{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,30]],"date-time":"2026-10-30T04:15:40Z","timestamp":1793333740496,"version":"4.5.0"},"reference-count":48,"publisher":"National Academy of Sciences","issue":"14","license":[{"start":{"date-parts":[[2019,3,15]],"date-time":"2019-03-15T00:00:00Z","timestamp":1552608000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["91731306"],"award-info":[{"award-number":["91731306"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"The Innovative Academy of Seed Design, Chinese Academy of Sciences","award":["The Innovative Academy of Seed Design"],"award-info":[{"award-number":["The Innovative Academy of Seed Design"]}]},{"name":"The Strategic Priority Research Program of the Chinese Academy of Sciences","award":["XDB27010305"],"award-info":[{"award-number":["XDB27010305"]}]},{"DOI":"10.13039\/501100001779","name":"Monash University","doi-asserted-by":"publisher","award":["Larkins Fellowship"],"award-info":[{"award-number":["Larkins Fellowship"]}],"id":[{"id":"10.13039\/501100001779","id-type":"DOI","asserted-by":"publisher"}]},{"name":"CAS President's International Fellowship for Visiting Scientists","award":["PIFI Fellow"],"award-info":[{"award-number":["PIFI Fellow"]}]}],"content-domain":{"domain":["www.pnas.org"],"crossmark-restriction":true},"short-container-title":["Proc. Natl. Acad. Sci. U.S.A."],"published-print":{"date-parts":[[2019,4,2]]},"abstract":"<jats:p>\n                    Rapid phenotypic changes in traits of adaptive significance are crucial for organisms to thrive in changing environments. How such phenotypic variation is achieved rapidly, despite limited genetic variation in species that experience a genetic bottleneck is unknown.\n                    <jats:italic>Capsella rubella<\/jats:italic>\n                    , an annual and inbreeding forb (Brassicaceae), is a great system for studying this basic question. Its distribution is wider than those of its congeneric species, despite an extreme genetic bottleneck event that severely diminished its genetic variation. Here, we demonstrate that transposable elements (TEs) are an important source of genetic variation that could account for its high phenotypic diversity. TEs are (\n                    <jats:italic>i<\/jats:italic>\n                    ) highly enriched in\n                    <jats:italic>C. rubella<\/jats:italic>\n                    compared with its outcrossing sister species\n                    <jats:italic>Capsella grandiflora<\/jats:italic>\n                    , and (\n                    <jats:italic>ii<\/jats:italic>\n                    ) 4.2% of polymorphic TEs in\n                    <jats:italic>C. rubella<\/jats:italic>\n                    are associated with variation in the expression levels of their adjacent genes. Furthermore, we show that frequent TE insertions at\n                    <jats:italic>FLOWERING LOCUS C (FLC)<\/jats:italic>\n                    in natural populations of\n                    <jats:italic>C. rubella<\/jats:italic>\n                    could explain 12.5% of the natural variation in flowering time, a key life history trait correlated with fitness and adaptation. In particular, we show that a recent TE insertion at the 3\u2032 UTR of\n                    <jats:italic>FLC<\/jats:italic>\n                    affects mRNA stability, which results in reducing its steady-state expression levels, to promote the onset of flowering. Our results highlight that TE insertions can drive rapid phenotypic variation, which could potentially help with adaptation to changing environments in a species with limited standing genetic variation.\n                  <\/jats:p>","DOI":"10.1073\/pnas.1811498116","type":"journal-article","created":{"date-parts":[[2019,3,15]],"date-time":"2019-03-15T21:34:43Z","timestamp":1552685683000},"page":"6908-6913","update-policy":"https:\/\/doi.org\/10.1073\/pnas.cm10313","source":"Crossref","is-referenced-by-count":160,"title":["Transposable elements drive rapid phenotypic variation in\n                    <i>Capsella rubella<\/i>"],"prefix":"10.1073","volume":"116","author":[{"given":"Xiao-Min","family":"Niu","sequence":"first","affiliation":[{"name":"State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 100093 Beijing, China;"},{"name":"University of Chinese Academy of Sciences, 100049 Beijing, China;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1378-4049","authenticated-orcid":false,"given":"Yong-Chao","family":"Xu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 100093 Beijing, China;"},{"name":"University of Chinese Academy of Sciences, 100049 Beijing, China;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zi-Wen","family":"Li","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 100093 Beijing, China;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yu-Tao","family":"Bian","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 100093 Beijing, China;"},{"name":"University of Chinese Academy of Sciences, 100049 Beijing, China;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xing-Hui","family":"Hou","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 100093 Beijing, China;"},{"name":"University of Chinese Academy of Sciences, 100049 Beijing, China;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0090-1979","authenticated-orcid":false,"given":"Jia-Fu","family":"Chen","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 100093 Beijing, China;"},{"name":"University of Chinese Academy of Sciences, 100049 Beijing, China;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yu-Pan","family":"Zou","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 100093 Beijing, China;"},{"name":"University of Chinese Academy of Sciences, 100049 Beijing, China;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juan","family":"Jiang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 100093 Beijing, China;"},{"name":"University of Chinese Academy of Sciences, 100049 Beijing, China;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qiong","family":"Wu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 100093 Beijing, China;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Song","family":"Ge","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 100093 Beijing, China;"},{"name":"University of Chinese Academy of Sciences, 100049 Beijing, China;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1057-2606","authenticated-orcid":false,"given":"Sureshkumar","family":"Balasubramanian","sequence":"additional","affiliation":[{"name":"School of Biological Sciences, Monash University, VIC 3800, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4643-4889","authenticated-orcid":false,"given":"Ya-Long","family":"Guo","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 100093 Beijing, China;"},{"name":"University of Chinese Academy of Sciences, 100049 Beijing, China;"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"341","published-online":{"date-parts":[[2019,3,15]]},"reference":[{"key":"e_1_3_4_1_2","doi-asserted-by":"crossref","first-page":"719","DOI":"10.1126\/science.aaf7671","article-title":"The broad footprint of climate change from genes to biomes to people","volume":"354","author":"Scheffers BR","year":"2016","unstructured":"BR Scheffers, , The broad footprint of climate change from genes to biomes to people. Science 354, 719 (2016).","journal-title":"Science"},{"key":"e_1_3_4_2_2","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1146\/annurev-ecolsys-121415-032116","article-title":"Is there a genetic paradox of biological invasion?","volume":"47","author":"Estoup A","year":"2016","unstructured":"A Estoup, , Is there a genetic paradox of biological invasion? Annu Rev Ecol Evol Syst 47, 51\u201372 (2016).","journal-title":"Annu Rev Ecol Evol Syst"},{"key":"e_1_3_4_3_2","doi-asserted-by":"crossref","first-page":"177","DOI":"10.1038\/nature02807","article-title":"Genetic variation increases during biological invasion by a Cuban lizard","volume":"431","author":"Kolbe JJ","year":"2004","unstructured":"JJ Kolbe, , Genetic variation increases during biological invasion by a Cuban lizard. Nature 431, 177\u2013181 (2004).","journal-title":"Nature"},{"key":"e_1_3_4_4_2","doi-asserted-by":"crossref","first-page":"385","DOI":"10.1038\/sj.hdy.6800634","article-title":"Resolving the genetic paradox in invasive species","volume":"94","author":"Frankham R","year":"2005","unstructured":"R Frankham, Resolving the genetic paradox in invasive species. Heredity (Edinb) 94, 385 (2005).","journal-title":"Heredity (Edinb)"},{"key":"e_1_3_4_5_2","doi-asserted-by":"crossref","first-page":"2241","DOI":"10.1111\/mec.13089","article-title":"Transposable elements as agents of rapid adaptation may explain the genetic paradox of invasive species","volume":"24","author":"Stapley J","year":"2015","unstructured":"J Stapley, AW Santure, SR Dennis, Transposable elements as agents of rapid adaptation may explain the genetic paradox of invasive species. Mol Ecol 24, 2241\u20132252 (2015).","journal-title":"Mol Ecol"},{"key":"e_1_3_4_6_2","doi-asserted-by":"crossref","first-page":"5495","DOI":"10.1038\/ncomms6495","article-title":"Transposable element islands facilitate adaptation to novel environments in an invasive species","volume":"5","author":"Schrader L","year":"2014","unstructured":"L Schrader, , Transposable element islands facilitate adaptation to novel environments in an invasive species. Nat Commun 5, 5495 (2014).","journal-title":"Nat Commun"},{"key":"e_1_3_4_7_2","doi-asserted-by":"crossref","first-page":"1503","DOI":"10.1111\/mec.12170","article-title":"The impact of transposable elements in environmental adaptation","volume":"22","author":"Casacuberta E","year":"2013","unstructured":"E Casacuberta, J Gonz\u00e1lez, The impact of transposable elements in environmental adaptation. Mol Ecol 22, 1503\u20131517 (2013).","journal-title":"Mol Ecol"},{"key":"e_1_3_4_8_2","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1038\/nrg.2016.139","article-title":"Regulatory activities of transposable elements: From conflicts to benefits","volume":"18","author":"Chuong EB","year":"2017","unstructured":"EB Chuong, NC Elde, C Feschotte, Regulatory activities of transposable elements: From conflicts to benefits. Nat Rev Genet 18, 71\u201386 (2017).","journal-title":"Nat Rev Genet"},{"key":"e_1_3_4_9_2","doi-asserted-by":"crossref","first-page":"561","DOI":"10.1146\/annurev-genet-120213-092359","article-title":"Population genomics of transposable elements in Drosophila","volume":"48","author":"Barr\u00f3n MG","year":"2014","unstructured":"MG Barr\u00f3n, AS Fiston-Lavier, DA Petrov, J Gonz\u00e1lez, Population genomics of transposable elements in Drosophila. Annu Rev Genet 48, 561\u2013581 (2014).","journal-title":"Annu Rev Genet"},{"key":"e_1_3_4_10_2","doi-asserted-by":"crossref","first-page":"2140","DOI":"10.1093\/gbe\/evy171","article-title":"Transposable elements contribute to the adaptation of Arabidopsis thaliana","volume":"10","author":"Li ZW","year":"2018","unstructured":"ZW Li, , Transposable elements contribute to the adaptation of Arabidopsis thaliana. Genome Biol Evol 10, 2140\u20132150 (2018).","journal-title":"Genome Biol Evol"},{"key":"e_1_3_4_11_2","doi-asserted-by":"crossref","first-page":"1160","DOI":"10.1038\/ng.942","article-title":"Identification of a functional transposon insertion in the maize domestication gene tb1","volume":"43","author":"Studer A","year":"2011","unstructured":"A Studer, Q Zhao, J Ross-Ibarra, J Doebley, Identification of a functional transposon insertion in the maize domestication gene tb1. Nat Genet 43, 1160\u20131163 (2011).","journal-title":"Nat Genet"},{"key":"e_1_3_4_12_2","doi-asserted-by":"crossref","first-page":"1135","DOI":"10.1038\/nature08498","article-title":"A transposon-induced epigenetic change leads to sex determination in melon","volume":"461","author":"Martin A","year":"2009","unstructured":"A Martin, , A transposon-induced epigenetic change leads to sex determination in melon. Nature 461, 1135\u20131138 (2009).","journal-title":"Nature"},{"key":"e_1_3_4_13_2","doi-asserted-by":"crossref","first-page":"102","DOI":"10.1038\/nature17951","article-title":"The industrial melanism mutation in British peppered moths is a transposable element","volume":"534","author":"Van\u2019t Hof AE","year":"2016","unstructured":"AE Van\u2019t Hof, , The industrial melanism mutation in British peppered moths is a transposable element. Nature 534, 102\u2013105 (2016).","journal-title":"Nature"},{"key":"e_1_3_4_14_2","doi-asserted-by":"crossref","first-page":"5246","DOI":"10.1073\/pnas.0808012106","article-title":"Recent speciation of Capsella rubella from Capsella grandiflora, associated with loss of self-incompatibility and an extreme bottleneck","volume":"106","author":"Guo YL","year":"2009","unstructured":"YL Guo, , Recent speciation of Capsella rubella from Capsella grandiflora, associated with loss of self-incompatibility and an extreme bottleneck. Proc Natl Acad Sci USA 106, 5246\u20135251 (2009).","journal-title":"Proc Natl Acad Sci USA"},{"key":"e_1_3_4_15_2","doi-asserted-by":"crossref","first-page":"5241","DOI":"10.1073\/pnas.0807679106","article-title":"Recent speciation associated with the evolution of selfing in Capsella","volume":"106","author":"Foxe JP","year":"2009","unstructured":"JP Foxe, , Recent speciation associated with the evolution of selfing in Capsella. Proc Natl Acad Sci USA 106, 5241\u20135245 (2009).","journal-title":"Proc Natl Acad Sci USA"},{"key":"e_1_3_4_16_2","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1007\/BF00987954","article-title":"Evolutionary processes in the genus Capsella (Brassicaceae)","volume":"206","author":"Hurka H","year":"1997","unstructured":"H Hurka, B Neuffer, Evolutionary processes in the genus Capsella (Brassicaceae). Plant Syst Evol 206, 295\u2013316 (1997).","journal-title":"Plant Syst Evol"},{"key":"e_1_3_4_17_2","doi-asserted-by":"crossref","first-page":"1070","DOI":"10.1126\/science.1143153","article-title":"The evolution of selfing in Arabidopsis thaliana","volume":"317","author":"Tang C","year":"2007","unstructured":"C Tang, , The evolution of selfing in Arabidopsis thaliana. Science 317, 1070\u20131072 (2007).","journal-title":"Science"},{"key":"e_1_3_4_18_2","doi-asserted-by":"crossref","first-page":"602","DOI":"10.1186\/1471-2164-15-602","article-title":"Mating system shifts and transposable element evolution in the plant genus Capsella","volume":"15","author":"\u00c5gren JA","year":"2014","unstructured":"JA \u00c5gren, , Mating system shifts and transposable element evolution in the plant genus Capsella. BMC Genomics 15, 602 (2014).","journal-title":"BMC Genomics"},{"key":"e_1_3_4_19_2","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1186\/s13059-017-1342-8","article-title":"Long-term balancing selection contributes to adaptation in Arabidopsis and its relatives","volume":"18","author":"Wu Q","year":"2017","unstructured":"Q Wu, , Long-term balancing selection contributes to adaptation in Arabidopsis and its relatives. Genome Biol 18, 217 (2017).","journal-title":"Genome Biol"},{"key":"e_1_3_4_20_2","doi-asserted-by":"crossref","first-page":"831","DOI":"10.1038\/ng.2669","article-title":"The Capsella rubella genome and the genomic consequences of rapid mating system evolution","volume":"45","author":"Slotte T","year":"2013","unstructured":"T Slotte, , The Capsella rubella genome and the genomic consequences of rapid mating system evolution. Nat Genet 45, 831\u2013835 (2013).","journal-title":"Nat Genet"},{"key":"e_1_3_4_21_2","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1038\/nprot.2008.211","article-title":"Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources","volume":"4","author":"Huang da W","year":"2009","unstructured":"W Huang da, BT Sherman, RA Lempicki, Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4, 44\u201357 (2009).","journal-title":"Nat Protoc"},{"key":"e_1_3_4_22_2","doi-asserted-by":"crossref","first-page":"2322","DOI":"10.1073\/pnas.1018222108","article-title":"Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata","volume":"108","author":"Hollister JD","year":"2011","unstructured":"JD Hollister, , Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata. Proc Natl Acad Sci USA 108, 2322\u20132327 (2011).","journal-title":"Proc Natl Acad Sci USA"},{"key":"e_1_3_4_23_2","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1007\/s11427-015-4993-2","article-title":"The effect of transposable elements on phenotypic variation: Insights from plants to humans","volume":"59","author":"Wei L","year":"2016","unstructured":"L Wei, X Cao, The effect of transposable elements on phenotypic variation: Insights from plants to humans. Sci China Life Sci 59, 24\u201337 (2016).","journal-title":"Sci China Life Sci"},{"key":"e_1_3_4_24_2","doi-asserted-by":"crossref","first-page":"1223","DOI":"10.1111\/j.1365-294X.2012.05460.x","article-title":"\u2018Missing link\u2019 species Capsella orientalis and Capsella thracica elucidate evolution of model plant genus Capsella (Brassicaceae)","volume":"21","author":"Hurka H","year":"2012","unstructured":"H Hurka, N Friesen, DA German, A Franzke, B Neuffer, \u2018Missing link\u2019 species Capsella orientalis and Capsella thracica elucidate evolution of model plant genus Capsella (Brassicaceae). Mol Ecol 21, 1223\u20131238 (2012).","journal-title":"Mol Ecol"},{"key":"e_1_3_4_25_2","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1104\/pp.111.189845","article-title":"Natural variation in Arabidopsis: From molecular genetics to ecological genomics","volume":"158","author":"Weigel D","year":"2012","unstructured":"D Weigel, Natural variation in Arabidopsis: From molecular genetics to ecological genomics. Plant Physiol 158, 2\u201322 (2012).","journal-title":"Plant Physiol"},{"key":"e_1_3_4_26_2","first-page":"3843","article-title":"Phenotypic plasticity and adaptive evolution contribute to advancing flowering phenology in response to climate change","volume":"279","author":"Anderson JT","year":"2012","unstructured":"JT Anderson, DW Inouye, AM McKinney, RI Colautti, T Mitchell-Olds, Phenotypic plasticity and adaptive evolution contribute to advancing flowering phenology in response to climate change. Proc Biol Sci 279, 3843\u20133852 (2012).","journal-title":"Proc Biol Sci"},{"key":"e_1_3_4_27_2","doi-asserted-by":"crossref","first-page":"1322","DOI":"10.1105\/tpc.18.00124","article-title":"Parallel evolution of common allelic variants confers flowering diversity in Capsella rubella","volume":"30","author":"Yang L","year":"2018","unstructured":"L Yang, , Parallel evolution of common allelic variants confers flowering diversity in Capsella rubella. Plant Cell 30, 1322\u20131336 (2018).","journal-title":"Plant Cell"},{"key":"e_1_3_4_28_2","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1560\/IJEE.57.1-2.91","article-title":"Relationships between flowering time and rainfall gradients across Mediterranean-desert Transects","volume":"57","author":"Kigel J","year":"2011","unstructured":"J Kigel, , Relationships between flowering time and rainfall gradients across Mediterranean-desert Transects. Isr J Ecol Evol 57, 91\u2013109 (2011).","journal-title":"Isr J Ecol Evol"},{"key":"e_1_3_4_29_2","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1111\/nph.12485","article-title":"Adaptation to spring heat and drought in northeastern Spanish Arabidopsis thaliana","volume":"201","author":"Wolfe MD","year":"2014","unstructured":"MD Wolfe, SJ Tonsor, Adaptation to spring heat and drought in northeastern Spanish Arabidopsis thaliana. New Phytol 201, 323\u2013334 (2014).","journal-title":"New Phytol"},{"key":"e_1_3_4_30_2","doi-asserted-by":"crossref","first-page":"1950","DOI":"10.3389\/fpls.2017.01950","article-title":"Early flowering as a drought escape mechanism in plants: How can it aid wheat production?","volume":"8","author":"Shavrukov Y","year":"2017","unstructured":"Y Shavrukov, , Early flowering as a drought escape mechanism in plants: How can it aid wheat production? Front Plant Sci 8, 1950 (2017).","journal-title":"Front Plant Sci"},{"key":"e_1_3_4_31_2","doi-asserted-by":"crossref","first-page":"352","DOI":"10.1038\/s41559-017-0423-0","article-title":"Genomic basis and evolutionary potential for extreme drought adaptation in Arabidopsis thaliana","volume":"2","author":"Exposito-Alonso M","year":"2018","unstructured":"M Exposito-Alonso, , Genomic basis and evolutionary potential for extreme drought adaptation in Arabidopsis thaliana. Nat Ecol Evol 2, 352\u2013358 (2018).","journal-title":"Nat Ecol Evol"},{"key":"e_1_3_4_32_2","doi-asserted-by":"crossref","first-page":"729","DOI":"10.1534\/genetics.112.143958","article-title":"Independent FLC mutations as causes of flowering-time variation in Arabidopsis thaliana and Capsella rubella","volume":"192","author":"Guo YL","year":"2012","unstructured":"YL Guo, M Todesco, J Hagmann, S Das, D Weigel, Independent FLC mutations as causes of flowering-time variation in Arabidopsis thaliana and Capsella rubella. Genetics 192, 729\u2013739 (2012).","journal-title":"Genetics"},{"key":"e_1_3_4_33_2","doi-asserted-by":"crossref","first-page":"160","DOI":"10.1104\/pp.107.102632","article-title":"Differential expression of genes important for adaptation in Capsella bursa-pastoris (Brassicaceae)","volume":"145","author":"Slotte T","year":"2007","unstructured":"T Slotte, K Holm, LM McIntyre, U Lagercrantz, M Lascoux, Differential expression of genes important for adaptation in Capsella bursa-pastoris (Brassicaceae). Plant Physiol 145, 160\u2013173 (2007).","journal-title":"Plant Physiol"},{"key":"e_1_3_4_34_2","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1371\/journal.pgen.0010006","article-title":"Diversity of flowering responses in wild Arabidopsis thaliana strains","volume":"1","author":"Lempe J","year":"2005","unstructured":"J Lempe, , Diversity of flowering responses in wild Arabidopsis thaliana strains. PLoS Genet 1, 109\u2013118 (2005).","journal-title":"PLoS Genet"},{"key":"e_1_3_4_35_2","doi-asserted-by":"crossref","first-page":"2873","DOI":"10.1101\/gad.1217304","article-title":"siRNAs targeting an intronic transposon in the regulation of natural flowering behavior in Arabidopsis","volume":"18","author":"Liu J","year":"2004","unstructured":"J Liu, Y He, R Amasino, X Chen, siRNAs targeting an intronic transposon in the regulation of natural flowering behavior in Arabidopsis. Genes Dev 18, 2873\u20132878 (2004).","journal-title":"Genes Dev"},{"key":"e_1_3_4_36_2","doi-asserted-by":"crossref","first-page":"16160","DOI":"10.1073\/pnas.1419030111","article-title":"Antisense COOLAIR mediates the coordinated switching of chromatin states at FLC during vernalization","volume":"111","author":"Csorba T","year":"2014","unstructured":"T Csorba, JI Questa, Q Sun, C Dean, Antisense COOLAIR mediates the coordinated switching of chromatin states at FLC during vernalization. Proc Natl Acad Sci USA 111, 16160\u201316165 (2014).","journal-title":"Proc Natl Acad Sci USA"},{"key":"e_1_3_4_37_2","doi-asserted-by":"crossref","first-page":"2527","DOI":"10.1105\/tpc.004564","article-title":"Different regulatory regions are required for the vernalization-induced repression of FLOWERING LOCUS C and for the epigenetic maintenance of repression","volume":"14","author":"Sheldon CC","year":"2002","unstructured":"CC Sheldon, AB Conn, ES Dennis, WJ Peacock, Different regulatory regions are required for the vernalization-induced repression of FLOWERING LOCUS C and for the epigenetic maintenance of repression. Plant Cell 14, 2527\u20132537 (2002).","journal-title":"Plant Cell"},{"key":"e_1_3_4_38_2","doi-asserted-by":"crossref","first-page":"397","DOI":"10.1038\/nrg2337","article-title":"Transposable elements and the evolution of regulatory networks","volume":"9","author":"Feschotte C","year":"2008","unstructured":"C Feschotte, Transposable elements and the evolution of regulatory networks. Nat Rev Genet 9, 397\u2013405 (2008).","journal-title":"Nat Rev Genet"},{"key":"e_1_3_4_39_2","doi-asserted-by":"crossref","first-page":"853","DOI":"10.1016\/j.molcel.2011.08.017","article-title":"Mechanisms and consequences of alternative polyadenylation","volume":"43","author":"Di Giammartino DC","year":"2011","unstructured":"DC Di Giammartino, K Nishida, JL Manley, Mechanisms and consequences of alternative polyadenylation. Mol Cell 43, 853\u2013866 (2011).","journal-title":"Mol Cell"},{"key":"e_1_3_4_40_2","doi-asserted-by":"crossref","first-page":"6232","DOI":"10.1093\/nar\/gkt296","article-title":"Arabidopsis thaliana LSM proteins function in mRNA splicing and degradation","volume":"41","author":"Golisz A","year":"2013","unstructured":"A Golisz, PJ Sikorski, K Kruszka, J Kufel, Arabidopsis thaliana LSM proteins function in mRNA splicing and degradation. Nucleic Acids Res 41, 6232\u20136249 (2013).","journal-title":"Nucleic Acids Res"},{"key":"e_1_3_4_41_2","doi-asserted-by":"crossref","first-page":"3612","DOI":"10.1093\/nar\/gkp223","article-title":"Alternative polyadenylation variants of the RNA binding protein, HuR: Abundance, role of AU-rich elements and auto-regulation","volume":"37","author":"Al-Ahmadi W","year":"2009","unstructured":"W Al-Ahmadi, M Al-Ghamdi, L Al-Haj, M Al-Saif, KS Khabar, Alternative polyadenylation variants of the RNA binding protein, HuR: Abundance, role of AU-rich elements and auto-regulation. Nucleic Acids Res 37, 3612\u20133624 (2009).","journal-title":"Nucleic Acids Res"},{"key":"e_1_3_4_42_2","doi-asserted-by":"crossref","first-page":"3641","DOI":"10.1038\/sj.emboj.7601788","article-title":"Heritable epigenetic mutation of a transposon-flanked Arabidopsis gene due to lack of the chromatin-remodeling factor DDM1","volume":"26","author":"Saze H","year":"2007","unstructured":"H Saze, T Kakutani, Heritable epigenetic mutation of a transposon-flanked Arabidopsis gene due to lack of the chromatin-remodeling factor DDM1. EMBO J 26, 3641\u20133652 (2007).","journal-title":"EMBO J"},{"key":"e_1_3_4_43_2","doi-asserted-by":"crossref","first-page":"14651","DOI":"10.1038\/ncomms14651","article-title":"Translational repression by a miniature inverted-repeat transposable element in the 3\u2032 untranslated region","volume":"8","author":"Shen J","year":"2017","unstructured":"J Shen, , Translational repression by a miniature inverted-repeat transposable element in the 3\u2032 untranslated region. Nat Commun 8, 14651 (2017).","journal-title":"Nat Commun"},{"key":"e_1_3_4_44_2","doi-asserted-by":"crossref","first-page":"e20777","DOI":"10.7554\/eLife.20777","article-title":"Population scale mapping of transposable element diversity reveals links to gene regulation and epigenomic variation","volume":"5","author":"Stuart T","year":"2016","unstructured":"T Stuart, , Population scale mapping of transposable element diversity reveals links to gene regulation and epigenomic variation. eLife 5, e20777 (2016).","journal-title":"eLife"},{"key":"e_1_3_4_45_2","first-page":"164","article-title":"PHYLIP-phylogeny inference package (version 3.2)","volume":"5","author":"Feisenstein J","year":"1989","unstructured":"J Feisenstein, PHYLIP-phylogeny inference package (version 3.2). Cladistics 5, 164\u2013166 (1989).","journal-title":"Cladistics"},{"key":"e_1_3_4_46_2","doi-asserted-by":"crossref","first-page":"607","DOI":"10.1111\/j.1600-0587.2009.06142.x","article-title":"ENMTools: A toolbox for comparative studies of environmental niche models","volume":"33","author":"Warren DL","year":"2010","unstructured":"DL Warren, RE Glor, M Turelli, ENMTools: A toolbox for comparative studies of environmental niche models. Ecography 33, 607\u2013611 (2010).","journal-title":"Ecography"},{"key":"e_1_3_4_47_2","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1038\/nmeth0809-550","article-title":"SHOREmap: Simultaneous mapping and mutation identification by deep sequencing","volume":"6","author":"Schneeberger K","year":"2009","unstructured":"K Schneeberger, , SHOREmap: Simultaneous mapping and mutation identification by deep sequencing. Nat Methods 6, 550\u2013551 (2009).","journal-title":"Nat Methods"},{"key":"e_1_3_4_48_2","doi-asserted-by":"crossref","first-page":"371","DOI":"10.1186\/1471-2105-9-371","article-title":"Kismeth: Analyzer of plant methylation states through bisulfite sequencing","volume":"9","author":"Gruntman E","year":"2008","unstructured":"E Gruntman, , Kismeth: Analyzer of plant methylation states through bisulfite sequencing. BMC Bioinformatics 9, 371 (2008).","journal-title":"BMC Bioinformatics"}],"container-title":["Proceedings of the National Academy of Sciences"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/www.pnas.org\/syndication\/doi\/10.1073\/pnas.1811498116","content-type":"unspecified","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/pnas.org\/doi\/pdf\/10.1073\/pnas.1811498116","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,7,15]],"date-time":"2024-07-15T17:05:08Z","timestamp":1721063108000},"score":1,"resource":{"primary":{"URL":"https:\/\/pnas.org\/doi\/full\/10.1073\/pnas.1811498116"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,3,15]]},"references-count":48,"journal-issue":{"issue":"14","published-print":{"date-parts":[[2019,4,2]]}},"alternative-id":["10.1073\/pnas.1811498116"],"URL":"https:\/\/doi.org\/10.1073\/pnas.1811498116","relation":{},"ISSN":["0027-8424","1091-6490"],"issn-type":[{"value":"0027-8424","type":"print"},{"value":"1091-6490","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,3,15]]},"assertion":[{"value":"2019-03-15","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}