title: Three groups of transposable elements with contrasting copy number dynamics and host responses in the maize (Zea mays ssp. mays) genome.
abstract: Most angiosperm nuclear DNA is repetitive and derived from silenced transposable elements (TEs). TE silencing requires substantial resources from the plant host, including the production of small interfering RNAs (siRNAs). Thus, the interaction between TEs and siRNAs is a critical aspect of both the function and the evolution of plant genomes. Yet the co-evolutionary dynamics between these two entities remain poorly characterized. Here we studied the organization of TEs within the maize (Zea mays ssp mays) genome, documenting that TEs fall within three groups based on the class and copy numbers. These groups included DNA elements, low copy RNA elements and higher copy RNA elements. The three groups varied statistically in characteristics that included length, location, age, siRNA expression and 24:22 nucleotide (nt) siRNA targeting ratios. In addition, the low copy retroelements encompassed a set of TEs that had previously been shown to decrease expression within a 24 nt siRNA biogenesis mutant (mop1). To investigate the evolutionary dynamics of the three groups, we estimated their abundance in two landraces, one with a genome similar in size to that of the maize reference and the other with a 30% larger genome. For all three accessions, we assessed TE abundance as well as 22 nt and 24 nt siRNA content within leaves. The high copy number retroelements are under targeted similarly by siRNAs among accessions, appear to be born of a rapid bust of activity, and may be currently transpositionally dead or limited. In contrast, the lower copy number group of retrolements are targeted more dynamically and have had a long and ongoing history of transposition in the maize genome.
authors.affiliation: Dept. of Ecology and Evolutionary Biology, UC Irvine, Irvine, California, United States of America; Departamento de Agronomía, Universidad de Córdoba, Campus de Excelencia Internacional Agroalimentario, ceiA3, Cordoba, Spain.
authors.forename: Concepcion M
authors.initials: CM
authors.lastname: Diez
authors.affiliation: Department of Mathematics, UC Irvine, Irvine, California, United States of America.
authors.forename: Esteban
authors.initials: E
authors.lastname: Meca
authors.affiliation: CNRS, UMR de Génétique Végétale, INRA/CNRS/Univ Paris-Sud/AgroParisTech, Ferme du Moulon, Gif-sur-Yvette, France.
authors.forename: Maud I
authors.initials: MI
authors.lastname: Tenaillon
authors.affiliation: Dept. of Ecology and Evolutionary Biology, UC Irvine, Irvine, California, United States of America.
authors.forename: Brandon S
authors.initials: BS
authors.lastname: Gaut
mesh_terms: D004251:DNA Transposable Elements / Q000235:genetics*; D019143:Evolution, Molecular; D018628:Gene Dosage / Q000235:genetics*; D018506:Gene Expression Regulation, Plant / Q000235:genetics; D018745:Genome, Plant / Q000235:genetics*; D034741:RNA, Small Interfering / Q000235:genetics; D018626:Retroelements / Q000235:genetics; D003313:Zea mays / Q000235:genetics*
chemical_list: D004251:DNA Transposable Elements; D034741:RNA, Small Interfering; D018626:Retroelements
references.citation: Genome Res. 2009 Aug;19(8):1419-28
references.pmid: 19478138
references.citation: Genome Res. 2009 Dec;19(12):2221-30
references.pmid: 19789376
references.citation: Proc Natl Acad Sci U S A. 2006 Nov 21;103(47):17644-9
references.pmid: 17101975
references.citation: Nat Rev Genet. 2007 Apr;8(4):272-85
references.pmid: 17363976
references.citation: Plant J. 2012 Feb;69(3):475-88
references.pmid: 21967390
references.citation: Genome Biol. 2013 Jun 12;14(6):R57
references.pmid: 23758703
references.citation: Genome Res. 2006 Oct;16(10):1252-61
references.pmid: 16954538
references.citation: Nat Rev Genet. 2007 Dec;8(12):973-82
references.pmid: 17984973
references.citation: Proc Natl Acad Sci U S A. 2008 Sep 30;105(39):14958-63
references.pmid: 18815367
references.citation: Genome Res. 2001 Oct;11(10):1725-9
references.pmid: 11591649
references.citation: Annu Rev Plant Biol. 2009;60:43-66
references.pmid: 19007329
references.citation: Mol Biol Evol. 2012 Oct;29(10):3193-203
references.pmid: 22593226
references.citation: Curr Opin Plant Biol. 2007 Apr;10(2):149-55
references.pmid: 17300983
references.citation: Proc Natl Acad Sci U S A. 2010 Dec 21;107(51):22184-9
references.pmid: 21135217
references.citation: Nat Rev Genet. 2010 Mar;11(3):204-20
references.pmid: 20142834
references.citation: Nat Struct Mol Biol. 2012 Sep;19(9):870-5
references.pmid: 22864289
references.citation: Genetics. 2012 Jul;191(3):883-94
references.pmid: 22542971
references.citation: BMC Bioinformatics. 2010 Feb 18;11:94
references.pmid: 20167110
references.citation: Genome Res. 2001 Oct;11(10):1660-76
references.pmid: 11591643
references.citation: Proc Natl Acad Sci U S A. 1997 Jun 24;94(13):6809-14
references.pmid: 11038553
references.citation: Plant Cell. 2010 Jan;22(1):17-33
references.pmid: 20086188
references.citation: Curr Biol. 2003 Mar 4;13(5):421-6
references.pmid: 12620192
references.citation: Science. 2009 Nov 20;326(5956):1112-5
references.pmid: 19965430
references.citation: Bioinformatics. 2010 Mar 1;26(5):589-95
references.pmid: 20080505
references.citation: Curr Opin Plant Biol. 2011 Apr;14(2):156-61
references.pmid: 21444239
references.citation: Nat Genet. 1998 Sep;20(1):43-5
references.pmid: 9731528
references.citation: PLoS Genet. 2012;8(12):e1003127
references.pmid: 23271981
references.citation: Plant Physiol. 2013 May;162(1):116-31
references.pmid: 23542151
references.citation: Genome Res. 2006 Oct;16(10):1262-9
references.pmid: 16963705
references.citation: New Phytol. 2013 Jul;199(1):264-276
references.pmid: 23550586
references.citation: Annu Rev Genet. 2012;46:651-75
references.pmid: 23145912
references.citation: Trends Plant Sci. 2010 Aug;15(8):471-8
references.pmid: 20541961
references.citation: PLoS Genet. 2009 Nov;5(11):e1000737
references.pmid: 19936292
references.citation: Genome Res. 2013 Oct;23(10):1663-74
references.pmid: 23739894
references.citation: PLoS Genet. 2009 Nov;5(11):e1000732
references.pmid: 19936065
references.citation: Nat Genet. 2012 Jun 03;44(7):803-7
references.pmid: 22660545
references.citation: Genome Res. 2004 May;14(5):860-9
references.pmid: 15078861
references.citation: Nat Genet. 2013 Sep;45(9):1029-39
references.pmid: 23852169
references.citation: Annu Rev Plant Biol. 2013;64:137-59
references.pmid: 23330790
references.citation: Cell. 2012 Sep 28;151(1):194-205
references.pmid: 23000270
references.citation: Genome Biol Evol. 2011;3:219-29
references.pmid: 21296765
references.citation: Nat Methods. 2008 Jul;5(7):621-8
references.pmid: 18516045
references.citation: Plant J. 2007 Nov;52(3):391-404
references.pmid: 17764504
references.citation: Genome Res. 2006 Oct;16(10):1276-88
references.pmid: 16954541
references.citation: PLoS Genet. 2009 Nov;5(11):e1000728
references.pmid: 19936048
references.citation: Genet Res. 2002 Dec;80(3):155-61
references.pmid: 12688654
references.citation: PLoS Genet. 2011 Nov;7(11):e1002372
references.pmid: 22125494
references.citation: Genome Res. 2010 Dec;20(12):1689-99
references.pmid: 21036921
references.citation: Curr Opin Plant Biol. 2012 Nov;15(5):511-6
references.pmid: 22824142
references.citation: Proc Natl Acad Sci U S A. 2012 Jun 26;109(26):10444-9
references.pmid: 22689990
references.citation: Genome Res. 2013 Oct;23(10):1651-62
references.pmid: 23739895
references.citation: PLoS Biol. 2006 Oct;4(10):e339
references.pmid: 16968137
references.citation: Cell. 2006 Dec 29;127(7):1309-21
references.pmid: 17190597
references.citation: Curr Opin Plant Biol. 2004 Dec;7(6):732-6
references.pmid: 15491923
references.citation: PLoS One. 2013 Apr 23;8(4):e61005
references.pmid: 23637782