Investigation of rice (Oryza sativa L.) retrotransposons in different taxa
Retrotransposons are the subclass of transposable elements and they can increase their copy numbers in the genome through their copy-paste transposition mechanism. Throughout evolutionary process, their transposition events result in mutations. Thus, they cause the formation of new gene alleles and,...
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description | Retrotransposons are the subclass of transposable elements and they can increase their copy numbers in the genome through their copy-paste transposition mechanism. Throughout evolutionary process, their transposition events result in mutations. Thus, they cause the formation of new gene alleles and, in the long term, speciation. In contrast, their transposition events might have harmful effects. Therefore most of the organisms have been developing various mechanisms for silencing retrotransposons throughout evolutionary processes. By this way they protect their genome from harmful transposition events. In this study, we investigated transposition events of four
Oryza sativa
LTR-retrotransposons (
Hopi
,
Houba
,
Osr30
and
RIRE1
) in
Oryza sativa
L. (rice),
Brachypodium distachyon
(L.) P. Beauv.,
Hordeum vulgare
L., (barley) and
Triticum aestivum
L. (wheat) by PCR based IRAP marker technique. PCR resulted in different band profiles and polymorphism ratios between individuals of each species. In four species, only rice showed significant polymorphisms between individuals. This result indicates that all tested retrotransposons are still active and cause genomic polymorphism between individuals of rice while they were silenced with various mechanisms in other species. Although these four plant species have a common ancestor, rice was distinguished from others more than 40 million years ago. This result might show that the mechanisms that repress the transposition events of retrotransposons were developed after this point. |
doi_str_mv | 10.1007/s10722-020-00919-2 |
format | Article |
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Oryza sativa
LTR-retrotransposons (
Hopi
,
Houba
,
Osr30
and
RIRE1
) in
Oryza sativa
L. (rice),
Brachypodium distachyon
(L.) P. Beauv.,
Hordeum vulgare
L., (barley) and
Triticum aestivum
L. (wheat) by PCR based IRAP marker technique. PCR resulted in different band profiles and polymorphism ratios between individuals of each species. In four species, only rice showed significant polymorphisms between individuals. This result indicates that all tested retrotransposons are still active and cause genomic polymorphism between individuals of rice while they were silenced with various mechanisms in other species. Although these four plant species have a common ancestor, rice was distinguished from others more than 40 million years ago. This result might show that the mechanisms that repress the transposition events of retrotransposons were developed after this point.</description><identifier>ISSN: 0925-9864</identifier><identifier>EISSN: 1573-5109</identifier><identifier>DOI: 10.1007/s10722-020-00919-2</identifier><language>eng</language><publisher>Dordrecht: Springer Netherlands</publisher><subject>Agriculture ; Biomedical and Life Sciences ; Brachypodium distachyon ; Genomes ; Hordeum vulgare ; Life Sciences ; Mutation ; Oryza sativa ; Plant Genetics and Genomics ; Plant Physiology ; Plant Sciences ; Plant species ; Plant Systematics/Taxonomy/Biogeography ; Polymorphism ; Research Article ; Retrotransposition ; Rice ; Speciation ; Species ; Transposition ; Triticum aestivum ; Wheat</subject><ispartof>Genetic resources and crop evolution, 2020-08, Vol.67 (6), p.1473-1479</ispartof><rights>Springer Nature B.V. 2020</rights><rights>Springer Nature B.V. 2020.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c2342-c36aba5e7d9c9e1c7f046ee3259e1f16d201c800e12b458f41dc38a3cdab79a33</citedby><cites>FETCH-LOGICAL-c2342-c36aba5e7d9c9e1c7f046ee3259e1f16d201c800e12b458f41dc38a3cdab79a33</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s10722-020-00919-2$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s10722-020-00919-2$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,780,784,27924,27925,41488,42557,51319</link.rule.ids></links><search><creatorcontrib>Tufan, Ayse Feyza</creatorcontrib><creatorcontrib>Ibisoglu, Merve Seda</creatorcontrib><creatorcontrib>Yilmaz, Sibel</creatorcontrib><creatorcontrib>Gozukirmizi, Nermin</creatorcontrib><title>Investigation of rice (Oryza sativa L.) retrotransposons in different taxa</title><title>Genetic resources and crop evolution</title><addtitle>Genet Resour Crop Evol</addtitle><description>Retrotransposons are the subclass of transposable elements and they can increase their copy numbers in the genome through their copy-paste transposition mechanism. Throughout evolutionary process, their transposition events result in mutations. Thus, they cause the formation of new gene alleles and, in the long term, speciation. In contrast, their transposition events might have harmful effects. Therefore most of the organisms have been developing various mechanisms for silencing retrotransposons throughout evolutionary processes. By this way they protect their genome from harmful transposition events. In this study, we investigated transposition events of four
Oryza sativa
LTR-retrotransposons (
Hopi
,
Houba
,
Osr30
and
RIRE1
) in
Oryza sativa
L. (rice),
Brachypodium distachyon
(L.) P. Beauv.,
Hordeum vulgare
L., (barley) and
Triticum aestivum
L. (wheat) by PCR based IRAP marker technique. PCR resulted in different band profiles and polymorphism ratios between individuals of each species. In four species, only rice showed significant polymorphisms between individuals. This result indicates that all tested retrotransposons are still active and cause genomic polymorphism between individuals of rice while they were silenced with various mechanisms in other species. Although these four plant species have a common ancestor, rice was distinguished from others more than 40 million years ago. This result might show that the mechanisms that repress the transposition events of retrotransposons were developed after this point.</description><subject>Agriculture</subject><subject>Biomedical and Life Sciences</subject><subject>Brachypodium distachyon</subject><subject>Genomes</subject><subject>Hordeum vulgare</subject><subject>Life Sciences</subject><subject>Mutation</subject><subject>Oryza sativa</subject><subject>Plant Genetics and Genomics</subject><subject>Plant Physiology</subject><subject>Plant Sciences</subject><subject>Plant species</subject><subject>Plant Systematics/Taxonomy/Biogeography</subject><subject>Polymorphism</subject><subject>Research Article</subject><subject>Retrotransposition</subject><subject>Rice</subject><subject>Speciation</subject><subject>Species</subject><subject>Transposition</subject><subject>Triticum aestivum</subject><subject>Wheat</subject><issn>0925-9864</issn><issn>1573-5109</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2020</creationdate><recordtype>article</recordtype><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNp9kMFKAzEQhoMoWKsv4CngRQ-pk2Q32RylWK0UetFzSLNJ2aJJTbbF-vRGV_DmaZjh-2eGD6FLChMKIG8zBckYAQYEQFFF2BEa0VpyUlNQx2gEitVENaI6RWc5b6BQUjQj9DQPe5f7bm36LgYcPU6ddfh6mQ6fBucy3Ru8mNzg5PoU-2RC3sYcQ8ZdwG3nvUsu9Lg3H-YcnXjzmt3Fbx2jl9n98_SRLJYP8-ndgljGK0YsF2ZlaidbZZWjVnqohHOc1aXzVLQMqG0AHGWrqm58RVvLG8Nta1ZSGc7H6GrYu03xfVee15u4S6Gc1KyiQjJBhSgUGyibYs7Jeb1N3ZtJB01BfzvTgzNdnOkfZ5qVEB9CucBh7dLf6n9SX-AobrE</recordid><startdate>20200801</startdate><enddate>20200801</enddate><creator>Tufan, Ayse Feyza</creator><creator>Ibisoglu, Merve Seda</creator><creator>Yilmaz, Sibel</creator><creator>Gozukirmizi, Nermin</creator><general>Springer Netherlands</general><general>Springer Nature B.V</general><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7X2</scope><scope>8FE</scope><scope>8FH</scope><scope>8FK</scope><scope>AFKRA</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>LK8</scope><scope>M0K</scope><scope>M7P</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope></search><sort><creationdate>20200801</creationdate><title>Investigation of rice (Oryza sativa L.) retrotransposons in different taxa</title><author>Tufan, Ayse Feyza ; Ibisoglu, Merve Seda ; Yilmaz, Sibel ; Gozukirmizi, Nermin</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c2342-c36aba5e7d9c9e1c7f046ee3259e1f16d201c800e12b458f41dc38a3cdab79a33</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2020</creationdate><topic>Agriculture</topic><topic>Biomedical and Life Sciences</topic><topic>Brachypodium distachyon</topic><topic>Genomes</topic><topic>Hordeum vulgare</topic><topic>Life Sciences</topic><topic>Mutation</topic><topic>Oryza sativa</topic><topic>Plant Genetics and Genomics</topic><topic>Plant Physiology</topic><topic>Plant Sciences</topic><topic>Plant species</topic><topic>Plant Systematics/Taxonomy/Biogeography</topic><topic>Polymorphism</topic><topic>Research Article</topic><topic>Retrotransposition</topic><topic>Rice</topic><topic>Speciation</topic><topic>Species</topic><topic>Transposition</topic><topic>Triticum aestivum</topic><topic>Wheat</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Tufan, Ayse Feyza</creatorcontrib><creatorcontrib>Ibisoglu, Merve Seda</creatorcontrib><creatorcontrib>Yilmaz, Sibel</creatorcontrib><creatorcontrib>Gozukirmizi, Nermin</creatorcontrib><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Agricultural Science Collection</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central UK/Ireland</collection><collection>Agricultural & Environmental Science Collection</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Biological Science Collection</collection><collection>Agricultural Science Database</collection><collection>Biological Science Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><jtitle>Genetic resources and crop evolution</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Tufan, Ayse Feyza</au><au>Ibisoglu, Merve Seda</au><au>Yilmaz, Sibel</au><au>Gozukirmizi, Nermin</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Investigation of rice (Oryza sativa L.) retrotransposons in different taxa</atitle><jtitle>Genetic resources and crop evolution</jtitle><stitle>Genet Resour Crop Evol</stitle><date>2020-08-01</date><risdate>2020</risdate><volume>67</volume><issue>6</issue><spage>1473</spage><epage>1479</epage><pages>1473-1479</pages><issn>0925-9864</issn><eissn>1573-5109</eissn><abstract>Retrotransposons are the subclass of transposable elements and they can increase their copy numbers in the genome through their copy-paste transposition mechanism. Throughout evolutionary process, their transposition events result in mutations. Thus, they cause the formation of new gene alleles and, in the long term, speciation. In contrast, their transposition events might have harmful effects. Therefore most of the organisms have been developing various mechanisms for silencing retrotransposons throughout evolutionary processes. By this way they protect their genome from harmful transposition events. In this study, we investigated transposition events of four
Oryza sativa
LTR-retrotransposons (
Hopi
,
Houba
,
Osr30
and
RIRE1
) in
Oryza sativa
L. (rice),
Brachypodium distachyon
(L.) P. Beauv.,
Hordeum vulgare
L., (barley) and
Triticum aestivum
L. (wheat) by PCR based IRAP marker technique. PCR resulted in different band profiles and polymorphism ratios between individuals of each species. In four species, only rice showed significant polymorphisms between individuals. This result indicates that all tested retrotransposons are still active and cause genomic polymorphism between individuals of rice while they were silenced with various mechanisms in other species. Although these four plant species have a common ancestor, rice was distinguished from others more than 40 million years ago. This result might show that the mechanisms that repress the transposition events of retrotransposons were developed after this point.</abstract><cop>Dordrecht</cop><pub>Springer Netherlands</pub><doi>10.1007/s10722-020-00919-2</doi><tpages>7</tpages></addata></record> |
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subjects | Agriculture Biomedical and Life Sciences Brachypodium distachyon Genomes Hordeum vulgare Life Sciences Mutation Oryza sativa Plant Genetics and Genomics Plant Physiology Plant Sciences Plant species Plant Systematics/Taxonomy/Biogeography Polymorphism Research Article Retrotransposition Rice Speciation Species Transposition Triticum aestivum Wheat |
title | Investigation of rice (Oryza sativa L.) retrotransposons in different taxa |
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