Validation of Direct Boiling Method for Simple and Efficient Genomic DNA Extraction and PCR‐based Macroalgal Species Determination
A rapid, simple, and cost‐effective total DNA extraction method referred to as a direct boiling method for PCR‐based algal species determination was validated using representative species of green, brown, and red algae. Each sample was briefly minced in two buffers, Tris‐EDTA (TE) or PCR buffer, and...
Gespeichert in:
| Veröffentlicht in: | Journal of phycology 2021-08, Vol.57 (4), p.1368-1372 |
|---|---|
| Hauptverfasser: | , , , , , |
| Format: | Artikel |
| Sprache: | eng |
| Schlagworte: | |
| Online-Zugang: | Volltext |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| container_end_page | 1372 |
|---|---|
| container_issue | 4 |
| container_start_page | 1368 |
| container_title | Journal of phycology |
| container_volume | 57 |
| creator | Shin, Sook Kyung Lee, Yeonhui Kwon, Hayoung Rhee, Jae‐Sung Kim, Jang Kyun Lane, C. |
| description | A rapid, simple, and cost‐effective total DNA extraction method referred to as a direct boiling method for PCR‐based algal species determination was validated using representative species of green, brown, and red algae. Each sample was briefly minced in two buffers, Tris‐EDTA (TE) or PCR buffer, and transferred to a heat block for boiling at 98°C for 5 min. No detergent was used in this experiment. The entire DNA isolation procedure was completed within 10 min. After brief centrifugation, the supernatant was directly used as a template for PCR. As a result, all genomic DNA markers were successfully amplified and sequenced from each algal taxon. Regardless of DNA quality, the direct boiling method is very suitable to identify unknown species of algae from a large amount of samples in a limited time and can be applied broadly to routine seasonal or annual monitoring of algae. DNA from an Undaria pinnatifida sporophyte, however, was not successfully extracted by this direct boiling method, probably due to a high concentration of polysaccharides. |
| doi_str_mv | 10.1111/jpy.13175 |
| format | Article |
| fullrecord | <record><control><sourceid>proquest_cross</sourceid><recordid>TN_cdi_proquest_journals_2559643141</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>2559643141</sourcerecordid><originalsourceid>FETCH-LOGICAL-c3535-10c44224461dfd87d8ee1776effeea2d31885584ca081c124e1283fabdfd444c3</originalsourceid><addsrcrecordid>eNp1kL9uFDEQhy0EIkdCkReILFGl2MTjP7tOGe4uAZSQiAAS1cpnjxOfdtcb757gOgoegGfkSXDuEjqmmeab7zf6EbIP7AjyHC_79REIqNQzMgHFTwqtoXpOJoxxXohSljvk1TAsGWNVqeAl2RFCCyk1m5BfX00TnBlD7Gj0dBYS2pG-jaEJ3S29xPEuOupjojeh7RukpnN07n2wAbuRnmMX22Dp7OMpnf8Yk7Eb0QN0Pf305-fvhRnQ0UtjUzTNrWnoTY_5dKAzHDG1odsk75EX3jQDvn7cu-TL2fzz9F1xcXX-fnp6UVihhCqAWSk5l7IE552unEaEqirRe0TDnQCtldLSGqbBApcIXAtvFpmWUlqxS95svX2K9yscxnoZV6nLkTVX6qSUAiRk6nBL5aeHIaGv-xRak9Y1sPqh7zr3XW_6zuzBo3G1aNH9I58KzsDxFvgeGlz_31R_uP62Vf4FGcWLIg</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2559643141</pqid></control><display><type>article</type><title>Validation of Direct Boiling Method for Simple and Efficient Genomic DNA Extraction and PCR‐based Macroalgal Species Determination</title><source>Wiley Online Library Journals Frontfile Complete</source><creator>Shin, Sook Kyung ; Lee, Yeonhui ; Kwon, Hayoung ; Rhee, Jae‐Sung ; Kim, Jang Kyun ; Lane, C.</creator><contributor>Lane, C.</contributor><creatorcontrib>Shin, Sook Kyung ; Lee, Yeonhui ; Kwon, Hayoung ; Rhee, Jae‐Sung ; Kim, Jang Kyun ; Lane, C. ; Lane, C.</creatorcontrib><description>A rapid, simple, and cost‐effective total DNA extraction method referred to as a direct boiling method for PCR‐based algal species determination was validated using representative species of green, brown, and red algae. Each sample was briefly minced in two buffers, Tris‐EDTA (TE) or PCR buffer, and transferred to a heat block for boiling at 98°C for 5 min. No detergent was used in this experiment. The entire DNA isolation procedure was completed within 10 min. After brief centrifugation, the supernatant was directly used as a template for PCR. As a result, all genomic DNA markers were successfully amplified and sequenced from each algal taxon. Regardless of DNA quality, the direct boiling method is very suitable to identify unknown species of algae from a large amount of samples in a limited time and can be applied broadly to routine seasonal or annual monitoring of algae. DNA from an Undaria pinnatifida sporophyte, however, was not successfully extracted by this direct boiling method, probably due to a high concentration of polysaccharides.</description><identifier>ISSN: 0022-3646</identifier><identifier>EISSN: 1529-8817</identifier><identifier>DOI: 10.1111/jpy.13175</identifier><identifier>PMID: 33834480</identifier><language>eng</language><publisher>United States: Wiley Subscription Services, Inc</publisher><subject>Algae ; algal species identification ; Boiling ; boiling method ; Buffers ; Centrifugation ; Centrifuging ; Deoxyribonucleic acid ; Detergents ; DNA ; DNA isolation ; Ethylenediaminetetraacetic acids ; Genomics ; Nucleotide sequence ; PCR ; Polymerase chain reaction ; Polysaccharides ; Saccharides ; Seaweeds ; Species ; Sporophytes</subject><ispartof>Journal of phycology, 2021-08, Vol.57 (4), p.1368-1372</ispartof><rights>2021 Phycological Society of America</rights><rights>This article is protected by copyright. All rights reserved.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c3535-10c44224461dfd87d8ee1776effeea2d31885584ca081c124e1283fabdfd444c3</citedby><cites>FETCH-LOGICAL-c3535-10c44224461dfd87d8ee1776effeea2d31885584ca081c124e1283fabdfd444c3</cites><orcidid>0000-0001-7008-6768</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1111%2Fjpy.13175$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1111%2Fjpy.13175$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>314,777,781,1412,27905,27906,45555,45556</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/33834480$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Lane, C.</contributor><creatorcontrib>Shin, Sook Kyung</creatorcontrib><creatorcontrib>Lee, Yeonhui</creatorcontrib><creatorcontrib>Kwon, Hayoung</creatorcontrib><creatorcontrib>Rhee, Jae‐Sung</creatorcontrib><creatorcontrib>Kim, Jang Kyun</creatorcontrib><creatorcontrib>Lane, C.</creatorcontrib><title>Validation of Direct Boiling Method for Simple and Efficient Genomic DNA Extraction and PCR‐based Macroalgal Species Determination</title><title>Journal of phycology</title><addtitle>J Phycol</addtitle><description>A rapid, simple, and cost‐effective total DNA extraction method referred to as a direct boiling method for PCR‐based algal species determination was validated using representative species of green, brown, and red algae. Each sample was briefly minced in two buffers, Tris‐EDTA (TE) or PCR buffer, and transferred to a heat block for boiling at 98°C for 5 min. No detergent was used in this experiment. The entire DNA isolation procedure was completed within 10 min. After brief centrifugation, the supernatant was directly used as a template for PCR. As a result, all genomic DNA markers were successfully amplified and sequenced from each algal taxon. Regardless of DNA quality, the direct boiling method is very suitable to identify unknown species of algae from a large amount of samples in a limited time and can be applied broadly to routine seasonal or annual monitoring of algae. DNA from an Undaria pinnatifida sporophyte, however, was not successfully extracted by this direct boiling method, probably due to a high concentration of polysaccharides.</description><subject>Algae</subject><subject>algal species identification</subject><subject>Boiling</subject><subject>boiling method</subject><subject>Buffers</subject><subject>Centrifugation</subject><subject>Centrifuging</subject><subject>Deoxyribonucleic acid</subject><subject>Detergents</subject><subject>DNA</subject><subject>DNA isolation</subject><subject>Ethylenediaminetetraacetic acids</subject><subject>Genomics</subject><subject>Nucleotide sequence</subject><subject>PCR</subject><subject>Polymerase chain reaction</subject><subject>Polysaccharides</subject><subject>Saccharides</subject><subject>Seaweeds</subject><subject>Species</subject><subject>Sporophytes</subject><issn>0022-3646</issn><issn>1529-8817</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2021</creationdate><recordtype>article</recordtype><recordid>eNp1kL9uFDEQhy0EIkdCkReILFGl2MTjP7tOGe4uAZSQiAAS1cpnjxOfdtcb757gOgoegGfkSXDuEjqmmeab7zf6EbIP7AjyHC_79REIqNQzMgHFTwqtoXpOJoxxXohSljvk1TAsGWNVqeAl2RFCCyk1m5BfX00TnBlD7Gj0dBYS2pG-jaEJ3S29xPEuOupjojeh7RukpnN07n2wAbuRnmMX22Dp7OMpnf8Yk7Eb0QN0Pf305-fvhRnQ0UtjUzTNrWnoTY_5dKAzHDG1odsk75EX3jQDvn7cu-TL2fzz9F1xcXX-fnp6UVihhCqAWSk5l7IE552unEaEqirRe0TDnQCtldLSGqbBApcIXAtvFpmWUlqxS95svX2K9yscxnoZV6nLkTVX6qSUAiRk6nBL5aeHIaGv-xRak9Y1sPqh7zr3XW_6zuzBo3G1aNH9I58KzsDxFvgeGlz_31R_uP62Vf4FGcWLIg</recordid><startdate>202108</startdate><enddate>202108</enddate><creator>Shin, Sook Kyung</creator><creator>Lee, Yeonhui</creator><creator>Kwon, Hayoung</creator><creator>Rhee, Jae‐Sung</creator><creator>Kim, Jang Kyun</creator><creator>Lane, C.</creator><general>Wiley Subscription Services, Inc</general><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7TN</scope><scope>F1W</scope><scope>H95</scope><scope>L.G</scope><scope>M7N</scope><orcidid>https://orcid.org/0000-0001-7008-6768</orcidid></search><sort><creationdate>202108</creationdate><title>Validation of Direct Boiling Method for Simple and Efficient Genomic DNA Extraction and PCR‐based Macroalgal Species Determination</title><author>Shin, Sook Kyung ; Lee, Yeonhui ; Kwon, Hayoung ; Rhee, Jae‐Sung ; Kim, Jang Kyun ; Lane, C.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c3535-10c44224461dfd87d8ee1776effeea2d31885584ca081c124e1283fabdfd444c3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>Algae</topic><topic>algal species identification</topic><topic>Boiling</topic><topic>boiling method</topic><topic>Buffers</topic><topic>Centrifugation</topic><topic>Centrifuging</topic><topic>Deoxyribonucleic acid</topic><topic>Detergents</topic><topic>DNA</topic><topic>DNA isolation</topic><topic>Ethylenediaminetetraacetic acids</topic><topic>Genomics</topic><topic>Nucleotide sequence</topic><topic>PCR</topic><topic>Polymerase chain reaction</topic><topic>Polysaccharides</topic><topic>Saccharides</topic><topic>Seaweeds</topic><topic>Species</topic><topic>Sporophytes</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Shin, Sook Kyung</creatorcontrib><creatorcontrib>Lee, Yeonhui</creatorcontrib><creatorcontrib>Kwon, Hayoung</creatorcontrib><creatorcontrib>Rhee, Jae‐Sung</creatorcontrib><creatorcontrib>Kim, Jang Kyun</creatorcontrib><creatorcontrib>Lane, C.</creatorcontrib><collection>PubMed</collection><collection>CrossRef</collection><collection>Oceanic Abstracts</collection><collection>ASFA: Aquatic Sciences and Fisheries Abstracts</collection><collection>Aquatic Science & Fisheries Abstracts (ASFA) 1: Biological Sciences & Living Resources</collection><collection>Aquatic Science & Fisheries Abstracts (ASFA) Professional</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><jtitle>Journal of phycology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Shin, Sook Kyung</au><au>Lee, Yeonhui</au><au>Kwon, Hayoung</au><au>Rhee, Jae‐Sung</au><au>Kim, Jang Kyun</au><au>Lane, C.</au><au>Lane, C.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Validation of Direct Boiling Method for Simple and Efficient Genomic DNA Extraction and PCR‐based Macroalgal Species Determination</atitle><jtitle>Journal of phycology</jtitle><addtitle>J Phycol</addtitle><date>2021-08</date><risdate>2021</risdate><volume>57</volume><issue>4</issue><spage>1368</spage><epage>1372</epage><pages>1368-1372</pages><issn>0022-3646</issn><eissn>1529-8817</eissn><abstract>A rapid, simple, and cost‐effective total DNA extraction method referred to as a direct boiling method for PCR‐based algal species determination was validated using representative species of green, brown, and red algae. Each sample was briefly minced in two buffers, Tris‐EDTA (TE) or PCR buffer, and transferred to a heat block for boiling at 98°C for 5 min. No detergent was used in this experiment. The entire DNA isolation procedure was completed within 10 min. After brief centrifugation, the supernatant was directly used as a template for PCR. As a result, all genomic DNA markers were successfully amplified and sequenced from each algal taxon. Regardless of DNA quality, the direct boiling method is very suitable to identify unknown species of algae from a large amount of samples in a limited time and can be applied broadly to routine seasonal or annual monitoring of algae. DNA from an Undaria pinnatifida sporophyte, however, was not successfully extracted by this direct boiling method, probably due to a high concentration of polysaccharides.</abstract><cop>United States</cop><pub>Wiley Subscription Services, Inc</pub><pmid>33834480</pmid><doi>10.1111/jpy.13175</doi><tpages>0</tpages><orcidid>https://orcid.org/0000-0001-7008-6768</orcidid></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 0022-3646 |
| ispartof | Journal of phycology, 2021-08, Vol.57 (4), p.1368-1372 |
| issn | 0022-3646 1529-8817 |
| language | eng |
| recordid | cdi_proquest_journals_2559643141 |
| source | Wiley Online Library Journals Frontfile Complete |
| subjects | Algae algal species identification Boiling boiling method Buffers Centrifugation Centrifuging Deoxyribonucleic acid Detergents DNA DNA isolation Ethylenediaminetetraacetic acids Genomics Nucleotide sequence PCR Polymerase chain reaction Polysaccharides Saccharides Seaweeds Species Sporophytes |
| title | Validation of Direct Boiling Method for Simple and Efficient Genomic DNA Extraction and PCR‐based Macroalgal Species Determination |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-18T13%3A53%3A06IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_cross&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Validation%20of%20Direct%20Boiling%20Method%20for%20Simple%20and%20Efficient%20Genomic%20DNA%20Extraction%20and%20PCR%E2%80%90based%20Macroalgal%20Species%20Determination&rft.jtitle=Journal%20of%20phycology&rft.au=Shin,%20Sook%20Kyung&rft.date=2021-08&rft.volume=57&rft.issue=4&rft.spage=1368&rft.epage=1372&rft.pages=1368-1372&rft.issn=0022-3646&rft.eissn=1529-8817&rft_id=info:doi/10.1111/jpy.13175&rft_dat=%3Cproquest_cross%3E2559643141%3C/proquest_cross%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=2559643141&rft_id=info:pmid/33834480&rfr_iscdi=true |