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Assembly-Free Detection and Quantification of Transposable Elements with dnaPipeTE

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Transposable Elements

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2607))

Abstract

The detection and quantification of transposable elements (TE) are notoriously challenging despite their relevance in evolutionary genomics and molecular ecology. The main hurdle is caused by the dependence of numerous tools on genome assemblies, whose level of completion directly affects the comparability of the results across species or populations. dnaPipeTE, whose use is demonstrated here, tackles this issue by directly performing TE detection, classification, and quantification from unassembled short reads. This chapter details all the required steps to perform a comparative analysis of the TE content between two related species, starting from the installation of a recently containerized version of the program to the post-processing of the outputs.

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References

  1. Hoen DR, Hickey G, Bourque G et al (2015) A call for benchmarking transposable element annotation methods. Mob DNA 6:1–9

    Article  Google Scholar 

  2. Bourque G, Burns KH, Gehring M et al (2018) Ten things you should know about transposable elements. https://doi.org/10.1186/s13059-018-1577-z

  3. Flynn JM, Hubley R, Goubert C et al (2020) RepeatModeler2 for automated genomic discovery of transposable element families. Proc Natl Acad Sci U S A 117:9451–9457

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Su W, Ou S, Hufford MB et al (2021) A tutorial of EDTA: extensive De Novo TE annotator. Methods Mol Biol 2250:55–67

    Article  CAS  PubMed  Google Scholar 

  5. Ou S, Su W, Liao Y et al (2019) Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline. Genome Biol 20:275

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Flutre T, Duprat E, Feuillet C et al (2011) Considering transposable element diversification in de novo annotation approaches. PLoS One 6:e16526

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Hoede C, Arnoux S, Moisset M et al (2014) PASTEC: an automatic transposable element classification tool. PLoS One 9:e91929

    Article  PubMed  PubMed Central  Google Scholar 

  8. Hotaling S, Kelley JL, Frandsen PB (2021) Toward a genome sequence for every animal: Where are we now?, https://doi.org/10.1073/pnas.2109019118

  9. Novak P, Neumann P, Pech J, et al (2013) RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads, https://doi.org/10.1093/bioinformatics/btt054

  10. Novák P, Neumann P, Macas J (2020) Global analysis of repetitive DNA from unassembled sequence reads using RepeatExplorer2. Nat Protoc 15:3745–3776

    Article  PubMed  Google Scholar 

  11. Koch P, Platzer M, Downie BR (2014) RepARK--de novo creation of repeat libraries from whole-genome NGS reads. Nucleic Acids Res 42:e80

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Goubert C, Modolo L, Vieira C et al (2015) De novo assembly and annotation of the Asian tiger mosquito (Aedes albopictus) repeatome with dnaPipeTE from raw genomic reads and comparative analysis with the yellow fever mosquito (Aedes aegypti). Genome Biol Evol 7:1192–1205

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Zytnicki M, Akhunov E, Quesneville H (2014) Tedna: a transposable element de novo assembler. Bioinformatics 30:2656–2658

    Article  CAS  PubMed  Google Scholar 

  14. Nelson MG, Linheiro RS, Bergman CM (2017) McClintock: an integrated pipeline for detecting transposable element insertions in whole-genome shotgun sequencing data. G3 7:2763–2778

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Weilguny L, Kofler R (2019) DeviaTE: assembly-free analysis and visualization of mobile genetic element composition. Mol Ecol Resour 19:1346–1354

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Novák P, Neumann P, Macas J (2010) Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data. BMC Bioinform 11:378

    Article  Google Scholar 

  17. Grabherr MG, Haas BJ, Yassour M et al (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29:644–652

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Storer J, Hubley R, Rosen J et al (2021) The Dfam community resource of transposable element families, sequence models, and genome annotations. Mob DNA 12:2

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Merkel D et al (2014) Docker: lightweight linux containers for consistent development and deployment. Linux J 2014:2

    Google Scholar 

  20. Kurtzer GM, Sochat V, Bauer MW (2017) Singularity: scientific containers for mobility of compute. PLoS One 12:e0177459

    Article  PubMed  PubMed Central  Google Scholar 

  21. Lerat E, Goubert C, Guirao-Rico S et al (2019) Population-specific dynamics and selection patterns of transposable element insertions in European natural populations. Mol Ecol 28:1506–1522

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Sessegolo C, Burlet N, Haudry A (2016) Strong phylogenetic inertia on genome size and transposable element content among 26 species of flies. Biol Lett 12:20160407

    Article  PubMed  PubMed Central  Google Scholar 

  23. Bracewell R, Chatla K, Nalley MJ et al (2019) Dynamic turnover of centromeres drives karyotype evolution in Drosophila. elife 8:e49002

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Brown EJ, Nguyen AH, Bachtrog D (2020) The Drosophila Y chromosome affects Heterochromatin integrity genome-wide. Mol Biol Evol 37:2808–2824

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Fonseca PM, Moura RD, Wallau GL et al (2019) The mobilome of Drosophila incompta, a flower-breeding species: comparison of transposable element landscapes among generalist and specialist flies. Chromosom Res 27:203–219

    Article  CAS  Google Scholar 

  26. Romero-Soriano V, Modolo L, Lopez-Maestre H et al (2017) Transposable element Misregulation is linked to the divergence between parental piRNA pathways in Drosophila hybrids. Genome Biol Evol 9:1450–1470

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Parisot N, Vargas-Chávez C, Goubert C et al (2021) The transposable element-rich genome of the cereal pest Sitophilus oryzae. BMC Biol 19:241

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Amorim IC, Melo ES, Moura RC et al (2020) Diverse mobilome of Dichotomius (Luederwaldtinia) schiffleri (Coleoptera: Scarabaeidae) reveals long-range horizontal transfer events of DNA transposons. Mol Gen Genomics 295:1339–1353

    Article  CAS  Google Scholar 

  29. Ferretti ABSM, Milani D, Palacios-Gimenez OM et al (2020) High dynamism for neo-sex chromosomes: satellite DNAs reveal complex evolution in a grasshopper. Heredity 125:124–137

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Shah A, Hoffman JI, Schielzeth H (2020) Comparative analysis of genomic repeat content in Gomphocerine grasshoppers reveals expansion of satellite DNA and Helitrons in species with unusually large genomes. Genome Biol Evol 12:1180–1193

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Milani D, Ruiz-Ruano FJ, Camacho JPM et al (2021) Out of patterns, the euchromatic B chromosome of the grasshopper Abracris flavolineata is not enriched in high-copy repeats. Heredity 127:475–483

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Martí E, Milani D, Bardella VB et al (2021) Cytogenomic analysis unveils mixed molecular evolution and recurrent chromosomal rearrangements sha** the multigene families on Schistocerca grasshopper genomes. Evolution 75:2027–2041

    Article  PubMed  Google Scholar 

  33. Kapheim KM, Pan H, Li C et al (2019) Draft genome assembly and population genetics of an agricultural pollinator, the solitary alkali bee (Halictidae: Nomia melanderi). G3 9:625–634

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. da Silva AF, Dezordi FZ, Loreto ELS et al (2018) Drosophila parasitoid wasps bears a distinct DNA transposon profile. Mob DNA 9:23

    Article  PubMed  PubMed Central  Google Scholar 

  35. Castro MRJ, Goubert C, Monteiro FA et al (2020) Homology-free detection of transposable elements unveils their dynamics in three ecologically distinct Rhodnius species. Genes 11:170

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Errbii M, Keilwagen J, Hoff KJ et al (2021) Transposable elements and introgression introduce genetic variation in the invasive ant Cardiocondyla obscurior. Mol Ecol 30:6211–6228

    Article  PubMed  Google Scholar 

  37. Talla V, Suh A, Kalsoom F et al (2017) Rapid increase in genome size as a consequence of transposable element hyperactivity in wood-white (Leptidea) butterflies. Genome Biol Evol 9:2491–2505

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Chak STC, Rubenstein DR (2019) TERAD: extraction of transposable element composition from RADseq data. Mol Ecol Resour 19:1681–1688

    Article  CAS  PubMed  Google Scholar 

  39. Schell T, Feldmeyer B, Schmidt H et al (2017) An annotated draft genome for Radix auricularia (Gastropoda, Mollusca). Genome Biol Evol 9:0

    Article  PubMed  PubMed Central  Google Scholar 

  40. Zarrella I, Herten K, Maes GE et al (2019) The survey and reference assisted assembly of the Octopus vulgaris genome. Sci Data 6:13

    Article  PubMed  PubMed Central  Google Scholar 

  41. Heath-Heckman E, Nishiguchi MK (2021) Leveraging short-read sequencing to explore the genomics of Sepiolid squid. Integr Comp Biol 61:1753–1761

    Article  CAS  PubMed  Google Scholar 

  42. Grosmaire M, Launay C, Siegwald M et al (2019) Males as somatic investment in a parthenogenetic nematode. Science 363:1210–1213

    Article  CAS  PubMed  Google Scholar 

  43. Blommaert J, Riss S, Hecox-Lea B et al (2019) Small, but surprisingly repetitive genomes: transposon expansion and not polyploidy has driven a doubling in genome size in a metazoan species complex. BMC Genomics 20:466

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Wong WY, Simakov O, Bridge DM et al (2019) Expansion of a single transposable element family is associated with genome-size increase and radiation in the genus Hydra. Proc Natl Acad Sci U S A 116:22915–22917

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Lamichhaney S, Catullo R, Keogh JS et al (2021) A bird-like genome from a frog: mechanisms of genome size reduction in the ornate burrowing frog. Platyplectrum ornatum Proc Natl Acad Sci U S A 118:e2011649118

    Article  CAS  PubMed  Google Scholar 

  46. Piégu B, Arensburger P, Beauclair L et al (2020) Variations in genome size between wild and domesticated lineages of fowls belonging to the Gallus gallus species. Genomics 112:1660–1673

    Article  PubMed  Google Scholar 

  47. Termignoni-Garcia F, Kirchman JJ, Clark J et al (2021) Comparative population genomics of cryptic speciation and adaptive divergence in Bicknell’s and Gray-cheeked thrushes (Aves: Catharus bicknelli and Catharus minimus). Genome Biol Evol 14:evab255

    Article  PubMed Central  Google Scholar 

  48. Li H (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM, http://arxiv.org/abs/1303.3997

  49. Quinlan AR (2014) BEDTools: the Swiss-Army tool for genome feature analysis. Curr Protoc Bioinformatics 47:11.12.1–34

    Article  PubMed  Google Scholar 

  50. Sherry S, **ao C, Durbrow K et al (2012) Ncbi sra toolkit technology for next generation sequence data. In: Plant and animal genome XX conference (January 14–18, 2012). Plant and animal genome

    Google Scholar 

  51. Lawlor MA, Cao W, Ellison CE (2021) A transposon expression burst accompanies the activation of Y-chromosome fertility genes during Drosophila spermatogenesis. Nat Commun 12:6854

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Li F, Rane RV, Luria V et al (2021) Phylogenomic analyses of the genus Drosophila reveals genomic signals of climate adaptation. Mol Ecol Resour 22:1559

    Article  PubMed  PubMed Central  Google Scholar 

  53. Tikariha H, Purohit HJ (2019) Assembling a genome for novel nitrogen-fixing bacteria with capabilities for utilization of aromatic hydrocarbons. Genomics 111:1824–1830

    Article  CAS  PubMed  Google Scholar 

  54. Gregory TR, Nicol JA, Tamm H et al (2007) Eukaryotic genome size databases. Nucleic Acids Res 35:D332–D338

    Article  CAS  PubMed  Google Scholar 

  55. Pflug JM, Holmes VR, Burrus C et al (2020) Measuring genome sizes using read-depth, k-mers, and flow cytometry: methodological comparisons in beetles (Coleoptera). G3: Genes|Genomes|Genetics 10:3047

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Elliott TA, Heitkam T, Hubley R et al (2021) TE Hub: a community-oriented space for sharing and connecting tools, data, resources, and methods for transposable element annotation. Mob DNA 12:1–5

    Google Scholar 

  57. Wicker T, Sabot F, Hua-Van A et al (2007) A unified classification system for eukaryotic transposable elements. Nat Rev Genet 8:973–982

    Article  CAS  PubMed  Google Scholar 

  58. Li W, Godzik A (2006) Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22:1658–1659

    Article  CAS  PubMed  Google Scholar 

  59. Huang W, Li L, Myers JR et al (2012) ART: a next-generation sequencing read simulator. Bioinformatics 28:593–594

    Article  PubMed  Google Scholar 

  60. Bao W, Kojima KK, Kohany O (2015) Repbase update, a database of repetitive elements in eukaryotic genomes. Mob DNA 6:11

    Article  PubMed  PubMed Central  Google Scholar 

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Acknowledgments

I warmly thank Stéphane Delmotte from the Laboratoire de Biométrie et Biologie Évolutive (LBBE, Lyon, France) who worked restlessly to produce the container version of dnaPipeTE. Many thanks to Paige Zhang for her help testing the scripts. I would also like to share my gratitude for the many users of dnaPipeTE over the years and their active involvement in the dnaPipeTE project.

Author information

Authors and Affiliations

  1. Canadian Centre for Computational Genomics, McGill University, Montreal, QC, Canada

    Clément Goubert

  2. McGill Genome Centre, Montreal, QC, Canada

    Clément Goubert

  3. Human Genetics, McGill University, Montreal, QC, Canada

    Clément Goubert

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  1. Clément Goubert
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Editors and Affiliations

  1. Faculty of Medicine and Dentistry, Blizard Institute, Queen Mary University of London, London, UK

    Miguel R. Branco

  2. School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK

    Alexandre de Mendoza Soler

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© 2023 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

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Goubert, C. (2023). Assembly-Free Detection and Quantification of Transposable Elements with dnaPipeTE. In: Branco, M.R., de Mendoza Soler, A. (eds) Transposable Elements. Methods in Molecular Biology, vol 2607. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2883-6_2

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  • DOI: https://doi.org/10.1007/978-1-0716-2883-6_2

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2882-9

  • Online ISBN: 978-1-0716-2883-6

  • eBook Packages: Springer Protocols

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