Parasitoid Wasps Bears a Distinct DNA Transposon Profile

Overview

Journal Mob DNA

Publisher Biomed Central

Specialty Genetics

Date 2018 Jul 14

PMID 30002736

Citations 4

Authors

Alexandre Freitas da Silva

Filipe Zimmer Dezordi

Elgion Lucio Silva Loreto

Gabriel Luz Wallau

Affiliations

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Abstract

Background: The majority of Eukaryotic genomes are composed of a small portion of stable (non-mobile) genes and a large fraction of parasitic mobile elements such as transposable elements and endogenous viruses: the Mobilome. Such important component of many genomes are normally underscored in genomic analysis and detailed characterized mobilomes only exists for model species. In this study, we used a combination of de novo and homology approaches to characterize the Mobilome of two non-model parasitoid wasp species.

Results: The different methodologies employed for TE characterization recovered TEs with different features as TE consensus number and size. Moreover, some TEs were detected only by one or few methodologies. RepeatExplorer and dnaPipeTE estimated a low TE content of 5.86 and 4.57% for Braconidae wasp and 5.22% and 7.42% for species, respectively. Both mobilomes are composed by a miscellaneous of ancient and recent elements. Braconidae wasps presented a large diversity of Class II TEs while other TE superfamilies were more equally diverse in both species. Phylogenetic analysis of reconstructed elements showed that vertical transfer is the main mode of transmission.

Conclusion: Different methodologies should be used complementarity in order to achieve better mobilome characterization. Both wasps genomes have one of the lower mobilome estimates among all Hymenoptera genomes studied so far and presented a higher proportion of Class II than Class I TEs. The large majority of superfamilies analyzed phylogenetically showed that the elements are being inherited by vertical transfer. Overall, we achieved a deep characterization of the mobilome in two non-model parasitoid wasps improving our understanding of their evolution.

Citing Articles

DNA Polymerase Diversity Reveals Multiple Incursions of Polintons During Nematode Evolution.

Jeong D, Sundrani S, Hall R, Krupovic M, Koonin E, Fire A Mol Biol Evol. 2023; 40(12).

PMID: 38069639 DOI: 10.1093/molbev/msad274.

Assembly-Free Detection and Quantification of Transposable Elements with dnaPipeTE.

Goubert C Methods Mol Biol. 2022; 2607:25-43.

PMID: 36449156 DOI: 10.1007/978-1-0716-2883-6_2.

Comparative Analysis of Genomic Repeat Content in Gomphocerine Grasshoppers Reveals Expansion of Satellite DNA and Helitrons in Species with Unusually Large Genomes.

Shah A, Hoffman J, Schielzeth H Genome Biol Evol. 2020; 12(7):1180-1193.

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The mobilome of Drosophila incompta, a flower-breeding species: comparison of transposable element landscapes among generalist and specialist flies.

Fonseca P, Moura R, Wallau G, Loreto E Chromosome Res. 2019; 27(3):203-219.

PMID: 31119502 DOI: 10.1007/s10577-019-09609-x.

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