Improved genomic resources and new bioinformatic workflow for the carcinogenic parasite Clonorchis sinensis: Biotechnological implications
Clonorchis sinensis (family Opisthorchiidae) is an important foodborne parasite that has a major socioeconomic impact on ~35 million people predominantly in China, Vietnam, Korea and the Russian Far East. In humans, infection with C. sinensis causes clonorchiasis, a complex hepatobiliary disease tha...
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Veröffentlicht in: | Biotechnology advances 2018-07, Vol.36 (4), p.894-904 |
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description | Clonorchis sinensis (family Opisthorchiidae) is an important foodborne parasite that has a major socioeconomic impact on ~35 million people predominantly in China, Vietnam, Korea and the Russian Far East. In humans, infection with C. sinensis causes clonorchiasis, a complex hepatobiliary disease that can induce cholangiocarcinoma (CCA), a malignant cancer of the bile ducts. Central to understanding the epidemiology of this disease is knowledge of genetic variation within and among populations of this parasite. Although most published molecular studies seem to suggest that C. sinensis represents a single species, evidence of karyotypic variation within C. sinensis and cryptic species within a related opisthorchiid fluke (Opisthorchis viverrini) emphasise the importance of studying and comparing the genes and genomes of geographically distinct isolates of C. sinensis. Recently, we sequenced, assembled and characterised a draft nuclear genome of a C. sinensis isolate from Korea and compared it with a published draft genome of a Chinese isolate of this species using a bioinformatic workflow established for comparing draft genome assemblies and their gene annotations. We identified that 50.6% and 51.3% of the Korean and Chinese C. sinensis genomic scaffolds were syntenic, respectively. Within aligned syntenic blocks, the genomes had a high level of nucleotide identity (99.1%) and encoded 15 variable proteins likely to be involved in diverse biological processes. Here, we review current technical challenges of using draft genome assemblies to undertake comparative genomic analyses to quantify genetic variation between isolates of the same species. Using a workflow that overcomes these challenges, we report on a high-quality draft genome for C. sinensis from Korea and comparative genomic analyses, as a basis for future investigations of the genetic structures of C. sinensis populations, and discuss the biotechnological implications of these explorations. |
doi_str_mv | 10.1016/j.biotechadv.2018.02.008 |
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In humans, infection with C. sinensis causes clonorchiasis, a complex hepatobiliary disease that can induce cholangiocarcinoma (CCA), a malignant cancer of the bile ducts. Central to understanding the epidemiology of this disease is knowledge of genetic variation within and among populations of this parasite. Although most published molecular studies seem to suggest that C. sinensis represents a single species, evidence of karyotypic variation within C. sinensis and cryptic species within a related opisthorchiid fluke (Opisthorchis viverrini) emphasise the importance of studying and comparing the genes and genomes of geographically distinct isolates of C. sinensis. Recently, we sequenced, assembled and characterised a draft nuclear genome of a C. sinensis isolate from Korea and compared it with a published draft genome of a Chinese isolate of this species using a bioinformatic workflow established for comparing draft genome assemblies and their gene annotations. We identified that 50.6% and 51.3% of the Korean and Chinese C. sinensis genomic scaffolds were syntenic, respectively. Within aligned syntenic blocks, the genomes had a high level of nucleotide identity (99.1%) and encoded 15 variable proteins likely to be involved in diverse biological processes. Here, we review current technical challenges of using draft genome assemblies to undertake comparative genomic analyses to quantify genetic variation between isolates of the same species. Using a workflow that overcomes these challenges, we report on a high-quality draft genome for C. sinensis from Korea and comparative genomic analyses, as a basis for future investigations of the genetic structures of C. sinensis populations, and discuss the biotechnological implications of these explorations.</description><identifier>ISSN: 0734-9750</identifier><identifier>EISSN: 1873-1899</identifier><identifier>DOI: 10.1016/j.biotechadv.2018.02.008</identifier><identifier>PMID: 29454982</identifier><language>eng</language><publisher>England: Elsevier Inc</publisher><subject>Animals ; Annotations ; Asia ; Assemblies ; Bioinformatics ; Biological activity ; Carcinogenesis ; Carcinogenic worm ; Carcinogens ; Clonorchiasis - parasitology ; Clonorchis sinensis ; Clonorchis sinensis - genetics ; Comparative genomics ; DNA, Helminth - genetics ; Epidemiology ; Genomes ; Genomics ; Genomics - methods ; Humans ; Molecular Diagnostic Techniques ; Parasitic diseases ; Populations ; Proteins ; Workflow ; Worms</subject><ispartof>Biotechnology advances, 2018-07, Vol.36 (4), p.894-904</ispartof><rights>2018 Elsevier Inc.</rights><rights>Copyright © 2018 Elsevier Inc. All rights reserved.</rights><rights>Copyright Elsevier Science Ltd. Jul/Aug 2018</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c505t-5a7d6ac75ad1969b0a1f0edccf788801550404bc5b5494e60f5d5e10a533e3a3</citedby><cites>FETCH-LOGICAL-c505t-5a7d6ac75ad1969b0a1f0edccf788801550404bc5b5494e60f5d5e10a533e3a3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://dx.doi.org/10.1016/j.biotechadv.2018.02.008$$EHTML$$P50$$Gelsevier$$H</linktohtml><link.rule.ids>314,780,784,3550,27924,27925,45995</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/29454982$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Wang, Daxi</creatorcontrib><creatorcontrib>Korhonen, Pasi K.</creatorcontrib><creatorcontrib>Gasser, Robin B.</creatorcontrib><creatorcontrib>Young, Neil D.</creatorcontrib><title>Improved genomic resources and new bioinformatic workflow for the carcinogenic parasite Clonorchis sinensis: Biotechnological implications</title><title>Biotechnology advances</title><addtitle>Biotechnol Adv</addtitle><description>Clonorchis sinensis (family Opisthorchiidae) is an important foodborne parasite that has a major socioeconomic impact on ~35 million people predominantly in China, Vietnam, Korea and the Russian Far East. In humans, infection with C. sinensis causes clonorchiasis, a complex hepatobiliary disease that can induce cholangiocarcinoma (CCA), a malignant cancer of the bile ducts. Central to understanding the epidemiology of this disease is knowledge of genetic variation within and among populations of this parasite. Although most published molecular studies seem to suggest that C. sinensis represents a single species, evidence of karyotypic variation within C. sinensis and cryptic species within a related opisthorchiid fluke (Opisthorchis viverrini) emphasise the importance of studying and comparing the genes and genomes of geographically distinct isolates of C. sinensis. Recently, we sequenced, assembled and characterised a draft nuclear genome of a C. sinensis isolate from Korea and compared it with a published draft genome of a Chinese isolate of this species using a bioinformatic workflow established for comparing draft genome assemblies and their gene annotations. We identified that 50.6% and 51.3% of the Korean and Chinese C. sinensis genomic scaffolds were syntenic, respectively. Within aligned syntenic blocks, the genomes had a high level of nucleotide identity (99.1%) and encoded 15 variable proteins likely to be involved in diverse biological processes. Here, we review current technical challenges of using draft genome assemblies to undertake comparative genomic analyses to quantify genetic variation between isolates of the same species. Using a workflow that overcomes these challenges, we report on a high-quality draft genome for C. sinensis from Korea and comparative genomic analyses, as a basis for future investigations of the genetic structures of C. sinensis populations, and discuss the biotechnological implications of these explorations.</description><subject>Animals</subject><subject>Annotations</subject><subject>Asia</subject><subject>Assemblies</subject><subject>Bioinformatics</subject><subject>Biological activity</subject><subject>Carcinogenesis</subject><subject>Carcinogenic worm</subject><subject>Carcinogens</subject><subject>Clonorchiasis - parasitology</subject><subject>Clonorchis sinensis</subject><subject>Clonorchis sinensis - genetics</subject><subject>Comparative genomics</subject><subject>DNA, Helminth - genetics</subject><subject>Epidemiology</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Genomics - methods</subject><subject>Humans</subject><subject>Molecular Diagnostic Techniques</subject><subject>Parasitic diseases</subject><subject>Populations</subject><subject>Proteins</subject><subject>Workflow</subject><subject>Worms</subject><issn>0734-9750</issn><issn>1873-1899</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2018</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkcFu1DAQhi0EokvhFZAlLlwSxkm8sbnRFdBKlbj0bjn2pOslsRc7uyteoU_NVFtA4sLJluf7_c_MzxgXUAsQ6w-7eghpQbe1_lg3IFQNTQ2gnrGVUH1bCaX1c7aCvu0q3Uu4YK9K2QEICbJ9yS4a3clOq2bFHm7mfU5H9PweY5qD4xlLOmSHhdvoecQTJ68Qx5Rnu1D9lPL3cUonTi982SJ3NrsQE-mpurfZlrAg30wppuy2ofASIsYSykd-de46pindB2cnHub9RJclpFhesxejnQq-eTov2d2Xz3eb6-r229ebzafbylH3SyVt79fW9dJ6odd6ACtGQO_c2CulaEQJHXSDkwON2OEaRuklCrCybbG17SV7f_6W5v5xwLKYORSH02QjpkMxDUDXrvteS0Lf_YPuaDWRmiNKq141Qmii1JlyOZWScTT7HGabfxoB5jEuszN_4zKPcRloDMVF0rdPBodhRv9H-DsfAq7OANJCjgGzKS5gdOhDRrcYn8L_XX4B5IOvBA</recordid><startdate>20180701</startdate><enddate>20180701</enddate><creator>Wang, Daxi</creator><creator>Korhonen, Pasi K.</creator><creator>Gasser, Robin B.</creator><creator>Young, Neil D.</creator><general>Elsevier Inc</general><general>Elsevier Science 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>7QQ</scope><scope>7SE</scope><scope>7TA</scope><scope>7TB</scope><scope>8FD</scope><scope>FR3</scope><scope>H8G</scope><scope>JG9</scope><scope>7X8</scope></search><sort><creationdate>20180701</creationdate><title>Improved genomic resources and new bioinformatic workflow for the carcinogenic parasite Clonorchis sinensis: Biotechnological implications</title><author>Wang, Daxi ; Korhonen, Pasi K. ; Gasser, Robin B. ; Young, Neil D.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c505t-5a7d6ac75ad1969b0a1f0edccf788801550404bc5b5494e60f5d5e10a533e3a3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2018</creationdate><topic>Animals</topic><topic>Annotations</topic><topic>Asia</topic><topic>Assemblies</topic><topic>Bioinformatics</topic><topic>Biological activity</topic><topic>Carcinogenesis</topic><topic>Carcinogenic worm</topic><topic>Carcinogens</topic><topic>Clonorchiasis - parasitology</topic><topic>Clonorchis sinensis</topic><topic>Clonorchis sinensis - genetics</topic><topic>Comparative genomics</topic><topic>DNA, Helminth - genetics</topic><topic>Epidemiology</topic><topic>Genomes</topic><topic>Genomics</topic><topic>Genomics - methods</topic><topic>Humans</topic><topic>Molecular Diagnostic Techniques</topic><topic>Parasitic diseases</topic><topic>Populations</topic><topic>Proteins</topic><topic>Workflow</topic><topic>Worms</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Wang, Daxi</creatorcontrib><creatorcontrib>Korhonen, Pasi K.</creatorcontrib><creatorcontrib>Gasser, Robin B.</creatorcontrib><creatorcontrib>Young, Neil D.</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Ceramic Abstracts</collection><collection>Corrosion Abstracts</collection><collection>Materials Business File</collection><collection>Mechanical & Transportation Engineering Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>Copper Technical Reference Library</collection><collection>Materials Research Database</collection><collection>MEDLINE - Academic</collection><jtitle>Biotechnology advances</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Wang, Daxi</au><au>Korhonen, Pasi K.</au><au>Gasser, Robin B.</au><au>Young, Neil D.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Improved genomic resources and new bioinformatic workflow for the carcinogenic parasite Clonorchis sinensis: Biotechnological implications</atitle><jtitle>Biotechnology advances</jtitle><addtitle>Biotechnol Adv</addtitle><date>2018-07-01</date><risdate>2018</risdate><volume>36</volume><issue>4</issue><spage>894</spage><epage>904</epage><pages>894-904</pages><issn>0734-9750</issn><eissn>1873-1899</eissn><abstract>Clonorchis sinensis (family Opisthorchiidae) is an important foodborne parasite that has a major socioeconomic impact on ~35 million people predominantly in China, Vietnam, Korea and the Russian Far East. In humans, infection with C. sinensis causes clonorchiasis, a complex hepatobiliary disease that can induce cholangiocarcinoma (CCA), a malignant cancer of the bile ducts. Central to understanding the epidemiology of this disease is knowledge of genetic variation within and among populations of this parasite. Although most published molecular studies seem to suggest that C. sinensis represents a single species, evidence of karyotypic variation within C. sinensis and cryptic species within a related opisthorchiid fluke (Opisthorchis viverrini) emphasise the importance of studying and comparing the genes and genomes of geographically distinct isolates of C. sinensis. Recently, we sequenced, assembled and characterised a draft nuclear genome of a C. sinensis isolate from Korea and compared it with a published draft genome of a Chinese isolate of this species using a bioinformatic workflow established for comparing draft genome assemblies and their gene annotations. We identified that 50.6% and 51.3% of the Korean and Chinese C. sinensis genomic scaffolds were syntenic, respectively. Within aligned syntenic blocks, the genomes had a high level of nucleotide identity (99.1%) and encoded 15 variable proteins likely to be involved in diverse biological processes. Here, we review current technical challenges of using draft genome assemblies to undertake comparative genomic analyses to quantify genetic variation between isolates of the same species. Using a workflow that overcomes these challenges, we report on a high-quality draft genome for C. sinensis from Korea and comparative genomic analyses, as a basis for future investigations of the genetic structures of C. sinensis populations, and discuss the biotechnological implications of these explorations.</abstract><cop>England</cop><pub>Elsevier Inc</pub><pmid>29454982</pmid><doi>10.1016/j.biotechadv.2018.02.008</doi><tpages>11</tpages></addata></record> |
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subjects | Animals Annotations Asia Assemblies Bioinformatics Biological activity Carcinogenesis Carcinogenic worm Carcinogens Clonorchiasis - parasitology Clonorchis sinensis Clonorchis sinensis - genetics Comparative genomics DNA, Helminth - genetics Epidemiology Genomes Genomics Genomics - methods Humans Molecular Diagnostic Techniques Parasitic diseases Populations Proteins Workflow Worms |
title | Improved genomic resources and new bioinformatic workflow for the carcinogenic parasite Clonorchis sinensis: Biotechnological implications |
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