Mitochondrial genomes of Trichinella species and genotypes – a basis for diagnosis, and systematic and epidemiological explorations
[Display omitted] •Deep sequencing of 15 mitochondrial (mt) genomes of Trichinella is reported.•The systematic relationships among taxa (T1–T12) were assessed.•A rich source of mitochondrial genetic markers was defined.•Broad applicability of a sequencing approach was used. In the present study we s...
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| Veröffentlicht in: | International journal for parasitology 2014-12, Vol.44 (14), p.1073-1080 |
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| container_title | International journal for parasitology |
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| creator | Mohandas, Namitha Pozio, Edoardo La Rosa, Giuseppe Korhonen, Pasi K. Young, Neil D. Koehler, Anson V. Hall, Ross S. Sternberg, Paul W. Boag, Peter R. Jex, Aaron R. Chang, Bill C.H. Gasser, Robin B. |
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•Deep sequencing of 15 mitochondrial (mt) genomes of Trichinella is reported.•The systematic relationships among taxa (T1–T12) were assessed.•A rich source of mitochondrial genetic markers was defined.•Broad applicability of a sequencing approach was used.
In the present study we sequenced or re-sequenced, assembled and annotated 15 mitochondrial genomes representing the 12 currently recognised taxa of Trichinella using a deep sequencing-coupled approach. We then defined and compared the gene order in individual mitochondrial genomes (∼14 to 17.7kb), evaluated genetic differences among species/genotypes and re-assessed the relationships among these taxa using the mitochondrial nucleic acid or amino acid sequence data sets. In addition, a rich source of mitochondrial genetic markers was defined that could be used in future systematic, epidemiological and population genetic studies of Trichinella. The sequencing-bioinformatic approach employed herein should be applicable to a wide range of eukaryotic parasites. |
| doi_str_mv | 10.1016/j.ijpara.2014.08.010 |
| format | Article |
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•Deep sequencing of 15 mitochondrial (mt) genomes of Trichinella is reported.•The systematic relationships among taxa (T1–T12) were assessed.•A rich source of mitochondrial genetic markers was defined.•Broad applicability of a sequencing approach was used.
In the present study we sequenced or re-sequenced, assembled and annotated 15 mitochondrial genomes representing the 12 currently recognised taxa of Trichinella using a deep sequencing-coupled approach. We then defined and compared the gene order in individual mitochondrial genomes (∼14 to 17.7kb), evaluated genetic differences among species/genotypes and re-assessed the relationships among these taxa using the mitochondrial nucleic acid or amino acid sequence data sets. In addition, a rich source of mitochondrial genetic markers was defined that could be used in future systematic, epidemiological and population genetic studies of Trichinella. The sequencing-bioinformatic approach employed herein should be applicable to a wide range of eukaryotic parasites.</description><identifier>ISSN: 0020-7519</identifier><identifier>EISSN: 1879-0135</identifier><identifier>DOI: 10.1016/j.ijpara.2014.08.010</identifier><identifier>PMID: 25245252</identifier><language>eng</language><publisher>England: Elsevier Ltd</publisher><subject>Amino Acid Sequence ; Animals ; Base Sequence ; Bioinformatics ; Deep sequencing ; DNA, Helminth - chemistry ; DNA, Helminth - genetics ; DNA, Mitochondrial - chemistry ; DNA, Mitochondrial - genetics ; Epidemiology ; Genetic relationships ; Genome, Helminth - genetics ; Genome, Mitochondrial - genetics ; Mitochondrial genome ; Molecular Sequence Annotation ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Population genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Systematics ; Trichinella ; Trichinella - classification ; Trichinella - genetics ; Trichinella/trichinellosis</subject><ispartof>International journal for parasitology, 2014-12, Vol.44 (14), p.1073-1080</ispartof><rights>2014 Australian Society for Parasitology Inc.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c395t-e9dbf588c4e7ef74c97f2b50c46744762d7db98dd0600d0c6190700b649d93fb3</citedby><cites>FETCH-LOGICAL-c395t-e9dbf588c4e7ef74c97f2b50c46744762d7db98dd0600d0c6190700b649d93fb3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://dx.doi.org/10.1016/j.ijpara.2014.08.010$$EHTML$$P50$$Gelsevier$$H</linktohtml><link.rule.ids>314,780,784,3550,27924,27925,45995</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/25245252$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Mohandas, Namitha</creatorcontrib><creatorcontrib>Pozio, Edoardo</creatorcontrib><creatorcontrib>La Rosa, Giuseppe</creatorcontrib><creatorcontrib>Korhonen, Pasi K.</creatorcontrib><creatorcontrib>Young, Neil D.</creatorcontrib><creatorcontrib>Koehler, Anson V.</creatorcontrib><creatorcontrib>Hall, Ross S.</creatorcontrib><creatorcontrib>Sternberg, Paul W.</creatorcontrib><creatorcontrib>Boag, Peter R.</creatorcontrib><creatorcontrib>Jex, Aaron R.</creatorcontrib><creatorcontrib>Chang, Bill C.H.</creatorcontrib><creatorcontrib>Gasser, Robin B.</creatorcontrib><title>Mitochondrial genomes of Trichinella species and genotypes – a basis for diagnosis, and systematic and epidemiological explorations</title><title>International journal for parasitology</title><addtitle>Int J Parasitol</addtitle><description>[Display omitted]
•Deep sequencing of 15 mitochondrial (mt) genomes of Trichinella is reported.•The systematic relationships among taxa (T1–T12) were assessed.•A rich source of mitochondrial genetic markers was defined.•Broad applicability of a sequencing approach was used.
In the present study we sequenced or re-sequenced, assembled and annotated 15 mitochondrial genomes representing the 12 currently recognised taxa of Trichinella using a deep sequencing-coupled approach. We then defined and compared the gene order in individual mitochondrial genomes (∼14 to 17.7kb), evaluated genetic differences among species/genotypes and re-assessed the relationships among these taxa using the mitochondrial nucleic acid or amino acid sequence data sets. In addition, a rich source of mitochondrial genetic markers was defined that could be used in future systematic, epidemiological and population genetic studies of Trichinella. The sequencing-bioinformatic approach employed herein should be applicable to a wide range of eukaryotic parasites.</description><subject>Amino Acid Sequence</subject><subject>Animals</subject><subject>Base Sequence</subject><subject>Bioinformatics</subject><subject>Deep sequencing</subject><subject>DNA, Helminth - chemistry</subject><subject>DNA, Helminth - genetics</subject><subject>DNA, Mitochondrial - chemistry</subject><subject>DNA, Mitochondrial - genetics</subject><subject>Epidemiology</subject><subject>Genetic relationships</subject><subject>Genome, Helminth - genetics</subject><subject>Genome, Mitochondrial - genetics</subject><subject>Mitochondrial genome</subject><subject>Molecular Sequence Annotation</subject><subject>Molecular Sequence Data</subject><subject>Phylogeny</subject><subject>Polymerase Chain Reaction</subject><subject>Population genetics</subject><subject>Sequence Alignment</subject><subject>Sequence Analysis, DNA</subject><subject>Systematics</subject><subject>Trichinella</subject><subject>Trichinella - classification</subject><subject>Trichinella - genetics</subject><subject>Trichinella/trichinellosis</subject><issn>0020-7519</issn><issn>1879-0135</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2014</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqNkU2O1DAQhS0EYpqBGyCUJQsSyo4TxxskNOJPGsRmWFuOXempVhIHO43oHRtOwA05Ce7ugSViU6Vnf-Un12PsKYeKA29f7iraLTbaSgCXFXQVcLjHNrxTugReN_fZBkBAqRquL9ijlHYAvKmlfMguRCNkk8uG_fhIa3C3YfaR7FhscQ4TpiIMxU0kd0szjqMt0oKO8rGd_QlZD0tWv77_LGzR20SpGEIsPNntHLJ6cQLTIa042ZXcSeJCHicKY9iSy1b4bRlDzNdhTo_Zg8GOCZ_c9Uv2-e2bm6v35fWndx-uXl-XrtbNWqL2_dB0nZOocFDSaTWIvgEnWyWlaoVXvted99ACeHAt16AA-lZqr-uhry_Z8_O7Swxf9phWM1Fyxy_OGPbJ8LaFWoMQ9X-geYdCKQ4ZlWfUxZBSxMEskSYbD4aDOWZlduaclTlmZaAzcBp7duew7yf0f4f-hJOBV2cA80q-EkaTcgqzQ08R3Wp8oH87_AZjlqnk</recordid><startdate>201412</startdate><enddate>201412</enddate><creator>Mohandas, Namitha</creator><creator>Pozio, Edoardo</creator><creator>La Rosa, Giuseppe</creator><creator>Korhonen, Pasi K.</creator><creator>Young, Neil D.</creator><creator>Koehler, Anson V.</creator><creator>Hall, Ross S.</creator><creator>Sternberg, Paul W.</creator><creator>Boag, Peter R.</creator><creator>Jex, Aaron R.</creator><creator>Chang, Bill C.H.</creator><creator>Gasser, Robin B.</creator><general>Elsevier Ltd</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>7SN</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>P64</scope><scope>RC3</scope></search><sort><creationdate>201412</creationdate><title>Mitochondrial genomes of Trichinella species and genotypes – a basis for diagnosis, and systematic and epidemiological explorations</title><author>Mohandas, Namitha ; Pozio, Edoardo ; La Rosa, Giuseppe ; Korhonen, Pasi K. ; Young, Neil D. ; Koehler, Anson V. ; Hall, Ross S. ; Sternberg, Paul W. ; Boag, Peter R. ; Jex, Aaron R. ; Chang, Bill C.H. ; Gasser, Robin B.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c395t-e9dbf588c4e7ef74c97f2b50c46744762d7db98dd0600d0c6190700b649d93fb3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2014</creationdate><topic>Amino Acid Sequence</topic><topic>Animals</topic><topic>Base Sequence</topic><topic>Bioinformatics</topic><topic>Deep sequencing</topic><topic>DNA, Helminth - chemistry</topic><topic>DNA, Helminth - genetics</topic><topic>DNA, Mitochondrial - chemistry</topic><topic>DNA, Mitochondrial - genetics</topic><topic>Epidemiology</topic><topic>Genetic relationships</topic><topic>Genome, Helminth - genetics</topic><topic>Genome, Mitochondrial - genetics</topic><topic>Mitochondrial genome</topic><topic>Molecular Sequence Annotation</topic><topic>Molecular Sequence Data</topic><topic>Phylogeny</topic><topic>Polymerase Chain Reaction</topic><topic>Population genetics</topic><topic>Sequence Alignment</topic><topic>Sequence Analysis, DNA</topic><topic>Systematics</topic><topic>Trichinella</topic><topic>Trichinella - classification</topic><topic>Trichinella - genetics</topic><topic>Trichinella/trichinellosis</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Mohandas, Namitha</creatorcontrib><creatorcontrib>Pozio, Edoardo</creatorcontrib><creatorcontrib>La Rosa, Giuseppe</creatorcontrib><creatorcontrib>Korhonen, Pasi K.</creatorcontrib><creatorcontrib>Young, Neil D.</creatorcontrib><creatorcontrib>Koehler, Anson V.</creatorcontrib><creatorcontrib>Hall, Ross S.</creatorcontrib><creatorcontrib>Sternberg, Paul W.</creatorcontrib><creatorcontrib>Boag, Peter R.</creatorcontrib><creatorcontrib>Jex, Aaron R.</creatorcontrib><creatorcontrib>Chang, Bill C.H.</creatorcontrib><creatorcontrib>Gasser, Robin B.</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 - Academic</collection><collection>Ecology Abstracts</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><jtitle>International journal for parasitology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Mohandas, Namitha</au><au>Pozio, Edoardo</au><au>La Rosa, Giuseppe</au><au>Korhonen, Pasi K.</au><au>Young, Neil D.</au><au>Koehler, Anson V.</au><au>Hall, Ross S.</au><au>Sternberg, Paul W.</au><au>Boag, Peter R.</au><au>Jex, Aaron R.</au><au>Chang, Bill C.H.</au><au>Gasser, Robin B.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Mitochondrial genomes of Trichinella species and genotypes – a basis for diagnosis, and systematic and epidemiological explorations</atitle><jtitle>International journal for parasitology</jtitle><addtitle>Int J Parasitol</addtitle><date>2014-12</date><risdate>2014</risdate><volume>44</volume><issue>14</issue><spage>1073</spage><epage>1080</epage><pages>1073-1080</pages><issn>0020-7519</issn><eissn>1879-0135</eissn><abstract>[Display omitted]
•Deep sequencing of 15 mitochondrial (mt) genomes of Trichinella is reported.•The systematic relationships among taxa (T1–T12) were assessed.•A rich source of mitochondrial genetic markers was defined.•Broad applicability of a sequencing approach was used.
In the present study we sequenced or re-sequenced, assembled and annotated 15 mitochondrial genomes representing the 12 currently recognised taxa of Trichinella using a deep sequencing-coupled approach. We then defined and compared the gene order in individual mitochondrial genomes (∼14 to 17.7kb), evaluated genetic differences among species/genotypes and re-assessed the relationships among these taxa using the mitochondrial nucleic acid or amino acid sequence data sets. In addition, a rich source of mitochondrial genetic markers was defined that could be used in future systematic, epidemiological and population genetic studies of Trichinella. The sequencing-bioinformatic approach employed herein should be applicable to a wide range of eukaryotic parasites.</abstract><cop>England</cop><pub>Elsevier Ltd</pub><pmid>25245252</pmid><doi>10.1016/j.ijpara.2014.08.010</doi><tpages>8</tpages></addata></record> |
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| ispartof | International journal for parasitology, 2014-12, Vol.44 (14), p.1073-1080 |
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| language | eng |
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| source | MEDLINE; Access via ScienceDirect (Elsevier) |
| subjects | Amino Acid Sequence Animals Base Sequence Bioinformatics Deep sequencing DNA, Helminth - chemistry DNA, Helminth - genetics DNA, Mitochondrial - chemistry DNA, Mitochondrial - genetics Epidemiology Genetic relationships Genome, Helminth - genetics Genome, Mitochondrial - genetics Mitochondrial genome Molecular Sequence Annotation Molecular Sequence Data Phylogeny Polymerase Chain Reaction Population genetics Sequence Alignment Sequence Analysis, DNA Systematics Trichinella Trichinella - classification Trichinella - genetics Trichinella/trichinellosis |
| title | Mitochondrial genomes of Trichinella species and genotypes – a basis for diagnosis, and systematic and epidemiological explorations |
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