Whole-genome sequencing of a Plasmodium vivax clinical isolate exhibits geographical characteristics and high genetic variation in China-Myanmar border area
Currently in China, the trend of Plasmodium vivax cases imported from Southeast Asia was increased especially in the China-Myanmar border area. Driven by the increase in P. vivax cases and stronger need for vaccine and drug development, several P. vivax isolates genome sequencing projects are underw...
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| Veröffentlicht in: | BMC genomics 2017-02, Vol.18 (1), p.131-131, Article 131 |
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| creator | Chen, Shen-Bo Wang, Yue Kassegne, Kokouvi Xu, Bin Shen, Hai-Mo Chen, Jun-Hu |
| description | Currently in China, the trend of Plasmodium vivax cases imported from Southeast Asia was increased especially in the China-Myanmar border area. Driven by the increase in P. vivax cases and stronger need for vaccine and drug development, several P. vivax isolates genome sequencing projects are underway. However, little is known about the genetic variability in this area until now.
The sequencing of the first P. vivax isolate from China-Myanmar border area (CMB-1) generated 120 million paired-end reads. A percentage of 10.6 of the quality-evaluated reads were aligned onto 99.9% of the reference strain Sal I genome in 62-fold coverage with an average of 4.8 SNPs per kb. We present a 539-SNP marker data set for P. vivax that can identify different parasites from different geographic origins with high sensitivity. We also identified exceptionally high levels of genetic variability in members of multigene families such as RBP, SERA, vir, MSP3 and AP2. The de-novo assembly yielded a database composed of 8,409 contigs with N50 lengths of 6.6 kb and revealed 661 novel predicted genes including 78 vir genes, suggesting a greater functional variation in P. vivax from this area.
Our result contributes to a better understanding of P. vivax genetic variation, and provides a fundamental basis for the geographic differentiation of vivax malaria from China-Myanmar border area using a direct sequencing approach without leukocyte depletion. This novel sequencing method can be used as an essential tool for the genomic research of P. vivax in the near future. |
| doi_str_mv | 10.1186/s12864-017-3523-y |
| format | Article |
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The sequencing of the first P. vivax isolate from China-Myanmar border area (CMB-1) generated 120 million paired-end reads. A percentage of 10.6 of the quality-evaluated reads were aligned onto 99.9% of the reference strain Sal I genome in 62-fold coverage with an average of 4.8 SNPs per kb. We present a 539-SNP marker data set for P. vivax that can identify different parasites from different geographic origins with high sensitivity. We also identified exceptionally high levels of genetic variability in members of multigene families such as RBP, SERA, vir, MSP3 and AP2. The de-novo assembly yielded a database composed of 8,409 contigs with N50 lengths of 6.6 kb and revealed 661 novel predicted genes including 78 vir genes, suggesting a greater functional variation in P. vivax from this area.
Our result contributes to a better understanding of P. vivax genetic variation, and provides a fundamental basis for the geographic differentiation of vivax malaria from China-Myanmar border area using a direct sequencing approach without leukocyte depletion. This novel sequencing method can be used as an essential tool for the genomic research of P. vivax in the near future.</description><identifier>ISSN: 1471-2164</identifier><identifier>EISSN: 1471-2164</identifier><identifier>DOI: 10.1186/s12864-017-3523-y</identifier><identifier>PMID: 28166727</identifier><language>eng</language><publisher>England: BioMed Central Ltd</publisher><subject>China ; Deoxyribonucleic acid ; Depletion ; DNA ; DNA sequencing ; Drug development ; Evolution, Molecular ; Gene sequencing ; Genes ; Genetic aspects ; Genetic diversity ; Genetic variability ; Genetic Variation ; Genomes ; Genomics ; Geography ; Humans ; Infections ; Leukocytes ; Malaria ; Manual workers ; Multigene Family - genetics ; Mutation ; Myanmar ; Nucleotide sequencing ; Parasites ; Plasmodium vivax ; Plasmodium vivax - genetics ; Plasmodium vivax - isolation & purification ; Single-nucleotide polymorphism ; Vaccines ; Vector-borne diseases ; Whole Genome Sequencing</subject><ispartof>BMC genomics, 2017-02, Vol.18 (1), p.131-131, Article 131</ispartof><rights>COPYRIGHT 2017 BioMed Central Ltd.</rights><rights>Copyright BioMed Central 2017</rights><rights>2017. This work is licensed under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>The Author(s). 2017</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c556t-681e3bde074c49eb6009bf6fd4dc043096a734244c81ec21f1b3c94484b43c603</citedby><cites>FETCH-LOGICAL-c556t-681e3bde074c49eb6009bf6fd4dc043096a734244c81ec21f1b3c94484b43c603</cites><orcidid>0000-0002-3765-0248</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5294834/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5294834/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,27924,27925,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/28166727$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Chen, Shen-Bo</creatorcontrib><creatorcontrib>Wang, Yue</creatorcontrib><creatorcontrib>Kassegne, Kokouvi</creatorcontrib><creatorcontrib>Xu, Bin</creatorcontrib><creatorcontrib>Shen, Hai-Mo</creatorcontrib><creatorcontrib>Chen, Jun-Hu</creatorcontrib><title>Whole-genome sequencing of a Plasmodium vivax clinical isolate exhibits geographical characteristics and high genetic variation in China-Myanmar border area</title><title>BMC genomics</title><addtitle>BMC Genomics</addtitle><description>Currently in China, the trend of Plasmodium vivax cases imported from Southeast Asia was increased especially in the China-Myanmar border area. Driven by the increase in P. vivax cases and stronger need for vaccine and drug development, several P. vivax isolates genome sequencing projects are underway. However, little is known about the genetic variability in this area until now.
The sequencing of the first P. vivax isolate from China-Myanmar border area (CMB-1) generated 120 million paired-end reads. A percentage of 10.6 of the quality-evaluated reads were aligned onto 99.9% of the reference strain Sal I genome in 62-fold coverage with an average of 4.8 SNPs per kb. We present a 539-SNP marker data set for P. vivax that can identify different parasites from different geographic origins with high sensitivity. We also identified exceptionally high levels of genetic variability in members of multigene families such as RBP, SERA, vir, MSP3 and AP2. The de-novo assembly yielded a database composed of 8,409 contigs with N50 lengths of 6.6 kb and revealed 661 novel predicted genes including 78 vir genes, suggesting a greater functional variation in P. vivax from this area.
Our result contributes to a better understanding of P. vivax genetic variation, and provides a fundamental basis for the geographic differentiation of vivax malaria from China-Myanmar border area using a direct sequencing approach without leukocyte depletion. This novel sequencing method can be used as an essential tool for the genomic research of P. vivax in the near future.</description><subject>China</subject><subject>Deoxyribonucleic acid</subject><subject>Depletion</subject><subject>DNA</subject><subject>DNA sequencing</subject><subject>Drug development</subject><subject>Evolution, Molecular</subject><subject>Gene sequencing</subject><subject>Genes</subject><subject>Genetic aspects</subject><subject>Genetic diversity</subject><subject>Genetic variability</subject><subject>Genetic Variation</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Geography</subject><subject>Humans</subject><subject>Infections</subject><subject>Leukocytes</subject><subject>Malaria</subject><subject>Manual workers</subject><subject>Multigene Family - genetics</subject><subject>Mutation</subject><subject>Myanmar</subject><subject>Nucleotide sequencing</subject><subject>Parasites</subject><subject>Plasmodium vivax</subject><subject>Plasmodium vivax - 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genetics</topic><topic>Mutation</topic><topic>Myanmar</topic><topic>Nucleotide sequencing</topic><topic>Parasites</topic><topic>Plasmodium vivax</topic><topic>Plasmodium vivax - genetics</topic><topic>Plasmodium vivax - isolation & purification</topic><topic>Single-nucleotide polymorphism</topic><topic>Vaccines</topic><topic>Vector-borne diseases</topic><topic>Whole Genome Sequencing</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Chen, Shen-Bo</creatorcontrib><creatorcontrib>Wang, Yue</creatorcontrib><creatorcontrib>Kassegne, Kokouvi</creatorcontrib><creatorcontrib>Xu, Bin</creatorcontrib><creatorcontrib>Shen, Hai-Mo</creatorcontrib><creatorcontrib>Chen, Jun-Hu</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: Science</collection><collection>ProQuest Central (Corporate)</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Chemoreception Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Neurosciences Abstracts</collection><collection>Toxicology Abstracts</collection><collection>ProQuest Health and Medical</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>ProQuest Biological Science Journals</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Publicly Available Content Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>BMC genomics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Chen, Shen-Bo</au><au>Wang, Yue</au><au>Kassegne, Kokouvi</au><au>Xu, Bin</au><au>Shen, Hai-Mo</au><au>Chen, Jun-Hu</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Whole-genome sequencing of a Plasmodium vivax clinical isolate exhibits geographical characteristics and high genetic variation in China-Myanmar border area</atitle><jtitle>BMC genomics</jtitle><addtitle>BMC Genomics</addtitle><date>2017-02-06</date><risdate>2017</risdate><volume>18</volume><issue>1</issue><spage>131</spage><epage>131</epage><pages>131-131</pages><artnum>131</artnum><issn>1471-2164</issn><eissn>1471-2164</eissn><abstract>Currently in China, the trend of Plasmodium vivax cases imported from Southeast Asia was increased especially in the China-Myanmar border area. Driven by the increase in P. vivax cases and stronger need for vaccine and drug development, several P. vivax isolates genome sequencing projects are underway. However, little is known about the genetic variability in this area until now.
The sequencing of the first P. vivax isolate from China-Myanmar border area (CMB-1) generated 120 million paired-end reads. A percentage of 10.6 of the quality-evaluated reads were aligned onto 99.9% of the reference strain Sal I genome in 62-fold coverage with an average of 4.8 SNPs per kb. We present a 539-SNP marker data set for P. vivax that can identify different parasites from different geographic origins with high sensitivity. We also identified exceptionally high levels of genetic variability in members of multigene families such as RBP, SERA, vir, MSP3 and AP2. The de-novo assembly yielded a database composed of 8,409 contigs with N50 lengths of 6.6 kb and revealed 661 novel predicted genes including 78 vir genes, suggesting a greater functional variation in P. vivax from this area.
Our result contributes to a better understanding of P. vivax genetic variation, and provides a fundamental basis for the geographic differentiation of vivax malaria from China-Myanmar border area using a direct sequencing approach without leukocyte depletion. This novel sequencing method can be used as an essential tool for the genomic research of P. vivax in the near future.</abstract><cop>England</cop><pub>BioMed Central Ltd</pub><pmid>28166727</pmid><doi>10.1186/s12864-017-3523-y</doi><tpages>1</tpages><orcidid>https://orcid.org/0000-0002-3765-0248</orcidid><oa>free_for_read</oa></addata></record> |
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| source | Springer Open Access; MEDLINE; DOAJ Directory of Open Access Journals; PubMed Central Open Access; EZB-FREE-00999 freely available EZB journals; PubMed Central; SpringerLink Journals - AutoHoldings |
| subjects | China Deoxyribonucleic acid Depletion DNA DNA sequencing Drug development Evolution, Molecular Gene sequencing Genes Genetic aspects Genetic diversity Genetic variability Genetic Variation Genomes Genomics Geography Humans Infections Leukocytes Malaria Manual workers Multigene Family - genetics Mutation Myanmar Nucleotide sequencing Parasites Plasmodium vivax Plasmodium vivax - genetics Plasmodium vivax - isolation & purification Single-nucleotide polymorphism Vaccines Vector-borne diseases Whole Genome Sequencing |
| title | Whole-genome sequencing of a Plasmodium vivax clinical isolate exhibits geographical characteristics and high genetic variation in China-Myanmar border area |
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