Deciphering the Draft Genome of Toxoplasma gondii RH Strain
Toxoplasmosis is a widespread parasitic infection by Toxoplasma gondii, a parasite with at least three distinct clonal lineages. This article reports the whole genome sequencing and de novo assembly of T. gondii RH (type I representative strain), as well as genome-wide comparison across major T. gon...
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| creator | Lau, Yee-Ling Lee, Wenn-Chyau Gudimella, Ranganath Zhang, GuiPing Ching, Xiao-Teng Razali, Rozaimi Aziz, Farhanah Anwar, Arif Fong, Mun-Yik |
| description | Toxoplasmosis is a widespread parasitic infection by Toxoplasma gondii, a parasite with at least three distinct clonal lineages. This article reports the whole genome sequencing and de novo assembly of T. gondii RH (type I representative strain), as well as genome-wide comparison across major T. gondii lineages. Genomic DNA was extracted from tachyzoites of T. gondii RH strain and its identity was verified by PCR and LAMP. Subsequently, whole genome sequencing was performed, followed by sequence filtering, genome assembly, gene annotation assignments, clustering of gene orthologs and phylogenetic tree construction. Genome comparison was done with the already archived genomes of T. gondii. From this study, the genome size of T. gondii RH strain was found to be 69.35Mb, with a mean GC content of 52%. The genome shares high similarity to the archived genomes of T. gondii GT1, ME49 and VEG strains. Nevertheless, 111 genes were found to be unique to T. gondii RH strain. Importantly, unique genes annotated to functions that are potentially critical for T. gondii virulence were found, which may explain the unique phenotypes of this particular strain. This report complements the genomic archive of T. gondii. Data obtained from this study contribute to better understanding of T. gondii and serve as a reference for future studies on this parasite. |
| doi_str_mv | 10.1371/journal.pone.0157901 |
| format | Article |
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This article reports the whole genome sequencing and de novo assembly of T. gondii RH (type I representative strain), as well as genome-wide comparison across major T. gondii lineages. Genomic DNA was extracted from tachyzoites of T. gondii RH strain and its identity was verified by PCR and LAMP. Subsequently, whole genome sequencing was performed, followed by sequence filtering, genome assembly, gene annotation assignments, clustering of gene orthologs and phylogenetic tree construction. Genome comparison was done with the already archived genomes of T. gondii. From this study, the genome size of T. gondii RH strain was found to be 69.35Mb, with a mean GC content of 52%. The genome shares high similarity to the archived genomes of T. gondii GT1, ME49 and VEG strains. Nevertheless, 111 genes were found to be unique to T. gondii RH strain. Importantly, unique genes annotated to functions that are potentially critical for T. gondii virulence were found, which may explain the unique phenotypes of this particular strain. This report complements the genomic archive of T. gondii. Data obtained from this study contribute to better understanding of T. gondii and serve as a reference for future studies on this parasite.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0157901</identifier><identifier>PMID: 27355363</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Algorithms ; Analysis ; Animals ; Annotations ; Assembly ; Base Composition ; Biology and Life Sciences ; Clustering ; Computational Biology ; Databases, Protein ; Deoxyribonucleic acid ; DNA ; DNA sequencing ; Education ; Filtration ; Gene expression ; Gene sequencing ; Genes ; Genetic aspects ; Genetic testing ; Genome, Protozoan ; Genomes ; Genomics ; Health aspects ; Infections ; Infectious diseases ; Medicine ; Medicine and Health Sciences ; Mice ; Molecular Sequence Annotation ; Nucleotide sequence ; Parasites ; Parasitology ; Phylogeny ; Physiological aspects ; Protozoa ; Research and Analysis Methods ; Species Specificity ; Tachyzoites ; Toxoplasma ; Toxoplasma - genetics ; Toxoplasma gondii ; Toxoplasmosis ; Toxoplasmosis - genetics ; Virulence</subject><ispartof>PloS one, 2016-06, Vol.11 (6), p.e0157901-e0157901</ispartof><rights>COPYRIGHT 2016 Public Library of Science</rights><rights>2016 Lau et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2016 Lau et al 2016 Lau et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c725t-27e0be41aa8c2d8895d73b38f530e006d4ea77af626a9a3e75a46c7af212c39b3</citedby><cites>FETCH-LOGICAL-c725t-27e0be41aa8c2d8895d73b38f530e006d4ea77af626a9a3e75a46c7af212c39b3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4927122/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4927122/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,725,778,782,862,883,2098,2917,23849,27907,27908,53774,53776,79351,79352</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/27355363$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Grigg, Michael E.</contributor><creatorcontrib>Lau, Yee-Ling</creatorcontrib><creatorcontrib>Lee, Wenn-Chyau</creatorcontrib><creatorcontrib>Gudimella, Ranganath</creatorcontrib><creatorcontrib>Zhang, GuiPing</creatorcontrib><creatorcontrib>Ching, Xiao-Teng</creatorcontrib><creatorcontrib>Razali, Rozaimi</creatorcontrib><creatorcontrib>Aziz, Farhanah</creatorcontrib><creatorcontrib>Anwar, Arif</creatorcontrib><creatorcontrib>Fong, Mun-Yik</creatorcontrib><title>Deciphering the Draft Genome of Toxoplasma gondii RH Strain</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Toxoplasmosis is a widespread parasitic infection by Toxoplasma gondii, a parasite with at least three distinct clonal lineages. This article reports the whole genome sequencing and de novo assembly of T. gondii RH (type I representative strain), as well as genome-wide comparison across major T. gondii lineages. Genomic DNA was extracted from tachyzoites of T. gondii RH strain and its identity was verified by PCR and LAMP. Subsequently, whole genome sequencing was performed, followed by sequence filtering, genome assembly, gene annotation assignments, clustering of gene orthologs and phylogenetic tree construction. Genome comparison was done with the already archived genomes of T. gondii. From this study, the genome size of T. gondii RH strain was found to be 69.35Mb, with a mean GC content of 52%. The genome shares high similarity to the archived genomes of T. gondii GT1, ME49 and VEG strains. Nevertheless, 111 genes were found to be unique to T. gondii RH strain. Importantly, unique genes annotated to functions that are potentially critical for T. gondii virulence were found, which may explain the unique phenotypes of this particular strain. This report complements the genomic archive of T. gondii. Data obtained from this study contribute to better understanding of T. gondii and serve as a reference for future studies on this parasite.</description><subject>Algorithms</subject><subject>Analysis</subject><subject>Animals</subject><subject>Annotations</subject><subject>Assembly</subject><subject>Base Composition</subject><subject>Biology and Life Sciences</subject><subject>Clustering</subject><subject>Computational Biology</subject><subject>Databases, Protein</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA sequencing</subject><subject>Education</subject><subject>Filtration</subject><subject>Gene expression</subject><subject>Gene sequencing</subject><subject>Genes</subject><subject>Genetic aspects</subject><subject>Genetic testing</subject><subject>Genome, Protozoan</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Health aspects</subject><subject>Infections</subject><subject>Infectious diseases</subject><subject>Medicine</subject><subject>Medicine and Health Sciences</subject><subject>Mice</subject><subject>Molecular Sequence Annotation</subject><subject>Nucleotide sequence</subject><subject>Parasites</subject><subject>Parasitology</subject><subject>Phylogeny</subject><subject>Physiological aspects</subject><subject>Protozoa</subject><subject>Research and Analysis Methods</subject><subject>Species Specificity</subject><subject>Tachyzoites</subject><subject>Toxoplasma</subject><subject>Toxoplasma - genetics</subject><subject>Toxoplasma gondii</subject><subject>Toxoplasmosis</subject><subject>Toxoplasmosis - genetics</subject><subject>Virulence</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2016</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><sourceid>DOA</sourceid><recordid>eNqNk21r1TAUx4sobk6_gWhBEH1xr3lsGgRhbLpdGAy26duQpie9ubRNbVqZ397c3W7cyl6MvEg4-Z1_zkNOkrzFaImpwF82fuxbXS8738ISYS4kws-SQywpWWQE0ed754PkVQgbhDjNs-xlckAE5Zxm9DD5egrGdWvoXVulwxrS017bIT2D1jeQepve-Fvf1To0Oq18WzqXXp2n10OvXfs6eWF1HeDNtB8lP398vzk5X1xcnq1Oji8WRhA-LIgAVADDWueGlHkueSloQXPLKQKEspKBFkLbjGRaagqCa5aZaCCYGCoLepS83-l2tQ9qyjsonCPECOFcRGK1I0qvN6rrXaP7v8prp-4Mvq-U7gdnalCWI24MNbEEkmVgC8uyAhMAaYpCaxu1vk2vjUUDpYE2JlvPROc3rVuryv9RTBKBCYkCnyaB3v8eIQyqccFAXesW_HgXdy4IjvhTUMxoLqWM6If_0McLMVGVjrm61voYotmKqmPGM844kyxSy0eouEponIn_ybponzl8njlEZoDbodJjCGp1ffV09vLXnP24x65B18M6-HocnG_DHGQ70PQ-hB7sQz8wUttxuK-G2o6DmsYhur3b7-WD0_3_p_8AOj8DQw</recordid><startdate>20160629</startdate><enddate>20160629</enddate><creator>Lau, Yee-Ling</creator><creator>Lee, Wenn-Chyau</creator><creator>Gudimella, Ranganath</creator><creator>Zhang, GuiPing</creator><creator>Ching, Xiao-Teng</creator><creator>Razali, Rozaimi</creator><creator>Aziz, Farhanah</creator><creator>Anwar, Arif</creator><creator>Fong, Mun-Yik</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>IOV</scope><scope>ISR</scope><scope>3V.</scope><scope>7QG</scope><scope>7QL</scope><scope>7QO</scope><scope>7RV</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TG</scope><scope>7TM</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>KB0</scope><scope>KL.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PDBOC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope></search><sort><creationdate>20160629</creationdate><title>Deciphering the Draft Genome of Toxoplasma gondii RH Strain</title><author>Lau, Yee-Ling ; Lee, Wenn-Chyau ; Gudimella, Ranganath ; Zhang, GuiPing ; Ching, Xiao-Teng ; Razali, Rozaimi ; Aziz, Farhanah ; Anwar, Arif ; Fong, Mun-Yik</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c725t-27e0be41aa8c2d8895d73b38f530e006d4ea77af626a9a3e75a46c7af212c39b3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2016</creationdate><topic>Algorithms</topic><topic>Analysis</topic><topic>Animals</topic><topic>Annotations</topic><topic>Assembly</topic><topic>Base Composition</topic><topic>Biology and Life Sciences</topic><topic>Clustering</topic><topic>Computational Biology</topic><topic>Databases, Protein</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>DNA sequencing</topic><topic>Education</topic><topic>Filtration</topic><topic>Gene expression</topic><topic>Gene sequencing</topic><topic>Genes</topic><topic>Genetic aspects</topic><topic>Genetic testing</topic><topic>Genome, Protozoan</topic><topic>Genomes</topic><topic>Genomics</topic><topic>Health aspects</topic><topic>Infections</topic><topic>Infectious diseases</topic><topic>Medicine</topic><topic>Medicine and Health Sciences</topic><topic>Mice</topic><topic>Molecular Sequence Annotation</topic><topic>Nucleotide sequence</topic><topic>Parasites</topic><topic>Parasitology</topic><topic>Phylogeny</topic><topic>Physiological aspects</topic><topic>Protozoa</topic><topic>Research and Analysis Methods</topic><topic>Species Specificity</topic><topic>Tachyzoites</topic><topic>Toxoplasma</topic><topic>Toxoplasma - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Lau, Yee-Ling</au><au>Lee, Wenn-Chyau</au><au>Gudimella, Ranganath</au><au>Zhang, GuiPing</au><au>Ching, Xiao-Teng</au><au>Razali, Rozaimi</au><au>Aziz, Farhanah</au><au>Anwar, Arif</au><au>Fong, Mun-Yik</au><au>Grigg, Michael E.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Deciphering the Draft Genome of Toxoplasma gondii RH Strain</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2016-06-29</date><risdate>2016</risdate><volume>11</volume><issue>6</issue><spage>e0157901</spage><epage>e0157901</epage><pages>e0157901-e0157901</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>Toxoplasmosis is a widespread parasitic infection by Toxoplasma gondii, a parasite with at least three distinct clonal lineages. This article reports the whole genome sequencing and de novo assembly of T. gondii RH (type I representative strain), as well as genome-wide comparison across major T. gondii lineages. Genomic DNA was extracted from tachyzoites of T. gondii RH strain and its identity was verified by PCR and LAMP. Subsequently, whole genome sequencing was performed, followed by sequence filtering, genome assembly, gene annotation assignments, clustering of gene orthologs and phylogenetic tree construction. Genome comparison was done with the already archived genomes of T. gondii. From this study, the genome size of T. gondii RH strain was found to be 69.35Mb, with a mean GC content of 52%. The genome shares high similarity to the archived genomes of T. gondii GT1, ME49 and VEG strains. Nevertheless, 111 genes were found to be unique to T. gondii RH strain. Importantly, unique genes annotated to functions that are potentially critical for T. gondii virulence were found, which may explain the unique phenotypes of this particular strain. This report complements the genomic archive of T. gondii. Data obtained from this study contribute to better understanding of T. gondii and serve as a reference for future studies on this parasite.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>27355363</pmid><doi>10.1371/journal.pone.0157901</doi><oa>free_for_read</oa></addata></record> |
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| subjects | Algorithms Analysis Animals Annotations Assembly Base Composition Biology and Life Sciences Clustering Computational Biology Databases, Protein Deoxyribonucleic acid DNA DNA sequencing Education Filtration Gene expression Gene sequencing Genes Genetic aspects Genetic testing Genome, Protozoan Genomes Genomics Health aspects Infections Infectious diseases Medicine Medicine and Health Sciences Mice Molecular Sequence Annotation Nucleotide sequence Parasites Parasitology Phylogeny Physiological aspects Protozoa Research and Analysis Methods Species Specificity Tachyzoites Toxoplasma Toxoplasma - genetics Toxoplasma gondii Toxoplasmosis Toxoplasmosis - genetics Virulence |
| title | Deciphering the Draft Genome of Toxoplasma gondii RH Strain |
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