Genetic exchange in eukaryotes through horizontal transfer: connected by the mobilome

Abstract

Background: All living species contain genetic information that was once shared by their common ancestor. DNA is being inherited through generations by vertical transmission (VT) from parents to offspring and from ancestor to descendant species. This process was considered the sole pathway by which biological entities exchange inheritable information. However, Horizontal Transfer (HT), the exchange of genetic information by other means than parents to offspring, was discovered in prokaryotes along with strong evidence showing that it is a very important process by which prokaryotes acquire new genes.

Main body: For some time now, it has been a scientific consensus that HT events were rare and non-relevant for evolution of eukaryotic species, but there is growing evidence supporting that HT is an important and frequent phenomenon in eukaryotes as well.

Conclusion: Here, we will discuss the latest findings regarding HT among eukaryotes, mainly HT of transposons (HTT), establishing HTT once and for all as an important phenomenon that should be taken into consideration to fully understand eukaryotes genome evolution. In addition, we will discuss the latest development methods to detect such events in a broader scale and highlight the new approaches which should be pursued by researchers to fill the knowledge gaps regarding HTT among eukaryotes.

Keywords: Detection methods; Horizontal transfer; Horizontal transmission; Impact on host genomes; Transposable elements.

Fig. 1

Pairwise regression plot of codon bias and synonymous substitution in which VHICA performs statistical analysis to detected TEs signal departure from host genes. ENC-dS gene estimates (grey circles), TE ENC-dS estimates (red circles), expected regression line (black dotted line), threshold line of p-value = 0.05 (green dotted line)

Fig. 2

a Residual distribution of host genes (grey dots) and TE (yellow - vertically transmitted TE; red dots - horizontally transmitted) ENC-dS from regression line. b Graphical representation of several pairwise species comparison and the TE significant departure from host genes distribution (red squares) or not (yellow squares). Red branches represent the TE evolution following vertical transmission among hosts species, white “X” represents the TE lost from the host genome and red arrows represent HTT events

Fig. 3

a Pairwise genome-wide nucleotide identity distribution extracted from non-overlapping 1 kb windows (grey dots). b Second filtering step of putative HTT events, true HTT should presents several highly similar copies corresponding to a transposition burst (red circle and histogram). Green dot and histogram represent a potential HTT event filtered out from further analysis

Fig. 4

Ecological networks proposed by Venner et al. 2017 which can capture the relationship complexity between species (nodes) and its connections by HTT (edges). Nodes and edges attributes can take into account the importance of a species as HTT hub, the particular presence of HTT catalyzers as parasites (arthropod and viruses), the intensity and directionality of HTT events as well as the type of ecological relationships existing between species

Fig. 5

Somatic TE invasion through HTT in eukaryotic organisms with few or no cell differentiation and asexual reproduction. a Organisms alternating sexual and asexual phases showing regenerative capacity - somatic TE invasion (# - green spot). Considering that new organisms can emerge by regeneration (asexual reproduction - As) or sexual reproduction (S), when gonads arise from the cell invaded by the TE, the descendants will bear the new horizontally transferred TE in their genome in different proportions. b In plants with cycles of sexual and asexual reproduction, a somatic TE invasion of a meristematic cell by horizontal transfer can give rise to descendants containing the TE insertion