A) Censor map of known Crassostrea gigas TEs JH816965.1 contig combined with the map of the RAG1L and RAG2L proteins. A short assembly gap is marked by NNNNNN. gi|405955968|gb|JH816965.1| 1849 2378 Helitron-N2f_CGi 70 591 d 0.7890 gi|405955968|gb|JH816965.1| 2396 2613 Helitron-N47_CGi 304 538 c 0.7668 gi|405955968|gb|JH816965.1| 2645 3127 DNA4-15_CGi 1 484 d 0.9194 gi|405955968|gb|JH816965.1| 3154 4179 Kolobok-N6_CGi 1 1042 c 0.9738 gi|405955968|gb|JH816965.1| 4184 4602 Kolobok-10_CGi 22 436 d 0.8849 gi|405955968|gb|JH816965.1| 4703 5029 Helitron-N19_CGi 1921 2230 d 0.7304 gi|405955968|gb|JH816965.1| 5038 5548 Helitron-N1C_CGi 80 590 d 0.8039 gi|405955968|gb|JH816965.1| 8132 8378 Helitron-N50_CGi 2365 2616 c 0.8097 gi|405955968|gb|JH816965.1| 8816 9061 DNA9-2B_CGi 216 460 c 0.9634 gi|405955968|gb|JH816965.1| 9131 9776 Helitron-N18_CGi 381 1029 c 0.9892 gi|405955968|gb|JH816965.1| 9777 9868 Helitron-N18_CGi 1 91 c 0.9783 gi|405955968|gb|JH816965.1| 10374 10715 SPRAG1L 463 579 d 0.3846 gi|405955968|gb|JH816965.1| 10787 11541 SPRAG1L 604 848 d 0.3896 gi|405955968|gb|JH816965.1| 11543 12473 SPRAG1L 546 849 c 0.4245 gi|405955968|gb|JH816965.1| 12476-12511 NNNNNN gi|405955968|gb|JH816965.1| 12516 13334 SPRAG2L 22 324 c 0.2500 gi|405955968|gb|JH816965.1| 13621 16666 Penelope-3_CGi 4 3106 c 0.9512 B) Alignment of the oyster RAG1L and RAG2L proteins with SPRAG1L and PMRAG2L gi|405955968|gb|JH816965.1| 11797 12300 SPRAG1L 604 770 c 0.3690 0.5714 295 < S: 12300 PFWNQISDENNHVSNVVCILPIKNKKEMLMQNRMNVKTNHVWICHKFSFFNSMVDDKRDRGDSGLQGSLS 12091 P I DEN+ ++ V + ++ ++ +L + M + H+F+ +NSM+D+K R GLQGS S Q: 604 PLLEAIGDENSASTSAVLMRKMEKERLILQNSIMTIHAGTYTRLHRFTIYNSMIDEKLARSSGGLQGSGS 673 S: 12090 KYLCTLCDADKHTAKELLESFVINRSVSECTNIAEILRVNPNVLSENELKILSKGVKSAPLTKIEPIQKG 11881 ++CTLC A K +AK L SF I+R+++E: + NP+ L+ +EL + GVK PL EP Q+ Q: 674 NFICTLCHATKTSAKTQLGSFKIDRTLTETQQTLTYITTNPDNLTPDELTTEAGGVKRKPLLTSEPKQQL 743 S: 11880 IDATHADISLGQLLYVKLLGSQNGNSHK 11797 +DATHADI LGQ- + K++ + : HK Q: 744 MDATHADIDLGQ-FFKKIIVREMAGVHK 770 gi|405955968|gb|JH816965.1| 10787 11290 SPRAG1L 604 770 d 0.3690 0.5714 295 < S: 10787 PFWNQISDENNHVSNVVCILPIKNKKEMLMQNRMNVKTNHVWICHKFSFFNSMVDDKRDRGDSGLQGSLS 10996 P I DEN+ ++ V + ++ ++ +L + M + H+F+ +NSM+D+K R GLQGS S Q: 604 PLLEAIGDENSASTSAVLMRKMEKERLILQNSIMTIHAGTYTRLHRFTIYNSMIDEKLARSSGGLQGSGS 673 S: 10997 KYLCTLCDADKHTAKELLESFVINRSVSECTNIAEILRVNPNVLSENELKILSKGVKSAPLTKIEPIQKG 11206 ++CTLC A K +AK L SF I+R+++E: + NP+ L+ +EL + GVK PL EP Q+ Q: 674 NFICTLCHATKTSAKTQLGSFKIDRTLTETQQTLTYITTNPDNLTPDELTTEAGGVKRKPLLTSEPKQQL 743 S: 11207 IDATHADISLGQLLYVKLLGSQNGNSHK 11290 +DATHADI LGQ- + K++ + : HK Q: 744 MDATHADIDLGQ-FFKKIIVREMAGVHK 770 gi|405955968|gb|JH816965.1| 10374 10715 SPRAG1L 463 579 d 0.3879 0.6121 211 < S: 10374 VFQAPRK-MESCENLFLPSAAVYQIMQGFVELATPNCLGVRFSYFDALSVSLQELEP*IVNGLENQGLNV 10580 V+ P K-+E ++ + + E A PNC+GV +SY +A++ +L+EL+ I G+ GLN Q: 463 VYHTPEKSLEEFDDHSMYEPIRINVRSKLTEFALPNCIGVAWSYPEAVAKTLEELDENIREGMLKVGLNP 532 S: 10581 E--KVILHTTVKNGCDGMGEVSIYKEKDFKMLPDKAFRFSFCIVKIE 10715 +-- +I+ TT+K+G DGMGE++++K K LPDKAFR SF ++K E Q: 533 DGPSIIIDTTLKDGADGMGEIAVHKMKSDTFLPDKAFRASFVVLKCE 579 gi|405955968|gb|JH816965.1| 12516 13334 SPRAG2L 22 324 c 0.2760 0.4982 230 < S: 13334 RVMRKKAVAD*I--NYFPPEGHVCL---------PINCYTYLYFGGARRGQESTWNMSNKLYRVSYVVD- 13161 ++ RKK +D -- Y+ EGH +---------P GGARRG +++W + ++--+ YVV+- Q: 22 KISRKKPQSDLKLNEYYLAEGHFAVMCPVLGAEEPEKKKRIFSSGGARRGGDNSWGDAGRI--IEYVVEM 89 S: 13160 --DNDINIENLLEIKLSGGQFPHLQSSDGFYISHKNCSFVWGGLNLSSFSMSNELYVV---KLNGTEGVE 12966 --++D+ + +++ K +GG+ P LQS+ :--I + +VWGG +L + ++L ++---+ G G Q: 90 DKNDDVTLASVVSCKTTGGRMPALQSAAA--IESDSRFYVWGGFDLMEYRCKDDLIILEEGRRRGATGAP 157 S: 12965 IIQPPCVISLRKL------------EGDIPSGRYGHSFTYFDCS--AVLHGGVCFPHRNSCIGSSLFTNV 12798 + V + +------------+G +P :R GH+ T +--A+L GGV -S + Q: 158 VFDIKYVPTTANMVASRRGNTVPVQKGTVPHARTGHTLTRLGETKEALLFGGVMEQEERKSF-SVEWELA 226 S: 12797 TNDSSFYMFDYERLFWT*LSV-SGSHPRAYHTATQMDIRGMKSVAYIGGVIKTERGLQRIPLSNVFVLKM 12591 : D +FY+ D + W + V-S:+ R YHTA ++ +A++GGV+ + RIP++ V +L M Q: 227 CRDGTFYILDLDTFIWRRVPVPSATLARTYHTAECLETVRSFVIAFVGGVMHDKNTTTRIPINEVLLLTM 296 S: 12590 ---DSDRHFHTEIWTFANFPAVGVSYHS 12516 ---D+D + + ++ P+ V Y S Q: 297 NSQDTDTAVLSTVTLASDGPSTPVPYIS 324 C) recent duplication of the RAG1L-coding region gi|405955968|gb|JH816965.1|_1 10614 11514 gi|405955968|gb|JH816965.1|_2 12443 11543 S=99.89% S: GGGTGTGATGGAATGGGGGAAGTTTCTATTTATAAAGAAAAAGATTTTAAAATGTTACCAGACAAAGCCT |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Q: GGGTGTGATGGAATGGGGGAAGTTTCTATTTATAAAGAAAAAGATTTTAAAATGTTACCAGACAAAGCCT S: TTAGATTTTCTTTTTGTATTGTTAAAATTGAAGCCGTACATCAAGGCACAAAAGTATGATGTGTTTACTG |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Q: TTAGATTTTCTTTTTGTATTGTTAAAATTGAAGCCGTACATCAAGGCACAAAAGTATGATGTGTTTACTG S: AGCCATTGCCAAACAGTGTTCGAACAAATAGACCCCTTTTGGAATCAAATTTCGGATGAAAATAACCATG |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Q: AGCCATTGCCAAACAGTGTTCGAACAAATAGACCCCTTTTGGAATCAAATTTCGGATGAAAATAACCATG S: TATCAAATGTTGTTTGCATTCTACCCATTAAAAATAAAAAAGAAATGTTAATGCAAAATCGCATGAATGT |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Q: TATCAAATGTTGTTTGCATTCTACCCATTAAAAATAAAAAAGAAATGTTAATGCAAAATCGCATGAATGT S: AAAAACAAACCACGTTTGGATATGTCATAAATTTTCATTTTTTAATTCAATGGTTGACGACAAAAGGGAC |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Q: AAAAACAAACCACGTTTGGATATGTCATAAATTTTCATTTTTTAATTCAATGGTTGACGACAAAAGGGAC S: AGAGGCGATTCTGGTCTTCAGGGTAGTTTGTCAAAATATTTATGTACATTATGTGATGCAGATAAACATA |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Q: AGAGGCGATTCTGGTCTTCAGGGTAGTTTGTCAAAATATTTATGTACATTATGTGATGCAGATAAACATA S: CTGCAAAAGAATTACTTGAATCTTTTGTAATTAATAGGTCAGTTTCTGAATGTACAAATATTGCTGAAAT |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Q: CTGCAAAAGAATTACTTGAATCTTTTGTAATTAATAGGTCAGTTTCTGAATGTACAAATATTGCTGAAAT S: TTTGCGTGTCAATCCAAATGTTTTGTCTGAAAATGAATTGAAAATATTATCAAAGGGTGTGAAATCTGCT |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Q: TTTGCGTGTCAATCCAAATGTTTTGTCTGAAAATGAATTGAAAATATTATCAAAGGGTGTGAAATCTGCT S: CCACTTACAAAAATTGAACCAATACAGAAAGGCATAGATGCCACACATGCAGATATCAGTTTAGGACAGT |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Q: CCACTTACAAAAATTGAACCAATACAGAAAGGCATAGATGCCACACATGCAGATATCAGTTTAGGACAGT S: TATTATACGTGAAATTGCTGGGGTCACAAAATGGGAACTCGCACAAGATGTTAAGTCATTAGTTCTAAGT |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Q: TATTATACGTGAAATTGCTGGGGTCACAAAATGGGAACTCGCACAAGATGTTAAGTCATTAGTTCTAAGT S: GCAGAATCATTGCTTGATCAACATTTGAAATTTAATTGTGGAATTAATCCCCAACTTATGTTGCCTGGCA |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Q: GCAGAATCATTGCTTGATCAACATTTGAAATTTAATTGTGGAATTAATCCCCAACTTATGTTGCCTGGCA S: ACTATGATAGGATTCTTTTTGAAACTCCCCATTCTGTTTAGTTAGAACTTATTTCAGATTCTACCAGAAA |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Q: ACTATGATAGGATTCTTTTTGAAACTCCCCATTCTGTTTAGTTAGAACTTATTTCAGATTCTACCAGAAA S: AGAATATCTTTCTTCTGTTTTTAGTATATATTTTTACAGCTTAGAAAGTTCTGTTTTGAGT ||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||| Q: AGAATATCTTTCTTCTGTTTTTAGTATATATTTGTACAGCTTAGAAAGTTCTGTTTTGAGT