title: Genome-wide comparative analysis of 20 miniature inverted-repeat transposable element families in Brassica rapa and B. oleracea.
abstract: Miniature inverted-repeat transposable elements (MITEs) are ubiquitous, non-autonomous class II transposable elements. Here, we conducted genome-wide comparative analysis of 20 MITE families in B. rapa, B. oleracea, and Arabidopsis thaliana. A total of 5894 and 6026 MITE members belonging to the 20 families were found in the whole genome pseudo-chromosome sequences of B. rapa and B. oleracea, respectively. Meanwhile, only four of the 20 families, comprising 573 members, were identified in the Arabidopsis genome, indicating that most of the families were activated in the Brassica genus after divergence from Arabidopsis. Copy numbers varied from 4 to 1459 for each MITE family, and there was up to 6-fold variation between B. rapa and B. oleracea. In particular, analysis of intact members showed that whereas eleven families were present in similar copy numbers in B. rapa and B. oleracea, nine families showed copy number variation ranging from 2- to 16-fold. Four of those families (BraSto-3, BraTo-3, 4, 5) were more abundant in B. rapa, and the other five (BraSto-1, BraSto-4, BraTo-1, 7 and BraHAT-1) were more abundant in B. oleracea. Overall, 54% and 51% of the MITEs resided in or within 2 kb of a gene in the B. rapa and B. oleracea genomes, respectively. Notably, 92 MITEs were found within the CDS of annotated genes, suggesting that MITEs might play roles in diversification of genes in the recently triplicated Brassica genome. MITE insertion polymorphism (MIP) analysis of 289 MITE members showed that 52% and 23% were polymorphic at the inter- and intra-species levels, respectively, indicating that there has been recent MITE activity in the Brassica genome. These recently activated MITE families with abundant MIP will provide useful resources for molecular breeding and identification of novel functional genes arising from MITE insertion.
authors.affiliation: Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea.
authors.forename: Perumal
authors.initials: P
authors.lastname: Sampath
authors.affiliation: Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea.
authors.forename: Jayakodi
authors.initials: J
authors.lastname: Murukarthick
authors.affiliation: Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea.
authors.forename: Nur Kholilatul
authors.initials: NK
authors.lastname: Izzah
authors.affiliation: Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea.
authors.forename: Jonghoon
authors.initials: J
authors.lastname: Lee
authors.affiliation: Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea.
authors.forename: Hong-Il
authors.initials: HI
authors.lastname: Choi
authors.affiliation: Department of Plant Genome Research, Kazusa DNA Research Institute, Chiba, Japan.
authors.forename: Kenta
authors.initials: K
authors.lastname: Shirasawa
authors.affiliation: National Instrumentation Center for Environmental Management, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea.
authors.forename: Beom-Soon
authors.initials: BS
authors.lastname: Choi
authors.affiliation: The Key Laboratory of Oil Crops Biology and Genetic Breeding, the Ministry of Agriculture, Oil Crops Research Institute, the Chinese Academy of Agricultural Sciences, Wuhan, China.
authors.forename: Shengyi
authors.initials: S
authors.lastname: Liu
authors.affiliation: Department of Horticulture, Sunchon National University, Suncheon, Republic of Korea.
authors.forename: Ill-Sup
authors.initials: IS
authors.lastname: Nou
authors.affiliation: Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea.
authors.forename: Tae-Jin
authors.initials: TJ
authors.lastname: Yang
mesh_terms: D001483:Base Sequence; D029741:Brassica rapa / Q000235:genetics*; D004251:DNA Transposable Elements / Q000235:genetics*; D018745:Genome, Plant / Q000235:genetics; D023281:Genomics; D055029:Inverted Repeat Sequences; D013045:Species Specificity
chemical_list: D004251:DNA Transposable Elements
references.citation: Nucleic Acids Res. 2008 Jan;36(Database issue):D154-8
references.pmid: 17991681
references.citation: Curr Opin Genet Dev. 1995 Dec;5(6):814-21
references.pmid: 8745082
references.citation: Methods Mol Biol. 2004;260:175-88
references.pmid: 15020809
references.citation: Proc Natl Acad Sci U S A. 2006 Nov 21;103(47):17620-5
references.pmid: 17101970
references.citation: Plant J. 1999 May;18(4):431-41
references.pmid: 10406126
references.citation: Mol Biol Evol. 2009 Jan;26(1):85-98
references.pmid: 18842687
references.citation: BMC Plant Biol. 2013 Apr 02;13:56
references.pmid: 23547712
references.citation: Genes Dev. 2006 May 15;20(10):1294-307
references.pmid: 16702403
references.citation: Curr Protoc Bioinformatics. 2009 Mar;Chapter 4:Unit 4.10
references.pmid: 19274634
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: Trends Plant Sci. 2012 Apr;17(4):204-12
references.pmid: 22326563
references.citation: J Mol Evol. 2004 Dec;59(6):747-60
references.pmid: 15599507
references.citation: Mol Biol Evol. 2012 Mar;29(3):1005-17
references.pmid: 22096216
references.citation: BMC Genomics. 2013 Sep 30;14:664
references.pmid: 24079801
references.citation: BMC Res Notes. 2014 Jun 20;7:379
references.pmid: 24948109
references.citation: Plant Physiol. 2011 Oct;157(2):552-62
references.pmid: 21844309
references.citation: Methods Mol Biol. 2000;132:365-86
references.pmid: 10547847
references.citation: Methods Mol Biol. 2012;859:1-28
references.pmid: 22367863
references.citation: Mol Biol Evol. 2006 Nov;23(11):2142-60
references.pmid: 16916944
references.citation: Curr Opin Genet Dev. 2007 Dec;17(6):505-12
references.pmid: 18006297
references.citation: Plant J. 2001 Jan;25(2):169-79
references.pmid: 11169193
references.citation: DNA Res. 2009 Apr;16(2):131-40
references.pmid: 19270311
references.citation: Nucleic Acids Res. 2010 Dec;38(22):e199
references.pmid: 20880995
references.citation: Gene. 2003 Jun 5;311:1-11
references.pmid: 12853133
references.citation: PLoS One. 2009;4(2):e4456
references.pmid: 19209240
references.citation: Nucleic Acids Res. 2003 Apr 1;31(7):1838-44
references.pmid: 12654999
references.citation: Cytogenet Genome Res. 2005;110(1-4):462-7
references.pmid: 16093699
references.citation: Theor Appl Genet. 2012 May;124(8):1429-38
references.pmid: 22294450
references.citation: Ann Bot. 2005 Jan;95(1):229-35
references.pmid: 15596470
references.citation: Theor Appl Genet. 2007 Feb;114(4):627-36
references.pmid: 17160537
references.citation: Genetics. 2010 Sep;186(1):59-66
references.pmid: 20610409
references.citation: Nat Rev Genet. 2008 May;9(5):397-405
references.pmid: 18368054
references.citation: Genome Res. 2009 Aug;19(8):1419-28
references.pmid: 19478138
references.citation: Nat Protoc. 2006;1(5):2320-5
references.pmid: 17406474
references.citation: Genome Res. 2009 Jan;19(1):42-56
references.pmid: 19037014
references.citation: Proc Natl Acad Sci U S A. 2000 Aug 29;97(18):10083-9
references.pmid: 10963671
references.citation: Plant Mol Biol. 2011 Sep;77(1-2):59-75
references.pmid: 21626236
references.citation: Mol Biol Evol. 2011 Oct;28(10):2731-9
references.pmid: 21546353
references.citation: Proc Natl Acad Sci U S A. 2001 Feb 13;98(4):1699-704
references.pmid: 11172014
references.citation: Nat Rev Genet. 2002 May;3(5):329-41
references.pmid: 11988759
references.citation: Nucleic Acids Res. 2003 Jul 1;31(13):3406-15
references.pmid: 12824337
references.citation: Nat Genet. 2011 Aug 28;43(10):1035-9
references.pmid: 21873998
references.citation: Nature. 2009 Oct 22;461(7267):1130-4
references.pmid: 19847266
references.citation: Plant J. 1998 Oct;16(1):79-85
references.pmid: 9807830
references.citation: Trends Genet. 2012 Dec;28(12):616-23
references.pmid: 23040327
references.citation: Nucleic Acids Res. 2003 Jul 1;31(13):3659-65
references.pmid: 12824388
references.citation: Nucleic Acids Res. 2014 Jan;42(Database issue):D1176-81
references.pmid: 24174541
references.citation: Science. 2004 Mar 12;303(5664):1626-32
references.pmid: 15016989
references.citation: Genome Biol. 2009;10(10):R111
references.pmid: 19821981
references.citation: Theor Appl Genet. 2012 May;124(7):1365-73
references.pmid: 22286503
references.citation: Plant Mol Biol. 2012 Nov;80(4-5):419-27
references.pmid: 22933118
references.citation: Gene. 2009 May 1;436(1-2):1-7
references.pmid: 19393167
references.citation: PLoS Genet. 2012 Sep;8(9):e1002953
references.pmid: 23028360
references.citation: Theor Appl Genet. 2002 Jan;104(1):104-10
references.pmid: 12579434
references.citation: Science. 2009 Sep 11;325(5946):1352-3
references.pmid: 19745141
references.citation: Proc Natl Acad Sci U S A. 2002 Jan 8;99(1):280-5
references.pmid: 11756687
references.citation: BMC Genomics. 2010 Sep 27;11:520
references.pmid: 20875122
references.citation: Genome Biol Evol. 2009 May 20;1:75-84
references.pmid: 20333179
references.citation: PLoS One. 2007 Feb 14;2(2):e203
references.pmid: 17301878
references.citation: PLoS One. 2012;7(5):e36599
references.pmid: 22662121
references.citation: Genome Biol. 2010;11(9):R94
references.pmid: 20875114
references.citation: Nat Rev Genet. 2007 Dec;8(12):973-82
references.pmid: 17984973
references.citation: BMC Bioinformatics. 2013 Jun 07;14:186
references.pmid: 23758809
references.citation: BMC Plant Biol. 2011 Oct 13;11:136
references.pmid: 21995777