Vertical inheritance and bursts of transposition have shaped the evolution of the BS non-LTR retrotransposon in Drosophila
Adriana Granzotto1, Fabrício R. Lopes1, Cristina Vieira2, Claudia M. A. Carareto1§
1 UNESP - São Paulo State University, Laboratory of Molecular Evolution, Department of Biology, 15054-000 São José do Rio Preto, São Paulo, Brazil
2 Université de Lyon; Université Lyon 1; CNRS; UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, 43 boulevard du 11 novembre 1918, Villeurbanne F-69622, France
§Corresponding author
Supplementary Material
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....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|
Dmelanogaster_TART KAPGKDLITNQLIKTLPTKATLYLILIYNSILRLGYYPEAWKHAQVKMILKPGKSANEPRSYRPISLLSGLSKIFERLLLKRLFKVDLFKKAIPLHQFGF
Dmelanogaster_Jockey ....E..LD.RT.RL..DQ.LQF.A..F..V.DV..F.K...S.SII..H.T..TPTDVD....T...PS.G..M...I.N..LTCKDVT....KF....
Dfunebris_Jockey ....E..LD.RT.RL..DQ.L...V..F.....V..F.K.RPT.SII...... QPLDVD....T...PS.G.ML...I.N.ILTSEEVTR...KF....
Bmori_Amy ....S.GVSYRV..L..VQLIVM.AS.F.AAMANCIF.AV..E.D.IG.H....PK.D.T...... MS.G.LY....Y...RDFVSS.GILIDE....
Dmelanogaster_Doc .S..Y....PRMLIE..KC.I.HIC.LF.A.AK...F.QK..KSTIV..P....DKTQ.S...... TC...L..KM..L.ISPHLRINNTL.T.....
Dmelanogaster_F .S..Y....PEM.IQ..HS.VR.ITKLF.A.TK...F.QR..MMKII..P....NHTVAS...... CI..L..KC..I..NQHQTYHNI..A.....
Dmelanogaster_X ....H.V.C.ATL.A..RQ.I..IT.VF.A.V..Q.F.YQ..LGIIS..H....PER..A...... PSI..V....IAV.IVSIMEAQGIT.E.....
Dmelanogaster_BS .S..I.NVC.ATL.A..VRTI...A....A...VQFF.KQ..M.AIL..H....PEES.E...... S...LW...IAN..NDIMTERRIL.D.....
Dsimulans_BS .S..I.NVC.ATL.A..VR.I...A....A...VQFF.KQ..M.AIL..H....PKES.E..-...... S...LW...IAN..DDIMTERRIL.D.....
Dsechellia_BS .S..I.NVC.ATL.V..VR.I...A....A...VQFF.KQ..M.AIL..Q....PEES.E...... S...LW...IAN..DDIMTERRIL.D.K...
Dyakuba_BS ------M.AIL..H....PEED.E...... S..Q.W...IAN..GDFIKERRIL.D...R.
Derecta_BS .T..I.NVC.ATL.A..LR.I..MAK.F.A.F.VQSF.KQ..M.AIL..H....PEED.E...... S....W...IAN..GDFIKERRIL.D.....
Dpersimilis_BS ....I.RVC.STL.A...R.I..IV..F.AM..MQFF.KQ..I.TIL..H....PEDD.E...... S...VW....AN..GGIIKERRIL.D.....
Dmelanogaster_BS .S..I.NVC.ATL.A..VRTI...A....A...VQFF.KQ..M.AIL..H....PEES.E...... S...LW...IAN..NDIMTERRIL.D.....
Dmojavensis_BS ....Y.RLS.ATL.A...R.IIFIA..F.AM..VEFF.KQ..M.AIV..H....PEDD.E...... S...VW...IAN..GNIISERHML.DN....
Dmelanogaster_Helena ------.F.A...IQVF.RQ..M.VIL..H....PEDD.E...... PS...LWK..FANLINDIIRQGNIV.D.....
Dsimulans_Helena ....I.R.CHATL.V..I..II.IA..F.A...IQVF.RQ..M.AIL..H....PEDD.E...... PS...LW...IAN.INDIIRQGNIL.D.....
Dsechellia_Helena ....I.R.CHATL.V..I..II.IA..F.A...IQVF.RQ..MPAIL..H....PEDD.E...... PS...LW...IAN.INDIIRQGNIL.D.....
Dyakuba_Helena ....Y.R.CHATL.V..I..II.IA..F.A...VQVF.RQ..M.VIM..H....PEAD.E...... PS...LW....V..INDIVRQGNIL.D.....
Derecta_Helena ------...... PS...LW...FANWINDIIRQGNIL.DP.C..
Dananassae_Helena ....I.RVCHATL.A.....I.FIA..FHA.I.IQVF.KQ..L.AIM..H....PEVD.E...... PC...LW...IAN.VKRIMTENNIL.D.....
Dmojavensis_Helena ....I.K.C.ATL.A...R.L..IA..F.A.I..QVF.RQ..L.AIL..H....PEED.E...... PS...LW..TIAN.INAIFRQSNIL.D.....
Dvirilis_Helena ------M...... PEED.E...... PS...LW..TIAN.ITAITSQSNIL.D.R...
Ctentans_NCR1th .S..L.DVN.I...N..P.GFE..KF.I..C.K.NHF.KV....K.IP.P....PT..VS...... V.SI...L..I..N.INDHLEDNNI..NQ.C..
Aaegypti_JuanA ....D.G.FYI...K..ESSLSF.VD.F.KCFQ.A.F.DK..N.K.VP....D.NPA.AS...... SI..L..KVI.N.MMAHINENSIFANE....
Cpipiens_JuanC ....E.G.FYI...K..EANLSC.VK.F.KCFD.A.F.SS..N.K.IP....D.NPA.AS...... SI..L...II.N.MMTHINENSIFADE....
110 120 130 140 150 160 170 180 190 200
....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|
Dmelanogaster_TART RKEHGSEQQIARVTQFILEAFERKE--YCSAVFLDISEAFDRVWHEGLLLKLAKI-LPYNLYIILESYLTNRTFEVKDQAGETSRTGQIGAGVPQGSNLG
Dmelanogaster_Jockey .LQ..TPE.LH..VN.A...M.N..--.AVGA....QQ...... P...Y.AKRL-F.PQ..LVVK.F.EE...H.SVD-.YK.SIKP.A...... V..
Dfunebris_Jockey .LQ..TPE.LH..VN.A...L.K..--.AGSC....QQ...... P...Y.AKSL-.SPQ.FQLIK.FWEG.K.S.TAD-.CR.SVKF.E...... V..
Bmori_Amy .TN.SCV..VH.L.EH..VGLN.PKPL.TG.L.F.VAK...K...N..IF..FNMGV.DS.VL.IRDF.S..S.RYRVE-.TR.SPRPLT...... V.S
Dmelanogaster_Doc .EK..TIE.VN.I.SE.RT...HR.--..T.I...VAQ...... LD...F.II.L-..Q.THKL.K...Y..V.AIRCD-TS...DCA.E...... V..
Dmelanogaster_F .ES..TIE.VN.I.TE.RT...YR.--..T.....V.Q...K..LD..MF.IKIS-..ESTHKL.K...YD.K.A.RCN-TA..TVHT.E...... V..
Dmelanogaster_X .AG.CTVE.LH..VEQ..T.YDS..--..NSL....R...... I..Q..IKQT-..APYFGL.K...EG.R.A.RFH-SAI.TEHNVA...... V..
Dmelanogaster_BS .QG.STVE.VH.L.KH..Q..DD..--..N...I.MQQ...... D..IS.VK.L-F.APY.GV.K...ED.R.M.RVR-NSY.IPRVMR...... V..
Dsimulans_BS .QG..CVE.VH.L.KH..Q..DDE.--..N...IVMQQT...... D...S.IK.--F.APY.GV.R...ED.K.M.RVR-NYY.TPCVMR...... V..
Dsechellia_BS .QG..TVE.VH.L.KH..Q..DD..--..Y...I.MQQ.....-.D...SQIK.L-F.APY.GV.R...ED.K.I.RVR-NSY.TPCVMR..A..C.V..
Dyakuba_BS .QG.STVE.VY.LVKH..Q..DDL.--..N...I.MQQ.....C.------
Derecta_BS .QG.STVE.VH.LVKH.IQ..DDL.--..N...I.MQQ...... I...C.IK.L-..APY.GV.K...ED.K.M.RVR-STY.TPCYMR...... V..
Dpersimilis_BS .EG..TVEEVH.LAGH..Q.YDDL.--..N...I.MQQ...... I...S.IK.L-F.APY.GV.R...EG.Q.M.RFR-NTH.TPC.MR...... V..
Dmelanogaster_BS .QG.STVE.VH.L.KH..Q..DD..--..N...I.MQQ...... D..IS.VK.L-F.APY.GV.K...ED.R.M.RVR-NSY.IPRVMR...... V..
Dmojavensis_BS ..G..TVE.VH.L.RH..Q..DDM.--..N...V.MQQ...... T...S.IKNL-F.APYFG..R...EG.Q.I.RVR-NTY.TPC.MR...... V..
Dmelanogaster_Helena ..G.ETIE.VH.LVKH..Q..DDC.--.SN...I.MQQ...K...V...C.IKTL-..APYFC..K...KE.Q.KITVR-NSY.SMYPMR...... V..
Dsimulans_Helena ..G..TIE.VH.LVKH..Q..DDC.--.SN...I.MQQ...K...V...C.IKTL-..APYFC..K...EE.Q.KITVR-NSY.SIYPMR...... V..
Dsechellia_Helena ..G..TIE.VH.LVKH..Q..DDC.--.SN...I.MQQ...K...V...C.IKTL-..APYFC..K...EE.E.KITVR-NSY.SIYPMR...... V..
Dyakuba_Helena ..G..TVE.VH.LVKH..Q.LDDC.--.SN...I.MQQ...K...V...C.IKTM-..APYFC..K...EG.E.KITVR-NNY.TVYPMR...... V..
Derecta_Helena ..R..TIE.VH.LVKH..Q..DDC.--SSL...I.MQQ...K...V...------KITVR-NSY.SMYPMR...... GV..
Dananassae_Helena .GG..TVE.VH.LV.H..Q..DDQ.--.SN...I.MQQ...K...D.....IKNL-..APY.GLFR...EV.E.K..VK-DSY.DNFLMR...... V..
Dmojavensis_Helena .EG.STVE.VH.LVKH..Q..DDS.--.SN...I.MQQ...K...D...Y.IKNL-..APY.GL.R...ED.V.Q..VK-DTL.S.YPMR...... V..
Dvirilis_Helena .EG.VTVE.VH.LLNH.MQ..DYL.--FSN...I.MQQ...K...D...C.IKNL-..APY.GL.R...ED.V.Q..VK-DTL.S.------
Ctentans_NCR1th .TGRSTSH.LIK.IKTAK.NINN.K--STGMI...VEK...... N...Y.ML.LRF.LP.IKTVR.F.SE...S.FIK-.QF.EIKE.KY.....AV.S
Aaegypti_JuanA .HG.STTH.LL...NLTRANKSEGY--STGLAL...EK...S...... IV..KNFNF.TYIVR.IQ...S...LQ.NY.-NSR.ERLPVR...... I..
Cpipiens_JuanC .LG.STTH.LL..SNL.RSNKSEGY--STAPAL...EK...S...K..IA..KRFNF.IYIVK.IQN...D..LQ.CY.-NSK.DQLPVR...... I..
210 220 230 240 250 260 270 280 290 300
....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|
Dmelanogaster_TART PLLYSIFSSDMPLPYIYRPSPTERIMLSTYADDTIVLSSDTLATAATRNNENYLKSFSDWADKWGISVNAA-KTGHVIFTLKNDLPT------SLRT
Dmelanogaster_Jockey .T...V.A....THTPVTEVDE.DVLIA...... A..TKSKSIL...SGLQE..DA.QQ..EN.NVRI..E-.CAN.T.ANRT--GS------CPG-
Dfunebris_Jockey .T.....TA...NQNAVTGLAEGEVLIA.....IA..TKS.CIVE..DALQE..DA.QE..V..NV.I..G-.CAN.T..--.AIRD------CPG-
Bmori_Amy ...F.L.VN.I.RSPPTH------.ALF....T.YY.SRNKSLIAKKLQSAALALGQ.FR..R.DI.P.-.STA.L.QRGSSTRISSRIRRRNLTPP-
Dmelanogaster_Doc .I..TLYTA.F.ID.------NLTT..F....AI..RSKCPIK..ALLSRH.T.VER.LAD.R..I.VQ-.CKQ.T...NK--Q.------CPP-
Dmelanogaster_F .T..L.YTA.I.TNS------.LTV..F....AI..RSRSPIQ..AQLAL..IDIKK.LSD.R.K..EQ-.CK..T...NR--QD------CPP-
Dmelanogaster_X ....CLY.H...Q.DVSLYG---KS..A.F...VC.TYRSRCEHD.ADGIQDFAYR..E..RR.N.GI.SS-.SNN.C....R--R.------PPP-
Dmelanogaster_BS .....V.TA.L.C.NA.HMADPRKAL.A.....IAL.Y.SNCCNE.A.GLQE..TTLAA.CKR.NLK..PQ-..INPC....TLS.V------TAP-
Dsimulans_BS .....V.TV.L.C.NAHHMY-PRKAL.A.------
Dsechellia_BS .....V.TA.L.C.NA.YMVDPMKAL.V....NIAL.Y.SNCCNV.A.GLQEH.TTLAA.CKR.NLE..PQ-..TNPC....PLN.V------PAP-
Dyakuba_BS ------
Derecta_BS ...... TA.L.C.NMHHMEAPRKAL.A.....IAL.Y.SSSC.E.A.GLQE..NTLAA.CKR.NLK..PH-..INPC....TLIRR------TPP-
Dpersimilis_BS ...... YTA.L.S.SEQHMEAPRKAL.A.....IAL.Y.SKCRLE.ADGLQE..Y.LAA.CKR.NLK..PL-..TNPC....ALIDH------TPP-
Dmelanogaster_BS .....V.TA.L.C.NA.HMADPRKAL.A.....IAL.Y.SNCCNE.A.GLQE..TTLAA.CKR.NLK..PQ-..INPC....TLS.V------TAP-
Dmojavensis_BS ...... YTA.L.S.SVRHMENPGKAL.A.....IA..Y.SKCP.E.ANGV.S..NTLVA.CKR.NMKI.PR-..TNTC....TFIRH------TPP-
Dmelanogaster_Helena ...--.PCTHY...EFRTHGS..QDSYCNLCRHRSCILGQRRGSKR.TGLQE.INALAA.CKR.NLKI.PL-..TNPC....TLI.N------TPP-
Dsimulans_Helena .....LYTA.I.C.SFEHMAAPN.TLIA.....IA.VYNSRDSRE.ANGLQE.INALAA.CKR.NLKI.PL-..TNPC....TLI.N------TPP-
Dsechellia_Helena .....LYTA.I.C.SFEHMAAPN.TLIA.....IA.VYNSRDSRETANGLQE.INDLAA.CKR.NLKI.PL-..TNPC....TLI.N------TPP-
Dyakuba_Helena .....LYTA.I.C.NFDHMEAPYKALMA.....IA.VY.SGDSRE.AKGLQE.INALAA.CKR.NLKI..T-..TNLC....TLIKK------TPP-
Derecta_Helena ...--.PCTHY...EFRTHGS..QDSYCNLCRHRSCILGQRRGSKR.T------
Dananassae_Helena .....LYTA.I.I.SSQHMVAPSKALIA.....IA.IYNYRCHRE.SKGLQE..FTLAA.CKR.NLKI.P--..TN.C....RLIIN------TPQ-
Dmojavensis_Helena ...F.LYT..I.S.SSQHMDAPSKAVIA.....IAIIYNSKNVVE.STGLQR..DTLA..CKR.NLK..PL-..LNPC....RLAMH------TPP-
Dvirilis_Helena ------
Ctentans_NCR1th .T..N..TY.IVRETTNN------IALF....ALYH.AENSADIVTQLLHTGRKVQQYM...K.NL.K--QKSQA..ITNRYSKQ------LP.-
Aaegypti_JuanA .I..N..T..L.------ELPQGCQK.LF....GLSAKGRSLRVICSRLQKS.DI..SYLQ..E..P..S-..QLI..PH.PKALY------LKPS
Cpipiens_JuanC .I..N..T..L.------DLPPGCQK.LF....SISAKARSLRVI..RLQKS.DI.NSYLKE.K.TP.VLS..QLI..PH.PRADF------LKPK
310 320 330 340 350 360 370 380 390 400
....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|
Dmelanogaster_TART ----MKIKGQVIKIESKQSYLGVILDSKLTLSSHVTKLMGKYTTAYRKMTWILNRRSKLPTKTKMLILKSVLSPIWQYAIAAWGPLVTDAQIRRIQVEEN
Dmelanogaster_Jockey ----VSLN.RL.RHHQAYK...IT..R...F.R.I.NIQQAFR.KVAR.S.LIAP.N..SLGC.VN.Y..I.A.CLF.GLQVY.-IAAKSHLNK.RILQA
Dfunebris_Jockey ----VT.N.SLLSHTHEYK...... RS..FRR.I.S.QHSFR.RIT..N.L.AA.N..SLDN.VK.Y.CIVA.GLF...QVY.-IAARTHLNK.R.LQA
Bmori_Amy ----ITLFR.P.PWAR.VK....T..ASM.FRP.IKSVRDRAAFILGRLYPMICK...MSLRN.VTLY.TCIR.VMT..SVVFA-HAARTH.DTL.SLQS
Dmelanogaster_Doc ----LVLNNIC.PQADEVT....H..RR..WRK.IEAKSKHLKLKA.NLH.LI.A..P.SLEF.A.LYN...K...T.GSEL..-NASRSN.DI..RAQS
Dmelanogaster_F ----LLLNSIPLPKADEVT....H..RR..WRR.IEAKKTQLKLKANNLH.LI.SG.P.SLDH.V.LYN.I.K...T.GSQL..-NASNSN.DI..RAQS
Dmelanogaster_X ----VY.EEVPVPQPNAAK....L..RR..F.K...DIRTRLRAKVA.HY.L.SS....SLSN.LT.Y.QI.A.N.K.GCQI..-.AC.SH.K...AIQ.
Dmelanogaster_BS ----IELE.VILDQP.QAK...IT..KR..FGP.LKATTRRCYQRMQQLR.L...K.TMTLRA.RAVYVHCVA...L.G.QI..-IAAKSNYN....LQ.
Dsimulans_BS ------VYVHYVA...L.G.QI..-ISANSNYNL...LQ.
Dsechellia_BS ----IELEDVILDQPLQAK...IT..KR..FGP.LKATARRCYQRMQQLR.RI..K.TMSLRA.RAVYVHYVA...L.G.QI..-ISEKSKNNL...LQ.
Dyakuba_BS ------
Derecta_BS ----IQFD.VTLEQPLQAK...IT..KR..FGP.LKAAARRCGQRMQQLR.LI....TMTLRA.RAVYAHCIA...L.GVQI..-IAAKSNYK..E.LQ.
Dpersimilis_BS ----I.LE.VTLDQPEQAK...IT..KR..FGP.LKATAR.CGQRMQQLR.LI....TMSLRA.RAVYVHCVA...L.GVQI..-IAAKSNYK....LQ.
Dmelanogaster_BS ----IELE.VILDQP.QAK...IT..KR..FGP.LKATTRRCYQRMQQLR.L...K.TMTLRA.RAVYVHCVA...L.G.QI..-IAAKSNYN....LQ.
Dmojavensis_BS ----IRLD.ETLDQP.QAK...IT..KR..FGP.LKAVARRCGQRMQQLR.LV....TMSLRA.RAVYVHCVA...L.GVQI..-ICAKSNFK....LQ.
Dmelanogaster_Helena ----IRLE---MNQPLQAT...IT..KR..FGP.LKNTVK.CGHRSQQLR.LM------
Dsimulans_Helena ----IRLE.VTLNQPLQAT...IT..KR..FGP.LKNTVK.CGHRSQQLR.LM....T.SMRC.RAVYAHCIV...L.G.QI..-IAAKSNYN....MQ.
Dsechellia_Helena ----IRLE.VTLNQTLQATH..IT..KR..FGP.LKNTVK.CGHRSQQLR.LM....T.SMRC.RAVYAHCIV...L.G.QI..-IAAKSNYN....MQ.
Dyakuba_Helena ----LQLE.VTLDQPLQAT...IT..------LR.LM...NT.SLRC.RAVYAHCIL...L.G.QI..-IAAKSNYK....MQ.
Derecta_Helena ------
Dananassae_Helena ----IQLE.VTLEQQNEAK...IT..KR..FGP.LKSTTK.CNMRVQQLR.MISK..TM.LRC.RAVYVHCIL.M.L.GVQI..-IAAKSNYK....LQ.
Dmojavensis_Helena ----IQMS.VTLQQPAQVK...IT..KR..FGP.LKATVK.CRHRLQQLR.LT..K.T..LRC.RAVYVHCIL...L.GVQI..-IAAKSNYK.V..LQ.
Dvirilis_Helena ------
Ctentans_NCR1th ------NNIKF.NENIK------.ESEANI.E------
Aaegypti_JuanA SRHVVTMR.VP.NWSDEVK...LM..KN..FKN.IEGIQA.CNKYIKCLYPLI..K...CL.N.L..F.QIFR.AML..VPI.T-SCCNTRKKAL.RIQ.
Cpipiens_JuanC SHHII.MNEVNL.W.DQVK...LGF.KN..YKD.IESIQV.CNKYIKCLYPLI..N.R.CL.N.L..Y.QIFR.AML..VPI.T-SCCLTRKKKL.RIQ.
410 420 430 440 450 460 470 480
....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|...
Dmelanogaster_TART RKMRDICRAGRYTSNQTIRD-----RYGIKTVEEFYQQALHRFSETIKSHPNIAVRRIFTRHY----IPNRLLRRIKKQEIQKFRGQP
Dmelanogaster_Jockey KTL.R.SG.PW.MRTRD.ER-----DLKVPKLGDKL.NIAQKYM.RLNV...SLA.KLG.AAVVNADPRT.VK..L.RHHPHDLPNLV
Dfunebris_Jockey KML.K.SG.PW.MRTRD.EC-----DLKVPKIGDKIREVAKKYH.RLD....SLA..LGVAAQRSASPRS.VR..L.RHHP.DLLDRA
Bmori_Amy .FC.LAVG.PWFVR.VDLH.-----DL.LESIRKYMKS.SE.YFDKAMR.D.RLG.LR------D.GNRT..TRQRGRRAT----
Dmelanogaster_Doc .IL.I.TG.PW.LR.EN.HR-----DLK..L.I.VIAEKKTKYN.KLTT.T.PLA.KL------.RVCSQS.LHRNDLPAQQ---
Dmelanogaster_F KIL.T.TG.PW.VRSEN.QR-----DLN.PS.TNAITELKEKYL------
Dmelanogaster_X KVA.L.TGCEWFVR.T.LHR-----DLKLA..FDEINKHSS.YHDRLER.R.RLASAL------NRS.PP..LNR------
Dmelanogaster_BS .A..A.TDCPY.VRGT.LHR-----DLNLH....QISKHTS.Y.DRLRR.HS.LA..L------L.A.P...L.RKGFA.TL...
Dsimulans_BS CA..A.TDCPY.VRGT.LHR-----DLNLH....QISTHTS.Y.DRLRR.HS.LA..L------L.A.P.....RKGFA.TL...
Dsechellia_BS .A..A.TDCPY.VRVT.LHR-----DLNLH....QISRHTS.Y.DRLRR.HS.LA..L------L.A...G.L.RKGFA.TL...
Dyakuba_BS --..A.ANCPY.VRGS.LHR-----DLNLH..K.QISRHTS.Y.DRL.R.HSMLAK.L------L.A.P...L.RKGFA.TI..L
Derecta_BS .A..A.TNCPY.VRSS.LHR-----DLNLH....QISRHTS.Y.DRL.R.HSMLA..L------L.A.P...L.RKGFA.TI..L
Dpersimilis_BS .A..Q.TNCPW.VRGS.LHR-----DLNLH....QIGRHTS.Y.DRLIR.HSMLA..L------L.AQ------
Dmelanogaster_BS .A..A.TDCPY.VRGT.LHR-----DLNLH....QISKHTS.Y.DRLRR.HS.LA..L------L.A.P...L.RKGFA.TL...
Dmojavensis_BS .VL.Q.TNCPW.VRGS.LHR-----DLKLF....QIGRHTS.Y.DRLAR.RSRLA..L------L.A.P...L.RLGFA.NIR--
Dmelanogaster_Helena ------
Dsimulans_Helena .AL.Q.TNCPW.VR.S.LHK-----DLN.H...SQIGRHTS.Y.DRLL..SSLLA..L------..A.P...L.R.GFA.TI..Q
Dsechellia_Helena .AL.Q.TNCPW.VNSS.LHK-----DLN.H...SQIGRHTS.Y.DRLL..SSLLA..L------..A.P...L.R.------
Dyakuba_Helena .AL.Q.TNCPW.VR.S.LHK-----DLNLY....QIGRHTS.Y.DRLQ..SSLLA..L------..A.P...L.R.GFA.TF..-
Derecta_Helena ------
Dananassae_Helena .ML.T.TGCPW.VRGS.LHR-----DLN.H....QINRHTS.Y.DRLLR.------
Dmojavensis_Helena .VL.Q.TNCPW.IRGS.LHR-----DLKLS....QINKHTS.Y.DRLVRYQSLLA.GL------T.A.P...L.R------
Dvirilis_Helena ------
Ctentans_NCR1th ------W------
Aaegypti_JuanA KILKM.L.LPPWY.TNELHRISMLKHWNKCQIQSLIISGKN.Y------.LLLP.L------M.YMFRLS------
Cpipiens_JuanC KILKM.PKLPPWF.TSELHQ-----LAEVD.LDVMSNKIIDA.RQKSLQSSAAL------I.SLYSL------
Fig S1. Alignment containing the sequences (RTases) used for the phylogenetic analysis. The sequences obtained in this study and other LINE elements based on their partial reverse transcriptase domains (see Methods for additional information) were manipulated using BioEdit (Hall 1999) and aligned with ClustalW (Thompson, Higgins et al. 1994). The dotsindicatesimilarity with the first sequence.
Table S1 Estimates of evolutionary divergence between BSreference sequences. Analyses were conducted using the Kimura 2-parameter model (Kimura 1980).
1 / 2 / 3 / 4 / 5 / 6 / 71. D. mel
2. D. sim / 0.057
3. D.sec / 0.061 / 0.051
4. D. yak / 0.221 / 0.236 / 0.242
5. D. ere / 0.232 / 0.235 / 0.234 / 0.088
6. D. pse / 0.296 / 0.317 / 0.325 / 0.315 / 0.283
7. D. per / 0.301 / 0.312 / 0.335 / 0.323 / 0.290 / 0.071
8. D. moj / 0.390 / 0.415 / 0.398 / 0.386 / 0.390 / 0.284 / 0.292
Table S2Estimates of evolutionary divergence between Adh sequences. Analyses were conducted using the Kimura 2-parameter model (Kimura 1980).
1 / 2 / 3 / 4 / 5 / 6 / 71. Dmel
2. Dsim / 0.012
3. Dsec / 0.015 / 0.012
4. Dyak / 0.035 / 0.032 / 0.040
5. Dere / 0.030 / 0.033 / 0.072 / 0.079
6. Dpse / 0.119 / 0.115 / 0.124 / 0.195 / 0.196
7. Dper / 0.119 / 0.115 / 0.124 / 0.191 / 0.192 / 0.001
8. Dmoj / 0.238 / 0.225 / 0.238 / 0.247 / 0.270 / 0.262 / 0.242
Table S3Sequences of the BS NLTR retrotransposon in the D. melanogaster sequenced genome.
Localization / Insertion orientation / Begin / End / Size(bp) / % identity with the reference BS
2LHet / + / 357,884 / 356,007 / 1,879 / 99.25
2RHet / - / 313,033 / 314,267 / 1,236 / 99.68
2RHet / - / 3,192,185 / 3,193,753 / 1,569 / 92.96
2RHet / + / 3,267,406 / 3,267,575 / 171 / 82.35
2RHet / + / 161,535 / 161,637 / 104 / 82.52
2RHet / + / 172,034 / 172,136 / 104 / 82.52
2RHet / + / 935,220 / 935,308 / 90 / 82.02
3LHet / - / 2,548,788 / 2,550,562 / 1,775 / 92.68
3LHet / - / 2,547,322 / 2,548,766 / 1,445 / 90.62
3L / - / 18,508,066 / 18,513,190 / 5,125 / 99.7
3L§ / - / 16,516,430 / 16,521,556 / 5,126 / -
3L / - / 24,299,797 / 24,300,538 / 742 / 97.18
3L / + / 6,988,050 / 6,988,585 / 537 / 99.25
3L / - / 24,300,541 / 24,300,679 / 140 / 97.12
3L / + / 7,123,125 / 7,123,236 / 113 / 100
3L / + / 19,108,816 / 19,108,912 / 98 / 100
3L / + / 5,919,512 / 5,919,601 / 91 / 100
3L / + / 16,724,100 / 16,724,211 / 113 / 91.96
3L / - / 20,705,034 / 20,704,945 / 91 / 91.11
3RHet / + / 1,484,369 / 1,489,114 / 4,746 / 97.87
3RHet / + / 2,330,390 / 2,333,164 / 2,775 / 96.78
3RHet / + / 2,335,021 / 2,335,806 / 786 / 96.84
3RHet / + / 2,496,004 / 2,496,117 / 115 / 90.35
3RHet / - / 2,209,845 / 2,209,927 / 84 / 95.18
XHet / + / 137,809 / 140,709 / 2,901 / 91.45
XHet / - / 148,103 / 150,969 / 2,867 / 91.14
§reference copy; sequences harboring indels; sequences harboring internal deletions; sequences harboring internal insertions
Table S4Sequences of theBS NLTR retrotransposon in the D. simulans sequenced genome.
Localization / Insertion orientation / Begin / End / Size(bp) / % Identity with the reference BS
ChrU / + / 367,761 / 368,767 / 1,007 / 91.74
ChrU / + / 505,681 / 505,982 / 303 / 92.08
ChrU / + / 607,803 / 608,444 / 642 / 91.72
ChrU / - / 793,089 / 793,795 / 707 / 89.14
ChrU / - / 1,281,253 / 1,282,007 / 755 / 88.94
ChrU / - / 1,760,288 / 1,761,741 / 1,454 / 94.64
ChrU / - / 1,762,568 / 1,763,533 / 966 / 93.94
ChrU / + / 2,046,421 / 2,047,379 / 959 / 94.54
ChrU / + / 2,179,775 / 2,179,963 / 189 / 95.77
ChrU / + / 2,181,370 / 2,184,512 / 3,143 / 96.50
ChrU / + / 2,539,475 / 2,540,485 / 1,011 / 93.24
ChrU / + / 4,199,857 / 4,200,180 / 324 / 96.3
ChrU / + / 4,358,853 / 4,359,305 / 453 / 93.95
ChrU / + / 5,818,292 / 5,819,110 / 819 / 91.52
ChrU § / + / 5,747,197 / 5,751,496 / 4,300 / -
ChrU / + / 6,115,844 / 6,117,327 / 1,484 / 94.73
ChrU / + / 7,600,908 / 7,601,461 / 554 / 90.96
ChrU / + / 8,125,180 / 8,126,150 / 971 / 92.63
ChrU / - / 9,841,781 / 9,842,484 / 704 / 91.43
ChrU / + / 10,774,408 / 10,775,135 / 728 / 92.59
ChrU / + / 12,626,625 / 12,627,170 / 546 / 90.83
ChrU / - / 12,954,313 / 12,954,571 / 259 / 88.03
ChrU / - / 13,147,952 / 13,148,681 / 731 / 90.83
ChrU / - / 14,466,864 / 14,467,567 / 704 / 91.09
ChrX_random / + / 5,629,190 / 5,629,436 / 247 / 97.17
ChrX_random / + / 5,629,711 / 5,631,052 / 1,342 / 96.37
ChrX_random / + / 5,634,148 / 5,634,598 / 451 / 94.90
Chr2h_random / - / 376,819 / 377,761 / 943 / 96.48
Chr2h_random / - / 378,098 / 379,189 / 1,092 / 92.34
Chr2h_random / + / 944,253 / 944,545 / 294 / 91.16
Chr3L / - / 19,315,055 / 19,315,305 / 251 / 95.75
Chr3L / - / 19,316,827 / 19,318,496 / 1,669 / 96.53
Chr3L_random / + / 1,032,446 / 1,032,576 / 131 / 81.68
Chr3L_random / + / 1,048,857 / 1,049,157 / 302 / 95.36
Chr2L / + / 20,941,146 / 20,941,452 / 308 / 89.29
Chr3h_random / + / 871,280 / 871,425 / 146 / 80.82
Chr3h_random / + / 1,366,192 / 1,366,454 / 264 / 90.53
Chr4 / - / 76,843 / 76,949 / 108 / 98.15
Chr3R / + / 15,009,955 / 15,010,121 / 167 / 80.24
§reference copy; sequences harboring indels; sequences harboring internal deletions; sequences harboring internal insertions
Table S5Sequences of the BS NLTR retrotransposon in the D. sechellia sequenced genome.
Localization / Insertion orientation / Begin / End / Size(bp) / % identity with the reference BS
super_2 / + / 4,064,552 / 4,064,647 / 96 / 93.75
super_5 / - / 5,802,082 / 5,802,313 / 235 / 96.60
super_11 / - / 78,966 / 789,562 / 100 / 95.00
super_26 / - / 46,917 / 47,371 / 455 / 96.27
super_26 / + / 49,444 / 49,528 / 85 / 98.82
super_29 / + / 688,191 / 689,224 / 1,034 / 95.06
super_29 / + / 695,397 / 696,294 / 898 / 96.16
super_39 / - / 180,289 / 18,019 / 100 / 94.00
super_48 / + / 138,634 / 138,727 / 101 / 88.12
super_49 / - / 121,127 / 123,395 / 2,269 / 94.96
super_54 / + / 111,849 / 111,945 / 97 / 91.75
super_63 / + / 18,364 / 18,448 / 90 / 92.22
super_70 / - / 5,209 / 7,634 / 2,426 / 95.88
super_70 / - / 8,145 / 8,615 / 471 / 92.87
super_133 / - / 17,841 / 19,276 / 1,436 / 95.27
super_133 / - / 20,174 / 20,908 / 735 / 94.63
super_133 / - / 20,980 / 24,575 / 3,596 / 95.02
super_133 / - / 27,342 / 29,360 / 2,019 / 94.49
super_139 / - / 15,401 / 19,272 / 3,872 / 92.74
super_176 § / + / 76,677 / 80,856 / 4,103 / -
super_194 / - / 38,520 / 41,175 / 2,656 / 95.50
super_194 / - / 49,653 / 50,345 / 704 / 94.03
super_214 / + / 25,456 / 26,027 / 572 / 94.90
super_263 / - / 4,162 / 5,058 / 897 / 96.13
super_263 / - / 11,028 / 11,714 / 687 / 95.15
super_274 / - / 3,415 / 5,838 / 2,424 / 95.33
super_274 / - / 7,357 / 7,844 / 489 / 95.71
super_274 / - / 8,130 / 8,222 / 93 / 82.80
super_348 / - / 4,448 / 4,775 / 328 / 92.58
super_348 / - / 38,298 / 39,318 / 1,021 / 95.06
super_348 / - / 3,696 / 3,850 / 156 / 92.31
super_348 / - / 35,740 / 35,989 / 250 / 93.20
super_433 / + / 3,789 / 4,822 / 1,034 / 96.43
super_433 / + / 7,190 / 7,669 / 480 / 93.77
super_433 / + / 8,267 / 8,639 / 373 / 93.55
super_491 / + / 7,080 / 8,324 / 1,245 / 89.55
super_736 / + / 4,356 / 4,826 / 471 / 91.55
super_764 / - / 1,302 / 1,655 / 354 / 95.58
super_790 / - / 7,357 / 7,844 / 489 / 95.71
super_1002 / - / 4,604 / 5,931 / 1,328 / 95.46
super_1012 / - / 25 / 795 / 771 / 95.41
super_1242 / + / 318 / 4,192 / 1,013 / 95.42
super_1754 / - / 656 / 1,689 / 1,034 / 95.50
super_1792 / - / 2,187 / 2,301 / 115 / 93.91
super_1835 / - / 1 / 102 / 102 / 95.37
super_2069 / - / 120 / 213 / 2,011 / 93.85
super_2712 / + / 55 / 1,075 / 1,021 / 96.20
super_2943 / - / 1 / 2,617 / 2,617 / 94.62
super_3296 / + / 4,178 / 4,987 / 810 / 96.22
Table S5 Continuation.
super_4247 / + / 115 / 823 / 328 / 92.58
super_4247 / + / 1,748 / 1,862 / 115 / 93.91
super_4756 / + / 3 / 1,131 / 1,129 / 88.88
super_5113 / + / 466 / 729 / 266 / 93.61
super_5135 / - / 1,115 / 2,091 / 977 / 96.82
super_5959 / - / 973 / 1,932 / 960 / 96.46
super_7676 / + / 831 / 1,673 / 843 / 96.19
super_7912 / - / 6 / 451 / 451 / 94.24
super_12591 / + / 49 / 893 / 845 / 93.32
super_12736 / - / 938 / 1,124 / 187 / 95.72
super_12896 / + / 258 / 1,107 / 850 / 100
super_12941 / - / 249 / 1,101 / 853 / 96.32
super_12971 / - / 1 / 1,098 / 1,098 / 99.17
super_13141 / + / 643 / 1,077 / 435 / 88.80
super_13295 / - / 37 / 1,054 / 1,018 / 95.22
super_13752 / - / 15 / 1,002 / 988 / 94.84
§reference copy; sequences harboring indels; sequences harboring internal deletions; sequences harboring internal insertions
Table S 4Sequences of the BS NLTR retrotransposon in the D. yakuba sequenced genome.
Localization / Insertion orientation / Begin / End / Size(bp) / % identity with the reference BS
Contig4.34 / + / 285,500 / 285,594 / 95 / 93.68
Contig4.38 / + / 172,920 / 173,133 / 214 / 89.72
Contig5.24 / + / 394,495 / 349,596 / 102 / 95.1
Contig11.4 / + / 484,992 / 485,112 / 121 / 93.39
Contig12.9 / + / 10,393 / 10,772 / 380 / 90.08
Contig13.5 / - / 126,620 / 126,841 / 222 / 93.69
Contig13.7 / - / 116,919 / 117,027 / 109 / 93.58
Contig39.36 / + / 1,511 / 1,754 / 244 / 88.52
Contig98.7 / - / 6,726 / 7,320 / 595 / 91.35
Contig105.4 / - / 31,587 / 31,701 / 116 / 90.52
Contig149.6 / - / 16,887 / 17,125 / 239 / 89.54
Contig156.5 / - / 49,013 / 49,527 / 515 / 86.61
Contig175.7 § / + / 10,651 / 11,895 / 1,245 / -
Contig278.3 / - / 1,418 / 1,657 / 240 / 89.17
Contig529.4 / + / 6,782 / 7,832 / 1,051 / 98.57
Contig577.2 / - / 1,572 / 1,710 / 139 / 93.53
Contig971.2 / + / 2,822 / 3,323 / 502 / 86.48
Contig1062.4 / - / 633 / 1,541 / 909 / 98.79
Contig1106.1 / + / 181 / 560 / 380 / 85.69
§reference copy; sequences harboring indels; sequences harboring internal deletions; sequences harboring internal insertions
Table S7Sequences of the BS NLTR retrotransposon in the D. erecta sequenced genome.
Localization / Insertion orientation / Begin / End / Size(bp) / % identity with the reference BS
scaffold_392 / - / 1,027 / 2,389 / 1,363 / 95.11
scaffold_542 / - / 1,471 / 2,157 / 687 / 97.67
scaffold_759 / - / 187 / 845 / 659 / 100
scaffold_985 / + / 2 / 832 / 831 / 99.16
scaffold_987 / - / 282 / 1,245 / 964 / 99.69
scaffold_1436 / - / 1,005 / 1,688 / 684 / 98.83
scaffold_1580 / + / 1 / 478 / 478 / 99.58
scaffold_1581 / + / 1 / 828 / 828 / 98.67
scaffold_1721 / - / 5,084 / 7,134 / 2,051 / 98.65
scaffold_2219 / - / 1 / 1,292 / 1,292 / 93.69
scaffold_2387 / + / 669 / 1,138 / 470 / 100
scaffold_2800 / - / 7,107 / 7,637 / 531 / 99.81
scaffold_3306 / + / 4,430 / 6,655 / 2,226 / 98.81
scaffold_3315 / + / 1,413 / 2,073 / 661 / 97.89
scaffold_3559 / + / 1 / 748 / 748 / 99.87
scaffold_3713 / - / 12 / 1,094 / 1,083 / 99.91
scaffold_4175 / - / 361 / 1,621 / 1,261 / 94.03
scaffold_4569 / - / 2,078 / 2,193 / 116 / 100
scaffold_4623 / - / 16 / 1,24 / 1,225 / 99.76
scaffold_4644 / - / 936,648 / 941,747 / 5,100 / 99.97
scaffold_4670 / - / 92,161 / 94,078 / 1,918 / 92.63
scaffold_4670 / - / 100,950 / 101,381 / 432 / 95.75
scaffold_4690 / + / 94,774 / 99,873 / 5,100 / 99.99
scaffold_4690 / + / 5,304,059 / 5,309,158 / 5,100 / 100
scaffold_4690 / + / 10,550,372 / 10,555,471 / 5,100 / 100
scaffold_4690 / - / 12,141,441 / 12,146,539 / 5,099 / 99.99
scaffold_4690 / + / 14,264,819 / 14,269,918 / 5,100 / 100
scaffold_4690 / + / 13,620,056 / 13,625,154 / 5,099 / 99.96
scaffold_4690 / - / 15,750,685 / 15,753,884 / 3,200 / 100
scaffold_4690 / + / 16,211,818 / 16,216,917 / 5,100 / 99.92
scaffold_4690 / - / 12,099,231 / 12,104,330 / 5,100 / 99.61
scaffold_4690 / + / 12,277,789 / 12,279,417 / 1,629 / 100
scaffold_4690 / - / 14,196,578 / 14,197,711 / 1,134 / 100
scaffold_4690 / + / 17,529,026 / 17,529,315 / 290 / 97.59
scaffold_4690 / - / 18,099,308 / 18,099,423 / 116 / 100
scaffold_4690 / - / 2,003,746 / 2,003,847 / 102 / 97.12
scaffold_4690 / - / 8,685,544 / 8,685,650 / 107 / 94.39
scaffold_4690 / - / 14,431,649 / 14,431,745 / 97 / 94.85
scaffold_4690 / - / 13,980,253 / 13,980,338 / 86 / 96.51
scaffold_4732 / + / 33,813 / 35,869 / 2,057 / 98.43
scaffold_4770 / - / 14,447,334 / 14,452,433 / 5,100 / 99.99
scaffold_4770 / + / 5,535,147 / 5,540,243 / 5,097 / 99.65
scaffold_4770 / - / 5,228,867 / 5,233,961 / 5,095 / 99.38
scaffold_4770 / + / 113,528 / 118,528 / 5,001 / 95.48
scaffold_4770 / + / 761,565 / 766,637 / 5,073 / 98.37
scaffold_4770 / + / 112,717 / 113,054 / 338 / 94.08
scaffold_4770 / + / 7,318,622 / 7,318,716 / 95 / 93.68
scaffold_4784 / - / 22,520,023 / 22,525,122 / 5,100 / 100
scaffold_4784 / + / 25,173,820 / 25,178,910 / 5,091 / 99.28
Table S7 Continuation.
scaffold_4784 / + / 25,663,719 / 25,667,762 / 4,044 / 94.45
scaffold_4784 / - / 22350870 / 22,351,438 / 569 / 98.68
scaffold_4784 / + / 7,404,350 / 7,405,677 / 1,328 / 95.37
scaffold_4784 / + / 21,538,552 / 21,538,653 / 102 / 94.38
scaffold_4820 / - / 2,761,673 / 2,766,772 / 5,100 / 99.84
scaffold_4820 / - / 8,996,891 / 9,001,984 / 5,094 / 99.50
scaffold_4820 / - / 9,973,341 / 9,978,434 / 5,094 / 99.50
scaffold_4820 / - / 8,594,716 / 8,594,831 / 116 / 100
scaffold_4845 / + / 9,333,338 / 9,338,437 / 5,100 / 99.97
scaffold_4845 / - / 18,626,870 / 18,631,969 / 5,100 / 99.90
scaffold_4845 / + / 1,361,901 / 1,363,210 / 1,310 / 93.49
scaffold_4845 / + / 3,329,569 / 3,329,653 / 85 / 97.65
scaffold_4851 / - / 2 / 1,792 / 1,791 / 94.84
scaffold_4929§ / + / 7,756,378 / 7,761,490 / 5,113 / -
scaffold_4929 / + / 25,112,986 / 25,115,518 / 2,533 / 94.42
scaffold_4929 / + / 25,116,895 / 25,119,058 / 2,164 / 96.41
scaffold_4929 / + / 22,307,341 / 22,311,800 / 4,460 / 92.84
scaffold_4929 / + / 20,913,515 / 20,914,866 / 1,352 / 95.49
scaffold_4929 / - / 17,699,536 / 17,699,643 / 108 / 95.37
scaffold_4929 / + / 19,760,111 / 19,760,199 / 89 / 94.38
scaffold_4929 / - / 19,818,148 / 19,818,248 / 101 / 92.08
§reference copy; sequences harboring indels; sequences harboring internal deletions; sequences harboring internal insertions
Table S8Sequences of the BS NLTR retrotransposon in the D. pseudoobscura sequenced genome.
Localization / Insertion orientation / Begin / End / Size(bp) / % identity with the reference BS
Ch2 / + / 18,327,761 / 18,328,567 / 807 / 91.40
Ch2 / - / 24,742,504 / 24,742,585 / 82 / 98.78
Unknown_group_2 / - / 76,512 / 78,598 / 2,087 / 89.35
Unknown_group_7 / + / 124,282 / 125,219 / 938 / 95.45
Unknown_group_42 / + / 23,608 / 25,762 / 2,155 / 91.92
Unknown_group_43 / - / 8,137 / 8,640 / 504 / 88.05
Unknown_group_108§ / - / 9,163 / 11,697 / 2,535 / -
Unknown_group_124 / + / 25,135 / 25,858 / 724 / 92.69
Unknown_group_124 / + / 26,206 / 26,947 / 742 / 91.38
Unknown_group_167 / + / 53,041 / 55,113 / 1,824 / 93.99
Unknown_group_264 / + / 1838 / 2,236 / 399 / 94.13
Unknown_group_338 / + / 10464 / 10,968 / 505 / 93.66
Unknown_group_359 / + / 7097 / 7,284 / 188 / 93.51
Unknown_group_391 / - / 1280 / 1,365 / 86 / 94.19
Unknown_group_391 / + / 1369 / 3,175 / 1,807 / 95.30
Unknown_singleton_400 / - / 152 / 638 / 487 / 93.62
Unknown_singleton_401 / - / 176 / 1,442 / 1,267 / 92.26
Unknown_group_443 / - / 112 / 2,638 / 2,527 / 90.75
Unknown_group_602 / + / 10,941 / 13,467 / 2,527 / 90.50
Unknown_group_602 / + / 4,364 / 6880 / 2,517 / 90.00
Unknown_group_821 / + / 1,138 / 2,563 / 1,426 / 87.42
Unknown_singleton_864 / + / 7,995 / 10,403 / 2,409 / 91.50
Unknown_singleton_1947 / - / 208 / 399 / 192 / 91.67
Unknown_singleton_2681 / - / 15 / 699 / 685 / 93.86
Unknown_singleton_3025 / + / 1 / 331 / 331 / 91.33
Unknown_singleton_3056 / - / 1 / 507 / 507 / 90.47
Unknown_singleton_3128 / + / 2 / 785 / 784 / 89.21
Unknown_singleton_3132 / - / 1 / 818 / 818 / 94.68
Unknown_singleton_3215 / + / 5 / 637 / 633 / 91.01
Unknown_singleton_3242 / + / 7 / 685 / 679 / 92.59
§reference copy; sequences harboring indels; sequences harboring internal deletions; sequences harboring internal insertions
Table S9Sequences of the BS NLTR retrotransposon in the D. persimilis sequenced genome.
Localization / Insertion orientation / Begin / End / Size(bp) / % identity with the reference BS
super_3 / + / 700,014 / 701,222 / 1,209 / 89.78
super_3 / - / 930,984 / 931,953 / 970 / 92.55
super_43 / - / 300,701 / 304,088 / 3,388 / 91.87
super_43 / - / 296,516 / 298,942 / 2,427 / 92.42
super_59 / - / 184,879 / 185,378 / 500 / 89.82
super_60 / - / 393,000 / 395,826 / 2,827 / 98.88
super_66 / + / 240,838 / 243,938 / 3,101 / 92.72
super_74 / + / 4,767 / 8,046 / 3,280 / 92.18
super_75 / - / 242,629 / 246,457 / 3,829 / 95.59
super_81 / - / 213,175 / 214,550 / 1,376 / 94.45
super_81 / - / 206,142 / 206,610 / 469 / 92.47
super_91 / - / 62209 / 63398 / 1,190 / 94.36
super_91 / - / 60,417 / 61,697 / 1,281 / 92.95
super_103 / - / 76,046 / 76,549 / 504 / 90.22
super_108 / - / 55,530 / 56,251 / 722 / 94.78
super_108 / - / 54,448 / 55,182 / 735 / 87.12
super_110 / + / 6,807 / 7,650 / 844 / 94.21
super_120 / - / 2,992 / 3,292 / 301 / 87.71
super_126 / + / 35,475 / 35,858 / 384 / 93.59
super_142 / + / 55,503 / 57,685 / 2,183 / 92.73
super_182 / - / 1 / 2,803 / 2,803 / 99.00
super_182 / - / 55,259 / 57,162 / 1,904 / 94.10
super_182 / - / 53,491 / 54,890 / 1,400 / 93.81
super_182 / - / 25,865 / 27,722 / 1,858 / 94.26
super_182 / - / 24,097 / 25,496 / 1,400 / 93.81
super_196 / + / 5,156 / 6,676 / 1,521 / 97.04
super_201 / - / 132,071 / 134,926 / 2,856 / 96.48
super_276 / + / 20,356 / 20,776 / 421 / 92.16
super_390§ / + / 1 / 3,832 / 3,832 / -
super_447 / + / 2,444 / 5,421 / 2,978 / 98.00
super_452 / + / 4,048 / 4,379 / 332 / 96.53
super_452 / + / 6,124 / 7,549 / 1,426 / 99.11
super_1087 / + / 4,442 / 7,057 / 2,616 / 99.35
super_1309 / + / 1 / 2,052 / 2,052 / 96.38
super_1395 / - / 4,369 / 6,749 / 2,381 / 97.65
super_1395 / - / 2,373 / 3,005 / 633 / 91.67
super_1426 / - / 4,741 / 5,376 / 636 / 93.79
super_2069 / + / 1 / 300 / 300 / 99.67
super_2376 / - / 5 / 957 / 953 / 97.14
super_2811 / + / 1,301 / 3,056 / 1,756 / 93.11
super_3237 / - / 1,830 / 2,600 / 771 / 92.58
super_3419 / - / 40 / 2,521 / 2,482 / 97.32
super_4187 / + / 97 / 1,800 / 1,704 / 94.85
super_4270 / + / 1 / 2,216 / 2,216 / 98.69
super_4294 / - / 1,448 / 2,096 / 649 / 93.71
super_4413 / + / 1 / 584 / 584 / 98.76
super_4413 / + / 583 / 2,145 / 1,563 / 98.14
super_4711 / - / 1 / 1,591 / 1591 / 98.10
super_6240 / + / 777 / 1,576 / 800 / 92.33
super_6487 / - / 573 / 1,535 / 963 / 96.97
super_6488 / + / 231 / 1,657 / 1,427 / 98.88
Table S9 Continuation.
super_7441 / + / 53 / 1,493 / 1,441 / 98.90
super_8716 / - / 4 / 1,294 / 1,291 / 92.24
super_9355 / + / 1 / 500 / 500 / 93.03
super_10695 / - / 792 / 1018 / 227 / 92.85
super_10994 / + / 864 / 971 / 108 / 95.41
super_11370 / + / 1 / 631 / 631 / 94.53
super_12040 / - / 4 / 106 / 103 / 95.19
§reference copy; sequences harboring indels; sequences harboring internal deletions; sequences harboring internal insertions
Table S10Sequences of the BS NLTR retrotransposon in the D. mojavensis sequenced genome.
Localization / Insertion orientation / Begin / End / Size(bp) / % identity with the reference BS
scaffold_704 / + / 101 / 373 / 273 / 99.30
scaffold_3539 / - / 1,676 / 1,187 / 490 / 100
scaffold_4956 / + / 219 / 569 / 373 / 99.43
scaffold_6308 / + / 1,494,585 / 1,494,796 / 212 / 93.40
scaffold_6359 / + / 2,420,095 / 2,420,650 / 556 / 99.64
scaffold_6360 / + / 58,976 / 59,325 / 351 / 99.15
scaffold_6469 / - / 4,496 / 4,845 / 351 / 99.15
scaffold_6473 / + / 16,823,350 / 16,824,160 / 811 / 88.50
scaffold_6473 / + / 16,583,622 / 16,587,732 / 4,111 / 98.54
scaffold_6473 / - / 1,963,020 / 1,963,180 / 162 / 99.38
scaffold_6473 / - / 8,947,223 / 8,947,346 / 125 / 99.20
scaffold_6473 / - / 5,636,454 / 5,636,541 / 88 / 92.05
scaffold_6473 / + / 8,639,792 / 8,639,689 / 104 / 85.58
scaffold_6473 / + / 13,853,669 / 13,853,910 / 242 / 80.17
scaffold_6482 / - / 1,068,114 / 1,068,506 / 393 / 100
scaffold_6482 / - / 1,394,406 / 1,394,791 / 386 / 90.50
scaffold_6482 / + / 1,852,293 / 1,852,731 / 439 / 99.32
scaffold_6482 / - / 1,837,065 / 1,837,505 / 441 / 98.41
scaffold_6482 / - / 1,063,123 / 1,063,290 / 168 / 98.81
scaffold_6494 / + / 148,975 / 149,840 / 867 / 99.54
scaffold_6496 / - / 25,484,898 / 25,485,514 / 617 / 98.38
scaffold_6496 / + / 23,047,848 / 2,3048,298 / 451 / 92.02
scaffold_6496 / + / 11,889,704 / 11,889,901 / 198 / 99.49
scaffold_6496 / - / 9,049,553 / 9,049,740 / 188 / 99.47
scaffold_6496 / + / 22,629,210 / 22,629,385 / 176 / 100
scaffold_6496 / - / 9,025,515 / 9,025,692 / 178 / 99.44
scaffold_6496 / - / 1,132,555 / 1,132,686 / 132 / 99.24
scaffold_6496 / + / 17,581,061 / 17,581,247 / 187 / 92.02
scaffold_6496 / + / 9,165,797 / 9,165,883 / 87 / 100
scaffold_6496 / + / 17,319,518 / 1,7319,630 / 113 / 92.04
scaffold_6496 / - / 9,389,702 / 9,389,804 / 103 / 93.20
scaffold_6496 / + / 2,110,701 / 2,110,781 / 81 / 96.30
scaffold_6496 / + / 18,763,569 / 18,763,673 / 105 / 91.43
scaffold_6496 / + / 6,182,722 / 6,182,808 / 87 / 93.10
scaffold_6498 / - / 1,950,134 / 1,954,137 / 4,004 / 96.45
scaffold_6500§ / + / 28,298,842 / 28,303,394 / 4,553 / -
scaffold_6500 / - / 28,261,147 / 28,260,536 / 612 / 93.6
scaffold_6500 / - / 28,282,148 / 28,283,786 / 1,639 / 99.45
scaffold_6500 / - / 24,821,341 / 24,821,823 / 483 / 99.17
scaffold_6500 / - / 10,544,045 / 10,544,387 / 343 / 99.71
scaffold_6500 / - / 9,358,915 / 9,359,065 / 151 / 94.04
scaffold_6500 / - / 26,069,113 / 26,069,231 / 119 / 99.16
scaffold_6500 / + / 10,017,426 / 10,017,537 / 112 / 100
scaffold_6500 / - / 16,293,731 / 16,293,817 / 87 / 98.85
scaffold_6500 / + / 26,175,878 / 26,176,003 / 126 / 90.48
scaffold_6500 / + / 26,069,037 / 26,069,116 / 80 / 97.50
scaffold_6500 / + / 15,042,622 / 15,042,710 / 89 / 94.38
scaffold_6500 / + / 8,357,373 / 8,357,473 / 101 / 89.62
scaffold_6540 / - / 319,282 / 320,728 / 1,447 / 97.27
scaffold_6540 / + / 3,414,078 / 3,414,736 / 659 / 88.55
Table S10 Continuation
scaffold_6540 / + / 309,305 / 310,408 / 1,104 / 97.20
scaffold_6540 / + / 307,986 / 308,130 / 145 / 96.55
scaffold_6540 / + / 5,589,546 / 5,589,892 / 347 / 99.14
scaffold_6540 / + / 19,738,759 / 19,738,914 / 156 / 97.44
scaffold_6540 / + / 19,748,452 / 19,748,550 / 99 / 96.97
scaffold_6540 / - / 21,570,142 / 21,570,232 / 91 / 98.90
scaffold_6540 / + / 19,268,692 / 19,268,774 / 83 / 85.54
scaffold_6668 / - / 1292 / 2,548 / 1,257 / 99.60
scaffold_6680 / + / 23,720,043 / 23,720,600 / 558 / 87.54
scaffold_6680 / + / 4,790,604 / 4,790,985 / 382 / 100
scaffold_6680 / + / 7,922,821 / 7,923,044 / 224 / 100
scaffold_6680 / - / 4,791,074 / 4,791,242 / 169 / 99.41
scaffold_6680 / + / 2,924,642 / 2,924,746 / 105 / 98.10
scaffold_6680 / - / 13,846,311 / 13,846,400 / 90 / 97.78
scaffold_6680 / - / 22,059,250 / 22,059,377 / 128 / 90.84
§reference copy; sequences harboring indels; sequences harboring internal deletions; sequences harboring internal insertions
Table S11P values of two-tailed Mann-Whitney U test (diagonal below) between the BS identity scores distribution in Drosophila species and correspondent significant values (diagonal above) (****: p<0.0001; ***: p<0.001; **: p<0.01; **p<0.01; *: p<0.05).
Species / 1 / 2 / 3 / 4 / 5 / 6 / 7 / 81.D. melanogaster / - / **
2. D.simulans / 0.0803 / - / ** / **** / ** / ****
3. D.sechellia / 0.7287 / 0.0064 / - / *** / **** / **** / ***
4. D.yakuba / 0.0783 / 0.2363 / 0.0006 / - / **** / ** / ***
5. D.erecta / 0.0014 / 0.0000 / 0.0000 / 0.0000 / - / **** / **** / *
6. D.pseudoobscura / 0.0891 / 0.4036 / 0.0000 / 0.3194 / 0.0000 / - / *** / ****
7. D.persimilis / 0.9438 / 0.0038 / 0.9462 / 0.0018 / 0.0000 / 0.0003 / - / **
8. D.mojavensis / 0.1059 / 0.0000 / 0.0002 / 0.0002 / 0.0130 / 0.0000 / 0.0019 / -------
Table S 12 Selective tests (dN, dS and dN/dS: ω) of BS intact coding regions in D. melanogaster (2 sequences) and D. erecta (18 sequences).
D. melanogaster / D. erectaORF1 / ORF2 / ORF1 / ORF2
dN / 0.0020 / 0.0029 / 0.0023 / 0.0011
dS / 0.0099 / 0.0091 / 0.0126 / 0.0056
ω / 0.2020 / 0.3187 / 0.1825 / 0.1964
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