Establishment of a Lotus japonicus gene tagging population using the exon‐targeting endogenous retrotransposon LORE1
Summary We established a gene tagging population of the model legume Lotus japonicus using an endogenous long terminal repeat (LTR) retrotransposon Lotus Retrotransposon 1 (LORE1). The population was composed of 2450 plant lines, from which a total of 4532 flanking sequence tags of LORE1 were recove...
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| Veröffentlicht in: | The Plant journal : for cell and molecular biology 2012-02, Vol.69 (4), p.720-730 |
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| container_title | The Plant journal : for cell and molecular biology |
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| creator | Fukai, Eigo Soyano, Takashi Umehara, Yosuke Nakayama, Shinobu Hirakawa, Hideki Tabata, Satoshi Sato, Shusei Hayashi, Makoto |
| description | Summary
We established a gene tagging population of the model legume Lotus japonicus using an endogenous long terminal repeat (LTR) retrotransposon Lotus Retrotransposon 1 (LORE1). The population was composed of 2450 plant lines, from which a total of 4532 flanking sequence tags of LORE1 were recovered by pyrosequencing. The two‐dimensional arrangement of the plant population, together with the use of multiple identifier sequences in the primers used to amplify the flanking regions, made it possible to trace insertions back to the original plant lines. The large‐scale detection of new LORE1 insertion sites revealed a preference for genic regions, especially in exons of protein‐coding genes, which is an interesting feature to consider in the interaction between host genomes and chromoviruses, to which LORE1 belongs, a class of retrotransposon widely distributed among plants. Forward screening of the symbiotic mutants from the population succeeded to identify five symbiotic mutants of known genes. These data suggest that LORE1 is robust as a genetic tool. |
| doi_str_mv | 10.1111/j.1365-313X.2011.04826.x |
| format | Article |
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We established a gene tagging population of the model legume Lotus japonicus using an endogenous long terminal repeat (LTR) retrotransposon Lotus Retrotransposon 1 (LORE1). The population was composed of 2450 plant lines, from which a total of 4532 flanking sequence tags of LORE1 were recovered by pyrosequencing. The two‐dimensional arrangement of the plant population, together with the use of multiple identifier sequences in the primers used to amplify the flanking regions, made it possible to trace insertions back to the original plant lines. The large‐scale detection of new LORE1 insertion sites revealed a preference for genic regions, especially in exons of protein‐coding genes, which is an interesting feature to consider in the interaction between host genomes and chromoviruses, to which LORE1 belongs, a class of retrotransposon widely distributed among plants. Forward screening of the symbiotic mutants from the population succeeded to identify five symbiotic mutants of known genes. These data suggest that LORE1 is robust as a genetic tool.</description><identifier>ISSN: 0960-7412</identifier><identifier>EISSN: 1365-313X</identifier><identifier>DOI: 10.1111/j.1365-313X.2011.04826.x</identifier><identifier>PMID: 22014259</identifier><language>eng</language><publisher>Oxford, UK: Blackwell Publishing Ltd</publisher><subject>Biological and medical sciences ; Data processing ; DNA Primers - genetics ; Exons ; Exons - genetics ; Fundamental and applied biological sciences. Psychology ; Gene expression ; gene tagging ; Gene Targeting ; Genic rearrangement. Recombination. Transposable element ; Genomes ; Host plants ; Insertion ; Legumes ; Long terminal repeat ; Loteae - genetics ; Lotus ; Lotus japonicus ; Lotus Retrotransposons 1 ; Molecular and cellular biology ; Molecular genetics ; Mutagenesis, Insertional - methods ; Mutation ; Parasitism and symbiosis ; Plant biology ; Plant physiology and development ; Plant populations ; Population genetics ; Primers ; Proteins ; pyrosequencing ; Retroelements - genetics ; retrotransposon ; Retrotransposons ; Sequence Analysis, DNA ; Symbiosis ; Terminal Repeat Sequences - genetics</subject><ispartof>The Plant journal : for cell and molecular biology, 2012-02, Vol.69 (4), p.720-730</ispartof><rights>2011 The Authors. The Plant Journal © 2011 Blackwell Publishing Ltd</rights><rights>2015 INIST-CNRS</rights><rights>2011 The Authors. The Plant Journal © 2011 Blackwell Publishing Ltd.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c5746-9100319feb7162c2ce73a8b786692c2dac0d08a5f5910ade9eca3b548691d7cd3</citedby><cites>FETCH-LOGICAL-c5746-9100319feb7162c2ce73a8b786692c2dac0d08a5f5910ade9eca3b548691d7cd3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1111%2Fj.1365-313X.2011.04826.x$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1111%2Fj.1365-313X.2011.04826.x$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>314,776,780,1411,1427,27903,27904,45553,45554,46387,46811</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=25502176$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/22014259$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Fukai, Eigo</creatorcontrib><creatorcontrib>Soyano, Takashi</creatorcontrib><creatorcontrib>Umehara, Yosuke</creatorcontrib><creatorcontrib>Nakayama, Shinobu</creatorcontrib><creatorcontrib>Hirakawa, Hideki</creatorcontrib><creatorcontrib>Tabata, Satoshi</creatorcontrib><creatorcontrib>Sato, Shusei</creatorcontrib><creatorcontrib>Hayashi, Makoto</creatorcontrib><title>Establishment of a Lotus japonicus gene tagging population using the exon‐targeting endogenous retrotransposon LORE1</title><title>The Plant journal : for cell and molecular biology</title><addtitle>Plant J</addtitle><description>Summary
We established a gene tagging population of the model legume Lotus japonicus using an endogenous long terminal repeat (LTR) retrotransposon Lotus Retrotransposon 1 (LORE1). The population was composed of 2450 plant lines, from which a total of 4532 flanking sequence tags of LORE1 were recovered by pyrosequencing. The two‐dimensional arrangement of the plant population, together with the use of multiple identifier sequences in the primers used to amplify the flanking regions, made it possible to trace insertions back to the original plant lines. The large‐scale detection of new LORE1 insertion sites revealed a preference for genic regions, especially in exons of protein‐coding genes, which is an interesting feature to consider in the interaction between host genomes and chromoviruses, to which LORE1 belongs, a class of retrotransposon widely distributed among plants. Forward screening of the symbiotic mutants from the population succeeded to identify five symbiotic mutants of known genes. These data suggest that LORE1 is robust as a genetic tool.</description><subject>Biological and medical sciences</subject><subject>Data processing</subject><subject>DNA Primers - genetics</subject><subject>Exons</subject><subject>Exons - genetics</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Gene expression</subject><subject>gene tagging</subject><subject>Gene Targeting</subject><subject>Genic rearrangement. Recombination. Transposable element</subject><subject>Genomes</subject><subject>Host plants</subject><subject>Insertion</subject><subject>Legumes</subject><subject>Long terminal repeat</subject><subject>Loteae - genetics</subject><subject>Lotus</subject><subject>Lotus japonicus</subject><subject>Lotus Retrotransposons 1</subject><subject>Molecular and cellular biology</subject><subject>Molecular genetics</subject><subject>Mutagenesis, Insertional - methods</subject><subject>Mutation</subject><subject>Parasitism and symbiosis</subject><subject>Plant biology</subject><subject>Plant physiology and development</subject><subject>Plant populations</subject><subject>Population genetics</subject><subject>Primers</subject><subject>Proteins</subject><subject>pyrosequencing</subject><subject>Retroelements - genetics</subject><subject>retrotransposon</subject><subject>Retrotransposons</subject><subject>Sequence Analysis, DNA</subject><subject>Symbiosis</subject><subject>Terminal Repeat Sequences - genetics</subject><issn>0960-7412</issn><issn>1365-313X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2012</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqNkc1u1DAUhS0EotPCK6AICdFNgn8SO16wqKrhTyMVoSKxsxzHSTPK2MF2YLrjEXhGnoQbZigSC4Q3vr7-ztG1D0IZwQWB9WJbEMarnBH2qaCYkAKXNeXF_h5a3V3cRyssOc5FSegJOo1xizERjJcP0QkFUUkruUJf1jHpZhzizc66lPku09nGpzlmWz15NxioeutslnTfD67PJj_No06Dd9kcl0a6sZnde_fj2_ekQ2_T0rSu9SDzoA42BZ-CdnHyEVSbqw9r8gg96PQY7ePjfoY-vlpfX77JN1ev315ebHJTiZLnkmDMiOxsIwinhhormK4bUXMu4dhqg1tc66qrgNStldZo1lRlzSVphWnZGXp-8J2C_zzbmNRuiMaOo3YWhlOSYsalJBTI83-SBNMaE8mEBPTpX-jWz8HBOxY_AmZCAFQfIBN8jMF2agrDTodbcFJLiGqrlqzUkpVaZOpXiGoP0idH_7nZ2fZO-Ds1AJ4dAR2NHjv4XDPEP1xVYUoEB-7lgfs6jPb2vwdQ1-_fLRX7CU4DufQ</recordid><startdate>201202</startdate><enddate>201202</enddate><creator>Fukai, Eigo</creator><creator>Soyano, Takashi</creator><creator>Umehara, Yosuke</creator><creator>Nakayama, Shinobu</creator><creator>Hirakawa, Hideki</creator><creator>Tabata, Satoshi</creator><creator>Sato, Shusei</creator><creator>Hayashi, Makoto</creator><general>Blackwell Publishing Ltd</general><general>Blackwell</general><scope>IQODW</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QO</scope><scope>7QP</scope><scope>7QR</scope><scope>7TM</scope><scope>8FD</scope><scope>FR3</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope></search><sort><creationdate>201202</creationdate><title>Establishment of a Lotus japonicus gene tagging population using the exon‐targeting endogenous retrotransposon LORE1</title><author>Fukai, Eigo ; Soyano, Takashi ; Umehara, Yosuke ; Nakayama, Shinobu ; Hirakawa, Hideki ; Tabata, Satoshi ; Sato, Shusei ; Hayashi, Makoto</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c5746-9100319feb7162c2ce73a8b786692c2dac0d08a5f5910ade9eca3b548691d7cd3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2012</creationdate><topic>Biological and medical sciences</topic><topic>Data processing</topic><topic>DNA Primers - genetics</topic><topic>Exons</topic><topic>Exons - genetics</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Gene expression</topic><topic>gene tagging</topic><topic>Gene Targeting</topic><topic>Genic rearrangement. Recombination. Transposable element</topic><topic>Genomes</topic><topic>Host plants</topic><topic>Insertion</topic><topic>Legumes</topic><topic>Long terminal repeat</topic><topic>Loteae - genetics</topic><topic>Lotus</topic><topic>Lotus japonicus</topic><topic>Lotus Retrotransposons 1</topic><topic>Molecular and cellular biology</topic><topic>Molecular genetics</topic><topic>Mutagenesis, Insertional - methods</topic><topic>Mutation</topic><topic>Parasitism and symbiosis</topic><topic>Plant biology</topic><topic>Plant physiology and development</topic><topic>Plant populations</topic><topic>Population genetics</topic><topic>Primers</topic><topic>Proteins</topic><topic>pyrosequencing</topic><topic>Retroelements - genetics</topic><topic>retrotransposon</topic><topic>Retrotransposons</topic><topic>Sequence Analysis, DNA</topic><topic>Symbiosis</topic><topic>Terminal Repeat Sequences - genetics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Fukai, Eigo</creatorcontrib><creatorcontrib>Soyano, Takashi</creatorcontrib><creatorcontrib>Umehara, Yosuke</creatorcontrib><creatorcontrib>Nakayama, Shinobu</creatorcontrib><creatorcontrib>Hirakawa, Hideki</creatorcontrib><creatorcontrib>Tabata, Satoshi</creatorcontrib><creatorcontrib>Sato, Shusei</creatorcontrib><creatorcontrib>Hayashi, Makoto</creatorcontrib><collection>Pascal-Francis</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Biotechnology Research Abstracts</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Chemoreception Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>The Plant journal : for cell and molecular biology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Fukai, Eigo</au><au>Soyano, Takashi</au><au>Umehara, Yosuke</au><au>Nakayama, Shinobu</au><au>Hirakawa, Hideki</au><au>Tabata, Satoshi</au><au>Sato, Shusei</au><au>Hayashi, Makoto</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Establishment of a Lotus japonicus gene tagging population using the exon‐targeting endogenous retrotransposon LORE1</atitle><jtitle>The Plant journal : for cell and molecular biology</jtitle><addtitle>Plant J</addtitle><date>2012-02</date><risdate>2012</risdate><volume>69</volume><issue>4</issue><spage>720</spage><epage>730</epage><pages>720-730</pages><issn>0960-7412</issn><eissn>1365-313X</eissn><abstract>Summary
We established a gene tagging population of the model legume Lotus japonicus using an endogenous long terminal repeat (LTR) retrotransposon Lotus Retrotransposon 1 (LORE1). The population was composed of 2450 plant lines, from which a total of 4532 flanking sequence tags of LORE1 were recovered by pyrosequencing. The two‐dimensional arrangement of the plant population, together with the use of multiple identifier sequences in the primers used to amplify the flanking regions, made it possible to trace insertions back to the original plant lines. The large‐scale detection of new LORE1 insertion sites revealed a preference for genic regions, especially in exons of protein‐coding genes, which is an interesting feature to consider in the interaction between host genomes and chromoviruses, to which LORE1 belongs, a class of retrotransposon widely distributed among plants. Forward screening of the symbiotic mutants from the population succeeded to identify five symbiotic mutants of known genes. These data suggest that LORE1 is robust as a genetic tool.</abstract><cop>Oxford, UK</cop><pub>Blackwell Publishing Ltd</pub><pmid>22014259</pmid><doi>10.1111/j.1365-313X.2011.04826.x</doi><tpages>11</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Biological and medical sciences Data processing DNA Primers - genetics Exons Exons - genetics Fundamental and applied biological sciences. Psychology Gene expression gene tagging Gene Targeting Genic rearrangement. Recombination. Transposable element Genomes Host plants Insertion Legumes Long terminal repeat Loteae - genetics Lotus Lotus japonicus Lotus Retrotransposons 1 Molecular and cellular biology Molecular genetics Mutagenesis, Insertional - methods Mutation Parasitism and symbiosis Plant biology Plant physiology and development Plant populations Population genetics Primers Proteins pyrosequencing Retroelements - genetics retrotransposon Retrotransposons Sequence Analysis, DNA Symbiosis Terminal Repeat Sequences - genetics |
| title | Establishment of a Lotus japonicus gene tagging population using the exon‐targeting endogenous retrotransposon LORE1 |
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