The gene order data set includes 85 genes shared between seven cpDNAs. The gene rps12 was coded as 55 and 74 in the cases when the first exon and the second exon are separated by other genes. Gene Name Code trnH-GUG 1 psbA 2 trnK-UUU 3 trnQ-UUG 4 psbK 5 psbI 6 trnS-GCU 7 trnR-UCU 8 atpA 9 atpF 10 atpF 11 atpH 12 atpI 13 rps2 14 rpoC2 15 rpoC1 16 rpoB 17 trnC-GCA 18 psbM 19 trnD-GUC 20 trnY-GUA 21 trnE-UUC 22 psbD 23 psbC 24 trnS-UGA 25 psbZ 26 trnG-GCC 27 trnfM 28 rps14 29 psaB 30 psaA 31 rps4 32 trnT-UGU 33 trnL-UAA 34 trnF-GAA 35 trnV-UAC 36 trnM-CAT 37 atpE 38 atpB 39 rbcL 40 ycf4 41 cemA 42 petA 43 psbJ 44 psbL 45 psbF 46 psbE 47 petL 48 petG 49 trnW-CCA 50 trnP-UGG 51 psaJ 52 rps18 53 rpl20 54 rps12 55 clpP 56 psbB 57 psbT 58 psbN 59 psbH 60 petB 61 petD 62 rpoA 63 rps11 64 rpl36 65 rps8 66 rpl14 67 rpl16 68 rps3 69 rps19 70 rpl2 71 rpl23 72 rps7 73 rps12, exon2 74 rrn16 75 trnI-GAU 76 trnA-UGC 77 rrn23 78 rrn5 79 trnR-ACG 80 trnN-GUU 81 ycf1 82 rpl32 83 trnL-UAG 84 ccsA 85 psaC 86 Gene orders >cv Chlorella -42 -2 86 -10 -11 -12 -13 -14 -33 6 -7 75 76 77 78 79 -24 -23 25 28 22 54 53 50 -51 52 55 73 41 -3 -26 -1 -8 -36 -44 -45 -46 -47 -36 84 -62 -61 -56 -27 19 -21 34 -60 59 -58 -57 31 30 -35 -4 -5 80 81 85 83 82 -18 17 16 15 40 29 27 37 -20 -32 -38 -39 -49 -48 -43 9 -63 -64 -65 -66 -67 -68 -69 -70 -71 -72 >cr Chlamydomonas 43 62 80 51 5 22 -18 -33 -9 -54 -25 -50 -56 -84 -61 65 72 71 70 68 67 66 31 27 32 75 76 77 78 79 -2 -7 -38 -73 -29 -19 -26 -85 -34 -31 -22 -60 59 -58 -57 -20 -63 -14 -53 -41 -47 -37 -17 -17 46 45 49 69 15 21 4 30 -8 -40 10 6 42 12 11 64 3 2 -79 -78 -77 -76 -75 -39 -82 55 -52 -13 -44 -31 -23 24 1 28 35 86 48 81 -16 -36 >no Nephroselmis 29 34 4 84 -19 37 2 39 38 -62 -61 -63 -64 -65 -66 -67 -68 -69 -70 -71 -72 -10 -11 -12 -13 -56 -1 -36 8 -18 17 16 15 14 28 23 24 -50 -51 52 55 73 41 42 43 48 49 3 5 35 27 -44 -45 -46 -47 -53 -32 -9 -54 20 -22 -26 25 -60 59 -58 -57 -33 -7 -6 -21 31 30 -40 75 76 77 78 79 80 85 -81 86 83 82 81 -85 -80 -79 -78 -77 -76 -75 40 >mv Mesostigma 23 24 -2 -56 57 58 -59 60 61 62 -63 -64 -65 -66 -67 -68 -69 -70 -71 -72 -40 39 38 37 -8 -9 -36 -10 -11 -12 -13 -14 -15 -16 -17 18 7 -6 -5 -4 31 30 29 28 3 35 -1 -19 -44 -45 -46 -47 -27 -26 25 -20 54 -53 -52 51 50 55 73 41 42 43 48 49 -22 -21 34 -32 33 75 76 77 78 79 80 86 81 -85 -82 -83 84 -80 -79 -78 -77 -76 -75 -33 >cg Chaetosphaeridium 74 73 19 -18 17 16 15 14 13 12 11 10 -9 -8 -3 -4 5 6 -7 -62 -61 -60 59 -58 -57 56 55 54 -53 -52 51 50 -49 -48 29 28 -21 -22 1 36 35 37 -38 -39 40 41 42 43 -44 -45 -46 -47 -27 -26 25 -24 -23 -2 -32 -33 34 31 30 20 -63 -64 -65 -66 -67 -68 -69 -70 -71 -72 75 76 77 78 79 80 -81 -83 84 85 -86 -82 81 -80 -79 -78 -77 -76 -75 >mp Marchantia 55 73 19 -18 17 16 15 14 13 12 11 10 -9 -8 7 -6 -5 4 3 2 1 -20 -21 -22 23 24 -25 26 27 -28 -29 -30 -31 -32 -33 34 35 -36 37 -38 -39 40 41 42 43 -44 -45 -46 -47 48 49 -50 -51 52 53 -54 -56 57 58 -59 60 61 62 -63 -64 -65 -66 -67 -68 -69 -70 -71 -72 75 76 77 78 79 80 -81 83 84 85 -86 -82 81 -80 -79 -78 -77 -76 -75 >nt Nicotiana -1 -2 -3 -4 5 6 -7 8 9 -10 -11 -12 -13 -14 -15 -16 -17 18 -19 -20 -21 -22 23 24 -25 26 27 -28 -29 -30 -31 -32 -33 34 35 -36 37 -38 -39 40 41 42 43 -44 -45 -46 -47 48 49 -50 -51 52 53 -54 -55 -56 57 58 -59 60 61 62 -63 -64 -65 -66 -67 -68 -69 -70 -71 -72 -73 -74 75 76 77 78 79 80 -81 82 83 84 85 -86 81 -80 -79 -78 -77 -76 -75 74 73 72 71 Cs for the data set >cv Chlorella 0.7093 >cr Chlamydomonas 0.8710 >no Nephroselmis 0.7742 >mv Mesostigma 0.7582 >cg Chaetosphaeridium 0.7174 >mp Marchantia 0.6703 >nt Nicotiana 0.6875 Cf for the data set (x1E-3) >cv Chlorella 19.51 >cr Chlamydomonas 33.97 >no Nephroselmis 19.64 >mv Mesostigma 22.58 >cg Chaetosphaeridium 23.16 >mp Marchantia 19.43 >nt Nicotiana 19.93 Inferred rearrangement phylogeny 1. Step 1, 5 IR-containing genomes Tree length=78 (no:24,(mv:16,(cg:4,(mp:0,nt:7):9):18):0); 2. Step 2, loss of IR occurred in C. vulgaris. nop, the inferred parent of N. olivaceae in Step 1. Tree length = 144 (cv:43,((cr:60,(nop:1,mv:15):13):3,no:9):0); 3. Resolved with the reference tree (mv:16,(no:12,(cv:43,cr:60):0):12,(cg:4,(mp:0,nt:7):9):18));