The Future of Transposable Element Annotation and Their Classification in the Light of Functional Genomics

The future of transposable element annotation and their classification in the light of functional genomics -what we can learn from the fables of Jean de la Fontaine? Peter Arensburger, Benoit Piegu, Yves Bigot

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Peter Arensburger, Benoit Piegu, Yves Bigot. The future of transposable element annotation and their classification in the light of functional genomics - what we can learn from thefables of Jean de la Fontaine?. Mobile Genetic Elements, Taylor & Francis, 2016, 6 (6), pp.e1256852. 10.1080/2159256X.2016.1256852. hal-02385838

HAL Id: hal-02385838 https://hal.archives-ouvertes.fr/hal-02385838 Submitted on 27 May 2020

HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Copyright Version postprint of Jean de la Fontaine?. Mobile Genetic Elements, 6(6), 1-17. DOI: 10.1080/2159256X.2016.1256852 Arensburger, P.,Piégu, B.,Bigot,Y. (2016). Thefuture oftransposable elementannotation and progressfurther in than aid genewere rather specifically developed to annotation to study TEs. We that argue subsequently developed. is genome whole Today, mostly annotation using done TE tools that David Finnegan near last the end the of century Transposable ideas sciencebysignificantly element influenced has (TE) pioneering the beenof Abstract transposableTE, element mobile geneticMGE, element Institute GIRI, Genetic Information ICE, integrative conjuga Abbreviations keywords address: author Corresponding Bi 2 1 Peter Arensburger functional genomics of future The element transposable annotation classification andtheir light the of in

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a TE taxonomy that that taxonomy a TE field 3 . In Table 1 ul ul Version postprint of Jean de la Fontaine?. Mobile Genetic Elements, 6(6), 1-17. DOI: 10.1080/2159256X.2016.1256852 Arensburger, P.,Piégu, B.,Bigot,Y. (2016). Thefuture oftransposable elementannotation and de laRecherche et de laTechnologie. STUDIUM and Ministère dethe Recherche Groupement the Nationale, CNRS 2157, de l’Education work This was by funded State University, California the Polytechnic C.N.R.S., the I.N.R.A., the Acknowledgments fable we it, disputeiswould Without great always “The of help. “Cat the andFox”: sleeping!” be a such certainly society of organization The would butto La bethe quote Fontaine challenging including theirbiology organiz role nuclear in scientificinternational societyvarious communities focused on that gathers several aspects TE of of taxonomy the TEs. However, emergence the may a a such be to first of committee step an and eukaryotic sides)prokaryotic take as as to the chargeof well virologists Transposable Taxonomy the of gather (ICTTE) researchers Element that would TE the on (both we In 2015 Concluding remarks phages,prokaryotic and TEs. ICEs have PhiGO used a such scheme and ACLAME create to this new to field, haswhile been previously Ariane Since early the Toussaint's used. 2000's team sequences novel of characterization taxonomic groups. Such new TE a of propo and discovery system. be shared clustered basedterms. their ontological would both This TEscould on allow thatforth a system base discussionthese aIn of course the of on recentmeeting international issues ICE and TEs. between(seeabove) strict since becertain a viruses, continuum may there too is likely phages, their classification inthe lightoffunctional genomics -whatwecan learnfromthe fables

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fundamental update to meet the challenge of their diversity and complexity. Piégu, B., Bire, S., Arensburger, P. & Bigot, Y. A survey of transposable element classification systems La Fontaine, J. ‘The Lion and Rat’ Book 2, Fable 11. La Fontaine, J. ‘The Wolf and Lamb’ Book 1, Fable 10. 29, wide characterization of eukaryotic repetitive elements next from Novak, P., Neumann, P., Pech, J., Steinhaisl, J. & Macas, J. RepeatExplor aegypti). dnaPipeTEwith from Raw Genomic Reads and Comparative Analysis thewith Yellow Fever Mosquito (Aedes Goubert, C. 1269 Bao,Automated Z. De Novo Identification of Repeat Sequence Families in Sequenced Genomes. Benson, Tandem G. repeats finder: programa to analyze sequencDNA Hubley, R. chicken genome. Mason, A. S., Fulton, E.,J. Hocking, M.P. & Burt, W.D. A new look at the L BMC Genomics repeats in the genome model of the red jungle Gallusfowl, gallus, using seriesa of de novo investigating tools. Guizard, S., Piégu, B., Arensburger, P., Guillou, & F. Bigot, DeepY. landscape Holt, R. A. Lander, E. S. A Smit, A, Hubley,F R. & Green, RepeatMaskerP. Open Microbiol. Haren Hoen, R. D. (2015). ences

792 – , L., , Ton 1276 (2002).

– 793 (2013). Genome Biol. Evol.

et al. 53, et al. et al. et al. et al.

- 245

Hoang, B. & Chandler, M. Integrating DNA: Transposases and Retroviral Integrases. 17,

The genome sequence of the malaria mosquito Anopheles gambiae. The Dfam Thedatabase Dfam of repetitive families.DNA

A call for benchmarking transposable element annotation methods. De Novo Assembly and Annotation of the Asian Tiger Mosquito ( BMC Genomics

Initial sequencinInitial – 659 (2016). 281 (1999).

Comment citer cedocument:

1192

17, g g and analysis of the human genome. –

688 (2016). 1205 (2015).

9 -

3.0. 3.0. 1996 Nucleic Acids Res. - 2010. (1996). - generation sequence reads. er: a er: Galaxy a es. TR retrotransposon contentof the Nature Nucleic Acids Res.

update of dispersed and tandem Mol. Phylogenet. Evol.

409,

44, - Aedes albopictus) Repeatome based web server for genome Science

D81 Mob. DNA 860 – – D89 (2016). 921 (2001).

298, 27,

Bioinformatics 6, 573 Genome Res.

129 (2002).

(2015).

Annu. Rev. 86, –

580 (1999). -

A call for a 90 –

109

12,

Version postprint of Jean de la Fontaine?. Mobile Genetic Elements, 6(6), 1-17. DOI: 10.1080/2159256X.2016.1256852 Arensburger, P.,Piégu, B.,Bigot,Y. (2016). Thefuture oftransposable elementannotation and 32. 31. 30. 29. 28. 27. 26. 25. 24. 23. 22. 21. 20. 19. 18. 17. 16. their classification inthe lightoffunctional genomics -whatwecan learnfromthe fables

Girgis, Girgis, H. Z. Red: an intelligent, rapid, accurate tool for detecting repeats de 21, Price, A. L., Jones, N. C. & Pevzner, A. P. De novo identification of repeat in families large genomes. Annotation Approaches. Flutre, Duprat, T., E., Feu A Smit, A, H.,F R. RepeatModeler Open La La Fontaine, J. ‘The Cat and Fox’ Book 9, Fable 14. Nucleic Acids Res. Leplae, R., Lima Microbiol. Toussaint, A., Lima Leplae, R. ACLAME: A CLAssification of Mobile genetic Elements. Analysis and Annotation of DNA Repeats and Dark Matter in Eukaryotic Genomes. in (2015). that generates target site duplications. Hickman, A. B. & Dyda, TheF. casposon Synthesizin Krupovic, M., Shmakov, S., Makarova, K. S., Forterre, & P. Koonin, E. V. Recent Mobility of Casposons, Self 4, Cu Repbase. Kapitonov, V. V. & Jurka, J. A universal classification of eukaryotic transposable elements implemented in (2007). Wicker, T. Finnegan, J.D. Eukaryotic transposable elements and genome evolution. Finnegan, J.D. Transposable elements. Ardeljan, D. Bioinformatics

865 rcio, M. J. & Derbyshire, K. M. The outs and ins of transposition: from mu to kangaroo.

i351 –

877 (2003). – Nat. Rev. Genet. i358 (2005).

158, et al. g g Transposons at the Origin of the CRISPR et al.

16,

567 - A unified cl Mendez, & Toussaint,G. A. ACLAME: A CLAssification of Mobile genetic Elements, update 2010.

Meeting Report: The Role of the Mobilome in Cancer. 38,

(2015). -

– Mendez, G. & Leplae, R. PhiGO, phagea ontology associated with the ACLAME database. 571 (2007).

D57

illet, C. & Quesneville, ConsideringH. Transposable Element Diversification in De Novo PLoS ONE 9, Comment citer cedocument: –

D61 (2010). assification system for eukaryotic transposable elements. 411 –

412 (2008).

e16526 (2011). - Curr. Opin.Dev. Genet. Nucleic A

- 1.0. 1.0. (2008).

encoded Cas1 protein from

cids Res.

- Cas Immunity.

43,

10576 2,

861 Nucleic Acids Res. – – Aciduliprofundum boonei 10587 (2015). 867 (1992). Genome Biol. Evol. Cancer Res Trends Genet. TIG - novo on the genomic scale.

76, 32,

Nat. Rev. Genet.

4316 45D

8, Nat. Rev. Mol. Cell Biol.

375 5, – – 49 (2004).

4319 (2016). 103 is a DNA DNA is a integrase – 386 (2016). – Bioinforma 107 (1989).

BMC 973 -

–

Res. 982 tics

102 Huang, S. – 114 (2016). et al.

Discovery of an Active RAG Transposon Illuminates the Origins of V(D)J Recombination.

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Version postprint of Jean de la Fontaine?. Mobile Genetic Elements, 6(6), 1-17. DOI: 10.1080/2159256X.2016.1256852 Arensburger, P.,Piégu, B.,Bigot,Y. (2016). Thefuture oftransposable elementannotation and Retron/msRNA RT features Class Group I intron (G1i) Intein host genes Machinery for excision of Class respectwith to the previous version indicated in italics just below the levels Orderof Class, and Superfamilies. Bibliographic refere in black, those in eukaryotes being in blue. Both colors are used for mixed superfamilies. The criteria used are  for prokaryotic a with TEs Classes TE rare for SSE an Classes with phenotype TE TEs  With With the exception of the Intein and Group intronI Classes, names of their classification inthe lightoffunctional genomics -whatwecan learnfromthe fables

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G1i G1i

retroposon phenotype

InBase (http://tools.neb.com/inbase/)InBase could inserted be proposed as used, in genesHost in which each intein specifically or site into host genes Phylogenetic relationships between HEN, and Superfamilies Introners Mobile introns lariat introns II Group Penelope, GIY GIYNeptune, Coprina, no GIY Athena, no GIY withLINEs both and AP PD msRNA Phylogenetic relationships between RT Superfamilies specifically could inserted also be used sitesHost in which each group intron I superfamilies found in prokaryotes are typed

- like - - YIG domain

elements YIG domain - - YIG domain

 YIG domain

nces of updated points

- (D/E)XK EN*