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Are “universal” DNA primers really universal?
“Universal” DNA primers LCO 1490 and HCO 2198 were originally designed from three coding and six anticoding strands by comparing highly conserved regions of mitochondrial cytochrome c oxidase subunit I ( COI ) genes across 15 taxa. These primers have been successful in amplifying a 710-bp fragment o...
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| Published in: | Journal of applied genetics 2014-11, Vol.55 (4), p.485-496 |
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| container_title | Journal of applied genetics |
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| creator | Sharma, Pranay Kobayashi, Tsuyoshi |
| description | “Universal” DNA primers LCO 1490 and HCO 2198 were originally designed from three coding and six anticoding strands by comparing highly conserved regions of mitochondrial cytochrome c oxidase subunit I (
COI
) genes across 15 taxa. These primers have been successful in amplifying a 710-bp fragment of highly conserved regions of the
COI
gene for more than 80 invertebrate species from 11 phyla. In the present study, 130,843 variations were reviewed in the primer region of mitochondrial molecular markers by comparing 725
COI
sequences from the kingdom Animalia. It was found that, for 177 invertebrate species, the forward primer (LCO 1490) showed only four conserved regions, compared to 12 in the original study. For ascidians, fungi and vertebrates, it showed approximately 50 % conserved regions, dropping to one conserved region for echinoderms. However, the reverse primer (HCO 2198) was highly conserved across 725
COI
primer sequences. A similar pattern was observed in amino acid distributions. There was a significant difference in the means of base pair differences from the level of family, genus and species for LCO 1490 [analysis of variance (ANOVA),
F
6,188
= 8.193,
P
|
| doi_str_mv | 10.1007/s13353-014-0218-9 |
| format | article |
| fullrecord | <record><control><sourceid>gale_proqu</sourceid><recordid>TN_cdi_proquest_miscellaneous_1635042672</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><galeid>A710733286</galeid><sourcerecordid>A710733286</sourcerecordid><originalsourceid>FETCH-LOGICAL-c514t-4716a6e52f92c2baaaef74c60d4022526287fdf9099fd737935eec0d62dd84253</originalsourceid><addsrcrecordid>eNp9kMtKAzEUQIMoWKsf4G7AjZvU5CaTx0pKfULRja5DnEnKlOlMTTqCu36I_ly_xAwjgiByF4Gbc-7iIHRKyYQSIi8iZSxnmFCOCVCF9R4aAdUEM6XYPhpRYBxTrdghOopxSQhTXMII0Wlw2W770TXVmwvR1rvtZ3b1MM3WoVqlRRacrev37Of_8hgdeFtHd_L9jtHzzfXT7A7PH2_vZ9M5LnLKN5hLKqxwOXgNBbxYa52XvBCk5AQgBwFK-tJrorUvJZOa5c4VpBRQlopDzsbofLi7Du1r5-LGrKpYuLq2jWu7aKhgOeEgJCT0bEAXtnamany7CbbocTOVlEjGQIlETf6g0pRuVRVt43yV9r8EOghFaGMMzps-ig3vhhLTVzdDdZOqm7660cmBwYmJbRYumGXbhSaF-kf6AtDcg1A</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>1635042672</pqid></control><display><type>article</type><title>Are “universal” DNA primers really universal?</title><source>Springer Nature</source><creator>Sharma, Pranay ; Kobayashi, Tsuyoshi</creator><creatorcontrib>Sharma, Pranay ; Kobayashi, Tsuyoshi</creatorcontrib><description>“Universal” DNA primers LCO 1490 and HCO 2198 were originally designed from three coding and six anticoding strands by comparing highly conserved regions of mitochondrial cytochrome c oxidase subunit I (
COI
) genes across 15 taxa. These primers have been successful in amplifying a 710-bp fragment of highly conserved regions of the
COI
gene for more than 80 invertebrate species from 11 phyla. In the present study, 130,843 variations were reviewed in the primer region of mitochondrial molecular markers by comparing 725
COI
sequences from the kingdom Animalia. It was found that, for 177 invertebrate species, the forward primer (LCO 1490) showed only four conserved regions, compared to 12 in the original study. For ascidians, fungi and vertebrates, it showed approximately 50 % conserved regions, dropping to one conserved region for echinoderms. However, the reverse primer (HCO 2198) was highly conserved across 725
COI
primer sequences. A similar pattern was observed in amino acid distributions. There was a significant difference in the means of base pair differences from the level of family, genus and species for LCO 1490 [analysis of variance (ANOVA),
F
6,188
= 8.193,
P
< 0.001] and at the level of genus and species for HCO 2198 (ANOVA,
F
6,77
= 2.538,
P
< 0.027). We conclude that, at different taxonomic levels, it is possible to design forward primers from reference sequences belonging to the level of order (maximum 5 bp differences), family (maximum 6 bp differences) or genus (maximum 1 bp difference). Reverse primers can be designed from the level of family (maximum 5 bp differences) or genus (maximum 2 bp differences).</description><identifier>ISSN: 1234-1983</identifier><identifier>EISSN: 2190-3883</identifier><identifier>DOI: 10.1007/s13353-014-0218-9</identifier><language>eng</language><publisher>Berlin/Heidelberg: Springer Berlin Heidelberg</publisher><subject>Analysis ; Animal Genetics and Genomics ; Animal Genetics • Original Paper ; Animalia ; Biomedical and Life Sciences ; Cytochrome oxidase ; DNA ; Human Genetics ; Life Sciences ; Marine ; Microbial Genetics and Genomics ; Plant Genetics and Genomics</subject><ispartof>Journal of applied genetics, 2014-11, Vol.55 (4), p.485-496</ispartof><rights>Institute of Plant Genetics, Polish Academy of Sciences, Poznan 2014</rights><rights>COPYRIGHT 2014 Springer</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c514t-4716a6e52f92c2baaaef74c60d4022526287fdf9099fd737935eec0d62dd84253</citedby><cites>FETCH-LOGICAL-c514t-4716a6e52f92c2baaaef74c60d4022526287fdf9099fd737935eec0d62dd84253</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,780,784,27923,27924</link.rule.ids></links><search><creatorcontrib>Sharma, Pranay</creatorcontrib><creatorcontrib>Kobayashi, Tsuyoshi</creatorcontrib><title>Are “universal” DNA primers really universal?</title><title>Journal of applied genetics</title><addtitle>J Appl Genetics</addtitle><description>“Universal” DNA primers LCO 1490 and HCO 2198 were originally designed from three coding and six anticoding strands by comparing highly conserved regions of mitochondrial cytochrome c oxidase subunit I (
COI
) genes across 15 taxa. These primers have been successful in amplifying a 710-bp fragment of highly conserved regions of the
COI
gene for more than 80 invertebrate species from 11 phyla. In the present study, 130,843 variations were reviewed in the primer region of mitochondrial molecular markers by comparing 725
COI
sequences from the kingdom Animalia. It was found that, for 177 invertebrate species, the forward primer (LCO 1490) showed only four conserved regions, compared to 12 in the original study. For ascidians, fungi and vertebrates, it showed approximately 50 % conserved regions, dropping to one conserved region for echinoderms. However, the reverse primer (HCO 2198) was highly conserved across 725
COI
primer sequences. A similar pattern was observed in amino acid distributions. There was a significant difference in the means of base pair differences from the level of family, genus and species for LCO 1490 [analysis of variance (ANOVA),
F
6,188
= 8.193,
P
< 0.001] and at the level of genus and species for HCO 2198 (ANOVA,
F
6,77
= 2.538,
P
< 0.027). We conclude that, at different taxonomic levels, it is possible to design forward primers from reference sequences belonging to the level of order (maximum 5 bp differences), family (maximum 6 bp differences) or genus (maximum 1 bp difference). Reverse primers can be designed from the level of family (maximum 5 bp differences) or genus (maximum 2 bp differences).</description><subject>Analysis</subject><subject>Animal Genetics and Genomics</subject><subject>Animal Genetics • Original Paper</subject><subject>Animalia</subject><subject>Biomedical and Life Sciences</subject><subject>Cytochrome oxidase</subject><subject>DNA</subject><subject>Human Genetics</subject><subject>Life Sciences</subject><subject>Marine</subject><subject>Microbial Genetics and Genomics</subject><subject>Plant Genetics and Genomics</subject><issn>1234-1983</issn><issn>2190-3883</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2014</creationdate><recordtype>article</recordtype><recordid>eNp9kMtKAzEUQIMoWKsf4G7AjZvU5CaTx0pKfULRja5DnEnKlOlMTTqCu36I_ly_xAwjgiByF4Gbc-7iIHRKyYQSIi8iZSxnmFCOCVCF9R4aAdUEM6XYPhpRYBxTrdghOopxSQhTXMII0Wlw2W770TXVmwvR1rvtZ3b1MM3WoVqlRRacrev37Of_8hgdeFtHd_L9jtHzzfXT7A7PH2_vZ9M5LnLKN5hLKqxwOXgNBbxYa52XvBCk5AQgBwFK-tJrorUvJZOa5c4VpBRQlopDzsbofLi7Du1r5-LGrKpYuLq2jWu7aKhgOeEgJCT0bEAXtnamany7CbbocTOVlEjGQIlETf6g0pRuVRVt43yV9r8EOghFaGMMzps-ig3vhhLTVzdDdZOqm7660cmBwYmJbRYumGXbhSaF-kf6AtDcg1A</recordid><startdate>20141101</startdate><enddate>20141101</enddate><creator>Sharma, Pranay</creator><creator>Kobayashi, Tsuyoshi</creator><general>Springer Berlin Heidelberg</general><general>Springer</general><scope>AAYXX</scope><scope>CITATION</scope><scope>7TM</scope><scope>7TN</scope><scope>8FD</scope><scope>F1W</scope><scope>FR3</scope><scope>H95</scope><scope>L.G</scope><scope>P64</scope><scope>RC3</scope></search><sort><creationdate>20141101</creationdate><title>Are “universal” DNA primers really universal?</title><author>Sharma, Pranay ; Kobayashi, Tsuyoshi</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c514t-4716a6e52f92c2baaaef74c60d4022526287fdf9099fd737935eec0d62dd84253</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2014</creationdate><topic>Analysis</topic><topic>Animal Genetics and Genomics</topic><topic>Animal Genetics • Original Paper</topic><topic>Animalia</topic><topic>Biomedical and Life Sciences</topic><topic>Cytochrome oxidase</topic><topic>DNA</topic><topic>Human Genetics</topic><topic>Life Sciences</topic><topic>Marine</topic><topic>Microbial Genetics and Genomics</topic><topic>Plant Genetics and Genomics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Sharma, Pranay</creatorcontrib><creatorcontrib>Kobayashi, Tsuyoshi</creatorcontrib><collection>CrossRef</collection><collection>Nucleic Acids Abstracts</collection><collection>Oceanic Abstracts</collection><collection>Technology Research Database</collection><collection>ASFA: Aquatic Sciences and Fisheries Abstracts</collection><collection>Engineering Research Database</collection><collection>Aquatic Science & Fisheries Abstracts (ASFA) 1: Biological Sciences & Living Resources</collection><collection>Aquatic Science & Fisheries Abstracts (ASFA) Professional</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><jtitle>Journal of applied genetics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Sharma, Pranay</au><au>Kobayashi, Tsuyoshi</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Are “universal” DNA primers really universal?</atitle><jtitle>Journal of applied genetics</jtitle><stitle>J Appl Genetics</stitle><date>2014-11-01</date><risdate>2014</risdate><volume>55</volume><issue>4</issue><spage>485</spage><epage>496</epage><pages>485-496</pages><issn>1234-1983</issn><eissn>2190-3883</eissn><abstract>“Universal” DNA primers LCO 1490 and HCO 2198 were originally designed from three coding and six anticoding strands by comparing highly conserved regions of mitochondrial cytochrome c oxidase subunit I (
COI
) genes across 15 taxa. These primers have been successful in amplifying a 710-bp fragment of highly conserved regions of the
COI
gene for more than 80 invertebrate species from 11 phyla. In the present study, 130,843 variations were reviewed in the primer region of mitochondrial molecular markers by comparing 725
COI
sequences from the kingdom Animalia. It was found that, for 177 invertebrate species, the forward primer (LCO 1490) showed only four conserved regions, compared to 12 in the original study. For ascidians, fungi and vertebrates, it showed approximately 50 % conserved regions, dropping to one conserved region for echinoderms. However, the reverse primer (HCO 2198) was highly conserved across 725
COI
primer sequences. A similar pattern was observed in amino acid distributions. There was a significant difference in the means of base pair differences from the level of family, genus and species for LCO 1490 [analysis of variance (ANOVA),
F
6,188
= 8.193,
P
< 0.001] and at the level of genus and species for HCO 2198 (ANOVA,
F
6,77
= 2.538,
P
< 0.027). We conclude that, at different taxonomic levels, it is possible to design forward primers from reference sequences belonging to the level of order (maximum 5 bp differences), family (maximum 6 bp differences) or genus (maximum 1 bp difference). Reverse primers can be designed from the level of family (maximum 5 bp differences) or genus (maximum 2 bp differences).</abstract><cop>Berlin/Heidelberg</cop><pub>Springer Berlin Heidelberg</pub><doi>10.1007/s13353-014-0218-9</doi><tpages>12</tpages></addata></record> |
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| source | Springer Nature |
| subjects | Analysis Animal Genetics and Genomics Animal Genetics • Original Paper Animalia Biomedical and Life Sciences Cytochrome oxidase DNA Human Genetics Life Sciences Marine Microbial Genetics and Genomics Plant Genetics and Genomics |
| title | Are “universal” DNA primers really universal? |
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