Efficient screening of long terminal repeat retrotransposons that show high insertion polymorphism via high-throughput sequencing of the primer binding site

Genome

Volumn 57, Issue 5, 2014, Pages 245-252

  Monden, Yuki ^a   Fujii, Nobuyuki ^b   Yamaguchi, Kentaro ^a   Ikeo, Kazuho ^b   Nakazawa, Yoshiko ^c   Waki, Takamitsu ^c   Hirashima, Keita ^d   Uchimura, Yosuke ^d   Tahara, Makoto ^a  

^a OKAYAMA UNIVERSITY   (Japan)

^b NATIONAL INSTITUTE OF GENETICS   (Japan)

^c Tochigi Prefectural Agricultural Experiment Station   (Japan)

^d FUKUOKA AGRICULTURAL RESEARCH CENTER   (Japan)

Author keywords

High throughput sequencing; Molecular markers; Polymorphism; Primer binding site; Retrotransposon

Indexed keywords

PLANT DNA; PRIMER DNA; RETROPOSON;

BINDING SITE; FRAGARIA; GENE EXPRESSION REGULATION; GENETIC POLYMORPHISM; GENETICS; HIGH THROUGHPUT SEQUENCING; LONG TERMINAL REPEAT; METABOLISM; NUCLEOTIDE SEQUENCE; PROCEDURES; RETROPOSON;

BASE SEQUENCE; BINDING SITES; CONSERVED SEQUENCE; DNA PRIMERS; DNA, PLANT; FRAGARIA; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MUTAGENESIS, INSERTIONAL; POLYMORPHISM, GENETIC; RETROELEMENTS; TERMINAL REPEAT SEQUENCES;

EID: 84909641057     PISSN: 08312796     EISSN: None     Source Type: Journal    
DOI: 10.1139/gen-2014-0031     Document Type: Article

References (50)

1. Antonius-Klemola K. Kalendar R. Schulman A.H. 2006. TRIM retrotransposons occur in apple and are polymorphic between varieties but not sports. Theor. Appl. Genet. 112 (6): 999-1008. 10.1007/s00122-005-0203-0. 16404583.
2. Benjamini Y. Hochberg Y. 1995. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. 57 (1): 289-300. Available from http://www.jstor.org/stable/2346101.
3. Ewing A.D. Kazazian H.H. 2011. Whole-genome resequencing allows detection of many rare LINE-1 insertion alleles in humans. Genome Res. 21 (6): 985-990. 10.1101/gr.114777.110. 20980553.
4. Feschotte C. Jiang N. Wessler S.R. 2002. Plant transposable elements: where genetics meets genomics. Nat. Rev. Genet. 3 (5): 329-341. 10.1038/nrg793. 11988759.
5. Flavell A.J. Knox M.R. Pearce S.R. Ellis T.H. 1998. Retrotransposon-based insertion polymorphisms (RBIP) for high throughput marker analysis. Plant J. 16 (5): 643-650. 10.1046/j.1365-313x.1998.00334.x. 10036780.
6. Havecker E.R. Gao X. Voytas D.F. 2004. The diversity of LTR retrotransposons. Genome Biol. 5 (6): 225. 10.1186/gb-2004-5-6-225. 15186483.
7. Hirakawa H. Shirasawa K. Kosugi S. Tashiro K. Nakayama S. Yamada M. et al 2014. Dissection of the octoploid strawberry genome by deep sequencing of the genomes of Fragaria species. DNA Res. 21 (2): 169-181. 10.1093/dnares/dst049. 24282021.
8. Hizi A. 2008. The reverse transcriptase of the Tf1 retrotransposon has a specific novel activity for generating the RNA self-primer that is functional in cDNA synthesis. J. Virol. 82 (21): 10906-10910. 10.1128/JVI.01370-08. 18753200.
9. Iskow R.C. McCabe M.T. Mills R.E. Torene S. Pittard W.S. Neuwald A.F. et al 2010. Natural mutagenesis of human genomes by endogenous retrotransposons. Cell, 141 (7): 1253-1261. 10.1016/j.cell.2010.05.020. 20603005.
10. Isobe S.N. Hirakawa H. Sato S. Maeda F. Ishikawa M. Mori T. et al 2013. Construction of an integrated high density simple sequence repeat linkage map in cultivated strawberry (Fragaria × ananassa) and its applicability. DNA Res. 20 (1): 79-92. 10.1093/dnares/dss035. 23248204.
11. Kalendar R. 2011. The use of retrotransposon-based molecular markers to analyze genetic diversity. Ratar. Povrt. 48 (2): 261-274. 10.5937/ratpov1102261K.
12. Kalendar R. Grob T. Regina M. Suoniemi A. Schulman A. 1999. IRAP and REMAP: two new retrotransposon-based DNA fingerprinting techniques. Theor. Appl. Genet. 98: 704-711. 10.1007/s001220051124.
13. Kalendar R. Antonius K. Smýkal P. Schulman A.H. 2010. iPBS: a universal method for DNA fingerprinting and retrotransposon isolation. Theor. Appl. Genet. 121 (8): 1419-1430. 10.1007/s00122-010-1398-2. 20623102.
14. Kalendar R. Flavell A.J. Ellis T.H.N. Sjakste T. Moisy C. Schulman A.H. 2011. Analysis of plant diversity with retrotransposon-based molecular markers. Heredity, 106 (4): 520-530. 10.1038/hdy.2010.93. 20683483.
15. Katoh K. Misawa K. Kuma K. Miyata T. 2002. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30 (14): 3059-3066. 10.1093/nar/gkf436. 12136088.
16. Kelly N.J. Palmer M.T. Morrow C.D. 2003. Selection of retroviral reverse transcription primer is coordinated with tRNA biogenesis. J. Virol. 77 (16): 8695-8701. 10.1128/JVI.77.16.8695-8701.2003. 12885888.
17. Kofler R. Betancourt A.J. Schlötterer C. 2012. Sequencing of pooled DNA samples (Pool-Seq) uncovers complex dynamics of transposable element insertions in Drosophila melanogaster. PLoS Genet. 8 (1): e1002487. 10.1371/journal.pgen.1002487. 22291611.
18. Krzywinski M. Schein J. Birol I. Connors J. Gascoyne R. Horsman D. et al 2009. Circos: an information aesthetic for comparative genomics. Genome Res. 19 (9): 1639-1645. 10.1101/gr.092759.109. 19541911.
19. Kumar A. Bennetzen J.L. 1999. Plant retrotransposons. Annu. Rev. Genet. 33: 479-532. 10.1146/annurev.genet.33.1.479. 10690416.
20. Kumar A. Hirochika H. 2001. Applications of retrotransposons as genetic tools in plant biology. Trends Plant Sci. 6 (3): 127-134. 10.1016/S1360-1385(00)01860-4. 11239612.
21. Levin H.L. Moran J.V. 2011. Dynamic interactions between transposable elements and their hosts. Nat. Rev. Genet. 12 (9): 615-627. 10.1038/nrg3030. 21850042.
22. Li H. Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25 (14): 1754-1760. 10.1093/bioinformatics/btp324. 19451168.
23. Li H. Handsaker B. Wysoker A. Fennell T. Ruan J. Homer N. et al 2009. The sequence alignment/map format and SAMtools. Bioinformatics, 25 (16): 2078-2079. 10.1093/bioinformatics/btp352. 19505943.
24. Lisch D. 2009. Epigenetic regulation of transposable elements in plants. Annu. Rev. Plant Biol. 60: 43-66. 10.1146/annurev.arplant.59.032607.092744. 19007329.
25. Macas J. Neumann P. Navrátilová A. 2007. Repetitive DNA in the pea (Pisum sativum L.) genome: comprehensive characterization using 454 sequencing and comparison to soybean and Medicago truncatula. BMC Genomics, 8: 427. 10.1186/1471-2164-8-427. 18031571.
26. Mak J. Kleiman L. 1997. Primer tRNAs for reverse transcription. J. Virol. 71 (11): 8087-8095. 9343157.
27. Marquet R. Isel C. Ehresmann C. Ehresmann B. 1995. tRNAs as primer of reverse transcriptases. Biochimie, 77: 113-124. 10.1016/0300-9084(96)88114-4. 7541250.
28. Mayer K.F.X. Waugh R. Brown J.W.S. Schulman A. Langridge P. et al 2012. A physical, genetic and functional sequence assembly of the barley genome. Nature, 491 (7426): 711-716. 10.1038/nature11543. 23075845.
29. McCarthy E.M. McDonald J.F. 2003. LTR-STRUC: a novel search and identification program for LTR retrotransposons. Bioinformatics, 19 (3): 362-367. 10.1093/bioinformatics/btf878. 12584121.
30. Monden Y. Yamamoto A. Shindo A. Tahara M. 2014. Efficient DNA fingerprinting based on the targeted sequencing of active retrotransposon insertion sites using a bench-top high-throughput sequencing platform. DNA Res. [Advance Access.] 10.1093/dnares/dsu015.
31. Novák P. Neumann P. Macas J. 2010. Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data. BMC Bioinformatics, 11: 378. 10.1186/1471-2105-11-378. 20633259.
32. Pagán H.J.T. Macas J. Novák P. McCulloch E.S. Stevens R.D. Ray D.A. 2012. Survey sequencing reveals elevated DNA transposon activity, novel elements, and variation in repetitive landscapes among vesper bats. Genome Biol. Evol. 4 (4): 575-585. 10.1093/gbe/evs038. 22491057.
33. Petit M. Guidat C. Daniel J. Denis E. Montoriol E. Bui QT. et al 2010. Mobilization of retrotransposons in synthetic allotetraploid tobacco. New Phytol. 186 (1): 135-147. 10.1111/j.1469-8137.2009.03140.x. 20074093.
34. Poczai P. Varga I. Laos M. Cseh A. Bell N. Valkonen J.P. Hyvönen J. 2013. Advances in plant gene-targeted and functional markers: a review. Plant Methods, 9 (1): 6. 10.1186/1746-4811-9-6. 23406322.
35. Quinlan A.R. Hall I.M. 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics, 26 (6): 841-842. 10.1093/bioinformatics/btq033. 20110278.
36. Rousseau-Gueutin M. Lerceteau-Köhler E. Barrot L. Sargent D.J. Monfort A. Simpson D. et al 2008. Comparative genetic mapping between octoploid and diploid Fragaria species reveals a high level of colinearity between their genomes and the essentially disomic behavior of the cultivated octoploid strawberry. Genetics, 179 (4): 2045-2060. 10.1534/genetics.107.083840. 18660542.
37. Sargent D.J. Fernandéz-Fernandéz F. Ruiz-Roja J.J. Sutherland B.G. Passey A. Whitehouse A.B. Simpson D.W. 2009. A genetic linkage map of the cultivated strawberry (Fragaria × ananassa) and its comparison to the diploid Fragaria reference map. Mol. Breed. 24 (3): 293-303. 10.1007/s11032-009-9292-9.
38. Sargent D.J. Passey T. Surbanovski N. Lopez Girona E. Kuchta P. Davik J. et al 2012. A microsatellite linkage map for the cultivated strawberry (Fragaria × ananassa) suggests extensive regions of homozygosity in the genome that may have resulted from breeding and selection. Theor. Appl. Genet. 124 (7): 1229-1240. 10.1007/s00122-011-1782-6. 22218676.
39. Schnable P.S. Ware D. Fulton R.S. Stein J.C. Wei F. Pasternak S. et al 2009. The B73 maize genome: complexity, diversity, and dynamics. Science, 326 (5956): 1112-1115. 10.1126/science.1178534. 19965430.
40. Shimizu K. Tsuda K. 2011. SlideSort: all pairs similarity search for short reads. Bioinformatics, 27 (4): 464-470. 10.1093/bioinformatics/btq677. 21148542.
41. Slotkin R.K. Martienssen R. 2007. Transposable elements and the epigenetic regulation of the genome. Nat. Rev. Genet. 8 (4): 272-285. 10.1038/nrg2072. 17363976.
42. Storey J.D. 2002. A direct approach to false discovery rates. J. R. Stat. Soc. Ser. B Stat. Methodol. 64 (3): 479-498. 10.1111/1467-9868.00346.
43. Syed N.H. Sureshsundar S. Wilkinson M.J. Bhau B.S. Cavalcanti J.J.V. Flavell A.J. 2005. Ty 1-copia retrotransposon-based SSAP marker development in cashew (Anacardium occidentale L.). Theor. Appl. Genet. 110 (7): 1195-1202. 10.1007/s00122-005-1948-1. 15761718.
44. Thorvaldsdóttir H. Robinson J.T. Mesirov J.P. 2013. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform. 14 (2): 178-192. 10.1093/bib/bbs017. 22517427.
45. Urbański D.F. Małolepszy A. Stougaard J. Andersen S.U. 2012. Genome-wide LORE 1 retrotransposon mutagenesis and high-throughput insertion detection in Lotus japonicus. Plant J. 69 (4): 731-741. 10.1111/j.1365-313X.2011.04827.x. 22014280.
46. Wang L. Feng Z. Wang X. Wang X. Zhang X. 2010. DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. Bioinformatics, 26 (1): 136-138. 10.1093/bioinformatics/btp612. 19855105.
47. Waugh R. McLean K. Flavell A.J. Pearce S.R. Kumar A. Thomas B.B. Powell W. 1997. Genetic distribution of Bare-1-like retrotransposable elements in the barley genome revealed by sequence-specific amplification polymorphisms (S-SAP). Mol. Gen. Genet. 253 (6): 687-694. 10.1007/s004380050372. 9079879.
48. Wessler S.R. 2006. Transposable elements and the evolution of eukaryotic genomes. Proc. Natl. Acad. Sci. U.S.A. 103 (47): 17600-17601. 10.1073/pnas.0607612103. 17101965.
49. Xing J. Witherspoon D.J. Jorde L.B. 2013. Mobile element biology: new possibilities with high-throughput sequencing. Trends Genet. 29 (5): 280-289. 10.1016/j.tig.2012.12.002. 23312846.
50. Zorrilla-Fontanesi Y. Cabeza A. Domínguez P. Medina J.J. Valpuesta V. Denoyes-Rothan B. et al 2011. Quantitative trait loci and underlying candidate genes controlling agronomical and fruit quality traits in octoploid strawberry (Fragaria × ananassa). Theor. Appl. Genet. 123 (5): 755-778. 10.1007/s00122-011-1624-6. 21667037.