LTR-retrotransposons and inter-retrotransposon amplified polymorphism (IRAP) analysis in Lilium species
LTR-retrotransposons are ubiquitous and highly abundant in plant genomes. Moreover, LTR-retrotransposons can often cause genome obesity in plants. Although Lilium species have been known carrying large genomes among flowering plants, reports on the LTR-retrotransposons in Lilium species are rather l...
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| Veröffentlicht in: | Genetica 2015-06, Vol.143 (3), p.343-352 |
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| creator | Lee, Sung-Il Kim, Jong-Hwa Park, Kyong-Cheul Kim, Nam-Soo |
| description | LTR-retrotransposons are ubiquitous and highly abundant in plant genomes. Moreover, LTR-retrotransposons can often cause genome obesity in plants. Although
Lilium
species have been known carrying large genomes among flowering plants, reports on the LTR-retrotransposons in
Lilium
species are rather limited. We isolated a novel
Ty3/gypsy
-like retrotransposon,
LIRE
-
del
, and two
Ty1/copia
-like retrotransposons, a
LIRE
-
del
and an unclassified, from a fosmid clone of
Lilium longiflorum
. Decayed internal ORF sequences indicated that they were non-autonomous elements. IRAP protocol was developed based on the LTR sequences of the isolated LTR-retrotransposons. Fourteen primer combinations showed clear distinctive PCR amplification bands that were highly informative in the analysis of species relationship among
Lilium
species. The phylogenetic relationship based on the IRAP profile revealed some discordant with phylogenetic studies based on the ITS sequences of 45S ribosomal gene and
matK
gene variations in a few species. Thus, the phylogenetic relationship among
Lilium
species may need to be re-evaluated with other tools such as cross compatibility and selectively neutral genetic markers. |
| doi_str_mv | 10.1007/s10709-015-9833-6 |
| format | Article |
| fullrecord | <record><control><sourceid>proquest_cross</sourceid><recordid>TN_cdi_proquest_miscellaneous_1701478359</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>3674083601</sourcerecordid><originalsourceid>FETCH-LOGICAL-c541t-f132f0fed465c1fa4f4de7fce12d799c14f5b2fc461e78fa118127a9a785e3c53</originalsourceid><addsrcrecordid>eNqFkcFq3DAQhkVpaDZJHyCXYuglOTjV2JZHOoYlSQMLLSE5C0WWEgXbcjX2Yd8-WjYtJVB6kmC-_xejj7FT4BfAOX4j4MhVyUGUStZ12X5gKxCYL1LgR7biHNqyRY6H7IjohXOusFWf2GElUGINasWeNvd3ZXJzinMyI02R4kiFGbsijLNL70eFGaY--OC6Yor9dohpeg40FGe3d5c_z3PO9FsKlMPFJvRhGQqanA2OTtiBNz25z2_nMXu4vrpffy83P25u15eb0ooG5tJDXXnuXde0woI3jW86h946qDpUykLjxWPlbdOCQ-kNgIQKjTIohautqI_Z2b53SvHX4mjWQyDr-t6MLi6kATk0KGuh_o-2kgNi_uiMfn2HvsQl5WV3FMoGK8mrTMGesikSJef1lMJg0lYD1zthei9MZ2F6J0y3OfPlrXl5HFz3J_HbUAaqPUB5ND659NfT_2x9BWvBoWg</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>1678472802</pqid></control><display><type>article</type><title>LTR-retrotransposons and inter-retrotransposon amplified polymorphism (IRAP) analysis in Lilium species</title><source>MEDLINE</source><source>Springer Nature - Complete Springer Journals</source><creator>Lee, Sung-Il ; Kim, Jong-Hwa ; Park, Kyong-Cheul ; Kim, Nam-Soo</creator><creatorcontrib>Lee, Sung-Il ; Kim, Jong-Hwa ; Park, Kyong-Cheul ; Kim, Nam-Soo</creatorcontrib><description>LTR-retrotransposons are ubiquitous and highly abundant in plant genomes. Moreover, LTR-retrotransposons can often cause genome obesity in plants. Although
Lilium
species have been known carrying large genomes among flowering plants, reports on the LTR-retrotransposons in
Lilium
species are rather limited. We isolated a novel
Ty3/gypsy
-like retrotransposon,
LIRE
-
del
, and two
Ty1/copia
-like retrotransposons, a
LIRE
-
del
and an unclassified, from a fosmid clone of
Lilium longiflorum
. Decayed internal ORF sequences indicated that they were non-autonomous elements. IRAP protocol was developed based on the LTR sequences of the isolated LTR-retrotransposons. Fourteen primer combinations showed clear distinctive PCR amplification bands that were highly informative in the analysis of species relationship among
Lilium
species. The phylogenetic relationship based on the IRAP profile revealed some discordant with phylogenetic studies based on the ITS sequences of 45S ribosomal gene and
matK
gene variations in a few species. Thus, the phylogenetic relationship among
Lilium
species may need to be re-evaluated with other tools such as cross compatibility and selectively neutral genetic markers.</description><identifier>ISSN: 0016-6707</identifier><identifier>EISSN: 1573-6857</identifier><identifier>DOI: 10.1007/s10709-015-9833-6</identifier><identifier>PMID: 25787319</identifier><language>eng</language><publisher>Cham: Springer International Publishing</publisher><subject>Animal Genetics and Genomics ; Biomedical and Life Sciences ; DNA, Plant - genetics ; Evolutionary Biology ; Flowering plants ; Genetic Markers ; Genome, Plant ; Human Genetics ; Life Sciences ; Lilium ; Lilium - genetics ; Lilium longiflorum ; Microbial Genetics and Genomics ; Phylogeny ; Plant Genetics and Genomics ; Polymorphism, Genetic ; Retroelements ; Sequence Analysis, DNA ; Terminal Repeat Sequences</subject><ispartof>Genetica, 2015-06, Vol.143 (3), p.343-352</ispartof><rights>Springer International Publishing Switzerland 2015</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c541t-f132f0fed465c1fa4f4de7fce12d799c14f5b2fc461e78fa118127a9a785e3c53</citedby><cites>FETCH-LOGICAL-c541t-f132f0fed465c1fa4f4de7fce12d799c14f5b2fc461e78fa118127a9a785e3c53</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/s10709-015-9833-6$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s10709-015-9833-6$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,778,782,27907,27908,41471,42540,51302</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/25787319$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Lee, Sung-Il</creatorcontrib><creatorcontrib>Kim, Jong-Hwa</creatorcontrib><creatorcontrib>Park, Kyong-Cheul</creatorcontrib><creatorcontrib>Kim, Nam-Soo</creatorcontrib><title>LTR-retrotransposons and inter-retrotransposon amplified polymorphism (IRAP) analysis in Lilium species</title><title>Genetica</title><addtitle>Genetica</addtitle><addtitle>Genetica</addtitle><description>LTR-retrotransposons are ubiquitous and highly abundant in plant genomes. Moreover, LTR-retrotransposons can often cause genome obesity in plants. Although
Lilium
species have been known carrying large genomes among flowering plants, reports on the LTR-retrotransposons in
Lilium
species are rather limited. We isolated a novel
Ty3/gypsy
-like retrotransposon,
LIRE
-
del
, and two
Ty1/copia
-like retrotransposons, a
LIRE
-
del
and an unclassified, from a fosmid clone of
Lilium longiflorum
. Decayed internal ORF sequences indicated that they were non-autonomous elements. IRAP protocol was developed based on the LTR sequences of the isolated LTR-retrotransposons. Fourteen primer combinations showed clear distinctive PCR amplification bands that were highly informative in the analysis of species relationship among
Lilium
species. The phylogenetic relationship based on the IRAP profile revealed some discordant with phylogenetic studies based on the ITS sequences of 45S ribosomal gene and
matK
gene variations in a few species. Thus, the phylogenetic relationship among
Lilium
species may need to be re-evaluated with other tools such as cross compatibility and selectively neutral genetic markers.</description><subject>Animal Genetics and Genomics</subject><subject>Biomedical and Life Sciences</subject><subject>DNA, Plant - genetics</subject><subject>Evolutionary Biology</subject><subject>Flowering plants</subject><subject>Genetic Markers</subject><subject>Genome, Plant</subject><subject>Human Genetics</subject><subject>Life Sciences</subject><subject>Lilium</subject><subject>Lilium - genetics</subject><subject>Lilium longiflorum</subject><subject>Microbial Genetics and Genomics</subject><subject>Phylogeny</subject><subject>Plant Genetics and Genomics</subject><subject>Polymorphism, Genetic</subject><subject>Retroelements</subject><subject>Sequence Analysis, DNA</subject><subject>Terminal Repeat Sequences</subject><issn>0016-6707</issn><issn>1573-6857</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2015</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNqFkcFq3DAQhkVpaDZJHyCXYuglOTjV2JZHOoYlSQMLLSE5C0WWEgXbcjX2Yd8-WjYtJVB6kmC-_xejj7FT4BfAOX4j4MhVyUGUStZ12X5gKxCYL1LgR7biHNqyRY6H7IjohXOusFWf2GElUGINasWeNvd3ZXJzinMyI02R4kiFGbsijLNL70eFGaY--OC6Yor9dohpeg40FGe3d5c_z3PO9FsKlMPFJvRhGQqanA2OTtiBNz25z2_nMXu4vrpffy83P25u15eb0ooG5tJDXXnuXde0woI3jW86h946qDpUykLjxWPlbdOCQ-kNgIQKjTIohautqI_Z2b53SvHX4mjWQyDr-t6MLi6kATk0KGuh_o-2kgNi_uiMfn2HvsQl5WV3FMoGK8mrTMGesikSJef1lMJg0lYD1zthei9MZ2F6J0y3OfPlrXl5HFz3J_HbUAaqPUB5ND659NfT_2x9BWvBoWg</recordid><startdate>20150601</startdate><enddate>20150601</enddate><creator>Lee, Sung-Il</creator><creator>Kim, Jong-Hwa</creator><creator>Park, Kyong-Cheul</creator><creator>Kim, Nam-Soo</creator><general>Springer International Publishing</general><general>Springer Nature B.V</general><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>3V.</scope><scope>7QL</scope><scope>7SN</scope><scope>7SS</scope><scope>7T7</scope><scope>7TK</scope><scope>7U9</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>8AO</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>P64</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>RC3</scope><scope>7X8</scope></search><sort><creationdate>20150601</creationdate><title>LTR-retrotransposons and inter-retrotransposon amplified polymorphism (IRAP) analysis in Lilium species</title><author>Lee, Sung-Il ; Kim, Jong-Hwa ; Park, Kyong-Cheul ; Kim, Nam-Soo</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c541t-f132f0fed465c1fa4f4de7fce12d799c14f5b2fc461e78fa118127a9a785e3c53</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2015</creationdate><topic>Animal Genetics and Genomics</topic><topic>Biomedical and Life Sciences</topic><topic>DNA, Plant - genetics</topic><topic>Evolutionary Biology</topic><topic>Flowering plants</topic><topic>Genetic Markers</topic><topic>Genome, Plant</topic><topic>Human Genetics</topic><topic>Life Sciences</topic><topic>Lilium</topic><topic>Lilium - genetics</topic><topic>Lilium longiflorum</topic><topic>Microbial Genetics and Genomics</topic><topic>Phylogeny</topic><topic>Plant Genetics and Genomics</topic><topic>Polymorphism, Genetic</topic><topic>Retroelements</topic><topic>Sequence Analysis, DNA</topic><topic>Terminal Repeat Sequences</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Lee, Sung-Il</creatorcontrib><creatorcontrib>Kim, Jong-Hwa</creatorcontrib><creatorcontrib>Park, Kyong-Cheul</creatorcontrib><creatorcontrib>Kim, Nam-Soo</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Ecology Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Neurosciences Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection (ProQuest)</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Genetica</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Lee, Sung-Il</au><au>Kim, Jong-Hwa</au><au>Park, Kyong-Cheul</au><au>Kim, Nam-Soo</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>LTR-retrotransposons and inter-retrotransposon amplified polymorphism (IRAP) analysis in Lilium species</atitle><jtitle>Genetica</jtitle><stitle>Genetica</stitle><addtitle>Genetica</addtitle><date>2015-06-01</date><risdate>2015</risdate><volume>143</volume><issue>3</issue><spage>343</spage><epage>352</epage><pages>343-352</pages><issn>0016-6707</issn><eissn>1573-6857</eissn><abstract>LTR-retrotransposons are ubiquitous and highly abundant in plant genomes. Moreover, LTR-retrotransposons can often cause genome obesity in plants. Although
Lilium
species have been known carrying large genomes among flowering plants, reports on the LTR-retrotransposons in
Lilium
species are rather limited. We isolated a novel
Ty3/gypsy
-like retrotransposon,
LIRE
-
del
, and two
Ty1/copia
-like retrotransposons, a
LIRE
-
del
and an unclassified, from a fosmid clone of
Lilium longiflorum
. Decayed internal ORF sequences indicated that they were non-autonomous elements. IRAP protocol was developed based on the LTR sequences of the isolated LTR-retrotransposons. Fourteen primer combinations showed clear distinctive PCR amplification bands that were highly informative in the analysis of species relationship among
Lilium
species. The phylogenetic relationship based on the IRAP profile revealed some discordant with phylogenetic studies based on the ITS sequences of 45S ribosomal gene and
matK
gene variations in a few species. Thus, the phylogenetic relationship among
Lilium
species may need to be re-evaluated with other tools such as cross compatibility and selectively neutral genetic markers.</abstract><cop>Cham</cop><pub>Springer International Publishing</pub><pmid>25787319</pmid><doi>10.1007/s10709-015-9833-6</doi><tpages>10</tpages></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 0016-6707 |
| ispartof | Genetica, 2015-06, Vol.143 (3), p.343-352 |
| issn | 0016-6707 1573-6857 |
| language | eng |
| recordid | cdi_proquest_miscellaneous_1701478359 |
| source | MEDLINE; Springer Nature - Complete Springer Journals |
| subjects | Animal Genetics and Genomics Biomedical and Life Sciences DNA, Plant - genetics Evolutionary Biology Flowering plants Genetic Markers Genome, Plant Human Genetics Life Sciences Lilium Lilium - genetics Lilium longiflorum Microbial Genetics and Genomics Phylogeny Plant Genetics and Genomics Polymorphism, Genetic Retroelements Sequence Analysis, DNA Terminal Repeat Sequences |
| title | LTR-retrotransposons and inter-retrotransposon amplified polymorphism (IRAP) analysis in Lilium species |
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