Comparison of orthologous and paralogous DNA flanking the wheat high molecular weight glutenin genes: sequence conservation and divergence, transposon distribution, and matrix-attachment regions
Extended flanking DNA sequences were characterized for five members of the wheat high molecular weight (HMW) glutenin gene family to understand more of the structure, control, and evolution of these genes. Analysis revealed more sequence conservation among orthologous regions than between paralogous...
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| Veröffentlicht in: | Genome 2002-04, Vol.45 (2), p.367-380 |
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| creator | Anderson, O.D Larka, L Christoffers, M.J McCue, K.F Gustafson, J.P |
| description | Extended flanking DNA sequences were characterized for five members of the wheat high molecular weight (HMW) glutenin gene family to understand more of the structure, control, and evolution of these genes. Analysis revealed more sequence conservation among orthologous regions than between paralogous regions, with differences mainly owing to transposition events involving putative retrotransposons and several miniature inverted transposable elements (MITEs). Both gyspy-like long terminal repeat (LTR) and non-LTR retrotransposon sequences are represented in the flanking DNAs. One of the MITEs is a novel class, but another MITE is related to the maize Stowaway family and is widely represented in Triticeae express sequence tags (ESTs). Flanking DNA of the longest sequence, a 20 425-bp fragment including and surrounding the HMW-glutenin Bx7 gene, showed additional cereal gene-like sequences both immediately 5' and 3' to the HMW-glutenin coding region. The transcriptional activities of sequences related to these flanking putative genes and the retrotransposon-related regions were indicated by matches to wheat and other Triticeae ESTs. Predictive analysis of matrix-attachment regions (MARs) of the HMW glutenin and several alpha-, gamma-, and omega-gliadin flanking DNAs indicate potential MARs immediately flanking each of the genes. Matrix binding activity in the predicted regions was confirmed for two of the HMW-glutenin genes. |
| doi_str_mv | 10.1139/g01-137 |
| format | Article |
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Analysis revealed more sequence conservation among orthologous regions than between paralogous regions, with differences mainly owing to transposition events involving putative retrotransposons and several miniature inverted transposable elements (MITEs). Both gyspy-like long terminal repeat (LTR) and non-LTR retrotransposon sequences are represented in the flanking DNAs. One of the MITEs is a novel class, but another MITE is related to the maize Stowaway family and is widely represented in Triticeae express sequence tags (ESTs). Flanking DNA of the longest sequence, a 20 425-bp fragment including and surrounding the HMW-glutenin Bx7 gene, showed additional cereal gene-like sequences both immediately 5' and 3' to the HMW-glutenin coding region. The transcriptional activities of sequences related to these flanking putative genes and the retrotransposon-related regions were indicated by matches to wheat and other Triticeae ESTs. Predictive analysis of matrix-attachment regions (MARs) of the HMW glutenin and several alpha-, gamma-, and omega-gliadin flanking DNAs indicate potential MARs immediately flanking each of the genes. Matrix binding activity in the predicted regions was confirmed for two of the HMW-glutenin genes.</description><identifier>ISSN: 0831-2796</identifier><identifier>EISSN: 1480-3321</identifier><identifier>DOI: 10.1139/g01-137</identifier><identifier>PMID: 11962634</identifier><language>eng</language><publisher>Ottawa, Canada: NRC Research Press</publisher><subject>3' Flanking Region - genetics ; 5' Flanking Region - genetics ; Base Sequence ; Cereals ; chemical structure ; Cloning, Molecular ; Conserved Sequence ; Databases, Genetic ; DNA ; DNA Transposable Elements - genetics ; DNA, Plant - genetics ; Evolution ; Evolution, Molecular ; Evolutionary genetics ; Expressed Sequence Tags ; genes ; Genes, Plant ; genetic variation ; glutenin ; glutenins ; Glutens - analogs & derivatives ; Glutens - chemistry ; Glutens - genetics ; Long terminal repeat ; Molecular Sequence Data ; Molecular Weight ; Nuclear Matrix - metabolism ; Nucleotide sequence ; Retrotransposons ; Sequence Analysis, DNA ; Terminal Repeat Sequences ; Transcription ; transcription (genetics) ; Transcription, Genetic ; Transposition ; transposon Gypsy ; Transposons ; Triticeae ; Triticum ; Triticum - genetics ; Triticum aestivum ; Zea mays</subject><ispartof>Genome, 2002-04, Vol.45 (2), p.367-380</ispartof><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c430t-3463a0297befe19042312ba8cc53e6e510c42a45574de3febc29eaa8b3bc0ff53</citedby><cites>FETCH-LOGICAL-c430t-3463a0297befe19042312ba8cc53e6e510c42a45574de3febc29eaa8b3bc0ff53</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://cdnsciencepub.com/doi/pdf/10.1139/g01-137$$EPDF$$P50$$Gnrcresearch$$H</linktopdf><linktohtml>$$Uhttps://cdnsciencepub.com/doi/full/10.1139/g01-137$$EHTML$$P50$$Gnrcresearch$$H</linktohtml><link.rule.ids>314,780,784,2932,27924,27925,64428,65234</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/11962634$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Anderson, O.D</creatorcontrib><creatorcontrib>Larka, L</creatorcontrib><creatorcontrib>Christoffers, M.J</creatorcontrib><creatorcontrib>McCue, K.F</creatorcontrib><creatorcontrib>Gustafson, J.P</creatorcontrib><title>Comparison of orthologous and paralogous DNA flanking the wheat high molecular weight glutenin genes: sequence conservation and divergence, transposon distribution, and matrix-attachment regions</title><title>Genome</title><addtitle>Génome</addtitle><description>Extended flanking DNA sequences were characterized for five members of the wheat high molecular weight (HMW) glutenin gene family to understand more of the structure, control, and evolution of these genes. Analysis revealed more sequence conservation among orthologous regions than between paralogous regions, with differences mainly owing to transposition events involving putative retrotransposons and several miniature inverted transposable elements (MITEs). Both gyspy-like long terminal repeat (LTR) and non-LTR retrotransposon sequences are represented in the flanking DNAs. One of the MITEs is a novel class, but another MITE is related to the maize Stowaway family and is widely represented in Triticeae express sequence tags (ESTs). Flanking DNA of the longest sequence, a 20 425-bp fragment including and surrounding the HMW-glutenin Bx7 gene, showed additional cereal gene-like sequences both immediately 5' and 3' to the HMW-glutenin coding region. The transcriptional activities of sequences related to these flanking putative genes and the retrotransposon-related regions were indicated by matches to wheat and other Triticeae ESTs. Predictive analysis of matrix-attachment regions (MARs) of the HMW glutenin and several alpha-, gamma-, and omega-gliadin flanking DNAs indicate potential MARs immediately flanking each of the genes. Matrix binding activity in the predicted regions was confirmed for two of the HMW-glutenin genes.</description><subject>3' Flanking Region - genetics</subject><subject>5' Flanking Region - genetics</subject><subject>Base Sequence</subject><subject>Cereals</subject><subject>chemical structure</subject><subject>Cloning, Molecular</subject><subject>Conserved Sequence</subject><subject>Databases, Genetic</subject><subject>DNA</subject><subject>DNA Transposable Elements - genetics</subject><subject>DNA, Plant - genetics</subject><subject>Evolution</subject><subject>Evolution, Molecular</subject><subject>Evolutionary genetics</subject><subject>Expressed Sequence Tags</subject><subject>genes</subject><subject>Genes, Plant</subject><subject>genetic variation</subject><subject>glutenin</subject><subject>glutenins</subject><subject>Glutens - analogs & derivatives</subject><subject>Glutens - chemistry</subject><subject>Glutens - genetics</subject><subject>Long terminal repeat</subject><subject>Molecular Sequence Data</subject><subject>Molecular Weight</subject><subject>Nuclear Matrix - metabolism</subject><subject>Nucleotide sequence</subject><subject>Retrotransposons</subject><subject>Sequence Analysis, DNA</subject><subject>Terminal Repeat Sequences</subject><subject>Transcription</subject><subject>transcription (genetics)</subject><subject>Transcription, Genetic</subject><subject>Transposition</subject><subject>transposon Gypsy</subject><subject>Transposons</subject><subject>Triticeae</subject><subject>Triticum</subject><subject>Triticum - genetics</subject><subject>Triticum aestivum</subject><subject>Zea mays</subject><issn>0831-2796</issn><issn>1480-3321</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2002</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkstu1TAQhiMEooeCeAPwqkhVA3acm9lVh3KRKlhA19HEGSeGxE5tp4XX48lwOJG6oqys8f9prn-SPGf0NWNcvOkpSxmvHiQ7ltc05TxjD5MdrTlLs0qUR8kT779TyigX7HFyxJgos5Lnu-T33k4zOO2tIVYR68JgR9vbxRMwHYkSbOG7z-dEjWB-aNOTMCC5HRACGXQ_kMmOKJcRHLnFGAfSj0tAow3p0aB_SzxeL2gkEmmNR3cDQceCa4VO36DrV-2MBAfGz3btpdM-ON0uK3f2F5wgfvxMIQSQw4QmEId9VP3T5JGC0eOz7T1Ort5ffNt_TC-_fPi0P79MZc5pSHlecqCZqFpUyATNM86yFmopC44lFozKPIO8KKq8Q66wlZlAgLrlraRKFfw4eXXIOzsbp_GhmbSXOMadYFxQU3NR1qISdSRP7iUrVlJRxmP8D2Q1p7FTeldbOuu9Q9XMTk_gfjWMNqsDmuiAJjogki-2lEs7YXfHbSePwOkBME469AhODvdkO_k3vEHN3KkIvjyACmwDfTRUc_U1o4zHjWd1Ljj_Ayfw1XE</recordid><startdate>20020401</startdate><enddate>20020401</enddate><creator>Anderson, O.D</creator><creator>Larka, L</creator><creator>Christoffers, M.J</creator><creator>McCue, K.F</creator><creator>Gustafson, J.P</creator><general>NRC Research Press</general><scope>FBQ</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>8FD</scope><scope>FR3</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><scope>7TM</scope></search><sort><creationdate>20020401</creationdate><title>Comparison of orthologous and paralogous DNA flanking the wheat high molecular weight glutenin genes: sequence conservation and divergence, transposon distribution, and matrix-attachment regions</title><author>Anderson, O.D ; Larka, L ; Christoffers, M.J ; McCue, K.F ; Gustafson, J.P</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c430t-3463a0297befe19042312ba8cc53e6e510c42a45574de3febc29eaa8b3bc0ff53</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2002</creationdate><topic>3' Flanking Region - genetics</topic><topic>5' Flanking Region - genetics</topic><topic>Base Sequence</topic><topic>Cereals</topic><topic>chemical structure</topic><topic>Cloning, Molecular</topic><topic>Conserved Sequence</topic><topic>Databases, Genetic</topic><topic>DNA</topic><topic>DNA Transposable Elements - genetics</topic><topic>DNA, Plant - genetics</topic><topic>Evolution</topic><topic>Evolution, Molecular</topic><topic>Evolutionary genetics</topic><topic>Expressed Sequence Tags</topic><topic>genes</topic><topic>Genes, Plant</topic><topic>genetic variation</topic><topic>glutenin</topic><topic>glutenins</topic><topic>Glutens - analogs & derivatives</topic><topic>Glutens - chemistry</topic><topic>Glutens - genetics</topic><topic>Long terminal repeat</topic><topic>Molecular Sequence Data</topic><topic>Molecular Weight</topic><topic>Nuclear Matrix - metabolism</topic><topic>Nucleotide sequence</topic><topic>Retrotransposons</topic><topic>Sequence Analysis, DNA</topic><topic>Terminal Repeat Sequences</topic><topic>Transcription</topic><topic>transcription (genetics)</topic><topic>Transcription, Genetic</topic><topic>Transposition</topic><topic>transposon Gypsy</topic><topic>Transposons</topic><topic>Triticeae</topic><topic>Triticum</topic><topic>Triticum - genetics</topic><topic>Triticum aestivum</topic><topic>Zea mays</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Anderson, O.D</creatorcontrib><creatorcontrib>Larka, L</creatorcontrib><creatorcontrib>Christoffers, M.J</creatorcontrib><creatorcontrib>McCue, K.F</creatorcontrib><creatorcontrib>Gustafson, J.P</creatorcontrib><collection>AGRIS</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>Nucleic Acids Abstracts</collection><jtitle>Genome</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Anderson, O.D</au><au>Larka, L</au><au>Christoffers, M.J</au><au>McCue, K.F</au><au>Gustafson, J.P</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Comparison of orthologous and paralogous DNA flanking the wheat high molecular weight glutenin genes: sequence conservation and divergence, transposon distribution, and matrix-attachment regions</atitle><jtitle>Genome</jtitle><addtitle>Génome</addtitle><date>2002-04-01</date><risdate>2002</risdate><volume>45</volume><issue>2</issue><spage>367</spage><epage>380</epage><pages>367-380</pages><issn>0831-2796</issn><eissn>1480-3321</eissn><abstract>Extended flanking DNA sequences were characterized for five members of the wheat high molecular weight (HMW) glutenin gene family to understand more of the structure, control, and evolution of these genes. Analysis revealed more sequence conservation among orthologous regions than between paralogous regions, with differences mainly owing to transposition events involving putative retrotransposons and several miniature inverted transposable elements (MITEs). Both gyspy-like long terminal repeat (LTR) and non-LTR retrotransposon sequences are represented in the flanking DNAs. One of the MITEs is a novel class, but another MITE is related to the maize Stowaway family and is widely represented in Triticeae express sequence tags (ESTs). Flanking DNA of the longest sequence, a 20 425-bp fragment including and surrounding the HMW-glutenin Bx7 gene, showed additional cereal gene-like sequences both immediately 5' and 3' to the HMW-glutenin coding region. The transcriptional activities of sequences related to these flanking putative genes and the retrotransposon-related regions were indicated by matches to wheat and other Triticeae ESTs. Predictive analysis of matrix-attachment regions (MARs) of the HMW glutenin and several alpha-, gamma-, and omega-gliadin flanking DNAs indicate potential MARs immediately flanking each of the genes. Matrix binding activity in the predicted regions was confirmed for two of the HMW-glutenin genes.</abstract><cop>Ottawa, Canada</cop><pub>NRC Research Press</pub><pmid>11962634</pmid><doi>10.1139/g01-137</doi><tpages>14</tpages></addata></record> |
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| language | eng |
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| source | NRC Research Press; MEDLINE |
| subjects | 3' Flanking Region - genetics 5' Flanking Region - genetics Base Sequence Cereals chemical structure Cloning, Molecular Conserved Sequence Databases, Genetic DNA DNA Transposable Elements - genetics DNA, Plant - genetics Evolution Evolution, Molecular Evolutionary genetics Expressed Sequence Tags genes Genes, Plant genetic variation glutenin glutenins Glutens - analogs & derivatives Glutens - chemistry Glutens - genetics Long terminal repeat Molecular Sequence Data Molecular Weight Nuclear Matrix - metabolism Nucleotide sequence Retrotransposons Sequence Analysis, DNA Terminal Repeat Sequences Transcription transcription (genetics) Transcription, Genetic Transposition transposon Gypsy Transposons Triticeae Triticum Triticum - genetics Triticum aestivum Zea mays |
| title | Comparison of orthologous and paralogous DNA flanking the wheat high molecular weight glutenin genes: sequence conservation and divergence, transposon distribution, and matrix-attachment regions |
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