title: Diversity of transposable elements and repeats in a 600 kb region of the fly Calliphora vicina.
abstract: BACKGROUND
  Transposable elements (TEs) are a very dynamic component of eukaryotic genomes with important implications (e.g., in evolution) and applications (e.g., as transgenic tools). They also represent a major challenge for the assembly and annotation of genomic sequences. However, they are still largely unknown in non-model species.
  
  
  RESULTS
  Here, we have annotated the repeats and transposable elements present in a 600 kb genomic region of the blowfly Calliphora vicina (Diptera: Calliphoridae) which contains most of the achaete-scute gene complex of this species. This is the largest genomic region to be sequenced and analyzed in higher flies outside the Drosophila genus. We find that the repeat content spans at least 24% of the sequence. It includes 318 insertions classified as 3 LTR retrotransposons, 21 LINEs, 14 cut-and-paste DNA transposons, 4 helitrons and 33 unclassified repeats.
  
  
  CONCLUSIONS
  This is the most detailed description of TEs and repeats in the Calliphoridae to date. This contribution not only adds to our knowledge about TE evolution but will also help in the annotation of repeats on Dipteran whole genome sequences.
authors.affiliation: Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK. bnegre@gmail.com.
authors.forename: Bárbara
authors.initials: B
authors.lastname: Negre
authors.forename: Pat
authors.initials: P
authors.lastname: Simpson
references.citation: Trends Ecol Evol. 2000 Mar;15(3):95-99
references.pmid: 10675923
references.citation: Nature. 2006 Oct 5;443(7111):521-4
references.pmid: 17024082
references.citation: Mol Genet Genomics. 2007 Jan;277(1):83-95
references.pmid: 17039376
references.citation: Proc Natl Acad Sci U S A. 2001 Jul 17;98(15):8714-9
references.pmid: 11447285
references.citation: J Mol Biol. 2000 Sep 8;302(1):205-17
references.pmid: 10964570
references.citation: Proc Natl Acad Sci U S A. 2003 May 27;100(11):6569-74
references.pmid: 12743378
references.citation: Nature. 2007 Nov 8;450(7167):203-18
references.pmid: 17994087
references.citation: Genet Mol Res. 2010 May 04;9(2):849-57
references.pmid: 20449818
references.citation: Genetics. 2007 Dec;177(4):2553-8
references.pmid: 17947403
references.citation: J Mol Biol. 1990 Oct 5;215(3):403-10
references.pmid: 2231712
references.citation: J Hered. 1997 Jan-Feb;88(1):72-6
references.pmid: 9048446
references.citation: Bioinformatics. 2007 Nov 1;23(21):2947-8
references.pmid: 17846036
references.citation: Mol Biol Evol. 2005 Jan;22(1):29-39
references.pmid: 15356275
references.citation: Science. 2007 Jun 22;316(5832):1718-23
references.pmid: 17510324
references.citation: Science. 2010 Oct 1;330(6000):86-8
references.pmid: 20929810
references.citation: Genome Biol. 2008;9(2):R39
references.pmid: 18291035
references.citation: Proc Natl Acad Sci U S A. 2007 Jul 3;104(27):11340-5
references.pmid: 17592135
references.citation: Gene. 2009 Dec 1;448(1):40-5
references.pmid: 19716865
references.citation: Gene. 2009 Dec 15;448(2):124-33
references.pmid: 19555747
references.citation: Nucleic Acids Res. 2012 Jan;40(Database issue):D706-14
references.pmid: 22127867
references.citation: Mol Biol Evol. 2011 May;28(5):1633-44
references.pmid: 21172826
references.citation: Insect Mol Biol. 2007 Dec;16(6):743-52
references.pmid: 18093003
references.citation: Trends Plant Sci. 2001 Mar;6(3):127-34
references.pmid: 11239612
references.citation: Mol Genet Genomics. 2011 Jun;285(6):447-60
references.pmid: 21505885
references.citation: Science. 2002 Oct 4;298(5591):129-49
references.pmid: 12364791
references.citation: Trends Ecol Evol. 2010 Sep;25(9):537-46
references.pmid: 20591532
references.citation: Curr Opin Genet Dev. 1992 Dec;2(6):861-7
references.pmid: 1335807
references.citation: Insect Mol Biol. 2010 Dec;19(6):707-15
references.pmid: 20636348
references.citation: Naturwissenschaften. 2004 Feb;91(2):51-65
references.pmid: 14991142
references.citation: Trends Genet. 2007 Oct;23(10):521-9
references.pmid: 17850916
references.citation: Nat Rev Genet. 2008 May;9(5):411-2; author reply 414
references.pmid: 18421312
references.citation: Genome Biol. 2006;7(11):R112
references.pmid: 17134480
references.citation: Genetics. 2001 Nov;159(3):1103-15
references.pmid: 11729156
references.citation: Nature. 2001 Feb 15;409(6822):860-921
references.pmid: 11237011
references.citation: Nucleic Acids Res. 2007 Jul;35(Web Server issue):W265-8
references.pmid: 17485477
references.citation: Heredity (Edinb). 2008 Jun;100(6):545-54
references.pmid: 18431403
references.citation: Genetica. 2011 Jan;139(1):41-52
references.pmid: 20725766
references.citation: Nucleic Acids Res. 2010 Jul;38(Web Server issue):W695-9
references.pmid: 20439314
references.citation: Nucleic Acids Res. 2011 Jul;39(Web Server issue):W13-7
references.pmid: 21558174
references.citation: Heredity (Edinb). 2010 Jun;104(6):520-33
references.pmid: 19935826
references.citation: Nat Rev Genet. 2007 Dec;8(12):973-82
references.pmid: 17984973
references.citation: Genetica. 2008 Jun;133(2):137-45
references.pmid: 17705057
references.citation: Bioessays. 2009 Jul;31(7):703-14
references.pmid: 19415638
references.citation: Genetica. 2002 May;115(1):49-63
references.pmid: 12188048