title: Selective acquisition and retention of genomic sequences by Pack-Mutator-like elements based on guanine-cytosine content and the breadth of expression.
abstract: The process of gene duplication followed by sequence and functional divergence is important for the generation of new genes. Pack-MULEs, nonautonomous Mutator-like elements (MULEs) that carry genic sequence(s), are potentially involved in generating new open reading frames and regulating parental gene expression. These elements are identified in many plant genomes and are most abundant in rice (Oryza sativa). Despite the abundance of Pack-MULEs, the mechanism by which parental genes are captured by Pack-MULEs remains largely unknown. In this study, we identified all MULEs in rice and examined factors likely important for sequence acquisition. Terminal inverted repeat MULEs are the predominant MULE type and account for the majority of the Pack-MULEs. In addition to genic sequences, rice MULEs capture guanine-cytosine (GC)-rich intergenic sequences, albeit at a much lower frequency. MULEs carrying nontransposon sequences have longer terminal inverted repeats and higher GC content in terminal and subterminal regions. An overrepresentation of genes with known functions and genes with orthologs among parental genes of Pack-MULEs is observed in rice, maize (Zea mays), and Arabidopsis (Arabidopsis thaliana), suggesting preferential acquisition for bona fide genes by these elements. Pack-MULEs selectively acquire/retain parental sequences through a combined effect of GC content and breadth of expression, with GC content playing a stronger role. Increased GC content and number of tissues with detectable expression result in higher chances of a gene being acquired by Pack-MULEs. Such selective acquisition/retention provides these elements greater chances of carrying functional sequences that may provide new genetic resources for the evolution of new genes or the modification of existing genes.
authors.affiliation: Department of Horticulture, Michigan State University, East Lansing, Michigan 48824.
authors.forename: Ann A
authors.initials: AA
authors.lastname: Ferguson
authors.forename: Dongyan
authors.initials: D
authors.lastname: Zhao
authors.forename: Ning
authors.initials: N
authors.lastname: Jiang
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D001482:Base Composition / Q000235:genetics*; D001483:Base Sequence; D004251:DNA Transposable Elements / Q000235:genetics*; D018744:DNA, Plant / Q000235:genetics*; D020862:GC Rich Sequence / Q000235:genetics; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant / Q000235:genetics*; D008969:Molecular Sequence Data; D016254:Mutagenesis, Insertional; D016366:Open Reading Frames / Q000235:genetics; D012275:Oryza / Q000235:genetics*; D020079:Terminal Repeat Sequences / Q000235:genetics; D003313:Zea mays / Q000235:genetics
chemical_list: D004251:DNA Transposable Elements; D018744:DNA, Plant
references.citation: Plant Cell. 2009 Jan;21(1):25-38
references.pmid: 19136648
references.citation: Theor Appl Genet. 1994 Jan;87(6):657-67
references.pmid: 24190408
references.citation: J Biol Chem. 1989 Feb 5;264(4):2331-7
references.pmid: 2521627
references.citation: Proc Natl Acad Sci U S A. 2006 Nov 21;103(47):17644-9
references.pmid: 17101975
references.citation: Trends Plant Sci. 2002 Nov;7(11):498-504
references.pmid: 12417150
references.citation: Plant Cell. 1997 Sep;9(9):1509-1514
references.pmid: 12237393
references.citation: Methods Mol Biol. 2008;453:3-31
references.pmid: 18712296
references.citation: Comp Funct Genomics. 2012;2012:695827
references.pmid: 22474413
references.citation: Genome Res. 2013 Feb;23(2):396-408
references.pmid: 23149293
references.citation: Plant Physiol. 2001 Mar;125(3):1293-303
references.pmid: 11244110
references.citation: Nucleic Acids Res. 2004 Mar 19;32(5):1792-7
references.pmid: 15034147
references.citation: Plant Cell. 2005 Oct;17(10):2619-32
references.pmid: 16141454
references.citation: New Phytol. 2009 Aug;183(3):557-564
references.pmid: 19555435
references.citation: Plant Cell Physiol. 2004 Jul;45(7):933-44
references.pmid: 15295077
references.citation: Nature. 2004 Sep 30;431(7008):569-73
references.pmid: 15457261
references.citation: Nature. 2013 May 30;497(7451):579-84
references.pmid: 23698360
references.citation: Plant J. 2007 Oct;52(2):342-51
references.pmid: 17764506
references.citation: BMC Evol Biol. 2007 Aug 29;7:152
references.pmid: 17727727
references.citation: Eukaryot Cell. 2005 Mar;4(3):615-24
references.pmid: 15755923
references.citation: Science. 2009 Nov 20;326(5956):1112-5
references.pmid: 19965430
references.citation: Plant J. 2012 Aug;71(3):492-502
references.pmid: 22443345
references.citation: Nature. 2010 Jan 14;463(7278):178-83
references.pmid: 20075913
references.citation: Proc Natl Acad Sci U S A. 2011 Jan 25;108(4):1537-42
references.pmid: 21220310
references.citation: Mol Cell Biol. 1997 Sep;17(9):5165-75
references.pmid: 9271394
references.citation: Nature. 2009 Jan 29;457(7229):551-6
references.pmid: 19189423
references.citation: Nucleic Acids Res. 2003 Apr 1;31(7):1838-44
references.pmid: 12654999
references.citation: Hum Mol Genet. 2005 Feb 1;14(3):421-7
references.pmid: 15590696
references.citation: Genome Res. 2004 Aug;14(8):1641-53
references.pmid: 15289482
references.citation: Proc Natl Acad Sci U S A. 2005 Dec 27;102(52):19243-8
references.pmid: 16357197
references.citation: Hum Mol Genet. 2003 Oct 1;12(19):2411-5
references.pmid: 12915446
references.citation: Nat Rev Genet. 2008 May;9(5):397-405
references.pmid: 18368054
references.citation: Genome Res. 2006 Oct;16(10):1262-9
references.pmid: 16963705
references.citation: Curr Opin Plant Biol. 2007 Apr;10(2):176-81
references.pmid: 17291821
references.citation: Nature. 2004 Jul 22;430(6998):471-6
references.pmid: 15269773
references.citation: Plant Cell. 2006 Aug;18(8):1791-802
references.pmid: 16829590
references.citation: Plant J. 2001 Jan;25(1):79-91
references.pmid: 11169184
references.citation: Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W33-6
references.pmid: 15215344
references.citation: Genome Biol. 2013 May 10;14(5):R41
references.pmid: 23663246
references.citation: Genetics. 2010 Aug;185(4):1507-17
references.pmid: 20457878
references.citation: Plant Physiol. 2004 Jun;135(2):801-13
references.pmid: 15173564
references.citation: Nat Rev Genet. 2007 Apr;8(4):272-85
references.pmid: 17363976
references.citation: Genetics. 2006 Dec;174(4):2215-28
references.pmid: 17028332
references.citation: Trends Ecol Evol. 2004 Jun;19(6):309-14
references.pmid: 16701276
references.citation: Mol Biol Evol. 1988 Sep;5(5):519-29
references.pmid: 2848175
references.citation: Nat Genet. 2005 Sep;37(9):997-1002
references.pmid: 16056225
references.citation: BMC Evol Biol. 2010 Feb 12;10:41
references.pmid: 20152032
references.citation: Rice (N Y). 2013 Feb 06;6(1):4
references.pmid: 24280374
references.citation: Genetics. 1999 Dec;153(4):1899-908
references.pmid: 10581294
references.citation: Nature. 2012 May 30;485(7400):635-41
references.pmid: 22660326
references.citation: Cell. 2004 Sep 3;118(5):555-66
references.pmid: 15339661
references.citation: BMC Genomics. 2010 May 16;11:308
references.pmid: 20470436
references.citation: Mol Biol Evol. 2006 Jun;23(6):1254-68
references.pmid: 16581939
references.citation: Genetics. 1991 Sep;129(1):261-70
references.pmid: 1657702
references.citation: Mol Biol Evol. 2003 Aug;20(8):1362-75
references.pmid: 12777515
references.citation: PLoS Biol. 2006 Jun;4(6):e180
references.pmid: 16700628
references.citation: Genetics. 2000 Dec;156(4):2019-31
references.pmid: 11102392
references.citation: Nature. 2005 Aug 11;436(7052):793-800
references.pmid: 16100779