Table 1.

Compilation of TE protein domestication events highlighted in the text that have been driven by selection to adapt to evolutionary conflicts.

Gene names	Ancestral TE	TE protein (domain)#	Originally discovered	Taxonomic distribution	Possible conflict	Function related to the conflict	References
abp1, cbh1, cbh2	Tc1/mariner/po go	Transposase (whole)	Schizosacchar omyces pombe	Schizosaccharo mycetale	TE vs. host / Centromere drive	LTR retrotransposons repression; chromatin silencing at centromere.	[44, 45]
ALP1	PIF/Harbinger	Transposase (whole)	Arabidopsis thaliana	Land plants	TE vs. host	Potential role in TE silencing through interaction with Polycomb Repressive Complex 2.	[49]
ancHTenv	Gammaretrovir uses	Envelope	Homo sapiens	Hominids	TE vs. host	Restrict viral entry into the host cell.	[42]
cag	Tc1/mariner/po go	Transposase (DBD)	Drosophila melanogaster	Unknown	Centromere drive	Predicted to bind centromeric DNA sequence.	[90]
Cas1	Casposon	Transposase (whole)	Bacteria	Archaea and bacteria	Host vs. pathogen	Defense response to virus and maintenance of CRISPR repeat elements.	[33]
Cas9	DNA transposon	tnpB	Bacteria	Archaea and bacteria	Host vs. pathogen	Integration of invading viral DNA into CRISPR locus.	[40]
CENPB	Tc1/mariner/pogo	Transposase (DBD)	Homo sapiens	Mammals	Centromere drive	Facilitates mitotic centromere formation, recognizes and binds a 17-bp sequence in the centromeric alpha satellite DNA.	[100, 101]
enJSRVenv	Betaretroviruses	Envelope	Sheep	Ovine/unknown	TE vs. host	Restrict viral entry into the host cell.	[41, 102]
Fv1	MuERV-L (gag) (class III)	Capsid Protein	Mus musculus	Mus subgenera	TE vs. host	Murine leukemia virus restriction.	[103]
L1TD1	L1	ORF1	Homo sapiens	Mammals	TE vs. host	Potential role in TE control.	[50]
MAIL1	Ty3/gypsy LTR retrotransposo n	Plant mobile domain	Arabidopsis thaliana	Unknown	TE vs. host	Silencing of TEs and genes. Condensation of pericentromeric heterochromatin.	[48]
MAIN	Ty3/gypsy LTR retrotransposo	Plant mobile domain	Arabidopsis thaliana	Unknown	TE vs. host	Silencing of TEs and genes. Condensation of pericentromeric heterochromatin.	[48]
PiggyMac	piggyBac	Transposase (DBD? + core)	Paramecium tetraurelia	Unknown	TE vs. host	Required for genome rearrangement in Paramecium tetraurelia.	[55]
RAG1	Transib	Transposase (core)	Homo sapiens	Jawed vertebrates	Host vs. pathogen	Important function in V(D)J combination and interacts with RAG2.	[26]
RAG2	Transib	Transposase	Homo sapiens	Jawed vertebrates	Host vs. pathogen	Important function in V(D)J combination and interacts with RAG1.	[26]
Refrex-1	Gammaretrovir uses	Envelope	Domestic cats	Feline/unknown	TE vs. host	Restrict viral entry into the host cell.	[41, 104]
Rmcf	Gammaretrovir uses	Envelope	Mus castaneus	Mus subgenera	TE vs. host	Defends against viral infection.	[41, 105]
Rmcf2	Gammaretrovir uses	Envelope	Mus castaneus	Mus subgenera	TE vs. host	Defends against viral infection.	[41, 106]
Suppressyn	HERV-F	Envelope	Homo sapiens	Simians	TE vs. host	Regulates syncytins and potential viral restriction into host cells.	[41, 107]
Syncytin A, Syncytin B	HERV-F or HERV-H	Envelope	Mus musculus	Murid rodents	Fetus vs. mother	Placenta formation; fusogenic activities ex vivo.	[69]
Syncytin 1, Syncytin 2	HERV-W	Envelope	Homo sapiens	Humans, apes, Old World monkeys	Fetus vs. mother	Cell fusion; placenta formation.	[69]
Syncytin-Car1	CarERV3 (class I)	Envelope	Carnivores	Carnivores	Fetus vs. mother	Placenta-specific expression, fusogenic activities.	[69]
Syncytin-Ory1	Type D retroviruses	Envelope	Rabbits and hares	Leporids: rabbits and hares	Fetus vs. mother	Placenta-specific expression, fusogenic activities.	[69]
Syncytin-rum1	vertebrate retrovirus	Envelope	Bos taurus	Bos taurus	Fetus vs. mother	Placenta-specific expression, fusogenic activities.	[69]
TERT	LINE-like retroelement?	Reverse transcriptase	Homo sapiens	Eukaryotes	TE vs. host	RNA-directed DNA polymerase activity; telomerase RNA reverse transcriptase activity.	[108]
TPB2	piggyBac	Transposase (DBD? + core)	Tetrahymena thermophila	Unknown	TE vs. host	Required for genome Rearrangement in Tetrahymena thermophile.	[60]
Prp8	Retroelement	Reverse transcriptase	Homo sapiens	Eukaryotes	mobile introns vs.	Generation of catalytic spliceosome for second transesterification step; mRNA 3’-splice site recognition.	[66]

^#DBD: DNA binding domain; Core: Catalytic core