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DNA Barcoding Using 18S rRNA Gene Fragments for Identification of Tick-Borne Protists in Ticks in the Republic of Korea
The objective of this study was to evaluate the diversity and prevalence of tick-borne protists in the Republic of Korea via DNA barcoding using 18S rRNA gene fragments and PCR. Between 2021 and 2022, questing ticks were collected using the flagging method, with a total of 13,375 ticks collected and...
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| Published in: | Pathogens (Basel) 2024-10, Vol.13 (11), p.941 |
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| creator | Alkathiri, Badriah Lee, Subin Ahn, KyuSung Youn, So Youn Yoo, Mi-Sun Lee, Hyang-Sim Cho, Yun Sang Jung, Jaeyun Seo, Kwangwon Kim, Soochong Umemiya-Shirafuji, Rika Xuan, Xuenan Kwak, Dongmi Shin, SungShik Lee, Seung-Hun |
| description | The objective of this study was to evaluate the diversity and prevalence of tick-borne protists in the Republic of Korea via DNA barcoding using 18S rRNA gene fragments and PCR. Between 2021 and 2022, questing ticks were collected using the flagging method, with a total of 13,375 ticks collected and pooled into 1003 samples. Of these, 50 tick pools were selected for DNA barcoding targeting the V4 and V9 regions of 18S rRNA using the MiSeq platform. A taxonomic analysis of the amplicon sequence variants identified three genera of protozoa, namely
,
, and
sp. However, the number and abundance of protists detected were different depending on the primer sets, and
was not identified in DNA barcoding. Furthermore, conventional PCR confirmed the presence of
,
,
, and
sp. in the collected ticks. This study identified
and
in
for the first time. It demonstrated that the results of DNA barcoding using 18S rRNA gene fragments can vary depending on the primer sets and further optimization is required for library construction to identify tick-borne protists in ticks. Despite these limitations, the findings highlight the potential of DNA barcoding using 18S rRNA gene fragments for screening the diversity of tick-borne protists in ticks. |
| doi_str_mv | 10.3390/pathogens13110941 |
| format | article |
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,
, and
sp. However, the number and abundance of protists detected were different depending on the primer sets, and
was not identified in DNA barcoding. Furthermore, conventional PCR confirmed the presence of
,
,
, and
sp. in the collected ticks. This study identified
and
in
for the first time. It demonstrated that the results of DNA barcoding using 18S rRNA gene fragments can vary depending on the primer sets and further optimization is required for library construction to identify tick-borne protists in ticks. Despite these limitations, the findings highlight the potential of DNA barcoding using 18S rRNA gene fragments for screening the diversity of tick-borne protists in ticks.</description><identifier>ISSN: 2076-0817</identifier><identifier>EISSN: 2076-0817</identifier><identifier>DOI: 10.3390/pathogens13110941</identifier><identifier>PMID: 39599494</identifier><language>eng</language><publisher>Switzerland: MDPI AG</publisher><subject>Analysis ; Arachnids ; Bacteria ; Bar codes ; Deoxyribonucleic acid ; DNA ; DNA barcoding ; Fragments ; Gene sequencing ; Genera ; Genes ; Genetic testing ; Lee, Y.S ; metabarcoding ; next-generation sequencing ; Nucleotide sequence ; Parasites ; Pathogens ; Phylogenetics ; Polymerase chain reaction ; Protozoa ; RNA ; rRNA 18S ; Taxonomy ; Theileria ; tick ; Tick-borne diseases ; tick-borne pathogen ; Ticks ; vector ; Veterinary medicine</subject><ispartof>Pathogens (Basel), 2024-10, Vol.13 (11), p.941</ispartof><rights>COPYRIGHT 2024 MDPI AG</rights><rights>2024 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2024 by the authors. 2024</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c443t-134ddd20075fadfb5c806186d96806b284dda19e9fe6adb32baab0deb6c2e68d3</cites><orcidid>0000-0002-6244-0381 ; 0000-0001-9575-1007 ; 0000-0003-2780-110X ; 0000-0003-1620-4916 ; 0000-0002-6739-9787 ; 0000-0001-7641-5526 ; 0000-0003-0876-3179 ; 0000-0003-1346-7067</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.proquest.com/docview/3133104129/fulltextPDF?pq-origsite=primo$$EPDF$$P50$$Gproquest$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.proquest.com/docview/3133104129?pq-origsite=primo$$EHTML$$P50$$Gproquest$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,885,25752,27923,27924,37011,37012,44589,53790,53792,74997</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/39599494$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Alkathiri, Badriah</creatorcontrib><creatorcontrib>Lee, Subin</creatorcontrib><creatorcontrib>Ahn, KyuSung</creatorcontrib><creatorcontrib>Youn, So Youn</creatorcontrib><creatorcontrib>Yoo, Mi-Sun</creatorcontrib><creatorcontrib>Lee, Hyang-Sim</creatorcontrib><creatorcontrib>Cho, Yun Sang</creatorcontrib><creatorcontrib>Jung, Jaeyun</creatorcontrib><creatorcontrib>Seo, Kwangwon</creatorcontrib><creatorcontrib>Kim, Soochong</creatorcontrib><creatorcontrib>Umemiya-Shirafuji, Rika</creatorcontrib><creatorcontrib>Xuan, Xuenan</creatorcontrib><creatorcontrib>Kwak, Dongmi</creatorcontrib><creatorcontrib>Shin, SungShik</creatorcontrib><creatorcontrib>Lee, Seung-Hun</creatorcontrib><title>DNA Barcoding Using 18S rRNA Gene Fragments for Identification of Tick-Borne Protists in Ticks in the Republic of Korea</title><title>Pathogens (Basel)</title><addtitle>Pathogens</addtitle><description>The objective of this study was to evaluate the diversity and prevalence of tick-borne protists in the Republic of Korea via DNA barcoding using 18S rRNA gene fragments and PCR. Between 2021 and 2022, questing ticks were collected using the flagging method, with a total of 13,375 ticks collected and pooled into 1003 samples. Of these, 50 tick pools were selected for DNA barcoding targeting the V4 and V9 regions of 18S rRNA using the MiSeq platform. A taxonomic analysis of the amplicon sequence variants identified three genera of protozoa, namely
,
, and
sp. However, the number and abundance of protists detected were different depending on the primer sets, and
was not identified in DNA barcoding. Furthermore, conventional PCR confirmed the presence of
,
,
, and
sp. in the collected ticks. This study identified
and
in
for the first time. It demonstrated that the results of DNA barcoding using 18S rRNA gene fragments can vary depending on the primer sets and further optimization is required for library construction to identify tick-borne protists in ticks. Despite these limitations, the findings highlight the potential of DNA barcoding using 18S rRNA gene fragments for screening the diversity of tick-borne protists in ticks.</description><subject>Analysis</subject><subject>Arachnids</subject><subject>Bacteria</subject><subject>Bar codes</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA barcoding</subject><subject>Fragments</subject><subject>Gene sequencing</subject><subject>Genera</subject><subject>Genes</subject><subject>Genetic testing</subject><subject>Lee, Y.S</subject><subject>metabarcoding</subject><subject>next-generation sequencing</subject><subject>Nucleotide sequence</subject><subject>Parasites</subject><subject>Pathogens</subject><subject>Phylogenetics</subject><subject>Polymerase chain reaction</subject><subject>Protozoa</subject><subject>RNA</subject><subject>rRNA 18S</subject><subject>Taxonomy</subject><subject>Theileria</subject><subject>tick</subject><subject>Tick-borne diseases</subject><subject>tick-borne pathogen</subject><subject>Ticks</subject><subject>vector</subject><subject>Veterinary medicine</subject><issn>2076-0817</issn><issn>2076-0817</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2024</creationdate><recordtype>article</recordtype><sourceid>PIMPY</sourceid><sourceid>DOA</sourceid><recordid>eNptUk1vEzEQXSEQrUp_ABe0EhcuKf5ar31CaaElogJU2rPltccbh40d7A2If483KaUFbMkez7z3xjOaqnqO0QmlEr3e6HEZewgZU4yRZPhRdUhQy2dI4PbxPfugOs55hcoSaHo_rQ6obKRkkh1WP95-nNenOplofejrmzydWHyp01UJXECA-jzpfg1hzLWLqV7YYnrnjR59DHV09bU3X2enMRXo5xRHnwvSh517Z4xLqK9gs-0Gbyb8h5hAP6ueOD1kOL69j6qb83fXZ-9nl58uFmfzy5lhjI4zTJm1liDUNk5b1zVGII4Ft5IXoyOihDWWIB1wbTtKOq07ZKHjhgAXlh5Vi72ujXqlNsmvdfqpovZq54ipVzqN3gygSEOxbDnhqMVMNqQTgkiNXMM6Jyw0RevNXqvUsgZrSiOSHh6IPowEv1R9_K4wbmRLOCkKr24VUvy2hTyqtc8GhkEHiNusKKaUcVS-UaAv_4Ku4jaF0qsdCiOGifyD6nWpwAcXS2Iziaq5wILxlrZT2pP_oMq2sPYmBnC--B8Q8J5gUsw5gbsrEiM1TZ_6Z_oK58X97twxfs8a_QUcVdUY</recordid><startdate>20241029</startdate><enddate>20241029</enddate><creator>Alkathiri, Badriah</creator><creator>Lee, Subin</creator><creator>Ahn, KyuSung</creator><creator>Youn, So Youn</creator><creator>Yoo, Mi-Sun</creator><creator>Lee, Hyang-Sim</creator><creator>Cho, Yun Sang</creator><creator>Jung, Jaeyun</creator><creator>Seo, Kwangwon</creator><creator>Kim, Soochong</creator><creator>Umemiya-Shirafuji, Rika</creator><creator>Xuan, Xuenan</creator><creator>Kwak, Dongmi</creator><creator>Shin, SungShik</creator><creator>Lee, Seung-Hun</creator><general>MDPI AG</general><general>MDPI</general><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7T7</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>LK8</scope><scope>M7P</scope><scope>P64</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope><orcidid>https://orcid.org/0000-0002-6244-0381</orcidid><orcidid>https://orcid.org/0000-0001-9575-1007</orcidid><orcidid>https://orcid.org/0000-0003-2780-110X</orcidid><orcidid>https://orcid.org/0000-0003-1620-4916</orcidid><orcidid>https://orcid.org/0000-0002-6739-9787</orcidid><orcidid>https://orcid.org/0000-0001-7641-5526</orcidid><orcidid>https://orcid.org/0000-0003-0876-3179</orcidid><orcidid>https://orcid.org/0000-0003-1346-7067</orcidid></search><sort><creationdate>20241029</creationdate><title>DNA Barcoding Using 18S rRNA Gene Fragments for Identification of Tick-Borne Protists in Ticks in the Republic of Korea</title><author>Alkathiri, Badriah ; Lee, Subin ; Ahn, KyuSung ; Youn, So Youn ; Yoo, Mi-Sun ; Lee, Hyang-Sim ; Cho, Yun Sang ; Jung, Jaeyun ; Seo, Kwangwon ; Kim, Soochong ; Umemiya-Shirafuji, Rika ; Xuan, Xuenan ; Kwak, Dongmi ; Shin, SungShik ; Lee, Seung-Hun</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c443t-134ddd20075fadfb5c806186d96806b284dda19e9fe6adb32baab0deb6c2e68d3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2024</creationdate><topic>Analysis</topic><topic>Arachnids</topic><topic>Bacteria</topic><topic>Bar codes</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>DNA barcoding</topic><topic>Fragments</topic><topic>Gene sequencing</topic><topic>Genera</topic><topic>Genes</topic><topic>Genetic testing</topic><topic>Lee, Y.S</topic><topic>metabarcoding</topic><topic>next-generation sequencing</topic><topic>Nucleotide sequence</topic><topic>Parasites</topic><topic>Pathogens</topic><topic>Phylogenetics</topic><topic>Polymerase chain reaction</topic><topic>Protozoa</topic><topic>RNA</topic><topic>rRNA 18S</topic><topic>Taxonomy</topic><topic>Theileria</topic><topic>tick</topic><topic>Tick-borne diseases</topic><topic>tick-borne pathogen</topic><topic>Ticks</topic><topic>vector</topic><topic>Veterinary medicine</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Alkathiri, Badriah</creatorcontrib><creatorcontrib>Lee, Subin</creatorcontrib><creatorcontrib>Ahn, KyuSung</creatorcontrib><creatorcontrib>Youn, So Youn</creatorcontrib><creatorcontrib>Yoo, Mi-Sun</creatorcontrib><creatorcontrib>Lee, Hyang-Sim</creatorcontrib><creatorcontrib>Cho, Yun Sang</creatorcontrib><creatorcontrib>Jung, Jaeyun</creatorcontrib><creatorcontrib>Seo, Kwangwon</creatorcontrib><creatorcontrib>Kim, Soochong</creatorcontrib><creatorcontrib>Umemiya-Shirafuji, Rika</creatorcontrib><creatorcontrib>Xuan, Xuenan</creatorcontrib><creatorcontrib>Kwak, Dongmi</creatorcontrib><creatorcontrib>Shin, SungShik</creatorcontrib><creatorcontrib>Lee, Seung-Hun</creatorcontrib><collection>PubMed</collection><collection>CrossRef</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>ProQuest Natural Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central</collection><collection>Engineering Research Database</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Biological Science Collection</collection><collection>Biological Science Database</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>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>Pathogens (Basel)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Alkathiri, Badriah</au><au>Lee, Subin</au><au>Ahn, KyuSung</au><au>Youn, So Youn</au><au>Yoo, Mi-Sun</au><au>Lee, Hyang-Sim</au><au>Cho, Yun Sang</au><au>Jung, Jaeyun</au><au>Seo, Kwangwon</au><au>Kim, Soochong</au><au>Umemiya-Shirafuji, Rika</au><au>Xuan, Xuenan</au><au>Kwak, Dongmi</au><au>Shin, SungShik</au><au>Lee, Seung-Hun</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>DNA Barcoding Using 18S rRNA Gene Fragments for Identification of Tick-Borne Protists in Ticks in the Republic of Korea</atitle><jtitle>Pathogens (Basel)</jtitle><addtitle>Pathogens</addtitle><date>2024-10-29</date><risdate>2024</risdate><volume>13</volume><issue>11</issue><spage>941</spage><pages>941-</pages><issn>2076-0817</issn><eissn>2076-0817</eissn><abstract>The objective of this study was to evaluate the diversity and prevalence of tick-borne protists in the Republic of Korea via DNA barcoding using 18S rRNA gene fragments and PCR. Between 2021 and 2022, questing ticks were collected using the flagging method, with a total of 13,375 ticks collected and pooled into 1003 samples. Of these, 50 tick pools were selected for DNA barcoding targeting the V4 and V9 regions of 18S rRNA using the MiSeq platform. A taxonomic analysis of the amplicon sequence variants identified three genera of protozoa, namely
,
, and
sp. However, the number and abundance of protists detected were different depending on the primer sets, and
was not identified in DNA barcoding. Furthermore, conventional PCR confirmed the presence of
,
,
, and
sp. in the collected ticks. This study identified
and
in
for the first time. It demonstrated that the results of DNA barcoding using 18S rRNA gene fragments can vary depending on the primer sets and further optimization is required for library construction to identify tick-borne protists in ticks. Despite these limitations, the findings highlight the potential of DNA barcoding using 18S rRNA gene fragments for screening the diversity of tick-borne protists in ticks.</abstract><cop>Switzerland</cop><pub>MDPI AG</pub><pmid>39599494</pmid><doi>10.3390/pathogens13110941</doi><orcidid>https://orcid.org/0000-0002-6244-0381</orcidid><orcidid>https://orcid.org/0000-0001-9575-1007</orcidid><orcidid>https://orcid.org/0000-0003-2780-110X</orcidid><orcidid>https://orcid.org/0000-0003-1620-4916</orcidid><orcidid>https://orcid.org/0000-0002-6739-9787</orcidid><orcidid>https://orcid.org/0000-0001-7641-5526</orcidid><orcidid>https://orcid.org/0000-0003-0876-3179</orcidid><orcidid>https://orcid.org/0000-0003-1346-7067</orcidid><oa>free_for_read</oa></addata></record> |
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| ispartof | Pathogens (Basel), 2024-10, Vol.13 (11), p.941 |
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| language | eng |
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| source | Publicly Available Content Database; PubMed Central |
| subjects | Analysis Arachnids Bacteria Bar codes Deoxyribonucleic acid DNA DNA barcoding Fragments Gene sequencing Genera Genes Genetic testing Lee, Y.S metabarcoding next-generation sequencing Nucleotide sequence Parasites Pathogens Phylogenetics Polymerase chain reaction Protozoa RNA rRNA 18S Taxonomy Theileria tick Tick-borne diseases tick-borne pathogen Ticks vector Veterinary medicine |
| title | DNA Barcoding Using 18S rRNA Gene Fragments for Identification of Tick-Borne Protists in Ticks in the Republic of Korea |
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