significantly enriched for genes with predicted signal sequences and single-exon genes and genes that are developmentally regulated at the transcriptional level. We validated 24 T. gondii ELs using comparative genomic hybridization; these data suggested significant copy number variation at these loci. High-molecular-weight Southern blotting for 3 T. gondii ELs revealed that copy number varies across T. gondii lineages and also between members of the same clonal lineage. Using similar methods, we identified 64 N. caninum ELs which were significantly enriched genes belonging to the SAG-related surface (SRS) antigen family. Moreover, there is significantly less overlap (30%) between the expanded gene sets in T. gondii and N. caninum than would be predicted by overall genomic synteny (81%). Consistent with this finding, only 59% of queried T. gondii ELs are similarly duplicated/expanded in H. hammondi despite over 99% genomic synteny between these species.</div></front></TEI></pubmed></double></record>Pour manipuler ce document sous Unix (Dilib)
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