Identification and Characterization of Microsatellite Markers Derived from the Whole Genome Analysis of Taenia solium
Infections with Taenia solium are the most common cause of adult acquired seizures worldwide, and are the leading cause of epilepsy in developing countries. A better understanding of the genetic diversity of T. solium will improve parasite diagnostics and transmission pathways in endemic areas there...
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| creator | Pajuelo, Mónica J Eguiluz, María Dahlstrom, Eric Requena, David Guzmán, Frank Ramirez, Manuel Sheen, Patricia Frace, Michael Sammons, Scott Cama, Vitaliano Anzick, Sarah Bruno, Dan Mahanty, Siddhartha Wilkins, Patricia Nash, Theodore Gonzalez, Armando García, Héctor H Gilman, Robert H Porcella, Steve Zimic, Mirko |
| description | Infections with Taenia solium are the most common cause of adult acquired seizures worldwide, and are the leading cause of epilepsy in developing countries. A better understanding of the genetic diversity of T. solium will improve parasite diagnostics and transmission pathways in endemic areas thereby facilitating the design of future control measures and interventions. Microsatellite markers are useful genome features, which enable strain typing and identification in complex pathogen genomes. Here we describe microsatellite identification and characterization in T. solium, providing information that will assist in global efforts to control this important pathogen.
For genome sequencing, T. solium cysts and proglottids were collected from Huancayo and Puno in Peru, respectively. Using next generation sequencing (NGS) and de novo assembly, we assembled two draft genomes and one hybrid genome. Microsatellite sequences were identified and 36 of them were selected for further analysis. Twenty T. solium isolates were collected from Tumbes in the northern region, and twenty from Puno in the southern region of Peru. The size-polymorphism of the selected microsatellites was determined with multi-capillary electrophoresis. We analyzed the association between microsatellite polymorphism and the geographic origin of the samples.
The predicted size of the hybrid (proglottid genome combined with cyst genome) T. solium genome was 111 MB with a GC content of 42.54%. A total of 7,979 contigs (>1,000 nt) were obtained. We identified 9,129 microsatellites in the Puno-proglottid genome and 9,936 in the Huancayo-cyst genome, with 5 or more repeats, ranging from mono- to hexa-nucleotide. Seven microsatellites were polymorphic and 29 were monomorphic within the analyzed isolates. T. solium tapeworms were classified into two genetic groups that correlated with the North/South geographic origin of the parasites.
The availability of draft genomes for T. solium represents a significant step towards the understanding the biology of the parasite. We report here a set of T. solium polymorphic microsatellite markers that appear promising for genetic epidemiology studies. |
| doi_str_mv | 10.1371/journal.pntd.0004316 |
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For genome sequencing, T. solium cysts and proglottids were collected from Huancayo and Puno in Peru, respectively. Using next generation sequencing (NGS) and de novo assembly, we assembled two draft genomes and one hybrid genome. Microsatellite sequences were identified and 36 of them were selected for further analysis. Twenty T. solium isolates were collected from Tumbes in the northern region, and twenty from Puno in the southern region of Peru. The size-polymorphism of the selected microsatellites was determined with multi-capillary electrophoresis. We analyzed the association between microsatellite polymorphism and the geographic origin of the samples.
The predicted size of the hybrid (proglottid genome combined with cyst genome) T. solium genome was 111 MB with a GC content of 42.54%. A total of 7,979 contigs (>1,000 nt) were obtained. We identified 9,129 microsatellites in the Puno-proglottid genome and 9,936 in the Huancayo-cyst genome, with 5 or more repeats, ranging from mono- to hexa-nucleotide. Seven microsatellites were polymorphic and 29 were monomorphic within the analyzed isolates. T. solium tapeworms were classified into two genetic groups that correlated with the North/South geographic origin of the parasites.
The availability of draft genomes for T. solium represents a significant step towards the understanding the biology of the parasite. We report here a set of T. solium polymorphic microsatellite markers that appear promising for genetic epidemiology studies.</description><identifier>ISSN: 1935-2735</identifier><identifier>ISSN: 1935-2727</identifier><identifier>EISSN: 1935-2735</identifier><identifier>DOI: 10.1371/journal.pntd.0004316</identifier><identifier>PMID: 26697878</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Adult ; Animals ; Base Sequence ; Bioinformatics ; Care and treatment ; Chromosome Mapping ; Cysts ; Developing countries ; Diagnosis ; DNA, Helminth - chemistry ; DNA, Helminth - genetics ; Epidemiology ; Epilepsy ; Genetic aspects ; Genetic Variation ; Genome, Helminth - genetics ; Genomes ; Genotype ; Geography ; High-Throughput Nucleotide Sequencing ; Humans ; Identification and classification ; Infection control ; Infections ; LDCs ; Microsatellite Repeats - genetics ; Microsatellites (Genetics) ; Molecular Sequence Data ; Parasites ; Pathogens ; Peru - epidemiology ; Pork tapeworm ; Public health ; Sequence Analysis, DNA ; Studies ; Taenia solium ; Taenia solium - genetics ; Taenia solium - isolation & purification ; Taeniasis - epidemiology ; Taeniasis - parasitology ; Virulence (Microbiology) ; Worms</subject><ispartof>PLoS neglected tropical diseases, 2015-12, Vol.9 (12), p.e0004316-e0004316</ispartof><rights>COPYRIGHT 2015 Public Library of Science</rights><rights>2015 Public Library of Science. 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: . PLoS Negl Trop Dis 9(12): e0004316. doi:10.1371/journal.pntd.0004316</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c590t-f3ced5e9159158f6afcddbf46961f85bc4a9e051191c7841679fed88be31d0b73</citedby><cites>FETCH-LOGICAL-c590t-f3ced5e9159158f6afcddbf46961f85bc4a9e051191c7841679fed88be31d0b73</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/PMC4689449/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4689449/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,2096,2915,23845,27901,27902,53766,53768,79569,79570</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/26697878$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Pajuelo, Mónica J</creatorcontrib><creatorcontrib>Eguiluz, María</creatorcontrib><creatorcontrib>Dahlstrom, Eric</creatorcontrib><creatorcontrib>Requena, David</creatorcontrib><creatorcontrib>Guzmán, Frank</creatorcontrib><creatorcontrib>Ramirez, Manuel</creatorcontrib><creatorcontrib>Sheen, Patricia</creatorcontrib><creatorcontrib>Frace, Michael</creatorcontrib><creatorcontrib>Sammons, Scott</creatorcontrib><creatorcontrib>Cama, Vitaliano</creatorcontrib><creatorcontrib>Anzick, Sarah</creatorcontrib><creatorcontrib>Bruno, Dan</creatorcontrib><creatorcontrib>Mahanty, Siddhartha</creatorcontrib><creatorcontrib>Wilkins, Patricia</creatorcontrib><creatorcontrib>Nash, Theodore</creatorcontrib><creatorcontrib>Gonzalez, Armando</creatorcontrib><creatorcontrib>García, Héctor H</creatorcontrib><creatorcontrib>Gilman, Robert H</creatorcontrib><creatorcontrib>Porcella, Steve</creatorcontrib><creatorcontrib>Zimic, Mirko</creatorcontrib><creatorcontrib>Cysticercosis Working Group in Peru</creatorcontrib><title>Identification and Characterization of Microsatellite Markers Derived from the Whole Genome Analysis of Taenia solium</title><title>PLoS neglected tropical diseases</title><addtitle>PLoS Negl Trop Dis</addtitle><description>Infections with Taenia solium are the most common cause of adult acquired seizures worldwide, and are the leading cause of epilepsy in developing countries. A better understanding of the genetic diversity of T. solium will improve parasite diagnostics and transmission pathways in endemic areas thereby facilitating the design of future control measures and interventions. Microsatellite markers are useful genome features, which enable strain typing and identification in complex pathogen genomes. Here we describe microsatellite identification and characterization in T. solium, providing information that will assist in global efforts to control this important pathogen.
For genome sequencing, T. solium cysts and proglottids were collected from Huancayo and Puno in Peru, respectively. Using next generation sequencing (NGS) and de novo assembly, we assembled two draft genomes and one hybrid genome. Microsatellite sequences were identified and 36 of them were selected for further analysis. Twenty T. solium isolates were collected from Tumbes in the northern region, and twenty from Puno in the southern region of Peru. The size-polymorphism of the selected microsatellites was determined with multi-capillary electrophoresis. We analyzed the association between microsatellite polymorphism and the geographic origin of the samples.
The predicted size of the hybrid (proglottid genome combined with cyst genome) T. solium genome was 111 MB with a GC content of 42.54%. A total of 7,979 contigs (>1,000 nt) were obtained. We identified 9,129 microsatellites in the Puno-proglottid genome and 9,936 in the Huancayo-cyst genome, with 5 or more repeats, ranging from mono- to hexa-nucleotide. Seven microsatellites were polymorphic and 29 were monomorphic within the analyzed isolates. T. solium tapeworms were classified into two genetic groups that correlated with the North/South geographic origin of the parasites.
The availability of draft genomes for T. solium represents a significant step towards the understanding the biology of the parasite. We report here a set of T. solium polymorphic microsatellite markers that appear promising for genetic epidemiology studies.</description><subject>Adult</subject><subject>Animals</subject><subject>Base Sequence</subject><subject>Bioinformatics</subject><subject>Care and treatment</subject><subject>Chromosome Mapping</subject><subject>Cysts</subject><subject>Developing countries</subject><subject>Diagnosis</subject><subject>DNA, Helminth - chemistry</subject><subject>DNA, Helminth - genetics</subject><subject>Epidemiology</subject><subject>Epilepsy</subject><subject>Genetic aspects</subject><subject>Genetic Variation</subject><subject>Genome, Helminth - genetics</subject><subject>Genomes</subject><subject>Genotype</subject><subject>Geography</subject><subject>High-Throughput Nucleotide Sequencing</subject><subject>Humans</subject><subject>Identification and classification</subject><subject>Infection control</subject><subject>Infections</subject><subject>LDCs</subject><subject>Microsatellite Repeats - genetics</subject><subject>Microsatellites (Genetics)</subject><subject>Molecular Sequence Data</subject><subject>Parasites</subject><subject>Pathogens</subject><subject>Peru - epidemiology</subject><subject>Pork tapeworm</subject><subject>Public health</subject><subject>Sequence Analysis, DNA</subject><subject>Studies</subject><subject>Taenia solium</subject><subject>Taenia solium - genetics</subject><subject>Taenia solium - isolation & purification</subject><subject>Taeniasis - epidemiology</subject><subject>Taeniasis - parasitology</subject><subject>Virulence (Microbiology)</subject><subject>Worms</subject><issn>1935-2735</issn><issn>1935-2727</issn><issn>1935-2735</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2015</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>DOA</sourceid><recordid>eNqNkl9rFDEUxQdRbK1-A9EBQXzZNdn8meRFWFatCy2-VHwMmeRmJ-vMZJvMFOqnN9Pdlt03IZCQ_HLuzckpircYzTGp8OdtGGOv2_muH-wcIUQJ5s-KcywJmy0qwp4frc-KVyltEWKSCfyyOFtwLitRifNiXFvoB--80YMPfal7W64aHbUZIPq_-83gymtvYkh6gLb1A5TXOv6BmMqvGboDW7oYunJooPzdhBbKS-hDB-Uy93effJoEbjT0XpcptH7sXhcvnG4TvDnMF8Wv799uVj9mVz8v16vl1cwwiYaZIwYsA4lZHsJx7Yy1taNccuwEqw3VEhDDWGJTCYp5JR1YIWog2KK6IhfF-73urg1JHRxLClecEiEEJplY7wkb9Fbtou90vFdBe_WwEeJG6Th404LC2iDLjLamcnTBobaICixM_g2OpUBZ68uh2lh3YE02Nur2RPT0pPeN2oQ7RbmQlMos8OkgEMPtCGlQnU8mW657COND3wvCBJLsP1CW0dwfzuiHPbrR-RW-dyEXNxOulpRxJAkhU_Mfj6gGdDs0-bPGKQDpFKR7cApEiuCeHoiRmpL56LOakqkOyczX3h2b83TpMYrkH6mE4is</recordid><startdate>20151201</startdate><enddate>20151201</enddate><creator>Pajuelo, Mónica J</creator><creator>Eguiluz, María</creator><creator>Dahlstrom, Eric</creator><creator>Requena, David</creator><creator>Guzmán, Frank</creator><creator>Ramirez, Manuel</creator><creator>Sheen, Patricia</creator><creator>Frace, Michael</creator><creator>Sammons, Scott</creator><creator>Cama, Vitaliano</creator><creator>Anzick, Sarah</creator><creator>Bruno, Dan</creator><creator>Mahanty, Siddhartha</creator><creator>Wilkins, Patricia</creator><creator>Nash, Theodore</creator><creator>Gonzalez, Armando</creator><creator>García, Héctor H</creator><creator>Gilman, Robert H</creator><creator>Porcella, Steve</creator><creator>Zimic, Mirko</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>7X8</scope><scope>8FD</scope><scope>FR3</scope><scope>P64</scope><scope>RC3</scope><scope>5PM</scope><scope>DOA</scope></search><sort><creationdate>20151201</creationdate><title>Identification and Characterization of Microsatellite Markers Derived from the Whole Genome Analysis of Taenia solium</title><author>Pajuelo, Mónica J ; Eguiluz, María ; Dahlstrom, Eric ; Requena, David ; Guzmán, Frank ; Ramirez, Manuel ; Sheen, Patricia ; Frace, Michael ; Sammons, Scott ; Cama, Vitaliano ; Anzick, Sarah ; Bruno, Dan ; Mahanty, Siddhartha ; Wilkins, Patricia ; Nash, Theodore ; Gonzalez, Armando ; García, Héctor H ; Gilman, Robert H ; Porcella, Steve ; Zimic, Mirko</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c590t-f3ced5e9159158f6afcddbf46961f85bc4a9e051191c7841679fed88be31d0b73</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2015</creationdate><topic>Adult</topic><topic>Animals</topic><topic>Base Sequence</topic><topic>Bioinformatics</topic><topic>Care and treatment</topic><topic>Chromosome Mapping</topic><topic>Cysts</topic><topic>Developing countries</topic><topic>Diagnosis</topic><topic>DNA, Helminth - chemistry</topic><topic>DNA, Helminth - genetics</topic><topic>Epidemiology</topic><topic>Epilepsy</topic><topic>Genetic aspects</topic><topic>Genetic Variation</topic><topic>Genome, Helminth - genetics</topic><topic>Genomes</topic><topic>Genotype</topic><topic>Geography</topic><topic>High-Throughput Nucleotide Sequencing</topic><topic>Humans</topic><topic>Identification and classification</topic><topic>Infection control</topic><topic>Infections</topic><topic>LDCs</topic><topic>Microsatellite Repeats - genetics</topic><topic>Microsatellites (Genetics)</topic><topic>Molecular Sequence Data</topic><topic>Parasites</topic><topic>Pathogens</topic><topic>Peru - epidemiology</topic><topic>Pork tapeworm</topic><topic>Public health</topic><topic>Sequence Analysis, DNA</topic><topic>Studies</topic><topic>Taenia solium</topic><topic>Taenia solium - genetics</topic><topic>Taenia solium - isolation & purification</topic><topic>Taeniasis - epidemiology</topic><topic>Taeniasis - parasitology</topic><topic>Virulence (Microbiology)</topic><topic>Worms</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Pajuelo, Mónica J</creatorcontrib><creatorcontrib>Eguiluz, María</creatorcontrib><creatorcontrib>Dahlstrom, Eric</creatorcontrib><creatorcontrib>Requena, David</creatorcontrib><creatorcontrib>Guzmán, Frank</creatorcontrib><creatorcontrib>Ramirez, Manuel</creatorcontrib><creatorcontrib>Sheen, Patricia</creatorcontrib><creatorcontrib>Frace, Michael</creatorcontrib><creatorcontrib>Sammons, Scott</creatorcontrib><creatorcontrib>Cama, Vitaliano</creatorcontrib><creatorcontrib>Anzick, Sarah</creatorcontrib><creatorcontrib>Bruno, Dan</creatorcontrib><creatorcontrib>Mahanty, Siddhartha</creatorcontrib><creatorcontrib>Wilkins, Patricia</creatorcontrib><creatorcontrib>Nash, Theodore</creatorcontrib><creatorcontrib>Gonzalez, Armando</creatorcontrib><creatorcontrib>García, Héctor H</creatorcontrib><creatorcontrib>Gilman, Robert H</creatorcontrib><creatorcontrib>Porcella, Steve</creatorcontrib><creatorcontrib>Zimic, Mirko</creatorcontrib><creatorcontrib>Cysticercosis Working Group in Peru</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - 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A better understanding of the genetic diversity of T. solium will improve parasite diagnostics and transmission pathways in endemic areas thereby facilitating the design of future control measures and interventions. Microsatellite markers are useful genome features, which enable strain typing and identification in complex pathogen genomes. Here we describe microsatellite identification and characterization in T. solium, providing information that will assist in global efforts to control this important pathogen.
For genome sequencing, T. solium cysts and proglottids were collected from Huancayo and Puno in Peru, respectively. Using next generation sequencing (NGS) and de novo assembly, we assembled two draft genomes and one hybrid genome. Microsatellite sequences were identified and 36 of them were selected for further analysis. Twenty T. solium isolates were collected from Tumbes in the northern region, and twenty from Puno in the southern region of Peru. The size-polymorphism of the selected microsatellites was determined with multi-capillary electrophoresis. We analyzed the association between microsatellite polymorphism and the geographic origin of the samples.
The predicted size of the hybrid (proglottid genome combined with cyst genome) T. solium genome was 111 MB with a GC content of 42.54%. A total of 7,979 contigs (>1,000 nt) were obtained. We identified 9,129 microsatellites in the Puno-proglottid genome and 9,936 in the Huancayo-cyst genome, with 5 or more repeats, ranging from mono- to hexa-nucleotide. Seven microsatellites were polymorphic and 29 were monomorphic within the analyzed isolates. T. solium tapeworms were classified into two genetic groups that correlated with the North/South geographic origin of the parasites.
The availability of draft genomes for T. solium represents a significant step towards the understanding the biology of the parasite. We report here a set of T. solium polymorphic microsatellite markers that appear promising for genetic epidemiology studies.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>26697878</pmid><doi>10.1371/journal.pntd.0004316</doi><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1935-2735 |
| ispartof | PLoS neglected tropical diseases, 2015-12, Vol.9 (12), p.e0004316-e0004316 |
| issn | 1935-2735 1935-2727 1935-2735 |
| language | eng |
| recordid | cdi_plos_journals_1764388813 |
| source | MEDLINE; DOAJ Directory of Open Access Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; PubMed Central; PubMed Central Open Access; Public Library of Science (PLoS) |
| subjects | Adult Animals Base Sequence Bioinformatics Care and treatment Chromosome Mapping Cysts Developing countries Diagnosis DNA, Helminth - chemistry DNA, Helminth - genetics Epidemiology Epilepsy Genetic aspects Genetic Variation Genome, Helminth - genetics Genomes Genotype Geography High-Throughput Nucleotide Sequencing Humans Identification and classification Infection control Infections LDCs Microsatellite Repeats - genetics Microsatellites (Genetics) Molecular Sequence Data Parasites Pathogens Peru - epidemiology Pork tapeworm Public health Sequence Analysis, DNA Studies Taenia solium Taenia solium - genetics Taenia solium - isolation & purification Taeniasis - epidemiology Taeniasis - parasitology Virulence (Microbiology) Worms |
| title | Identification and Characterization of Microsatellite Markers Derived from the Whole Genome Analysis of Taenia solium |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-02-19T13%3A02%3A05IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Identification%20and%20Characterization%20of%20Microsatellite%20Markers%20Derived%20from%20the%20Whole%20Genome%20Analysis%20of%20Taenia%20solium&rft.jtitle=PLoS%20neglected%20tropical%20diseases&rft.au=Pajuelo,%20M%C3%B3nica%20J&rft.aucorp=Cysticercosis%20Working%20Group%20in%20Peru&rft.date=2015-12-01&rft.volume=9&rft.issue=12&rft.spage=e0004316&rft.epage=e0004316&rft.pages=e0004316-e0004316&rft.issn=1935-2735&rft.eissn=1935-2735&rft_id=info:doi/10.1371/journal.pntd.0004316&rft_dat=%3Cgale_plos_%3EA456093330%3C/gale_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1752354811&rft_id=info:pmid/26697878&rft_galeid=A456093330&rft_doaj_id=oai_doaj_org_article_1ac0d5cadc7f426ebd04818c13761980&rfr_iscdi=true |