{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,18]],"date-time":"2026-06-18T13:09:41Z","timestamp":1781788181245,"version":"3.54.5"},"reference-count":86,"publisher":"Wiley","issue":"4","license":[{"start":{"date-parts":[[2017,10,9]],"date-time":"2017-10-09T00:00:00Z","timestamp":1507507200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"funder":[{"DOI":"10.13039\/501100005908","name":"Bundesministerium f\u00fcr Ern\u00e4hrung und Landwirtschaft","doi-asserted-by":"publisher","award":["22031714"],"award-info":[{"award-number":["22031714"]}],"id":[{"id":"10.13039\/501100005908","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["The Plant Journal"],"published-print":{"date-parts":[[2017,11]]},"abstract":"<jats:title>Summary<\/jats:title><jats:p>Short interspersed nuclear elements (<jats:styled-content style=\"fixed-case\">SINE<\/jats:styled-content>s) are non\u2010autonomous transposable elements which are propagated by retrotransposition and constitute an inherent part of the genome of most eukaryotic species. Knowledge of heterogeneous and highly abundant <jats:styled-content style=\"fixed-case\">SINE<\/jats:styled-content>s is crucial for <jats:italic>de novo<\/jats:italic> (or improvement of) annotation of whole genome sequences. We scanned Poaceae genome sequences of six important cereals (<jats:italic>Oryza sativa<\/jats:italic>,<jats:italic> Triticum aestivum<\/jats:italic>,<jats:italic> Hordeum vulgare<\/jats:italic>,<jats:italic> Panicum virgatum<\/jats:italic>,<jats:italic> Sorghum bicolor<\/jats:italic>,<jats:italic> Zea mays<\/jats:italic>) and <jats:italic>Brachypodium distachyon<\/jats:italic> to examine the diversity and evolution of <jats:styled-content style=\"fixed-case\">SINE<\/jats:styled-content> populations. We comparatively analyzed the structural features, distribution, evolutionary relation and abundance of 32 <jats:styled-content style=\"fixed-case\">SINE<\/jats:styled-content> families and subfamilies within grasses, comprising 11\u00a0052 individual copies. The investigation of activity profiles within the Poaceae provides insights into their species\u2010specific diversification and amplification. We found that Poaceae <jats:styled-content style=\"fixed-case\">SINE<\/jats:styled-content>s (PoaS) fall into two length categories: simple <jats:styled-content style=\"fixed-case\">SINE<\/jats:styled-content>s of up to 180\u00a0bp and dimeric <jats:styled-content style=\"fixed-case\">SINE<\/jats:styled-content>s larger than 240\u00a0bp. Detailed analysis at the nucleotide level revealed that multimerization of related and unrelated <jats:styled-content style=\"fixed-case\">SINE<\/jats:styled-content> copies is an important evolutionary mechanism of <jats:styled-content style=\"fixed-case\">SINE<\/jats:styled-content> formation. We conclude that PoaS families diversify by massive reshuffling between <jats:styled-content style=\"fixed-case\">SINE<\/jats:styled-content> families, likely caused by insertion of truncated copies, and provide a model for this evolutionary scenario. Twenty\u2010eight of 32 PoaS families and subfamilies show significant conservation, in particular either in the 5\u2032 or 3\u2032 regions, across Poaceae species and share large sequence stretches with one or more other PoaS families.<\/jats:p>","DOI":"10.1111\/tpj.13676","type":"journal-article","created":{"date-parts":[[2017,8,31]],"date-time":"2017-08-31T11:43:53Z","timestamp":1504179833000},"page":"676-695","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["Evolutionary modes of emergence of short interspersed nuclear element (<scp>SINE<\/scp>) families in grasses"],"prefix":"10.1111","volume":"92","author":[{"given":"Anja","family":"K\u00f6gler","sequence":"first","affiliation":[{"name":"Institute of Botany Technische Universit\u00e4t Dresden Dresden 01069 Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas","family":"Schmidt","sequence":"additional","affiliation":[{"name":"Institute of Botany Technische Universit\u00e4t Dresden Dresden 01069 Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Torsten","family":"Wenke","sequence":"additional","affiliation":[{"name":"Institute of Botany Technische Universit\u00e4t Dresden Dresden 01069 Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2017,10,9]]},"reference":[{"key":"e_1_2_7_2_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1469-8137.2011.03972.x"},{"key":"e_1_2_7_3_1","doi-asserted-by":"publisher","DOI":"10.1038\/35048692"},{"key":"e_1_2_7_4_1","doi-asserted-by":"publisher","DOI":"10.1105\/tpc.114.135954"},{"key":"e_1_2_7_5_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1000732"},{"key":"e_1_2_7_6_1","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-arplant-050213-035811"},{"key":"e_1_2_7_7_1","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.2001.5369"},{"key":"e_1_2_7_8_1","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M310450200"},{"key":"e_1_2_7_9_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.tplants.2009.10.001"},{"key":"e_1_2_7_10_1","doi-asserted-by":"publisher","DOI":"10.1038\/ng0597-6"},{"key":"e_1_2_7_11_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature11650"},{"key":"e_1_2_7_12_1","doi-asserted-by":"publisher","DOI":"10.1006\/geno.2002.6843"},{"key":"e_1_2_7_13_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkg496"},{"key":"e_1_2_7_14_1","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msp076"},{"key":"e_1_2_7_15_1","doi-asserted-by":"publisher","DOI":"10.1007\/s11568-007-9002-9"},{"key":"e_1_2_7_16_1","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msi071"},{"key":"e_1_2_7_17_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.089789.108"},{"key":"e_1_2_7_18_1","doi-asserted-by":"publisher","DOI":"10.1038\/nrg2640"},{"key":"e_1_2_7_19_1","first-page":"43","volume-title":"The Impact of Short, Interspersed Elements (SINEs) on the Host Genome","author":"Deininger P.L.","year":"1995"},{"key":"e_1_2_7_20_1","doi-asserted-by":"publisher","DOI":"10.1016\/0168-9525(92)90262-3"},{"key":"e_1_2_7_21_1","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2011-12-12-236"},{"key":"e_1_2_7_22_1","doi-asserted-by":"publisher","DOI":"10.1080\/10635150601047843"},{"key":"e_1_2_7_23_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.132102"},{"key":"e_1_2_7_24_1","doi-asserted-by":"publisher","DOI":"10.1038\/ng1223"},{"key":"e_1_2_7_25_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature12817"},{"key":"e_1_2_7_26_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1574-6941.2006.00060.x"},{"key":"e_1_2_7_27_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btq461"},{"key":"e_1_2_7_28_1","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msw130"},{"key":"e_1_2_7_29_1","doi-asserted-by":"publisher","DOI":"10.1007\/s11103-006-0026-7"},{"key":"e_1_2_7_30_1","doi-asserted-by":"publisher","DOI":"10.1093\/oxfordjournals.molbev.a003721"},{"key":"e_1_2_7_31_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.gene.2011.01.020"},{"key":"e_1_2_7_32_1","doi-asserted-by":"publisher","DOI":"10.1038\/294626a0"},{"key":"e_1_2_7_33_1","doi-asserted-by":"publisher","DOI":"10.1046\/j.1469-8137.2002.00352.x"},{"key":"e_1_2_7_34_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature08939"},{"key":"e_1_2_7_35_1","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1242\/jcs.100.1.15","article-title":"The molecular cytogenetics of plants","volume":"100","author":"Heslop\u2010Harrison J.","year":"1991","journal-title":"J. Cell Sci."},{"key":"e_1_2_7_36_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature03895"},{"key":"e_1_2_7_37_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature22971"},{"key":"e_1_2_7_38_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkn772"},{"key":"e_1_2_7_39_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.94.5.1872"},{"key":"e_1_2_7_40_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0092-8674(02)01041-3"},{"key":"e_1_2_7_41_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0074-7696(05)47004-7"},{"key":"e_1_2_7_42_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.3910705"},{"key":"e_1_2_7_43_1","doi-asserted-by":"publisher","DOI":"10.1093\/oxfordjournals.molbev.a025836"},{"key":"e_1_2_7_44_1","doi-asserted-by":"publisher","DOI":"10.1093\/oxfordjournals.molbev.a003778"},{"key":"e_1_2_7_45_1","doi-asserted-by":"publisher","DOI":"10.1159\/000084976"},{"key":"e_1_2_7_46_1","doi-asserted-by":"publisher","DOI":"10.1038\/nrg3374"},{"key":"e_1_2_7_47_1","doi-asserted-by":"publisher","DOI":"10.1016\/0092-8674(93)90078-5"},{"key":"e_1_2_7_48_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ygeno.2013.08.005"},{"key":"e_1_2_7_49_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature22043"},{"key":"e_1_2_7_50_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature11543"},{"key":"e_1_2_7_51_1","doi-asserted-by":"publisher","DOI":"10.1038\/35052098"},{"key":"e_1_2_7_52_1","doi-asserted-by":"publisher","DOI":"10.1093\/oxfordjournals.molbev.a004020"},{"key":"e_1_2_7_53_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.5255506"},{"key":"e_1_2_7_54_1","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msh225"},{"key":"e_1_2_7_55_1","doi-asserted-by":"publisher","DOI":"10.1007\/PL00000058"},{"key":"e_1_2_7_56_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0378-1119(97)00409-5"},{"key":"e_1_2_7_57_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.205701"},{"key":"e_1_2_7_58_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.2693004"},{"key":"e_1_2_7_59_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.152300"},{"key":"e_1_2_7_60_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.81.24.8014"},{"key":"e_1_2_7_61_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.tree.2010.06.001"},{"key":"e_1_2_7_62_1","doi-asserted-by":"publisher","DOI":"10.1007\/BF01253964"},{"key":"e_1_2_7_63_1","doi-asserted-by":"publisher","DOI":"10.1159\/000337117"},{"key":"e_1_2_7_64_1","doi-asserted-by":"publisher","DOI":"10.1016\/S1055-7903(03)00060-5"},{"key":"e_1_2_7_65_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.1178534"},{"key":"e_1_2_7_66_1","doi-asserted-by":"publisher","DOI":"10.1101\/gad.1018902"},{"key":"e_1_2_7_67_1","doi-asserted-by":"publisher","DOI":"10.1111\/tpj.13103"},{"key":"e_1_2_7_68_1","doi-asserted-by":"publisher","DOI":"10.1111\/tpj.13170"},{"key":"e_1_2_7_69_1","doi-asserted-by":"publisher","DOI":"10.1093\/oxfordjournals.molbev.a004191"},{"key":"e_1_2_7_70_1","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msm092"},{"key":"e_1_2_7_71_1","doi-asserted-by":"publisher","DOI":"10.1266\/ggs.83.227"},{"key":"e_1_2_7_72_1","doi-asserted-by":"publisher","DOI":"10.1038\/312171a0"},{"key":"e_1_2_7_73_1","doi-asserted-by":"publisher","DOI":"10.1266\/jjg.66.569"},{"key":"e_1_2_7_74_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature08747"},{"key":"e_1_2_7_75_1","doi-asserted-by":"publisher","DOI":"10.3835\/plantgenome2015.04.0021"},{"key":"e_1_2_7_76_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0955-0674(02)00338-1"},{"key":"e_1_2_7_77_1","doi-asserted-by":"publisher","DOI":"10.1007\/s11103-009-9542-6"},{"key":"e_1_2_7_78_1","doi-asserted-by":"publisher","DOI":"10.1105\/tpc.111.088682"},{"key":"e_1_2_7_79_1","doi-asserted-by":"publisher","DOI":"10.1266\/ggs.80.161"},{"key":"e_1_2_7_80_1","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms1855"},{"key":"e_1_2_7_81_1","doi-asserted-by":"publisher","DOI":"10.1266\/ggs.86.19"},{"key":"e_1_2_7_82_1","doi-asserted-by":"publisher","DOI":"10.1007\/s001220051668"},{"key":"e_1_2_7_83_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.90.14.6562"},{"key":"e_1_2_7_84_1","doi-asserted-by":"publisher","DOI":"10.1007\/s00239-004-0259-5"},{"key":"e_1_2_7_85_1","doi-asserted-by":"publisher","DOI":"10.1089\/10665270050081478"},{"key":"e_1_2_7_86_1","doi-asserted-by":"publisher","DOI":"10.1007\/BF00163213"},{"key":"e_1_2_7_87_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.3421505"}],"container-title":["The Plant Journal"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.wiley.com\/onlinelibrary\/tdm\/v1\/articles\/10.1111%2Ftpj.13676","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/tpj.13676","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,9,17]],"date-time":"2023-09-17T08:00:25Z","timestamp":1694937625000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1111\/tpj.13676"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,10,9]]},"references-count":86,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2017,11]]}},"alternative-id":["10.1111\/tpj.13676"],"URL":"https:\/\/doi.org\/10.1111\/tpj.13676","archive":["Portico"],"relation":{},"ISSN":["0960-7412","1365-313X"],"issn-type":[{"value":"0960-7412","type":"print"},{"value":"1365-313X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,10,9]]},"assertion":[{"value":"2017-07-15","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2017-08-22","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2017-10-09","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}