Unraveling the evolutionary scenario of the hobo element in populations of Drosophila melanogaster and D. simulans in South America using the TPE repeats as markers

Abstract

Transposable elements (TEs) are nucleotide sequences found in most studied genomes. These elements are highly diversified and have a large variation in nucleotide structure and mechanisms of transposition. hobo is a member of class II, belonging to hAT superfamily, described inDrosophila melanogaster, and it presents in its Open Reading Frame, a repetitive region encoding the amino acids threonine-proline-glutamic acid (TPE), which shows variability in the number of repeats in some regions of the world. Due to this variability some evolutionary scenarios of the hobo element are discussed, such as the scenario of the invasion of hobo element in populations ofD. melanogaster. In the present study, we investigated 22 DNA sequences of D. melanogaster and seven sequences ofD. simulans, both from South America, to check the number of repetitions of TPE, in order to clarify the evolutionary scenario of thehobo element in these populations. Our results showed a monomorphism in populations of both species in South America, with only three TPE repeats. Hence, we discuss and propose an evolutionary scenario of the invasion of the hobo element in populations of D. melanogaster and D. simulans.

Birth, School, Work, Death, and Resurrection: The Life Stages and Dynamics of Transposable Element Proliferation

“…This suggests that an active version of the hobo element was present in an ancestor of all D. melanogaster , was lost, but now has proliferated to the extent that it can cause hybrid dysgenesis. This new hobo variant also appears among close relatives that include D. simulans [78,79,80,81]. Finally, a similar scenario is observed in the hybrid dysgenesis syndrome of Drosophila virilis .…”

LoRTE: Detecting transposon-induced genomic variants using low coverage PacBio long read sequences

“…The vast majority of these new insertions are due to Hobo elements, a hAT DNA transposon known to have been recently acquired in D. melanogaster. Hobo elements are subject to a fast and ongoing expansion in the genome and might generated frequent cut-and-paste in somatic tissues [23] (Figs. 3 and 4).…”

LoRTE: Detecting transposon-induced genomic variants using low coverage PacBio long read sequences

“…Conversely, the number of new TE insertions observed in the PacBio reads increased linearly with the reads coverage's ( Fig 1C). The vast majority of these new insertions are due to Hobo elements, a hAT DNA transposon known to have been recently acquired in D. melanogaster and subject to a fast and ongoing expansion in the genome (Ragagnin, et al, 2016)( Supplementary Fig S2). Among the 30 new insertions identified using a coverage of 40X, only 12 were validated in the 90X genome assembly.…”