Draft genome sequencing of giardia intestinalis assemblage B isolate GS: is human giardiasis caused by two different species?
Giardia intestinalis is a major cause of diarrheal disease worldwide and two major Giardia genotypes, assemblages A and B, infect humans. The genome of assemblage A parasite WB was recently sequenced, and the structurally compact 11.7 Mbp genome contains simplified basic cellular machineries and met...
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| creator | Franzén, Oscar Jerlström-Hultqvist, Jon Castro, Elsie Sherwood, Ellen Ankarklev, Johan Reiner, David S Palm, Daniel Andersson, Jan O Andersson, Björn Svärd, Staffan G |
| description | Giardia intestinalis is a major cause of diarrheal disease worldwide and two major Giardia genotypes, assemblages A and B, infect humans. The genome of assemblage A parasite WB was recently sequenced, and the structurally compact 11.7 Mbp genome contains simplified basic cellular machineries and metabolism. We here performed 454 sequencing to 16x coverage of the assemblage B isolate GS, the only Giardia isolate successfully used to experimentally infect animals and humans. The two genomes show 77% nucleotide and 78% amino-acid identity in protein coding regions. Comparative analysis identified 28 unique GS and 3 unique WB protein coding genes, and the variable surface protein (VSP) repertoires of the two isolates are completely different. The promoters of several enzymes involved in the synthesis of the cyst-wall lack binding sites for encystation-specific transcription factors in GS. Several synteny-breaks were detected and verified. The tetraploid GS genome shows higher levels of overall allelic sequence polymorphism (0.5 versus |
| doi_str_mv | 10.1371/journal.ppat.1000560 |
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The genome of assemblage A parasite WB was recently sequenced, and the structurally compact 11.7 Mbp genome contains simplified basic cellular machineries and metabolism. We here performed 454 sequencing to 16x coverage of the assemblage B isolate GS, the only Giardia isolate successfully used to experimentally infect animals and humans. The two genomes show 77% nucleotide and 78% amino-acid identity in protein coding regions. Comparative analysis identified 28 unique GS and 3 unique WB protein coding genes, and the variable surface protein (VSP) repertoires of the two isolates are completely different. The promoters of several enzymes involved in the synthesis of the cyst-wall lack binding sites for encystation-specific transcription factors in GS. Several synteny-breaks were detected and verified. The tetraploid GS genome shows higher levels of overall allelic sequence polymorphism (0.5 versus <0.01% in WB). The genomic differences between WB and GS may explain some of the observed biological and clinical differences between the two isolates, and it suggests that assemblage A and B Giardia can be two different species.</description><identifier>ISSN: 1553-7374</identifier><identifier>ISSN: 1553-7366</identifier><identifier>EISSN: 1553-7374</identifier><identifier>DOI: 10.1371/journal.ppat.1000560</identifier><identifier>PMID: 19696920</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Animals ; Base Sequence ; Biologi ; Biology ; Causes of ; DNA sequencing ; Gene Frequency ; Genetic aspects ; Genetics and Genomics/Comparative Genomics ; Genome, Bacterial - genetics ; Genome, Protozoan ; Genomics ; Giardia ; Giardia lamblia ; Giardia lamblia - classification ; Giardia lamblia - genetics ; Giardiasis ; Giardiasis - parasitology ; Humans ; Infectious Diseases/Gastrointestinal Infections ; Infectious Diseases/Neglected Tropical Diseases ; Infectious Diseases/Protozoal Infections ; Introns ; Microbiology ; Molecular Sequence Data ; NATURAL SCIENCES ; NATURVETENSKAP ; Nucleotide sequencing ; Parasites ; Phylogeny ; Physiological aspects ; Polymorphism, Genetic ; Porphyromonas gingivalis - genetics ; Promoter Regions, Genetic ; Proteins ; Protozoan Proteins - genetics ; Protozoan Proteins - metabolism ; RNA Splicing ; RNA, Messenger - metabolism ; RNA, Protozoan - genetics ; Sequence Alignment ; Studies ; Synteny</subject><ispartof>PLoS pathogens, 2009-08, Vol.5 (8), p.e1000560-e1000560</ispartof><rights>COPYRIGHT 2009 Public Library of Science</rights><rights>Franzén et al. 2009</rights><rights>2009 Franzén et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Franzén O, Jerlström-Hultqvist J, Castro E, Sherwood E, Ankarklev J, et al. (2009) Draft Genome Sequencing of Giardia intestinalis Assemblage B Isolate GS: Is Human Giardiasis Caused by Two Different Species? PLoS Pathog 5(8): e1000560. doi:10.1371/journal.ppat.1000560</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c773t-fc9e031417ab095a45c853bb5aa276143d0795402aa016b75d95b5dfe52810e03</citedby><cites>FETCH-LOGICAL-c773t-fc9e031417ab095a45c853bb5aa276143d0795402aa016b75d95b5dfe52810e03</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/PMC2723961/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723961/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,550,723,776,780,860,881,2096,2915,23847,27903,27904,53769,53771,79346,79347</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/19696920$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-127462$$DView record from Swedish Publication Index$$Hfree_for_read</backlink><backlink>$$Uhttp://kipublications.ki.se/Default.aspx?queryparsed=id:119503943$$DView record from Swedish Publication Index$$Hfree_for_read</backlink></links><search><contributor>Petri, William</contributor><creatorcontrib>Franzén, Oscar</creatorcontrib><creatorcontrib>Jerlström-Hultqvist, Jon</creatorcontrib><creatorcontrib>Castro, Elsie</creatorcontrib><creatorcontrib>Sherwood, Ellen</creatorcontrib><creatorcontrib>Ankarklev, Johan</creatorcontrib><creatorcontrib>Reiner, David S</creatorcontrib><creatorcontrib>Palm, Daniel</creatorcontrib><creatorcontrib>Andersson, Jan O</creatorcontrib><creatorcontrib>Andersson, Björn</creatorcontrib><creatorcontrib>Svärd, Staffan G</creatorcontrib><title>Draft genome sequencing of giardia intestinalis assemblage B isolate GS: is human giardiasis caused by two different species?</title><title>PLoS pathogens</title><addtitle>PLoS Pathog</addtitle><description>Giardia intestinalis is a major cause of diarrheal disease worldwide and two major Giardia genotypes, assemblages A and B, infect humans. The genome of assemblage A parasite WB was recently sequenced, and the structurally compact 11.7 Mbp genome contains simplified basic cellular machineries and metabolism. We here performed 454 sequencing to 16x coverage of the assemblage B isolate GS, the only Giardia isolate successfully used to experimentally infect animals and humans. The two genomes show 77% nucleotide and 78% amino-acid identity in protein coding regions. Comparative analysis identified 28 unique GS and 3 unique WB protein coding genes, and the variable surface protein (VSP) repertoires of the two isolates are completely different. The promoters of several enzymes involved in the synthesis of the cyst-wall lack binding sites for encystation-specific transcription factors in GS. Several synteny-breaks were detected and verified. The tetraploid GS genome shows higher levels of overall allelic sequence polymorphism (0.5 versus <0.01% in WB). The genomic differences between WB and GS may explain some of the observed biological and clinical differences between the two isolates, and it suggests that assemblage A and B Giardia can be two different species.</description><subject>Animals</subject><subject>Base Sequence</subject><subject>Biologi</subject><subject>Biology</subject><subject>Causes of</subject><subject>DNA sequencing</subject><subject>Gene Frequency</subject><subject>Genetic aspects</subject><subject>Genetics and Genomics/Comparative Genomics</subject><subject>Genome, Bacterial - genetics</subject><subject>Genome, Protozoan</subject><subject>Genomics</subject><subject>Giardia</subject><subject>Giardia lamblia</subject><subject>Giardia lamblia - classification</subject><subject>Giardia lamblia - genetics</subject><subject>Giardiasis</subject><subject>Giardiasis - parasitology</subject><subject>Humans</subject><subject>Infectious Diseases/Gastrointestinal Infections</subject><subject>Infectious Diseases/Neglected Tropical Diseases</subject><subject>Infectious Diseases/Protozoal Infections</subject><subject>Introns</subject><subject>Microbiology</subject><subject>Molecular Sequence Data</subject><subject>NATURAL SCIENCES</subject><subject>NATURVETENSKAP</subject><subject>Nucleotide sequencing</subject><subject>Parasites</subject><subject>Phylogeny</subject><subject>Physiological aspects</subject><subject>Polymorphism, Genetic</subject><subject>Porphyromonas gingivalis - genetics</subject><subject>Promoter Regions, Genetic</subject><subject>Proteins</subject><subject>Protozoan Proteins - genetics</subject><subject>Protozoan Proteins - metabolism</subject><subject>RNA Splicing</subject><subject>RNA, Messenger - metabolism</subject><subject>RNA, Protozoan - genetics</subject><subject>Sequence Alignment</subject><subject>Studies</subject><subject>Synteny</subject><issn>1553-7374</issn><issn>1553-7366</issn><issn>1553-7374</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2009</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>D8T</sourceid><sourceid>DOA</sourceid><recordid>eNqVk01v1DAQhiMEoqXwDxBY4oCQ2MUfcZxwAC0tlJUqkChwtSbOJPU2iUOcUHrgv-PtptBIcEA-ZDR53ncy40wUPWR0yYRiLzZu7Fuol10Hw5JRSmVCb0X7TEqxUELFt2_Ee9E97zeUxkyw5G60x7IkHE73o59HPZQDqbB1DRKP30ZsjW0r4kpSWegLC8S2A_rBhmLWE_Aem7yGCskbYr2rYUByfPoyxORsbKC9lvmQMDB6LEh-SYYLRwpblthjOxDfobHoX9-P7pRQe3wwPQ-iL-_efj58vzj5eLw-XJ0sjFJiWJQmQypYzBTkNJMQS5NKkecSgKuExaKgKpMx5QCUJbmSRSZzWZQoecpokB5Ej3e-Xe28nibnNeNpRqWkWRyI9Y4oHGx019sG-kvtwOqrhOsrDf1gTY2aAjOMszRWhsVpAdl2rqVMeSopp3ESvBY7L3-B3ZjP3KbUeYhQS5kIvq39_J_8kf26uqo-juFzVZzwgL-amhnzBgsTBtpDPVPN37T2TFfuu-aKiyxhweDpZNC7cN9-0I31BusaWnSj10qITLHQTSCf7MgKQuO2LV0wNFtarzhVikrF00At_0KFU2BjjWuxtCE_EzybCQIz4I-hCn-L1-vTT__Bfpiz8Y41vfO-x_L3UBjV26W5vnq9XRo9LU2QPbo50D-iaUvELxKuExA</recordid><startdate>20090801</startdate><enddate>20090801</enddate><creator>Franzén, Oscar</creator><creator>Jerlström-Hultqvist, Jon</creator><creator>Castro, Elsie</creator><creator>Sherwood, Ellen</creator><creator>Ankarklev, Johan</creator><creator>Reiner, David S</creator><creator>Palm, Daniel</creator><creator>Andersson, Jan O</creator><creator>Andersson, Björn</creator><creator>Svärd, Staffan G</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>ISN</scope><scope>ISR</scope><scope>7X8</scope><scope>5PM</scope><scope>ADTPV</scope><scope>AOWAS</scope><scope>DF2</scope><scope>D8T</scope><scope>ZZAVC</scope><scope>DOA</scope></search><sort><creationdate>20090801</creationdate><title>Draft genome sequencing of giardia intestinalis assemblage B isolate GS: is human giardiasis caused by two different species?</title><author>Franzén, Oscar ; Jerlström-Hultqvist, Jon ; Castro, Elsie ; Sherwood, Ellen ; Ankarklev, Johan ; Reiner, David S ; Palm, Daniel ; Andersson, Jan O ; Andersson, Björn ; Svärd, Staffan G</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c773t-fc9e031417ab095a45c853bb5aa276143d0795402aa016b75d95b5dfe52810e03</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2009</creationdate><topic>Animals</topic><topic>Base Sequence</topic><topic>Biologi</topic><topic>Biology</topic><topic>Causes of</topic><topic>DNA sequencing</topic><topic>Gene Frequency</topic><topic>Genetic aspects</topic><topic>Genetics and Genomics/Comparative Genomics</topic><topic>Genome, Bacterial - genetics</topic><topic>Genome, Protozoan</topic><topic>Genomics</topic><topic>Giardia</topic><topic>Giardia lamblia</topic><topic>Giardia lamblia - classification</topic><topic>Giardia lamblia - genetics</topic><topic>Giardiasis</topic><topic>Giardiasis - parasitology</topic><topic>Humans</topic><topic>Infectious Diseases/Gastrointestinal Infections</topic><topic>Infectious Diseases/Neglected Tropical Diseases</topic><topic>Infectious Diseases/Protozoal Infections</topic><topic>Introns</topic><topic>Microbiology</topic><topic>Molecular Sequence Data</topic><topic>NATURAL SCIENCES</topic><topic>NATURVETENSKAP</topic><topic>Nucleotide sequencing</topic><topic>Parasites</topic><topic>Phylogeny</topic><topic>Physiological aspects</topic><topic>Polymorphism, Genetic</topic><topic>Porphyromonas gingivalis - genetics</topic><topic>Promoter Regions, Genetic</topic><topic>Proteins</topic><topic>Protozoan Proteins - genetics</topic><topic>Protozoan Proteins - metabolism</topic><topic>RNA Splicing</topic><topic>RNA, Messenger - metabolism</topic><topic>RNA, Protozoan - genetics</topic><topic>Sequence Alignment</topic><topic>Studies</topic><topic>Synteny</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Franzén, Oscar</creatorcontrib><creatorcontrib>Jerlström-Hultqvist, Jon</creatorcontrib><creatorcontrib>Castro, Elsie</creatorcontrib><creatorcontrib>Sherwood, Ellen</creatorcontrib><creatorcontrib>Ankarklev, Johan</creatorcontrib><creatorcontrib>Reiner, David S</creatorcontrib><creatorcontrib>Palm, Daniel</creatorcontrib><creatorcontrib>Andersson, Jan O</creatorcontrib><creatorcontrib>Andersson, Björn</creatorcontrib><creatorcontrib>Svärd, Staffan G</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Gale In Context: Canada</collection><collection>Gale In Context: Science</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>SwePub</collection><collection>SwePub Articles</collection><collection>SWEPUB Uppsala universitet</collection><collection>SWEPUB Freely available online</collection><collection>SwePub Articles full text</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PLoS pathogens</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Franzén, Oscar</au><au>Jerlström-Hultqvist, Jon</au><au>Castro, Elsie</au><au>Sherwood, Ellen</au><au>Ankarklev, Johan</au><au>Reiner, David S</au><au>Palm, Daniel</au><au>Andersson, Jan O</au><au>Andersson, Björn</au><au>Svärd, Staffan G</au><au>Petri, William</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Draft genome sequencing of giardia intestinalis assemblage B isolate GS: is human giardiasis caused by two different species?</atitle><jtitle>PLoS pathogens</jtitle><addtitle>PLoS Pathog</addtitle><date>2009-08-01</date><risdate>2009</risdate><volume>5</volume><issue>8</issue><spage>e1000560</spage><epage>e1000560</epage><pages>e1000560-e1000560</pages><issn>1553-7374</issn><issn>1553-7366</issn><eissn>1553-7374</eissn><abstract>Giardia intestinalis is a major cause of diarrheal disease worldwide and two major Giardia genotypes, assemblages A and B, infect humans. The genome of assemblage A parasite WB was recently sequenced, and the structurally compact 11.7 Mbp genome contains simplified basic cellular machineries and metabolism. We here performed 454 sequencing to 16x coverage of the assemblage B isolate GS, the only Giardia isolate successfully used to experimentally infect animals and humans. The two genomes show 77% nucleotide and 78% amino-acid identity in protein coding regions. Comparative analysis identified 28 unique GS and 3 unique WB protein coding genes, and the variable surface protein (VSP) repertoires of the two isolates are completely different. The promoters of several enzymes involved in the synthesis of the cyst-wall lack binding sites for encystation-specific transcription factors in GS. Several synteny-breaks were detected and verified. The tetraploid GS genome shows higher levels of overall allelic sequence polymorphism (0.5 versus <0.01% in WB). The genomic differences between WB and GS may explain some of the observed biological and clinical differences between the two isolates, and it suggests that assemblage A and B Giardia can be two different species.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>19696920</pmid><doi>10.1371/journal.ppat.1000560</doi><oa>free_for_read</oa></addata></record> |
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| subjects | Animals Base Sequence Biologi Biology Causes of DNA sequencing Gene Frequency Genetic aspects Genetics and Genomics/Comparative Genomics Genome, Bacterial - genetics Genome, Protozoan Genomics Giardia Giardia lamblia Giardia lamblia - classification Giardia lamblia - genetics Giardiasis Giardiasis - parasitology Humans Infectious Diseases/Gastrointestinal Infections Infectious Diseases/Neglected Tropical Diseases Infectious Diseases/Protozoal Infections Introns Microbiology Molecular Sequence Data NATURAL SCIENCES NATURVETENSKAP Nucleotide sequencing Parasites Phylogeny Physiological aspects Polymorphism, Genetic Porphyromonas gingivalis - genetics Promoter Regions, Genetic Proteins Protozoan Proteins - genetics Protozoan Proteins - metabolism RNA Splicing RNA, Messenger - metabolism RNA, Protozoan - genetics Sequence Alignment Studies Synteny |
| title | Draft genome sequencing of giardia intestinalis assemblage B isolate GS: is human giardiasis caused by two different species? |
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