title: Evolutionary dynamics of microsatellite distribution in plants: insight from the comparison of sequenced brassica, Arabidopsis and other angiosperm species.
abstract: Despite their ubiquity and functional importance, microsatellites have been largely ignored in comparative genomics, mostly due to the lack of genomic information. In the current study, microsatellite distribution was characterized and compared in the whole genomes and both the coding and non-coding DNA sequences of the sequenced Brassica, Arabidopsis and other angiosperm species to investigate their evolutionary dynamics in plants. The variation in the microsatellite frequencies of these angiosperm species was much smaller than those for their microsatellite numbers and genome sizes, suggesting that microsatellite frequency may be relatively stable in plants. The microsatellite frequencies of these angiosperm species were significantly negatively correlated with both their genome sizes and transposable elements contents. The pattern of microsatellite distribution may differ according to the different genomic regions (such as coding and non-coding sequences). The observed differences in many important microsatellite characteristics (especially the distribution with respect to motif length, type and repeat number) of these angiosperm species were generally accordant with their phylogenetic distance, which suggested that the evolutionary dynamics of microsatellite distribution may be generally consistent with plant divergence/evolution. Importantly, by comparing these microsatellite characteristics (especially the distribution with respect to motif type) the angiosperm species (aside from a few species) all clustered into two obviously different groups that were largely represented by monocots and dicots, suggesting a complex and generally dichotomous evolutionary pattern of microsatellite distribution in angiosperms. Polyploidy may lead to a slight increase in microsatellite frequency in the coding sequences and a significant decrease in microsatellite frequency in the whole genome/non-coding sequences, but have little effect on the microsatellite distribution with respect to motif length, type and repeat number. Interestingly, several microsatellite characteristics seemed to be constant in plant evolution, which can be well explained by the general biological rules.
authors.affiliation: Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China.
authors.forename: Jiaqin
authors.initials: J
authors.lastname: Shi
authors.forename: Shunmou
authors.initials: S
authors.lastname: Huang
authors.forename: Donghui
authors.initials: D
authors.lastname: Fu
authors.forename: Jinyin
authors.initials: J
authors.lastname: Yu
authors.forename: Xinfa
authors.initials: X
authors.lastname: Wang
authors.forename: Wei
authors.initials: W
authors.lastname: Hua
authors.forename: Shengyi
authors.initials: S
authors.lastname: Liu
authors.forename: Guihua
authors.initials: G
authors.lastname: Liu
authors.forename: Hanzhong
authors.initials: H
authors.lastname: Wang
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D005075:Biological Evolution; D001937:Brassica / Q000235:genetics*; D018745:Genome, Plant / Q000235:genetics; D019684:Magnoliopsida / Q000145:classification / Q000235:genetics*; D018895:Microsatellite Repeats / Q000235:genetics*; D010802:Phylogeny
references.citation: Plant J. 2000 Jul;23(2):233-43
references.pmid: 10929117
references.citation: Annu Rev Genet. 2010;44:445-77
references.pmid: 20809801
references.citation: Trends Plant Sci. 2006 Nov;11(11):535-42
references.pmid: 17029932
references.citation: J Mol Evol. 2010 Mar;70(3):275-88
references.pmid: 20217059
references.citation: DNA Res. 2007 Feb 28;14(1):37-45
references.pmid: 17452422
references.citation: Genome Res. 2006 Jul;16(7):934-46
references.pmid: 16760422
references.citation: Nat Genet. 2011 Aug 28;43(10):1035-9
references.pmid: 21873998
references.citation: PLoS One. 2011;6(6):e21298
references.pmid: 21713003
references.citation: Proc Natl Acad Sci U S A. 2004 Dec 28;101(52):18058-63
references.pmid: 15596718
references.citation: Nat Rev Genet. 2004 Jun;5(6):435-45
references.pmid: 15153996
references.citation: Theor Appl Genet. 2003 Feb;106(3):411-22
references.pmid: 12589540
references.citation: PLoS One. 2011;6(7):e22306
references.pmid: 21799819
references.citation: Brief Bioinform. 2008 Sep;9(5):355-66
references.pmid: 18621747
references.citation: Nat Genet. 2002 Feb;30(2):194-200
references.pmid: 11799393
references.citation: Int J Mol Sci. 2012;13(7):8549-61
references.pmid: 22942719
references.citation: Plant Cell. 2006 Jun;18(6):1339-47
references.pmid: 16632644
references.citation: Proc Natl Acad Sci U S A. 2004 Apr 13;101(15):5589-94
references.pmid: 15064405
references.citation: Proc Natl Acad Sci U S A. 1997 Feb 4;94(3):1041-6
references.pmid: 9023379
references.citation: Proc Natl Acad Sci U S A. 2006 Jul 25;103(30):11228-33
references.pmid: 16844788
references.citation: Proc Natl Acad Sci U S A. 2010 Oct 26;107(43):18724-8
references.pmid: 20921408
references.citation: Genome. 2008 Jun;51(6):399-408
references.pmid: 18521118
references.citation: Science. 2009 May 29;324(5931):1213-6
references.pmid: 19478187
references.citation: Eukaryot Cell. 2007 Aug;6(8):1380-91
references.pmid: 17557878
references.citation: Curr Opin Plant Biol. 2007 Apr;10(2):168-75
references.pmid: 17300984
references.citation: Trends Biotechnol. 2007 Nov;25(11):490-8
references.pmid: 17945369
references.citation: Genome Biol. 2006;7(2):R14
references.pmid: 16507170
references.citation: Trends Ecol Evol. 1999 Sep;14(9):348-352
references.pmid: 10441308
references.citation: Mol Biol Evol. 2004 Jun;21(6):991-1007
references.pmid: 14963101
references.citation: Genomics. 2009 Apr;93(4):323-31
references.pmid: 19146945
references.citation: Genetics. 1997 Jul;146(3):769-79
references.pmid: 9215886
references.citation: Mol Ecol. 2002 Dec;11(12):2453-65
references.pmid: 12453231
references.citation: Genetics. 2005 Jul;170(3):1239-45
references.pmid: 15911583
references.citation: Science. 1994 Apr 15;264(5157):421-4
references.pmid: 17836906
references.citation: Mol Genet Genomics. 2001 Nov;266(3):471-80
references.pmid: 11713677
references.citation: Trends Biotechnol. 2005 Jan;23(1):48-55
references.pmid: 15629858
references.citation: Proc Natl Acad Sci U S A. 2004 Mar 9;101(10):3504-9
references.pmid: 14993601
references.citation: Mol Biol Evol. 2001 Jul;18(7):1161-7
references.pmid: 11420357
references.citation: Science. 2005 Jun 10;308(5728):1630-4
references.pmid: 15947188
references.citation: Genetics. 2008 May;179(1):581-92
references.pmid: 18493073
references.citation: PLoS One. 2007 Aug 29;2(8):e795
references.pmid: 17726525
references.citation: J Appl Genet. 2011 Nov;52(4):391-401
references.pmid: 21769669
references.citation: BMC Plant Biol. 2011 Jan 19;11:15
references.pmid: 21247422
references.citation: Genome Biol Evol. 2012;4(3):265-77
references.pmid: 22275519
references.citation: Microbiol Mol Biol Rev. 2008 Dec;72(4):686-727
references.pmid: 19052325
references.citation: Genet Mol Biol. 2009 Oct;32(4):822-33
references.pmid: 21637460
references.citation: Am J Hum Genet. 2000 Aug;67(2):345-56
references.pmid: 10889045
references.citation: Mol Biol Evol. 2002 Aug;19(8):1251-60
references.pmid: 12140237
references.citation: Proc Natl Acad Sci U S A. 1989 Aug;86(16):6201-5
references.pmid: 2762323
references.citation: Mol Biol Evol. 1998 Dec;15(12):1751-60
references.pmid: 9866209
references.citation: BMC Genomics. 2010 Oct 15;11:569
references.pmid: 20950470
references.citation: Plant J. 2008 Dec;56(6):1030-44
references.pmid: 18764926
references.citation: Genome Res. 2006 Oct;16(10):1252-61
references.pmid: 16954538
references.citation: Plant Mol Biol. 2011 Oct;77(3):225-33
references.pmid: 21805197
references.citation: Genome Biol. 2010;11(9):R94
references.pmid: 20875114
references.citation: Mol Genet Genomics. 2011 Aug;286(2):161-70
references.pmid: 21766184
references.citation: Planta. 2007 Feb;225(3):603-14
references.pmid: 16953430
references.citation: Plant Cell. 2007 Nov;19(11):3403-17
references.pmid: 18024568
references.citation: Plant Cell. 2006 Jun;18(6):1348-59
references.pmid: 16632643