Multiple Independent Evolutions of Trans-Splicing

Supplementary Figure 2 Alignments of Group II Introns ccmFCi829 and sdh3i100 from Physcomitrella patens and Megaceros aenigmaticus

[ 10 20 30 40 50 60 70 80 90 100] [ ...... ]

Phy_ccmFC_IN GTGCGACCCG GCAGCTTATG CGCGACCATC TCGTGTTTAA GCTCACGCCC ACATGGCGTG AACTCTGGTT GAATTCGGGT TCTAAATCCC GCCGCTGAGA [100] Meg_ccmFC_IN ....A..TT. CTGA....C...... ATCGC...C. .GC...... T ..GC.CT..T C...T..... T...... CT.C...T.. ..T...... [100]

[ 110 120 130 140 150 160 170 180 190 200] [ ...... ]

Phy_ccmFC_IN TGCTCAGTCG ACTCTTGAAC CTTGATGGGA AGACGGCTTC TTCCCAAATT AGTGCAAAA------GGT TCCAGGACTT A---GGATGA ACTTAATGTG [189] Meg_ccmFC_IN C.T.....T. ....C...... A...... T...... GA..... C...... A AAAAGAG..G ..AG...... TTA...... GCC.-.... [199]

[ 210 220 230 240 250 260 270 280 290 300] [ ...... ]

Phy_ccmFC_IN AATGAGTATA AGCTTCGCTG CTCAAAAACA CCCAGTATTG ACCACACTGA GAGACTTGCC AATGGCAAGA AAGGCCGCGG ---GTAACGC TAGTTGGCGA [286] Meg_ccmFC_IN ....GA.G.C ...... G....A. .T..C.GC.A ...... GCCGG TG..AGG... GG...... CGG..C...T C...... G [299]

[ 310 320 330 340 350 360 370 380 390 400] [ ...... ]

Phy_ccmFC_IN AATGGCGTTA AGCATTCCTA GCGATACGGA AAGAGAGGTC GTGATGGATG ATATCATCTA CGTTCGTACT GTTCCTCGTG GAGTAAATCT CACATCCAAA [386] Meg_ccmFC_IN GCG...C... ----...... G....A. .G....A...... --- -...T...... ----..A .C...... T ...... A. .G...... - [386]

[ 410 420 430 440 450 460 470 480 490 500] [ ...... ]

Phy_ccmFC_IN AATCTAACCA GGGAACGGGA TAATTCCCAT TAAGTTCCAG TAAAACTGGC AGGCCAGCCG GGCCG------TAAGCTA------GT [460] Meg_ccmFC_IN ---.C.TAA. A..G...A.G A...... GC ...... T...... AA...... TACTGAT AGGAGACAGG AT.C...C.A AACCATTC.. [483]

[ 510 520 530 540 550 560 570 580 590 600] [ ...... ]

Phy_ccmFC_IN GGGAAC------AGGATTC TCC------CGAAAA GACAAAACCT TCGAGGCAAA CGCTCACTTT GCTCGCGTTA ------GTGAA- [527] Meg_ccmFC_IN C..GG.GAAG CAG...CCA. .T.AGTTGCA TTAG.AT.G. ATG.GGG... CA..A.A.T. A.T.TC...A T...C.AC.. CTACCAAAAA GCAG.C...T [583]

[ 610 620 630 640 650 660 670 680 690 700] [ ...... ]

Phy_ccmFC_IN ------GTAAATCTC GAAGAAA------AGGCCG ACGCGGGGAC TCAGGGCGCA GCATAACGAA TGGTGAAGAG TTCGTATGA- GCAGAATGAA [608] Meg_ccmFC_IN GAAGGCCGAA C.A.GG..G. ...TG..TGG GTGA...... T..A... .A...A...G ..G...... A.CA.G.GA .GAAC.GA.T A..A.G.AGT [683]

[ 710 720 730 740 750 760 770 780 790 800] 2

[ ...... ]

Phy_ccmFC_IN CAGAAAAAAA AGATTT------TTAGGCG AATGCCATGT ------AAATCTCCG CTTTATTAT------[659] Meg_ccmFC_IN T.ATTC..GC G...C.CTGA CGGTCCCTGT CCA....TTA G.CT..T.A. TAGCCAGGGC A..GCT..T. .C.C...T.A GTGAGGCGGG GAAGGAGATT [783]

[ 810 820 830 840 850 860 870 880 890 900] [ ...... ]

Phy_ccmFC_IN ------TTATTATTC GGT--TTTCA GGTTCCCCCT GAGAAGAGCC GTATGAGGCC GTAGGCTCAC GTACGGTTCG [726] Meg_ccmFC_IN AAAAGTTTGC TGCAAATAAG CAAACTTTCT C....CTA.G ...GG.C..C ..C..TT.A. ..A...... G...... AG.....T...... [883]

[ 910 920 930 940 950 960 970 980 990 1000] [ ...... ]

Phy_ccmFC_IN GAAGCCAAGC CCCTGCAGTG ATGCTGTGGC TTAGGTTAAC ------[766] Meg_ccmFC_IN ..-...G...... G...... CA.. ...A...... CGACACAGAA AAGATACAGT TTACTCAACA AACAACTATG GTCATTGGGT TTTGAACTCT [982]

[ 1010 1020 1030 1040 1050 1060 1070 1080] [ ...... ]

Phy_ccmFC_IN ------[766] Meg_ccmFC_IN ATCTATCTAT CTATCTATCT ATCTATCTAT CTATCTATCT ATCTATCTAT CTATCAAAGG AGAAAAGCAC CTTGTTGCAA GG [1064] 3

[ 10 20 30 40 50 60 70 80 90 100] [ ...... ]

Phy_sdh3_IN GGGCGGCCGT TAGATCACTT GTGATTACAA CAAAGGCACT ACTGCTCGAG GGG------[53] Mega_sdh3_IN ...... T.. ...C.T..C...... G. AGC.ACTTTG C.GC.CGA.. .AAGGAAGGA AGGAAGGAAG GAAGGAAGGA AGGAAGGAAG GAAGGAAGGA [100]

[ 110 120 130 140 150 160 170 180 190 200] [ ...... ]

Phy_sdh3_IN ------CTCA GGGCTTACCT GATAGCGAAG GAAAGGAAGC [87] Mega_sdh3_IN AGGAAGGAAG GAAGGAAGGA AGGAAGGAAG GAAGGAAGGA AGGAAGGAAG GAAGGAAGGA AGGCGC.CTG ...... T. ACCT.GCGG. .G.GC..... [200]

[ 210 220 230 240 250 260 270 280 290 300] [ ...... ]

Phy_sdh3_IN ATGCCACAGA AGCTGCGATA A--AGGAGAT ATTCGTCGGC TGTTGGCTAG TTTATCGGCC TGCTCAATAA TCAATCCTCC GCGAGTCCGC TGGCGCTTGC [185] Mega_sdh3_IN ...... A. ...A..AGCG GTG...G..A .A...... A. ..------. ....C.A...... C.G.G.. ..T-..TG.T .TT..C...... A.....A. [292]

[ 310 320 330 340 350 360 370 380 390 400] [ ...... ]

Phy_sdh3_IN TAAATGAAAT ATATATATTT ATATGAAATA TATATATATT TCATTTAGCA TGAGATGATA AAGCAGAATC GCAGTTCTTT TCGGGTCAGC CTGCCCTACA [285] Mega_sdh3_IN G.CGGAT... CC.C------.------.G..G G--.GG...- -...C..T.C C-.A...... G...... C...... C.T.. .CTA.AGC.. [367]

[ 410 420 430 440 450 460 470 480 490 500] [ ...... ]

Phy_sdh3_IN ACCAGTGCGG AAAAAATGCA CGCGGGGAAT CGCACGAACG AACACTGTTA TGCTTTCGGC CTGCTGGCGG CTAAGAACGG TAAGGACAAA AAAAATAGAT [385] Mega_sdh3_IN ...... A. ....---...... --- -...... ---...A...... C..T .------G.C ..G..GT.G. ...TTGT.G. [451]

[ 510 520 530 540 550 560 570 580 590 600] [ ...... ]

Phy_sdh3_IN ATATTTTTAC GCATGGAAGC AGATTACCCA AATTAATGGG GACAGAGAAC TAAACGACAT CTCAAGCGCT ATA----GCT CACAGGTGAT ATCGGCGAGA [481] Mega_sdh3_IN T.T.C.GCCT ...... G.....TT.. TT.CTT..A...... TATA...... A..C-C GG...... T. [550]

[ 610 620 630 640 650 660 670 680 690 700] [ ...... ]

Phy_sdh3_IN TCCAACCGTA CACTATGGTC --CGAGTTGG AAGTCAGAGG ACCCA--TAG TACCTGCCTA ATCCTAAAAG AACCGTGTAA ACGGCAAACT TGCGGATTGA [577] Mega_sdh3_IN .....TAACT TTG.TCC.C. GC.....C.. G...... TTAC.T. C..T.A...... TGA.G.G. ..G....CG. ....G..G.A CTA.T.A.-. [649] 4

[ 710 720 730 740 750 760 770 780 790 800] [ ...... ]

Phy_sdh3_IN GTAAAAGGCG AAGGGGTCTA TGCAC----C TGCCTAGTCT GGCAGGTTTT ACTCTCCAAA ACTCAA-AAA AGAAACGGCA AATATATCTA TCTATTTTTT [672] Mega_sdh3_IN ...... A .....A...... T..GTAC. ....AG.G.G ...... G.. .GC.G.TGG. .T...AT.T. TTC.A.G.C. CGA.GGCGAA [749]

[ 810 820 830 840 850 860 870 880 890 900] [ ...... ]

Phy_sdh3_IN GT------CGCGCCCT ATTAACATCA AGATGTTAAT ACATTATATA TGATGATAC- ATCCAGTGCC ATCGATAATC CGATCAGTAG GGCAGGCACC [761] Mega_sdh3_IN ..GAAAAAGA GG....AAGC GC.G.GG.GG TCTC.GCGGC G...... T CTT.AT.TTT ..G..TCATG .G.-...... TTCCTT.G.C AT.-..TT.G [847]

[ 910 920 930 940 950 960 970 980 990 1000] [ ...... ]

Phy_sdh3_IN CAACGAGCCG CAGTCAATGG AGCCCGTCTC C-TATGAGTT GGATC-AGGA GAGTTAGTGA GCCGTATGAT GGGAGACTAT CACGTACGGT TCGGAGAGCA [859] Mega_sdh3_IN ....A.ATTT .CT.GG.GCC G...TC.TA. .A..C...GC ....AG.AA. .G.AAG.A.. .T..GTGAGC C.T..G--.G .T...... ---.... [942]

[ 1010 1020 1030 1040 1050 1060 ] [ ...... ]

Phy_sdh3_IN CTTAGTAGGC AGGCCGTAGG TCATCACTTC CTACCGAAGT TTGACTCTAT ------[909] Mega_sdh3_IN .C....C... T..A-..GAA .G...... G..T....C .C...... CCACTATGTT TTGT [1005]