Kawahara et al./Breeding Science doi: 10.1270/jsbbs.19097 Supplemental Table 6. Mandarin (C. clementina and C. unshiu ) specific gene groups and annotation ID Num. in C. celementine Num in C. unshiu Num in P.trifoliata Note GO InterPro Members in C.clementine Members in C.unshiu Members in P.trifoliata scaffold_1_mRNA_511.1,scaffold_3_mR NA_14.1,scaffold_3_mRNA_1514.1,scaf fold_3_mRNA_220.1,scaffold_3_mRNA _3574.1,scaffold_3_mRNA_3785.1,scaff C_unshiu_00008_mRNA_15.1,C_unshiu old_4_mRNA_760.1,scaffold_5_mRNA_ _00016_mRNA_48.1,C_unshiu_00141_ 3887.1,scaffold_5_mRNA_4369.1,scaffo mRNA_26.1,C_unshiu_00185_mRNA_9 ld_5_mRNA_4932.1,scaffold_6_mRNA_ .1,C_unshiu_00217_mRNA_43.1,C_unsh GF0000019 21 10 0 Hypothetical protein (31) - 1884.1,scaffold_7_mRNA_1009.1,scaffo iu_00310_mRNA_22.1,C_unshiu_00514 ld_7_mRNA_1036.1,scaffold_7_mRNA_ _mRNA_15.1,C_unshiu_00627_mRNA_ 1928.1,scaffold_7_mRNA_1995.1,scaffo 3.1,C_unshiu_00919_mRNA_9.1,C_unsh ld_7_mRNA_460.1,scaffold_7_mRNA_5 iu_01313_mRNA_3.1 01.1,scaffold_7_mRNA_864.1,scaffold_ 8_mRNA_3093.1,scaffold_9_mRNA_22 9.1,scaffold_9_mRNA_3409.1 scaffold_1_mRNA_1502.1,scaffold_2_m nucleic acid binding [GO:0003676 Zinc finger, CCHC-type [IPR001878] RNA_324.1,scaffold_6_mRNA_441.1,sc C_unshiu_00128_mRNA_34.1,C_unshiu molecular_function] (10); zinc ion (10); Peptidase A2A, retrovirus, catalytic affold_6_mRNA_530.1,scaffold_6_mRN _00219_mRNA_10.1,C_unshiu_00219_ binding [GO:0008270 [IPR001995] (7); Viral movement protein A_635.1,scaffold_8_mRNA_1564.1,scaf mRNA_13.1,C_unshiu_00538_mRNA_1 GF0000066 12 7 0 Hypothetical protein (19) molecular_function] (10); proteolysis [IPR028919] (6); Aspartic peptidase - fold_8_mRNA_1587.1,scaffold_8_mRN 3.1,C_unshiu_00724_mRNA_19.1,C_un [GO:0006508 biological_process] (7); domain [IPR021109] (6); Reverse A_1595.1,scaffold_8_mRNA_1635.1,sca shiu_01568_mRNA_13.1,C_unshiu_019 aspartic-type endopeptidase activity transcriptase domain [IPR000477] (5); ffold_8_mRNA_1691.1,scaffold_9_mRN 25_mRNA_6.1 [GO:0004190 molecular_function] (7) Retropepsins [IPR018061] (1) A_2229.1,scaffold_9_mRNA_2297.1 scaffold_1_mRNA_1036.1,scaffold_1_m RNA_963.1,scaffold_2_mRNA_2490.1,s caffold_3_mRNA_1756.1,scaffold_3_m GF0000242 10 1 0 Hypothetical protein (11) RNA_3222.1,scaffold_3_mRNA_4688.1, C_unshiu_00170_mRNA_44.1 - scaffold_6_mRNA_290.1,scaffold_6_mR NA_604.1,scaffold_7_mRNA_1891.1,sc affold_9_mRNA_1608.1 scaffold_4_mRNA_1603.1,scaffold_4_m RNA_1606.1,scaffold_5_mRNA_3949.1, C_unshiu_00041_mRNA_39.1,C_unshiu scaffold_5_mRNA_3954.1,scaffold_6_m _00218_mRNA_32.1,C_unshiu_00298_ GF0000111 10 6 0 Hypothetical protein (16) RNA_669.1,scaffold_7_mRNA_1910.1,s mRNA_26.1,C_unshiu_00447_mRNA_3 - caffold_8_mRNA_1431.1,scaffold_9_m 2.1,C_unshiu_00582_mRNA_5.1,C_unsh RNA_3174.1,scaffold_9_mRNA_3287.1, iu_02743_mRNA_3.1 scaffold_9_mRNA_3332.1 scaffold_2_mRNA_954.1,scaffold_3_mR NA_12.1,scaffold_3_mRNA_3572.1,scaf fold_5_mRNA_4934.1,scaffold_6_mRN GF0000477 8 1 0 Hypothetical protein (9) C_unshiu_00627_mRNA_1.1 - A_170.1,scaffold_7_mRNA_2644.1,scaf fold_8_mRNA_1523.1,scaffold_8_mRN A_2176.1 scaffold_3_mRNA_3570.1,scaffold_4_m RNA_756.1,scaffold_5_mRNA_4367.1,s C_unshiu_00404_mRNA_12.1,C_unshiu GF0000499 7 2 0 Hypothetical protein (9) caffold_5_mRNA_486.1,scaffold_5_mR - _01313_mRNA_7.1 NA_4935.1,scaffold_7_mRNA_1535.1,s caffold_8_mRNA_3091.1 scaffold_5_mRNA_2779.1,scaffold_5_m RNA_2857.1,scaffold_5_mRNA_438.1,s C_unshiu_00004_mRNA_3.1,C_unshiu_ Hypothetical protein (9); Monosacharide DNA binding [GO:0003677 Myb-like domain [IPR017877] (1); GF0000387 7 3 0 caffold_8_mRNA_480.1,scaffold_8_mR 00271_mRNA_7.1,C_unshiu_00378_mR - transport protein (1) molecular_function] (1) Homeobox domain-like [IPR009057] (1) NA_957.1,scaffold_9_mRNA_1498.1,sc NA_20.1 affold_9_mRNA_3365.1 scaffold_3_mRNA_1363.1,scaffold_3_m C_unshiu_00137_mRNA_4.1,C_unshiu_ RNA_5073.1,scaffold_5_mRNA_1401.1, 00760_mRNA_4.1,C_unshiu_01260_mR GF0000275 6 5 0 Hypothetical protein (11) - scaffold_5_mRNA_3344.1,scaffold_6_m NA_8.1,C_unshiu_01382_mRNA_2.1,C RNA_1789.1,scaffold_9_mRNA_2959.1 _unshiu_02154_mRNA_2.1 Reverse transcriptase, RNA-dependent DNA polymerase [IPR013103] (7); nucleic acid binding [GO:0003676 Ribonuclease H-like domain scaffold_4_mRNA_1134.1,scaffold_5_m Retrotransposon protein, putative, Ty1- molecular_function] (5); zinc ion binding [IPR012337] (5); Integrase, catalytic core RNA_1957.1,scaffold_6_mRNA_1003.1, C_unshiu_00323_mRNA_5.1,C_unshiu_ GF0000949 5 2 0 copia subclass (6); Cysteine-rich RLK [GO:0008270 molecular_function] (4); - [IPR001584] (4); Zinc finger, CCHC- scaffold_8_mRNA_1396.1,scaffold_8_m 00413_mRNA_4.1 (RECEPTOR-like protein kinase) 8 (1) DNA integration [GO:0015074 type [IPR001878] (4); GAG-pre- RNA_1625.1 biological_process] (4) integrase domain [IPR025724] (3); Viral movement protein [IPR028919] (1) scaffold_1_mRNA_306.1,scaffold_5_mR NA_1301.1,scaffold_5_mRNA_2602.1,s C_unshiu_00233_mRNA_12.1,C_unshiu GF0000805 5 2 0 Monosacharide transport protein (7) - caffold_8_mRNA_472.1,scaffold_9_mR _00800_mRNA_3.1 NA_3209.1 GAG-pre-integrase domain [IPR025724] nucleic acid binding [GO:0003676 (6); Zinc finger, CCHC-type scaffold_1_mRNA_1631.1,scaffold_4_m Retrotransposon protein, putative, Ty1- molecular_function] (6); zinc ion binding [IPR001878] (6); Reverse transcriptase, RNA_1135.1,scaffold_5_mRNA_3554.1, C_unshiu_00424_mRNA_4.1,C_unshiu_ GF0000784 5 2 0 copia subclass (6); Putative retroelement [GO:0008270 molecular_function] (6); RNA-dependent DNA polymerase - scaffold_9_mRNA_1737.1,scaffold_9_m 00434_mRNA_24.1 pol polyprotein (1) DNA integration [GO:0015074 [IPR013103] (4); Ribonuclease H-like RNA_2941.1 biological_process] (3) domain [IPR012337] (4); Integrase, catalytic core [IPR001584] (3) scaffold_2_mRNA_172.1,scaffold_3_mR C_unshiu_00361_mRNA_9.1,C_unshiu_ NA_2036.1,scaffold_3_mRNA_4464.1,s 01106_mRNA_1.1,C_unshiu_02358_mR GF0000326 5 5 0 Hypothetical protein (10) LOG family [IPR031100] (10) - caffold_4_mRNA_1996.1,scaffold_5_m NA_1.1,C_unshiu_02458_mRNA_3.1,C RNA_601.1 _unshiu_02747_mRNA_1.1 scaffold_5_mRNA_2696.1,scaffold_6_m GF0002260 4 1 0 Hypothetical protein (5) RNA_2058.1,scaffold_6_mRNA_2059.1, C_unshiu_01636_mRNA_5.1 - scaffold_6_mRNA_319.1 scaffold_2_mRNA_839.1,scaffold_3_mR GF0001952 4 1 0 Hypothetical protein (5) NA_3305.1,scaffold_5_mRNA_1156.1,s C_unshiu_00066_mRNA_20.1 - caffold_8_mRNA_2127.1 scaffold_2_mRNA_3057.1,scaffold_3_m Putative retroelement pol polyprotein (4); hydrolase activity [GO:0016787 Pectinacetylesterase/NOTUM GF0001907 4 1 0 RNA_3146.1,scaffold_5_mRNA_3216.1, C_unshiu_00003_mRNA_1.1 - Hypothetical protein (1) molecular_function] (1) [IPR004963] (1) scaffold_6_mRNA_117.1 scaffold_2_mRNA_2323.1,scaffold_3_m GF0001883 4 1 0 Hypothetical protein (5) RNA_1910.1,scaffold_3_mRNA_1986.1, C_unshiu_00138_mRNA_38.1 - scaffold_9_mRNA_2255.1 Retrotransposon gag domain Gag protease polyprotein (3); Cellular [IPR005162] (5); Zinc finger, CCHC- nucleic acid binding [GO:0003676 scaffold_1_mRNA_1954.1,scaffold_2_m nucleic acid-binding protein (1); type [IPR001878] (5); LDOC1-related GF0001765 4 1 0 molecular_function] (5); zinc ion binding RNA_187.1,scaffold_9_mRNA_2057.1,s C_unshiu_00016_mRNA_9.1 - DNA/RNA polymerases superfamily [IPR032567] (2); Aspartic peptidase [GO:0008270 molecular_function] (5) caffold_9_mRNA_2916.1 protein (1) domain [IPR021109] (1); Retroviral aspartyl protease [IPR013242] (1) DNA integration [GO:0015074 Ribonuclease H-like domain biological_process] (6); nucleic acid [IPR012337] (6); Integrase, catalytic core scaffold_4_mRNA_1666.1,scaffold_5_m binding [GO:0003676 C_unshiu_00140_mRNA_28.1,C_unshiu GF0001444 4 2 0 Orf764 protein (6) [IPR001584] (6); Ribonuclease H domain RNA_1151.1,scaffold_7_mRNA_1363.1, - molecular_function] (6); RNA-DNA _00716_mRNA_14.1 [IPR002156] (4); Retrotransposon gag scaffold_7_mRNA_2242.1 hybrid ribonuclease activity domain [IPR005162] (1) [GO:0004523 molecular_function] (4) scaffold_1_mRNA_751.1,scaffold_2_mR C_unshiu_00947_mRNA_4.1,C_unshiu_ GF0001186 4 2 0 Putative retroelement pol polyprotein (6) NA_661.1,scaffold_3_mRNA_705.1,scaf - 01928_mRNA_5.1 fold_5_mRNA_615.1 C_unshiu_00124_mRNA_19.1,C_unshiu _00215_mRNA_2.1,C_unshiu_00406_m RNA_9.1,C_unshiu_00556_mRNA_19.1 scaffold_2_mRNA_2854.1,scaffold_2_m ,C_unshiu_00722_mRNA_10.1,C_unshiu GF0000142 4 10 0 Hypothetical protein (14) LOG family [IPR031100] (1) RNA_2860.1,scaffold_6_mRNA_310.1,s - _01049_mRNA_5.1,C_unshiu_01704_m caffold_8_mRNA_1550.1 RNA_1.1,C_unshiu_01716_mRNA_1.1, C_unshiu_02577_mRNA_3.1,C_unshiu_ 02711_mRNA_1.1 Tetratricopeptide-like helical domain [IPR011990] (4); Tetratricopeptide repeat [IPR019734] (4); Eukaryotic translation initiation factor 3 protein binding [GO:0005515 Tetratricopeptide repeat-containing scaffold_7_mRNA_1733.1,scaffold_7_m GF0004477 3 1 0 subunit, putative (2); Hypothetical protein C_unshiu_00766_mRNA_2.1 - molecular_function] (4) domain [IPR013026] (4); CLU central RNA_1742.1,scaffold_7_mRNA_1759.1 (2) domain [IPR033646] (3); Winged helix- turn-helix DNA-binding domain [IPR011991] (3) Ribonuclease H-like domain nucleic acid binding [GO:0003676 [IPR012337] (4); hAT-like transposase, molecular_function] (4); protein RNase-H fold [IPR025525] (4); HAT, C- BED zinc finger,hAT family dimerization scaffold_6_mRNA_388.1,scaffold_8_mR GF0004380 3 1 0 dimerization activity [GO:0046983 terminal dimerisation domain C_unshiu_00474_mRNA_21.1 - domain isoform 1 (4) NA_2483.1,scaffold_9_mRNA_1810.1 molecular_function] (4); DNA binding [IPR008906] (4); Zinc finger, BED-type [GO:0003677 molecular_function] (4) [IPR003656] (3); Zinc finger C2H2-type [IPR013087]