Table 1.
Examples of horizontally acquired transposable elements with documented evolutionary or phenotypic impact
| TE name | Locus | Species | TE size (bp) | TE type | Type of impact | Evidence for HTT* | References |
|---|---|---|---|---|---|---|---|
| P | Multiple copies and P neogenes | Drosophila | 2900 | Class 2; P | Hybrid dysgenesis; P neogenes involved in repression of P activity | see References column | [16,17,79,80] |
| hobo | Multiple copies | Drosophila | 3016 | Class 2; hAT | Hybrid dysgenesis | see References column | [81,82] |
| SPIN | Spider gene (NM_183088.2) | Murid rodents | 2867 | Class 2; hAT | Exaptation of transposase domain inferred from purifying selection on an orthologous copy shared by mouse and rats; unknown function | see References column | [83] |
| Helibat | Multiple | Vespertilionid bats | Class 2; Helitron | Capture, duplication, fusion of genes and regulatory region; remodeling of gene expression | see References column | [67] | |
| Bari1 | Juvenile hormone epoxy hydrolase (Jheh) genes | Drosophila | 1750 | Class 2; Tc1/Mariner | Adaptive insertion in intergenic region between Jheh2 and Jheh3 genes, downregulates expression of both genes | see References column | [14,22,84] |
| Rider | Sun gene; phytoene synthase gene PSY1; FER gene | Tomato (Solanum lycopersicum) | 4867 | Class 1; Copia | TE-mediated gene duplication causing a change in fruit shape; insertion into PSY1 inducing the production of yellow flesh; insertion into FER gene resulting in iron deficiency | Closest copy in spinach (107 My**), 79% identical over 4239 bp; dS TE = 1.1; lowest dS gene = 1.34; Rider was also found to be horizontally transferred in Arabidopsis [85] | [70,71,85–87] |
| Tsc2 | Ruby gene | Blood orange (Citrus sinensis) | 5454 | Class 1; Copia | TE induces cold-dependent modification of Ruby expression, which encodes an activator of anthocyanin production | Closest copy in asparagus (148 My), 82% identical over 4010 bp; dS TE = 0.48; lowest dS gene = 0.78 | [72,88] |
| Tip100 | CHS-D gene | Morning glory (Ipomoea purpurea) | 3873 | Class 2; hAT | TE insertion into CHS-D intron suppresses anthocyanin production | Closest copy in cannabis (110 My), 80% identical over 2426 bp; dS TE = 0.47; lowest dS gene = 0.74 | [69] |
| Hsmarl | SETMAR gene | Anthropoid primates | 1035 | Class 2; Mariner | Exaptation of Transposase domain giving birth to a new gene involved in DNA replication/repair | Closest copy in ant Ooceraea biroi (500 My), 73% identical over 1106 bp; dS TE = 0.6; lowest dS gene = 1.2 | [89,90] |
| SORE-1 | GmphyA2 gene | Soybean (Glycine max) | 6238 | Class 1; Copia | TE insertion inactivates GmphyA2 and induces photoperiod-insensitivity | Closest copy in banana (148 My), 85% identical over 5540 bp; dS TE = 0.57; lowest dS gene = 1.3 | [91] |
| ONSEN (ATCOPIA 78) | Abscisic acid (ABA) responsive gene | Arabidopsis (Arabidopsis thaliana) | 4077 | Class 1; Copia | Insertion of ONSEN into ABA responsive gene induces ABA-insensitive phenotype | Closest copy in asparagus (148 Myrs), 89% identical over 4077 bp; dS TE = 0.52; lowest dS gene= 1.14 | [92] |
| raider | Genes upregulated under UV stress | Maize (Zea mais) | 6527 | Class 1; Copia | Copies of raider are enriched within 1 kb of the TSS of genes up-regulated under UV stress. Stimulate stress-responsive gene expression | Closest copy in rice (40 Myrs), 88% identical over 4356 bp; dS TE = 0.35; lowest dS gene = 42 | [93] |
HTT of TEs for which a function has been demonstrated was searched using each TE copy as a query in blastn (megablast option) on the Whole Genome Sequences Genbank database. Hits from different species were retained when nucleotide identity was equal or higher to 79% for plants diverging from the original species by at least 40 myrs or 73% between insects and primates. The TE copy from the best hit was in each case submitted to further analysis, which consisted in comparing the global and synonymous (dS) TE distance to the dS calculated for five conserved genes evolving under purifying selection. These genes are SMC1, SMC2, MSH1, MLH1 and MCM5, taken from Zhang et al. (2012) [94]for plants and RPSA, RPLP0, RPL7, RPS5, RPL12 for the comparison between primates and insects. In all comparisons the dS calculated between TE copies was lower than the lowest dS calculated between the five conserved genes, strongly supporting HT of these TEs.
Indicates the time since when the two species in which the TE copy was found diverged, according to [95]