Assembly-Free Detection and Quantification of Transposable Elements with DnaPipeTE

Overview

Journal Methods Mol Biol

Specialty Molecular Biology

Date 2022 Nov 30

PMID 36449156

Authors

Clement Goubert

Affiliations

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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

Flynn J, Hubley R, Goubert C, Rosen J, Clark A, Feschotte C . RepeatModeler2 for automated genomic discovery of transposable element families. Proc Natl Acad Sci U S A. 2020; 117(17):9451-9457. PMC: 7196820. DOI: 10.1073/pnas.1921046117. View

Su W, Ou S, Hufford M, Peterson T . A Tutorial of EDTA: Extensive De Novo TE Annotator. Methods Mol Biol. 2021; 2250:55-67. DOI: 10.1007/978-1-0716-1134-0_4. View

Ou S, Su W, Liao Y, Chougule K, Agda J, Hellinga A . Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline. Genome Biol. 2019; 20(1):275. PMC: 6913007. DOI: 10.1186/s13059-019-1905-y. View

Flutre T, Duprat E, Feuillet C, Quesneville H . Considering transposable element diversification in de novo annotation approaches. PLoS One. 2011; 6(1):e16526. PMC: 3031573. DOI: 10.1371/journal.pone.0016526. View

Hoede C, Arnoux S, Moisset M, Chaumier T, Inizan O, Jamilloux V . PASTEC: an automatic transposable element classification tool. PLoS One. 2014; 9(5):e91929. PMC: 4008368. DOI: 10.1371/journal.pone.0091929. View

Novak P, Neumann P, Macas J . Global analysis of repetitive DNA from unassembled sequence reads using RepeatExplorer2. Nat Protoc. 2020; 15(11):3745-3776. DOI: 10.1038/s41596-020-0400-y. View

Koch P, Platzer M, Downie B . RepARK--de novo creation of repeat libraries from whole-genome NGS reads. Nucleic Acids Res. 2014; 42(9):e80. PMC: 4027187. DOI: 10.1093/nar/gku210. View

Goubert C, Modolo L, Vieira C, ValienteMoro C, Mavingui P, Boulesteix M . 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. 2015; 7(4):1192-205. PMC: 4419797. DOI: 10.1093/gbe/evv050. View

Zytnicki M, Akhunov E, Quesneville H . Tedna: a transposable element de novo assembler. Bioinformatics. 2014; 30(18):2656-8. DOI: 10.1093/bioinformatics/btu365. View

10.

Nelson M, Linheiro R, Bergman C . McClintock: An Integrated Pipeline for Detecting Transposable Element Insertions in Whole-Genome Shotgun Sequencing Data. G3 (Bethesda). 2017; 7(8):2763-2778. PMC: 5555480. DOI: 10.1534/g3.117.043893. View

11.

Weilguny L, Kofler R . DeviaTE: Assembly-free analysis and visualization of mobile genetic element composition. Mol Ecol Resour. 2019; 19(5):1346-1354. PMC: 6791034. DOI: 10.1111/1755-0998.13030. View

12.

Grabherr M, Haas B, Yassour M, Levin J, Thompson D, Amit I . Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 2011; 29(7):644-52. PMC: 3571712. DOI: 10.1038/nbt.1883. View

13.

Storer J, Hubley R, Rosen J, Wheeler T, Smit A . The Dfam community resource of transposable element families, sequence models, and genome annotations. Mob DNA. 2021; 12(1):2. PMC: 7805219. DOI: 10.1186/s13100-020-00230-y. View

14.

Kurtzer G, Sochat V, Bauer M . Singularity: Scientific containers for mobility of compute. PLoS One. 2017; 12(5):e0177459. PMC: 5426675. DOI: 10.1371/journal.pone.0177459. View

15.

Lerat E, Goubert C, Guirao-Rico S, Merenciano M, Dufour A, Vieira C . Population-specific dynamics and selection patterns of transposable element insertions in European natural populations. Mol Ecol. 2018; 28(6):1506-1522. PMC: 6849870. DOI: 10.1111/mec.14963. View

16.

Sessegolo C, Burlet N, Haudry A . Strong phylogenetic inertia on genome size and transposable element content among 26 species of flies. Biol Lett. 2016; 12(8). PMC: 5014035. DOI: 10.1098/rsbl.2016.0407. View

17.

Bracewell R, Chatla K, Nalley M, Bachtrog D . Dynamic turnover of centromeres drives karyotype evolution in Drosophila. Elife. 2019; 8. PMC: 6795482. DOI: 10.7554/eLife.49002. View

18.

Brown E, Nguyen A, Bachtrog D . The Drosophila Y Chromosome Affects Heterochromatin Integrity Genome-Wide. Mol Biol Evol. 2020; 37(10):2808-2824. PMC: 7530609. DOI: 10.1093/molbev/msaa082. View

19.

Romero-Soriano V, Modolo L, Lopez-Maestre H, Mugat B, Pessia E, Chambeyron S . Transposable Element Misregulation Is Linked to the Divergence between Parental piRNA Pathways in Drosophila Hybrids. Genome Biol Evol. 2017; 9(6):1450-1470. PMC: 5499732. DOI: 10.1093/gbe/evx091. View

20.

Parisot N, Vargas-Chavez C, Goubert C, Baa-Puyoulet P, Balmand S, Beranger L . The transposable element-rich genome of the cereal pest Sitophilus oryzae. BMC Biol. 2021; 19(1):241. PMC: 8576890. DOI: 10.1186/s12915-021-01158-2. View