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Horizontal transfer of retrotransposons in eukaryotes
Novikova O.S.
PhD scientific researcher
Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
Horizontal transfer or horizontal transmission (HT) can be defined as the process by which
genes move between reproductively isolated species. It is not surprising that many examples of
HT of transposable elements (TEs) have been identified in eukaryotes. TEs have the capacity to
insert themselves into the chromosomes of possible vectors and, subsequently, into host
chromosomes. They were found virtually in all investigated eukaryotes and represent the
ubiquitous components of eukaryotic genomes (Bannert, Kurth, 2004; Vitte, Panaud, 2005).
Recent evidence suggests that TEs may provide the genome with potent agents to generate
genetic and genomic plasticity (Kidwell, Lisch, 1997). Two major classes of TEs are
recognized (Wicker et al., 2007). Class I elements use RNA-mediated mechanisms for their
transposition and are called retrotransposons. Two major orders of retrotransposons are
recognized: LTR retrotransposons, which have long terminal repeats (LTRs); and non-LTR
retrotransposons, which lack LTRs (Wicker et al., 2007). Class II elements transpose through
DNA-mediated mechanisms and are called DNA transposons (Feschotte, Pritham, 2007). HT is
well known for DNA transposons and LTR retrotransposons (Robertson, 1993; Silva, Kidwell,
2004). However non-LTR retrotransposons rarely undergo HT, and their phylogenies are
largely congruent to those of their hosts (Malik et al., 1999).
Three criteria can be used for HT event recognition. The first criterion is the inconsistence
between the phylogenies of TEs and host species. There are potential problems with application
of this criterion for HT detection. Multiple TEs lineages can be present within genomes.
Moreover, TEs are multicopy components of genomes. Comparisons of paralogous TE copies
instead of orthologs along with varying rates of their sequence evolution are the main sources
for incongruence in phylogenetic analysis, which could be misidentified as HT. The second
criterion, which seems to offer the strongest evidence, is a higher degree of observed sequence
similarity for TEs than for functional genes, so called ‘slowdown effect on evolutionary rates’.
Once inserted, a new copy of transposable element is presumed to evolve without functional
constrains. Thus, all types of mutations should have an equal chance to be fixed (Volff et al.,
2000; Bensasson et al., 2001). The third criterion of inferring HT is the discontinuous
distribution of TEs among closely related taxa, i.e., presence of a TE in one lineage and its
absence in a sister lineage (Kaplan et al., 1985; Lohe et al., 1995).
We are combining a search of retrotransposons in publicly available eukaryotic genomes
using bioinformatic approaches and an experimental analysis of diverse eukaryotic species in
order to identify putative HT events. The whole genome mining of retrotransposable elements
uGENE was designed in collaboration with UniPro Company (htt
p://unipro.ru/) as an
interactive visual software system aimed to simplify work with DNA sequences, alignments
and annotations. The standard molecular biology methods are used in experimental analysis:
PCR and cloning followed by sequencing of individual clones.
The bioinformatic whole genomes analysis of number eukaryotic species (35 fungi, two
plants and three insect species) allowed us to describe three putative HT so far: (i) for CR1B
non-LTR retrotransposons which have been transmitted between Bombycidae moths and
Lycaenidae butterflies; (ii) for Tad-like non-LTR retrotransposons which have been transferred
between Eurotiomycetes and Sordariomycetes fungi; and (iii) for Ty3 LTR retrotransposons
which were presumably transmitted between basidiomycetes (Fungi) and mosses (Bryophyta,
Plantae). The actual mechanisms of horizontal transfer are still unknown for eukaryotic TEs
since it is not possible to show experimentally how the HT can occur. Parasites, symbionts,
bacteria, or viruses all could be suggested as potential vectors for horizontal transfer.