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Table 1 Candidate TEs located nearby immune-related genes. TE length is indicated as full-length (FL) or truncated (T). In the case of truncated elements, whether the insertion is a solo LTR, a TIR or 5′ truncated (5′) is also indicated. NS, not significant. NA, not analyzed

From: Regulatory regions in natural transposable element insertions drive interindividual differences in response to immune challenges in Drosophila

TE TE family (class) TE start position TE length Evidences of selection Gene (position) Immune-related evidence
FBti0019457 pogo (DNA) 3R: 29760415 1146 bp (T: TIR) Fst, nSL [52] kay (4434 bp 5′) Expression. Component of the JNK pathway, essential for antimicrobial peptide release [56, 57]. Upregulated in imd and bsk mutant LPS-induced S2 cells, and downregulated in Rel mutants [58]. Upregulated in larvae infected with P. entomophila (gram-negative) [46], and after 4 h of infection with P. entomophila [41].
FBti0020046 Doc (non-LTR) 3 L: 6040416 2305 bp (T: 5′) Allele age [59] Jon65Aiv (281 bp 3′) Expression. Upregulated after septic injury with mixed bacteria: M. luteus (gram-positive) and E. coli (gram-negative) [60]. Downregulated after 4 h of infection with P. entomophila [41]. Downregulated after oral infection with the avirulent gacA P. entomophila [61].
FBti0020057 BS (non-LTR) 3 L: 7130011 126 bp (T: 5′) H12, nSL [52] CG15829 (338 bp 3′) Expression. Upregulated after infection by septic injury with mixed bacteria (gram-positive and gram-negative), and regulated by Rel [60]. Upregulated after 4 h of infection with P. entomophila [41]. Upregulated in transgenic flies expressing a SINV replicon (alphavirus) [62].
CG8628 (739 bp 5′) Expression. Upregulated in microbiota associated flies vs. germ free flies [63], after infection with several pathogens (gram-positive and gram-negative, fungi, protozoa) [64], and downregulated after 4 h of infection with P. entomophila [41].
FBti0018883 Burdock (LTR) 2R: 9151357 6413 bp (T: LTR) NS CG8008 136 bp 3′) Expression. Induced by LPS (gram-negative) in an IKK-dependent manner in S2 cell cultures [65]. Upregulated after E. coli (gram-negative) infection in S2 cells [66].
FBti0019381 Juan (non-LTR) 3R: 15132112 2995 bp (T: 5′) NS CG42788 (180 bp 5′) Expression. Downregulated in response to P. rettgeri (gram-negative) infection in females [67].
FBti0019602 Juan (non-LTR) X: 8031495 4249 bp (FL) NS CG2233 (12 bp 3′) Expression. Downregulated in PEBP1 mutant L3 larvae, which are more resistant to M. luteus (gram-positive) and E. coli (gram-negative) infection [68]. Latitudinal expression differentiation after infection with E. coli and M. luteus mix in temperate vs. tropical populations [69].
FBti0061105 G5 (non-LTR) 2R: 7317828 51 bp (T: 5′) NS Dscam1 (46 bp 3′) Expression. Required in hemocytes for efficient phagocytosis and binds to E. coli (gram-negative) [70].
FBti0062242 BS (non-LTR) 3R: 16041234 102 bp (T: 5′) NS Pnr (3′UTR) Expression. pnr is a modifier of the Toll pathway and RNAi mutants show Imd pathway hyperactivation when infected with E. cloacae (gram-negative) and M. luteus and E. faecalis (gram-positive) [71].
tdn4 BS (non-LTR) 2R: 18807871 800 bp (T: 5′) NA CG15096 (479 bp 3′) Expression. Downregulated in Oregon R and Rel-mutant flies with microbiota compared to axenic flies [72], and after P. entomophila infection [41].
tdn8 Transpac (LTR) 3 L: 12863675 5500 bp (FL) NA CG10943 (816 bp 5′) Expression. Upregulated in Oregon R and Rel-mutant flies with microbiota compared to axenic flies [72], 24 h after infection with O. muscaedomesticae (protozoan) [64], and after P. entomophila infection [41].
tdn17 pogo (DNA) X: 21399382 2067 bp (FL) NA lcs (2,067 bp 5′) Expression. Involved in virus response, downregulated in males infected with sigma virus [73]. Upregulated in young fly guts [72].
FBti0019386 invader4 (LTR) 3R: 16189464 347 bp (T: solo LTR) CL test, TajimaD, Phenotypic [74] Bin1 (5′UTR) Survival. Mutant larvae are more sensitive to fungal A. fumigatus (fungi) infection [75].
FBti0019985 roo (LTR) 2R: 9871090 434 bp (T: solo LTR) TajimaD, iHS, H12, Phenotypic [76] cbx (first intron) Survival. Mutant flies are more sensitive to S. aureus (gram-positive) septic infection, but not to S. typhimurium (gram-negative) infection [77].
FBti0019564 mdg1 (LTR) X: 3785867 189 bp (T: LTR) TajimaD [78] tlk (intron) Survival. Involved in antimicrobial humoral response to gram-negative [57]. tlk knockdown, together with other five genes knocked-down, reduces phagocytosis of E. coli (gram-negative) and S. aureus (gram-positive) in S2 cells [79].
FBti0020119 S (DNA) 3 L: 15554974 1732 bp (FL) NS AGO2 (first intron) Survival. Involved in defense response to virus infections [80, 81], and interacts with Imd pathway proteins during gram-negative infection [82].
FBti0020137 S (DNA) 3 L: 17799864 1732 bp (FL) NS NUCB1 (first intron) Survival. Mutants are more resistant to V. cholerae (gram-negative) oral infection [83].
FBti0061506 1360 (DNA) 2 L: 17432071 48 bp (T: TIR) iHS [52] Dif (first intron) Survival and expression. Transcription factor involved in defense response to fungus and gram-positive bacteria and mediates Toll pathway activation [84,85,86,87,88]. Dif mutants are susceptible to fungi and gram-positive bacterial infection [88, 89]. Upregulated in guts from P. entomophila infected flies [41].
FBti0018877 BS (non-LTR) 2R: 9945496 131 bp (T: 5′) NS Mef2 (first intron) Survival and expression. Adult Mef2 mutant males are more sensitive to E. cloacae (gram-negative) and M. marinum (gram-positive) septic infection [90]. Upregulated after 4 h of infection with P. entomophila (gram-negative) [41].
FBti0018868 297 (LTR) 2R: 23877783 414 bp (T: LTR) NS TM4SF (1 bp 5′) A tetraspanin transmembrane protein, which modulate immune-signaling in Drosophila [53].
ken (340 bp 3′) JAK-STAT. Member of JAK-STAT pathway [91]. JAK-STAT pathway plays a role in immune response in D. melanogaster [54].