Mobilome characterization of the beetle Euchroma gigantea (Buprestidae) uncovers multiple long range Tc1-Mariner horizontal transfer events

Igor C Amorim; Catarine A A Mello; Aline P Félix; Crislaine Xavier; Gabriel L Wallau; Rita C Moura

doi:10.1016/j.gene.2023.147785

Mobilome characterization of the beetle Euchroma gigantea (Buprestidae) uncovers multiple long range Tc1-Mariner horizontal transfer events

Gene. 2023 Dec 20:888:147785. doi: 10.1016/j.gene.2023.147785. Epub 2023 Sep 9.

Authors

Igor C Amorim¹, Catarine A A Mello², Aline P Félix³, Crislaine Xavier², Gabriel L Wallau⁴, Rita C Moura⁵

Affiliations

¹ Laboratório de Biodiversidade e Genética de Insetos, Instituto de Ciências Biológicas, Universidade de Pernambuco, Recife, Pernambuco, Brazil; Departamento de Tecnologia e Ciências Sociais, Universidade do Estado da Bahia, Juazeiro, BA, Brasil.
² Laboratório de Biodiversidade e Genética de Insetos, Instituto de Ciências Biológicas, Universidade de Pernambuco, Recife, Pernambuco, Brazil.
³ Laboratório de Biodiversidade e Genética de Insetos, Instituto de Ciências Biológicas, Universidade de Pernambuco, Recife, Pernambuco, Brazil; Pós-Graduação em Genética e Biologia Molecular, Centro de Ciências Biológicas (CB), Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil; Departamento de Entomologia e Núcleo de Bioinformática, Instituto Aggeu Magalhães - Fundação Oswaldo Cruz, Recife, Pernambuco, Brazil.
⁴ Departamento de Entomologia e Núcleo de Bioinformática, Instituto Aggeu Magalhães - Fundação Oswaldo Cruz, Recife, Pernambuco, Brazil; Department of Arbovirology and Entomology, Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Center for Arbovirus and Hemorrhagic Fever Reference and Research, National Reference Center for Tropical Infectious Diseases, Bernhard-Nocht-Straße 74, 20359 Hamburg, Germany. Electronic address: gabriel.wallau@fiocruz.br.
⁵ Laboratório de Biodiversidade e Genética de Insetos, Instituto de Ciências Biológicas, Universidade de Pernambuco, Recife, Pernambuco, Brazil; Pós-Graduação em Genética e Biologia Molecular, Centro de Ciências Biológicas (CB), Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil. Electronic address: rita.moura@upe.br.

PMID: 37689222
DOI: 10.1016/j.gene.2023.147785

Abstract

Transposable elements (TEs) are mobile repetitive DNA sequences that can transfer horizontally between species. Due to their mutagenic characteristics, TEs are associated with different evolutionary events, including chromosomal rearrangements that are abundant in the beetle Euchroma gigantea. In order to understand more in depth the impact of TEs on the genomic evolution of E. gigantea, we characterized the E. gigantea mobilome and evaluated the horizontal transfer of Tc1-Mariner elements. Genomic sequencing data was generated on the Illumina Hiseq plataform, from a specimen (Northeast lineage) collected in Recife, Pernambuco - Brazil. The TEs were characterized by two independent approaches based on the clustering and assembly of highly repetitive sequences, the RepeatExplorer and dnaPipeTE. The sequences obtained were further characterized using ORFfinder and CD-Search, to obtain the TEs' potential coding proteins and verify the presence and integrity of known TE domains. Evidence for horizontal transfer was evaluated by nucleotide and protein genetic distance between TEs from E. gigantea and other species and phylogenetic incongruences detected between TEs and hosts phylogenetic trees. The mobilome of E. gigantea represents about 21 to 26% of its genome. This mobilome is composed of TEs from 31 superfamilies, belonging to different classes and most known orders of TEs. Several types of TEs with intact domains were observed with emphasis on Tc1-Mariner suggesting the presence of potentially autonomous elements. This superfamily also stands out for having the greatest abundance and diversity, with TEs being classified into four families. When compared to TEs deposited in databases, Mariner TEs stood out as having the highest nucleotide identity (above 90%) with TEs from phylogenetically distant species, such as ants and bees. Altogether these results suggest that E. gigantea Mariner TEs underwent multiple horizontal transfer events to other insect species.

Keywords: Horizontal transmission; Host switch; Phylogenetic incongruence; Transposable elements.

MeSH terms

Animals
Coleoptera* / genetics
DNA Transposable Elements / genetics
Evolution, Molecular
Genomics
Humans
Nucleotides
Phylogeny

Substances

DNA Transposable Elements
Nucleotides