Suggested Absence of Horizontal Transfer of Retrotransposons between Humans and Domestic Mammal Species.

Nicole Wanner,Christopher Faulk

doi:10.3390/genes12081223

Abstract

Transposable element sequences are usually vertically inherited but have also spread across taxa via horizontal transfer. Previous investigations of ancient horizontal transfer of transposons have compared consensus sequences, but this method resists detection of recent single or low copy number transfer events. The relationship between humans and domesticated animals represents an opportunity for potential horizontal transfer due to the consistent shared proximity and exposure to parasitic insects, which have been identified as plausible transfer vectors. The relatively short period of extended human–animal contact (tens of thousands of years or less) makes horizontal transfer of transposons between them unlikely. However, the availability of high-quality reference genomes allows individual element comparisons to detect low copy number events. Using pairwise all-versus-all megablast searches of the complete suite of retrotransposons of thirteen domestic animals against human, we searched a total of 27,949,823 individual TEs. Based on manual comparisons of stringently filtered BLAST search results for evidence of vertical inheritance, no plausible instances of HTT were identified. These results indicate that significant recent HTT between humans and domesticated animals has not occurred despite the close proximity, either due to the short timescale, inhospitable recipient genomes, a failure of vector activity, or other factors.

Highlights

Transposable elements (TEs) are DNA sequences that can move or copy themselves to new locations in genomes [1]
Reference genomes and retrotransposon genomic intervals for human (GRCh38/hg38) and thirteen domestic animal species were downloaded from UCSC Table Browser using the RepeatMasker track
TE sequences were extracted to multifasta files with the Biostrings package version 2.54.0 [30] in R version 3.6.1, and reference genomes downloaded from UCSC

Summary

Introduction

Transposable elements (TEs) are DNA sequences that can move or copy themselves to new locations in genomes [1]. HTT is inferred by a higher than expected sequence identity between TEs across species compared to divergence based on vertical inheritance from the last common ancestor [9]. While HTT is generally more common in lower animals such as insects [16], evidence for the phenomenon has been found in domesticated mammal species.

Results

Conclusion