title: Detection and characterization of megasatellites in orthologous and nonorthologous genes of 21 fungal genomes.
abstract: Megasatellites are large DNA tandem repeats, originally described in Candida glabrata, in protein-coding genes. Most of the genes in which megasatellites are found are of unknown function. In this work, we extended the search for megasatellites to 20 additional completely sequenced fungal genomes and extracted 216 megasatellites in 203 out of 142,121 genes, corresponding to the most exhaustive description of such genetic elements available today. We show that half of the megasatellites detected encode threonine-rich peptides predicted to be intrinsically disordered, suggesting that they may interact with several partners or serve as flexible linkers. Megasatellite motifs were clustered into several families. Their distribution in fungal genes shows that different motifs are found in orthologous genes and similar motifs are found in unrelated genes, suggesting that megasatellite formation or spreading does not necessarily track the evolution of their host genes. Altogether, these results suggest that megasatellites are created and lost during evolution of fungal genomes, probably sharing similar functions, although their primary sequences are not necessarily conserved.
authors.affiliation: Unité de Génétique Moléculaire des Levures, Département Génomes & Génétique, Institut Pasteur, Paris, France.
authors.forename: Fredj
authors.initials: F
authors.lastname: Tekaia
authors.forename: Bernard
authors.initials: B
authors.lastname: Dujon
authors.forename: Guy-Franck
authors.initials: GF
authors.lastname: Richard
mesh_terms: D000595:Amino Acid Sequence; D001203:Ascomycota / Q000145:classification / Q000235:genetics*; D001487:Basidiomycota / Q000145:classification / Q000235:genetics*; D019143:Evolution, Molecular; D005656:Fungal Proteins / Q000145:classification / Q000235:genetics*; D016681:Genome, Fungal; D008969:Molecular Sequence Data; D005810:Multigene Family; D010802:Phylogeny; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment; D020080:Tandem Repeat Sequences; D013912:Threonine / Q000235:genetics
chemical_list: D005656:Fungal Proteins; D013912:Threonine
references.citation: Mol Biol Evol. 2000 Apr;17(4):540-52
references.pmid: 10742046
references.citation: Nucleic Acids Res. 2000 Jan 1;28(1):235-42
references.pmid: 10592235
references.citation: Bioinformatics. 2009 May 1;25(9):1189-91
references.pmid: 19151095
references.citation: Genes Dev. 2003 Sep 15;17(18):2245-58
references.pmid: 12952896
references.citation: Nucleic Acids Res. 2010 Aug;38(14):4731-9
references.pmid: 20360043
references.citation: Genome Biol. 2008;9(5):R77
references.pmid: 18460219
references.citation: EMBO J. 2002 Mar 15;21(6):1465-76
references.pmid: 11889052
references.citation: Nature. 2006 Nov 2;444(7115):97-101
references.pmid: 17080091
references.citation: Eukaryot Cell. 2007 Aug;6(8):1380-91
references.pmid: 17557878
references.citation: J Mol Evol. 1999 Nov;49(5):591-600
references.pmid: 10552040
references.citation: Nature. 2005 Dec 22;438(7071):1105-15
references.pmid: 16372000
references.citation: J Chem Biol. 2010 Mar;3(1):19-35
references.pmid: 19898886
references.citation: Nature. 2005 Dec 22;438(7071):1157-61
references.pmid: 16372010
references.citation: Nat Genet. 2005 Sep;37(9):986-90
references.pmid: 16086015
references.citation: Mol Microbiol. 2000 Jul;37(1):207-15
references.pmid: 10931317
references.citation: Genome Res. 2000 Jul;10(7):899-907
references.pmid: 10899139
references.citation: FEMS Yeast Res. 2006 May;6(3):428-41
references.pmid: 16630283
references.citation: Gene. 2012 Jan 15;492(1):199-211
references.pmid: 22056699
references.citation: Eukaryot Cell. 2006 Oct;5(10):1664-73
references.pmid: 16936142
references.citation: Mol Microbiol. 2002 Oct;46(2):479-92
references.pmid: 12406223
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D225-9
references.pmid: 21109532
references.citation: Science. 2004 Apr 9;304(5668):304-7
references.pmid: 15001715
references.citation: BMC Genomics. 2008 Sep 16;9 Suppl 2:S25
references.pmid: 18831791
references.citation: Trends Biochem Sci. 1999 May;24(5):181-5
references.pmid: 10322433
references.citation: Nature. 2002 Feb 21;415(6874):871-80
references.pmid: 11859360
references.citation: Nucleic Acids Res. 1994 Nov 11;22(22):4828-36
references.pmid: 7984436
references.citation: Genome Res. 2003 Sep;13(9):2005-17
references.pmid: 12952872
references.citation: Mol Microbiol. 2003 Oct;50(1):245-57
references.pmid: 14507378
references.citation: Nat Biotechnol. 2009 Jun;27(6):561-6
references.pmid: 19465926
references.citation: Microbiology (Reading). 2005 Mar;151(Pt 3):673-681
references.pmid: 15758214
references.citation: Gene. 1995 Dec 29;167(1-2):GC1-10
references.pmid: 8566757
references.citation: Nucleic Acids Res. 2008 Oct;36(18):5970-82
references.pmid: 18812401
references.citation: Science. 1999 Jul 23;285(5427):578-82
references.pmid: 10417386
references.citation: Genome Res. 2009 Dec;19(12):2231-44
references.pmid: 19745113
references.citation: Nucleic Acids Res. 1999 Jan 15;27(2):573-80
references.pmid: 9862982
references.citation: Nature. 2004 Jul 1;430(6995):35-44
references.pmid: 15229592
references.citation: Proc Natl Acad Sci U S A. 2002 Dec 10;99(25):16029-34
references.pmid: 12461176
references.citation: Cell Mol Life Sci. 2010 Mar;67(5):671-6
references.pmid: 19946728
references.citation: Int J Biochem Cell Biol. 2011 Aug;43(8):1090-103
references.pmid: 21501695
references.citation: J Mol Biol. 2007 Jan 5;365(1):146-59
references.pmid: 17046787
references.citation: Genome Res. 2009 Oct;19(10):1696-709
references.pmid: 19525356
references.citation: Nature. 2005 Dec 22;438(7071):1151-6
references.pmid: 16372009
references.citation: FEMS Microbiol Rev. 2002 Aug;26(3):239-56
references.pmid: 12165426
references.citation: Science. 2000 Mar 10;287(5459):1809-15
references.pmid: 10710307
references.citation: Biochim Biophys Acta. 2010 Jun;1804(6):1231-64
references.pmid: 20117254
references.citation: Tuber Lung Dis. 1999;79(6):329-42
references.pmid: 10694977
references.citation: Nature. 1998 Jun 11;393(6685):537-44
references.pmid: 9634230
references.citation: EMBO Rep. 2003 Jun;4(6):628-32
references.pmid: 12776183
references.citation: Nat Biotechnol. 2007 Mar;25(3):319-26
references.pmid: 17334359
references.citation: BMC Genomics. 2006 Dec 05;7:307
references.pmid: 17147802
references.citation: Trends Microbiol. 2012 Feb;20(2):59-65
references.pmid: 22099004
references.citation: PLoS One. 2009 Aug 05;4(8):e6515
references.pmid: 19654869
references.citation: J Clin Invest. 2001 Mar;107(6):657-62
references.pmid: 11254662
references.citation: FEMS Microbiol Lett. 2008 Aug;285(2):137-45
references.pmid: 18616597
references.citation: Science. 1996 Oct 25;274(5287):546, 563-7
references.pmid: 8849441
references.citation: Microbiol Mol Biol Rev. 2008 Dec;72(4):686-727
references.pmid: 19052325
references.citation: Nucleic Acids Res. 1997 Sep 1;25(17):3389-402
references.pmid: 9254694
references.citation: BMC Evol Biol. 2009 Aug 10;9:195
references.pmid: 19664262
references.citation: Nucleic Acids Res. 2002 Apr 1;30(7):1575-84
references.pmid: 11917018
references.citation: G3 (Bethesda). 2012 Feb;2(2):299-311
references.pmid: 22384408
references.citation: Nat Rev Genet. 2010 Jul;11(7):512-24
references.pmid: 20559329
references.citation: Trends Microbiol. 2001 Apr;9(4):176-80
references.pmid: 11286882
references.citation: Proc Natl Acad Sci U S A. 2004 May 11;101(19):7329-34
references.pmid: 15123810
references.citation: Mol Biol Evol. 2009 Mar;26(3):591-602
references.pmid: 19056904
references.citation: Cell. 2000 Apr 14;101(2):199-210
references.pmid: 10786835
references.citation: Microbiology (Reading). 2001 Aug;147(Pt 8):2321-2332
references.pmid: 11496009
references.citation: Nucleic Acids Res. 1994 Nov 11;22(22):4673-80
references.pmid: 7984417