Insights on genome size evolution from a miniature inverted repeat transposon driving a satellite DNA

Molecular Phylogenetics and Evolution

Volumn 81, Issue , 2014, Pages 1-9

  Scalvenzi, Thibault ^a   Pollet, Nicolas ^a  

^a UNIVERSITÉ D EVRY VAL D ESSONNE   (France)

Author keywords

Amphibian; Genome; Miniature inverted repeat; Satellite DNA; Tc1 mariner; Transposon

Indexed keywords

SATELLITE DNA; TRANSPOSON;

ANIMAL; DNA SEQUENCE; GENETICS; GENOME SIZE; MOLECULAR EVOLUTION; NUCLEOTIDE SEQUENCE; PHYLOGENY; SEQUENCE HOMOLOGY; TRANSPOSON; XENOPUS;

ANIMALS; BASE SEQUENCE; CONSERVED SEQUENCE; DNA TRANSPOSABLE ELEMENTS; DNA, SATELLITE; EVOLUTION, MOLECULAR; GENOME SIZE; PHYLOGENY; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, NUCLEIC ACID; XENOPUS;

EID: 84907553085     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2014.08.014     Document Type: Article

References (48)

1. Bergemann M., Lespinet O., M'Barek S.B., Daboussi M.-J., Dufresne M. Genome-wide analysis of the Fusarium oxysporum mimp family of MITEs and mobilization of both native and de novo created mimps. J. Mol. Evol. 2008, 67:631-642. 10.1007/s00239-008-9164-7.
2. Bureau T.E., Wessler S.R. Tourist: a large family of small inverted repeat elements frequently associated with maize genes. Plant Cell 1992, 4:1283-1294.
3. Crooks G.E., Hon G., Chandonia J.-M., Brenner S.E. WebLogo: a sequence logo generator. Genome Res. 2004, 14:1188-1190. 10.1101/gr.849004.
4. Deen P.M., Terwel D., Bussemakers M.J., Roubos E.W., Martens G.J. Structural analysis of the entire proopiomelanocortin gene of Xenopus laevis. Eur. J. Biochem. FEBS 1991, 201:129-137.
5. Deen P.M., Bussemakers M.J., Terwel D., Roubos E.W., Martens G.J. Comparative structural analysis of the transcriptionally active proopiomelanocortin genes A and B of Xenopus laevis. Mol. Biol. Evol. 1992, 9:483-494.
6. Edgar R.C. Search and clustering orders of magnitude faster than BLAST. Bioinform. Oxf. Engl. 2010, 26:2460-2461. 10.1093/bioinformatics/btq461.
7. Feschotte, C., Zhang, X., Wessler, S.R., 2002. Miniature inverted-repeat transposable elements (MITEs) and their relationship with established DNA transposons. In: Craig, N., Craigie, R., Gellert, M., Lambowitz, A. (Eds.), Mobile DNA II. ASM press, Washington D.C., pp. 1147-1158.
8. Feschotte C., Swamy L., Wessler S.R. Genome-wide analysis of mariner-like transposable elements in rice reveals complex relationships with stowaway miniature inverted repeat transposable elements (MITEs). Genetics 2003, 163:747-758.
9. Feschotte C., Osterlund M.T., Peeler R., Wessler S.R. DNA-binding specificity of rice mariner-like transposases and interactions with Stowaway MITEs. Nucleic Acids Res. 2005, 33:2153-2165. 10.1093/nar/gki509.
10. Fleetwood D.J., Khan A.K., Johnson R.D., Young C.A., Mittal S., Wrenn R.E., Hesse U., Foster S.J., Schardl C.L., Scott B. Abundant degenerate miniature inverted-repeat transposable elements in genomes of epichloid fungal endophytes of grasses. Genome Biol. Evol. 2011, 3:1253-1264. 10.1093/gbe/evr098.
11. Gregory T.R. The Evolution of the Genome 2005, Elsevier Academic, Burlington, MA.
12. Guindon S., Dufayard J.-F., Lefort V., Anisimova M., Hordijk W., Gascuel O. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol. 2010, 59:307-321. 10.1093/sysbio/syq010.
13. Hellsten U., Harland R.M., Gilchrist M.J., Hendrix D., Jurka J., Kapitonov V., Ovcharenko I., Putnam N.H., Shu S., Taher L., Blitz I.L., Blumberg B., Dichmann D.S., Dubchak I., Amaya E., Detter J.C., Fletcher R., Gerhard D.S., Goodstein D., Graves T., Grigoriev I.V., Grimwood J., Kawashima T., Lindquist E., Lucas S.M., Mead P.E., Mitros T., Ogino H., Ohta Y., Poliakov A.V., Pollet N., Robert J., Salamov A., Sater A.K., Schmutz J., Terry A., Vize P.D., Warren W.C., Wells D., Wills A., Wilson R.K., Zimmerman L.B., Zorn A.M., Grainger R., Grammer T., Khokha M.K., Richardson P.M., Rokhsar D.S. The genome of the Western clawed frog Xenopus tropicalis. Science 2010, 328:633-636. 10.1126/science.1183670.
14. Hikosaka A., Kawahara A. A systematic search and classification of T2 family miniature inverted-repeat transposable elements (MITEs) in Xenopus tropicalis suggests the existence of recently active MITE subfamilies. Mol. Genet. Genom. MGG 2010, 283:49-62. 10.1007/s00438-009-0496-9.
15. Hikosaka A., Nishimura K., Hikosaka-Katayama T., Kawahara A. Recent transposition activity of Xenopus T2 family miniature inverted-repeat transposable elements. Mol. Genet. Genom. MGG 2011, 285:219-224. 10.1007/s00438-010-0599-3.
16. Hua-Van A., Le Rouzic A., Boutin T.S., Filée J., Capy P. The struggle for life of the genome's selfish architects. Biol. Direct 2011, 6:19. 10.1186/1745-6150-6-19.
17. Jiang N., Feschotte C., Zhang X., Wessler S.R. Using rice to understand the origin and amplification of miniature inverted repeat transposable elements (MITEs). Curr. Opin. Plant Biol. 2004, 7:115-119. 10.1016/j.pbi.2004.01.004.
18. Jurka J., Kapitonov V.V., Pavlicek A., Klonowski P., Kohany O., Walichiewicz J. Repbase Update, a database of eukaryotic repetitive elements. Cytogenet. Genome Res. 2005, 110:462-467. 10.1159/000084979.
19. Kapitonov V.V., Jurka J. Helitrons on a roll: eukaryotic rolling-circle transposons. Trends Genet. TIG 2007, 23:521-529. 10.1016/j.tig.2007.08.004.
20. Krüger J., Vogel F. Population genetics of unequal crossing over. J. Mol. Evol. 1975, 4:201-247. 10.1007/BF01732983.
21. Levinson G., Gutman G.A. Slipped-strand mispairing: a major mechanism for DNA sequence evolution. Mol. Biol. Evol. 1987, 4:203-221.
22. Lisch D. How important are transposons for plant evolution?. Nat. Rev. Genet. 2013, 14:49-61. 10.1038/nrg3374.
23. Lu C., Chen J., Zhang Y., Hu Q., Su W., Kuang H. Miniature Inverted-Repeat Transposable Elements (MITEs) have been accumulated through amplification bursts and play important roles in gene expression and species diversity in Oryza sativa. Mol. Biol. Evol. 2012, 29:1005-1017. 10.1093/molbev/msr282.
24. Luo G., Ivics Z., Izsvák Z., Bradley A. Chromosomal transposition of a Tc1/mariner-like element in mouse embryonic stem cells. Proc. Natl. Acad. Sci. 1998, 95:10769-10773.
25. Metcalfe C.J., Filée J., Germon I., Joss J., Casane D. Evolution of the Australian lungfish (Neoceratodus forsteri) genome: a major role for CR1 and L2 LINE elements. Mol. Biol. Evol. 2012, 29:3529-3539. 10.1093/molbev/mss159.
26. Meyerhof W., Korge E., Knöchel W. Characterization of repetitive DNA transcripts isolated from a Xenopus laevis gastrula-stage cDNA clone bank. Rouxs Arch. Dev. Biol. 1987, 196:22-29. 10.1007/BF00376019.
27. Meyerhof W., Stalder J., Köster M., Wirthmüller U., Knöchel W. Sequence analysis of the upstream regions of Xenopus laevis beta-globin genes and arrangement of repetitive elements within the globin gene clusters. Mol. Biol. Rep. 1990, 14:17-26.
28. Nachman M.W. Variation in recombination rate across the genome: evidence and implications. Curr. Opin. Genet. Dev. 2002, 12:657-663.
29. Negoua A., Rouault J.-D., Chakir M., Capy P. Internal deletions of transposable elements: the case of Lemi elements. Genetica 2013, 141:369-379. 10.1007/s10709-013-9736-3.
30. Okumura K., Kiyama R., Oishi M. Sequence analyses of extrachromosomal Sau3A and related family DNA: analysis of recombination in the excision event. Nucleic Acids Res. 1987, 15:7477-7489.
31. Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 1999, 27:573-580.
32. Plohl M., Luchetti A., Mestrović N., Mantovani B. Satellite DNAs between selfishness and functionality: structure, genomics and evolution of tandem repeats in centromeric (hetero)chromatin. Gene 2008, 409:72-82. 10.1016/j.gene.2007.11.013.
33. Plohl M., Meštrović N., Mravinac B. Satellite DNA evolution. Genome Dyn. 2012, 7:126-152. 10.1159/000337122.
34. Pollet N., Mazabraud A. Insights from Xenopus genomes. Genome Dyn. 2006, 2:138-153. 10.1159/000095101.
35. Šatović E., Plohl M. Tandem repeat-containing MITEs in the clam Donax trunculus. Genome Biol. Evol. 2013, 5:2549-2559. 10.1093/gbe/evt202.
36. Shen J.J., Dushoff J., Bewick A.J., Chain F.J.J., Evans B.J. Genomic dynamics of transposable elements in the western clawed frog (Silurana tropicalis). Genome Biol. Evol. 2013, 5:998-1009. 10.1093/gbe/evt065.
37. Sievers F., Wilm A., Dineen D., Gibson T.J., Karplus K., Li W., Lopez R., McWilliam H., Remmert M., Söding J., Thompson J.D., Higgins D.G. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol. Syst. Biol. 2011, 7:539. 10.1038/msb.2011.75.
38. Sinzelle L., Pollet N., Bigot Y., Mazabraud A. Characterization of multiple lineages of Tc1-like elements within the genome of the amphibian Xenopus tropicalis. Gene 2005, 349:187-196. 10.1016/j.gene.2004.12.023.
39. Sinzelle L., Chesneau A., Bigot Y., Mazabraud A., Pollet N. The mariner transposons belonging to the irritans subfamily were maintained in chordate genomes by vertical transmission. J. Mol. Evol. 2006, 62:53-65. 10.1007/s00239-005-0013-7.
40. Sinzelle L., Izsvák Z., Ivics Z. Molecular domestication of transposable elements: from detrimental parasites to useful host genes. Cell. Mol. Life Sci. CMLS 2009, 66:1073-1093. 10.1007/s00018-009-8376-3.
41. Sinzelle L., Carradec Q., Paillard E., Bronchain O.J., Pollet N. Characterization of a Xenopus tropicalis endogenous retrovirus with developmental and stress-dependent expression. J. Virol. 2011, 85:2167-2179. 10.1128/JVI.01979-10.
42. Smith G.P. Evolution of repeated DNA sequences by unequal crossover. Science 1976, 191:528-535.
43. Sonnhammer E.L., Durbin R. A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis. Gene 1995, 167:GC1-GC10.
44. Sun C., Shepard D.B., Chong R.A., López Arriaza J., Hall K., Castoe T.A., Feschotte C., Pollock D.D., Mueller R.L. LTR retrotransposons contribute to genomic gigantism in plethodontid salamanders. Genome Biol. Evol. 2012, 4:168-183. 10.1093/gbe/evr139.
45. Walsh J.B. Persistence of tandem arrays: implications for satellite and simple-sequence DNAs. Genetics 1987, 115:553-567.
46. Wicker T., Sabot F., Hua-Van A., Bennetzen J.L., Capy P., Chalhoub B., Flavell A., Leroy P., Morgante M., Panaud O., Paux E., SanMiguel P., Schulman A.H. A unified classification system for eukaryotic transposable elements. Nat. Rev. Genet. 2007, 8:973-982. 10.1038/nrg2165.
47. Yang H.-P., Barbash D.A. Abundant and species-specific DINE-1 transposable elements in 12 Drosophila genomes. Genome Biol. 2008, 9:R39. 10.1186/gb-2008-9-2-r39.
48. Yang G., Fattash I., Lee C.-N., Liu K., Cavinder B. Birth of three stowaway-like MITE families via microhomology-mediated miniaturization of a Tc1/Mariner element in the yellow fever mosquito. Genome Biol. Evol. 2013, 5:1937-1948. 10.1093/gbe/evt146.