High frequency of horizontal transfer in Jockey families (LINE order) of drosophilids

Abstract

BackgroundThe use of large-scale genomic analyses has resulted in an improvement of transposable element sampling and a significant increase in the number of reported HTT (horizontal transfer of transposable elements) events by expanding the sampling of transposable element sequences in general and of specific families of these elements in particular, which were previously poorly sampled. In this study, we investigated the occurrence of HTT events in a group of elements that, until recently, were uncommon among the HTT records in Drosophila – the Jockey elements, members of the LINE (long interspersed nuclear element) order of non-LTR (long terminal repeat) retrotransposons. The sequences of 111 Jockey families deposited in Repbase that met the criteria of the analysis were used to identify Jockey sequences in 48 genomes of Drosophilidae (genus Drosophila, subgenus Sophophora: melanogaster, obscura and willistoni groups; subgenus Drosophila: immigrans, melanica, repleta, robusta, virilis and grimshawi groups; subgenus Dorsilopha: busckii group; genus/subgenus Zaprionus and genus Scaptodrosophila).ResultsPhylogenetic analyses revealed 72 Jockey families in 41 genomes. Combined analyses revealed 15 potential HTT events between species belonging to different genera and species groups of Drosophilidae, providing evidence for the flow of genetic material favoured by the spatio-temporal sharing of these species present in the Palaeartic or Afrotropical region.ConclusionsOur results provide phylogenetic, biogeographic and temporal evidence of horizontal transfers of the Jockey elements, increase the number of rare records of HTT in specific families of LINE elements, increase the number of known occurrences of these events, and enable a broad understanding of the evolutionary dynamics of these elements and the host species.

Evolutionary study of the412/mdg1lineage of theTy3/gypsygroup of LTR retrotransposons in Diptera

“…The phylogenetic reconstruction of the analyzed species was based on the nuclear gene Amyrel . Sequences were downloaded using the access number provided by Tambones et al [37] (S2 Table). Additional sequences were obtained directly from NCBI, using D. melanogaster as a query or another related species when no results were recovered.…”

Comparative Analysis of Transposable Elements Reveals the Diversity of Transposable Elements in Decapoda and Their Effects on Genomic Evolution

“…What's more, the phylogenetic relationship of the WSSV-speci c JLSs among the eight decapoda species was not consistent with their species phylogeny. According to the criteria of Tambones et al (Tambones et al 2019) for TE horizontal transfer, we speculated that the above JLSs might be derived from the endogenous WSSV sequence, and horizontal transfer occurred in the genomes of the eight decapoda species with WSSV as the carrier.…”

Turnover of retroelements and satellite DNA drives centromere reorganization over short evolutionary timescales in Drosophila

“…To better understand the evolutionary history of this specific retroelement, we inferred the phylogeny for all G2/Jockey-3 ORFs in the D. melanogaster clade assemblies. G2/Jockey-3 has two open reading frames (ORFs), but we only used ORF2 for inferring phylogenies, as ORF1 is more evolutionarily labile across species 41 6B). That is, 53% of all G2/Jockey-3 insertions are centromeric in D. simulans and D. sechellia, which is more than expected if these TEs were randomly distributed in the genome (Fisher's exact tests: Psim < 10 -16 ; Psec < 10 -16 ;).…”