Abstract
BackgroundTransposable elements (TEs) are highly abundant genomic parasites in eukaryote genomes. Although several genomes have been screened for TEs, so far very limited information is available regarding avian TEs and their evolutionary histories. Taking advantage of the rich genomic data available for birds, we characterized the evolutionary history of the galluhop element, originally described in Gallus gallus, through the use of several bioinformatic analyses.Resultsgalluhop homologous sequences were found in 6 of 72 genomes analyzed: 5 species of Galliformes (Gallus gallus, Meleagris gallopavo, Coturnix japonica, Colinus virginianus, Lyrurus tetrix) and one Buceritiformes (Buceros rhinoceros). The copy number ranged from 5 to 10,158, in the genomes of C. japonica and G. gallus respectively. All 6 species possessed short elements, suggesting the presence of Miniature Inverted repeats Transposable Elements (MITEs), which underwent an ancient massive amplification in the G. gallus and M. gallopavo genomes. Only 4 species showed potential MITE full-length partners, although no potential coding copies were detected. Phylogenetic analysis of reconstructed coding sequences showed that galluhop homolog sequences form a new mariner subfamily, which we termed Gallus. Inter-species and intragenomic galluhop distance analyses indicated a high identity between the consensus of B. rhinoceros and the other 5 related species, and different emergence ages of the element between the Galliformes species and B. rhinocerus, suggesting that horizontal transfer took place from Galliformes to a Buceritiformes ancestor, probably through an intermediate species.ConclusionsOverall, our results showed that mariner elements have amplified to high copy numbers in some avian species, and that this transposition burst probably occurred in the common ancestor of G. gallus and M. gallopavo. In addition, although no coding sequences could be found currently, they probably existed, allowing an ancient massive MITE amplification in these 2 species. The other 4 species also have MITEs, suggesting that this new mariner family is prone to give rise to such non-autonomous derivatives. Last, our results suggest that a horizontal transfer event of a galluhop element occurred between Galliformes and Buceritiformes.
Highlights
Transposable elements (TEs) are highly abundant genomic parasites in eukaryote genomes
C. virginianus and L. tetrix showed amplification of Miniature inverted repeats transposable element (MITE) on a smaller scale, and C. japonica and B. rhinocerus possessed only MITEs elements and no trace of their possible autonomous counterparts (Fig. 1). These findings suggest that MITEs originated independently in this new mariner subfamily, which probably affected the fate of these elements leading to the extinction of the TE family in all avian genomes studied
The evolution of transposable elements usually shows complex patterns, such as patchy distributions within taxa, associated with a high similarity of TEs in host species that diverged long ago. The presence of such patterns can be explained by an exchange of TEs by these species or independent acquisitions from a third source, which characterizes a phenomenon known as Horizontal Transposon Transfer (HTT)
Summary
Transposable elements (TEs) are highly abundant genomic parasites in eukaryote genomes. Around 2853 Horizontal Transposon Transfer (HTT) events have been reported [13]. The mariner family of Class II DNA transposons has the highest number of HTT cases reported (52) [13, 14]. Such events have been characterized in a wide variety of taxa, including insects and mammals [14,15,16]. In birds, considering all TE families of Class I and II, only seven HTT events have been reported so far: two retrotransposons (AviRTE), which took place between several bird species ancestors and human pathogenic nematodes [17]
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