Table II.
Conserved orthologous genes of organelles in C. merolae and C. reinhardtii
The reciprocal top pair of genes was shown to be orthologs as a result of BLAST analyses. When there were paralogous genes, two or more IDs are indicated in the column, and the corresponding orthologous gene is in bold. In cases of many paralogous genes (more than five), the number of genes is shown in parentheses, and the ID is indicated in supplemental data. The gene without the E-value was used to judge the relationship based on annotation.
| Description | KOG No. | C. merolae Gene ID | C. reinhardtii Protein ID | E-Value |
|---|---|---|---|---|
| Double membrane-bound organelles | ||||
| Nucleus | ||||
| Nucleolus | ||||
| Nucleolar protein NOL1/NOP2 | KOG1122 | CMP349C, CMT214C | 155441, 157957, 161814, 163585 | 8.70E-33 |
| Ribosome biogenesis protein Nop56p/Sik1p | KOG2573 | CMQ185C | 154535 | 6.00E-114 |
| Ribosome biogenesis protein Nop58p/Nop5p | KOG2572 | CMT605C | 156639 | 1.00E-113 |
| 60S ribosomal protein 15.5 kD/SNU13, NHP2/L7A family | KOG3387 | CMP335C | 169550 | 1.40E-36 |
| H/ACA snRNP component GAR1 | KOG3262 | CMI184C | 154459 | 6.30E-18 |
| Pseudouridine synthase | KOG2529 | CMM044C | 159827, 165705, 171730 | 9.00E-152 |
| Box H/ACA snoRNP component | KOG3167 | CMN132C | 160832, 168319 | 9.00E-28 |
| H/ACA snoRNP complex, subunit NOP10 | KOG3503 | CMH198C | ||
| Nucleolar protein fibrillarin NOP77 (RRM superfamily) | KOG0127 | CMR019C | 162436 | 5.20E-28 |
| WD40 repeat nucleolar protein Bop1, involved in ribosome biogenesis | KOG0650 | CMP117C | 168381, 168382 | 3.60E-52 |
| Fibrillarin and related nucleolar RNA-binding proteins | KOG1596 | CMN074C | 167674 | 1.90E-90 |
| Nucleolar RNA-associated protein (NRAP) | KOG2054 | CMT453C | 152756 | 2.40E-11 |
| Nucleolar protein involved in 40S ribosome biogenesis | KOG2147 | 159619 | ||
| Predicted nucleolar protein involved in ribosome biogenesis | KOG2154 | CMP203C | 153823 | |
| Cell growth-regulating nucleolar protein | KOG2186 | 170784 | ||
| Proliferation-associated nucleolar protein (NOL1) | KOG2360 | CMQ219C | 166986 | |
| Chromatin | ||||
| Chromatin remodeling complex WSTF-ISWI, small subunit | KOG0385 | CMJ200C, CMQ363C | 155935, 166121, 166985, 169081 | |
| Chromatin remodeling complex SWI/SNF | KOG0386 | CMH195C, CMM316C, CMJ053C, CMS028C | 155069, 158183, 165564 | |
| Chromatin remodeling protein HARP/SMARCAL1 | KOG1000 | CMR070C | 154676, 155886, 162842, 162843 | 7.40E-30 |
| Chromatin assembly complex 1 subunit B/CAC2 | KOG1009 | CMP030C | 159982 | 3.40E-18 |
| Retinoblastoma pathway protein LIN-9/chromatin-associated protein Aly | KOG1019 | 171468 | ||
| Chromatin remodeling complex WSTF-ISWI, large subunit | KOG1245 | CMJ244C | ||
| Chromatin remodeling factor subunit and related transcription factors | KOG1279 | CML061C, CMM233C | ||
| SWI-SNF chromatin remodeling complex, Snf5 subunit | KOG1649 | CMT559C | ||
| Chromatin remodeling protein, contains PHD zinc finger | KOG1973 | CMQ358C | 171356, 160490, 154083 | |
| Chromosome maintenance | ||||
| Structural maintenance of chromosome protein 1 (SMC1) | KOG0018 | CMI192C | 169433, 153089, 155233 | 1.70E-54 |
| Structural maintenance of chromosome protein 2 (SMC2) | KOG0933 | CMG189C | 164464, 169433 | 3.00E-154 |
| Structural maintenance of chromosome protein 3 (SMC3) | KOG0964 | CML027C | 162769, 167971 | |
| Structural maintenance of chromosome protein 4 (SMC4) | KOG0996 | CME029C | 156651, 169433 | |
| DNA repair protein RAD18 (SMC family protein) | KOG0250 | CMA066C | 154558, 154532 | 8.70E-69 |
| DNA repair protein RAD50, ABC-type ATPase/SMC superfamily | KOG0962 | CMQ187C | 164776 | 8.80E-13 |
| Structural maintenance of chromosome protein SMC5/Spr18 | KOG0979 | CMH246C | 156651, 156652 | |
| Regulator of spindle pole body duplication | KOG1849 | CMD159C | 164991 | 7.60E-09 |
| Conserved protein related to condensin complex subunit 1 | KOG0413 | CMQ236C | ||
| Chromosome condensation complex condensin, subunit D2 | KOG0414 | CMR484C | 155341 | 7.50E-15 |
| Chromosome condensation complex condensin, subunit G | KOG2025 | CMS422C | 168195 | |
| Chromosome condensation complex condensin, subunit H | KOG2328 | CMF069C | 169845 | |
| Histone | ||||
| Histone H1 | KOG4012 | CMN183C | 152784, 154462, 166540 | |
| Histone H2A | KOG1756 | CMN170C, CMN174C | 161746 + [26] | 2.10E-47 |
| Histone H2B | KOG1744 | CMN145C, CMN173C | 153803 + [24] | 1.60E-31 |
| Histone H3 | KOG1745 | CMN165C, CMN176C, CME099C | 152775 + [35] | 4.10E-52 |
| Histone H4 | KOG3467 | CMN166C, CMN169C | 161832 + [32] | 5.00E-35 |
| CENP-A | KOG1745 | CME099C | ||
| & Transport | ||||
| Karyopherin (importin) α | KOG0166 | CMT096C | 154475, 157323, 166294, 168625, 171096 | 2.00E-136 |
| Karyopherin (importin) β1 | KOG1241 | CMO056C | 161223 | 3.20E-82 |
| Karyopherin (importin) β3 | KOG2171 | CMI255C | 159427, 162988, 165758 | 1.90E-15 |
| Nuclear architecture-related protein | KOG2439 | CML104C | 154604, 154613, 163470 | 3.70E-25 |
| Nuclear pore complex, Nup155 component | KOG1900 | CMH179C | 163504 | 1.00E-24 |
| Nuclear pore complex, Nup98 component | KOG0845 | CMB112C | 157262, 164460, 164461 | |
| Nuclear pore complex, p54 component | KOG3091 | 170132 | ||
| Nuclear pore complex, rNup107 component | KOG1964 | CMC129C | 171545 | |
| Nuclear porin | KOG2196 | 167348 | ||
| Exportin 1 (Xpo1; CRM1/MSN5) | KOG2020 | CMS276C | 166838 | 0 |
| Nuclear transport receptor KAP120 | KOG1993 | 164435, 167577 | ||
| Nuclear transport receptor Karyopherin-β2/Transportin | KOG2023 | 157342 | ||
| Nuclear transport receptor RanBP16 | KOG1410 | 160790, 160794, 163343, 163345 | ||
| Nuclear transport receptor RANBP7/RANBP8 | KOG1991 | 166497 | ||
| Nucleolar GTPase/ATPase p130 | KOG2992 | 156312, 158268 | ||
| Predicted importin 9 | KOG2274 | 154841 | ||
| Ran GTPase-activating protein | KOG1909 | CMG035C | 154033, 156666, 165921, 171967 | 6.30E-19 |
| Small GTP-binding protein of Ran | KOG0096 | CMT257C | 164622 | 5.60E-90 |
| Ran-binding protein RANBP1 and related RanBD domain proteins | KOG0864 | 163501, 163502 | ||
| Spliceosomes | ||||
| U1 snRNP component | KOG3168 | 157199, 166414 | ||
| Spliceosomal protein snRNP-U1A/U2B | KOG4206 | 159384, 167958 | ||
| U3 snoRNP component | KOG2781 | 163262 | ||
| KOG4655 | 163626 | |||
| KOG2600 | 171407 | |||
| U4/U6 small nuclear ribonucleoprotein Prp4 | KOG0272 | 158503, 168282, 168801 | ||
| U5 snRNP spliceosome subunit | KOG1795 | 162021 | ||
| U5 snRNP-specific protein | KOG0468 | CMK208C | 171910 | 4.30E-43 |
| U6 snRNP-associated Sm-like protein | KOG1775 | 166844 | ||
| Splicing factor 3b, subunit 4 (U2 snRNP) | KOG0131 | CME063C | 158080 | |
| Box C/D snoRNP and U4 snRNP component Snu13p | KOG3387 | CMP335C | 169550 | 1.40E-36 |
| Thioredoxin-like U5 snRNP component dim1 | KOG3414 | CMN033C, CMS018C | 158362 | 4.70E-22 |
| snRNP core Sm-like protein SmX5 | KOG3448 | CMB130C | 156627, 155338 | 1.80E-20 |
| Mitochondria | ||||
| Translocons | ||||
| Tom20 | 171301 | |||
| Tom22 | CMG115C | |||
| Tom40 | KOG3296 | CMF062C | 161559 | 2.60E-41 |
| Tom70 | 159288 | |||
| Tim8 | KOG3489 | CMI216C | ||
| Tim9 | 154330 | |||
| Tim10 | KOG3480 | CMG033C | 157296 | |
| Tim13 | KOG1733 | CMB148C | ||
| Tim17 | KOG1652 | CMS471C | 163245, 158395 | 5.50E-41 |
| Tim22 | KOG3225 | CMS209C | 163831 | 6.10E-15 |
| Tim23 | 156509 | |||
| Tim44 | KOG2580 | CMJ253C | 168938 | 1.10E-06 |
| Tim54 | KOG2832 | CMN179C | 164180 | 9.30E-43 |
| Division | ||||
| Dynamin-related protein | 171301 | |||
| Organelle division protein FtsZ | CMG115C | |||
| Plastid | ||||
| Translocons | ||||
| Toc34 | CMP284C | 153364, 156483 | 5.80E-14 | |
| Toc64 | KOG1211 | 156765, 157654, 165871 | ||
| Toc75 | CMJ202C | 170954, 165731 | ||
| Toc159 | KOG1211 | 153364 | ||
| Tic20 | 155153 | |||
| Tic22 | CMC181C, CMJ105C | 162599 | ||
| Tic40 | KOG1308 | 166119, 168128 | ||
| Tic62 | 161722 | |||
| Tic110 | CMQ342C | 163303 | ||
| Division | ||||
| Dynamin-related protein | CMN262C | 155446 | 2.00E-138 | |
| Plastid division protein FtsZ | CMS004C, CMO089C | 152672 | 1.10E-89 | |
| MinE | 158874 | |||
| MinD | 157354 | |||
| Single membrane-bound organelles | ||||
| Endoplasmic reticulum | ||||
| ER lumen protein retaining receptor | KOG3106 | CMR190C | 158379, 166543, 172038 | 2.10E-57 |
| ER-to-Golgi transport protein/RAD50-interacting protein 1 | KOG2218 | 169153 | ||
| ER vesicle integral membrane protein | KOG2729 | CME060C | 161292 | 5.20E-14 |
| Membrane component of ER protein translocation complex | KOG2927 | 164494 | ||
| Membrane protein involved in ER to Golgi transport | KOG2887 | 157838, 169932 | ||
| Signal recognition particle receptor, α-subunit | KOG0781 | CME016C | 167087 | 8.60E-74 |
| Signal recognition particle receptor, β-subunit | KOG0090 | CMM147C | 159090 | |
| Signal recognition particle, subunit Srp54 | KOG0780 | CMC066C | 157035, 165958 | 1.30E-49 |
| Signal recognition particle, subunit Srp54 | KOG0780 | CMO152C | 171457 | |
| Signal recognition particle, subunit Srp68 | KOG2460 | CML086C | 161743 | |
| Signal recognition particle, subunit Srp72 | KOG2376 | CMQ194C | 156546 | |
| Signal recognition particle, subunit Srp19 | KOG3198 | CMR091C | ||
| Vesicle coat complex AP-1, γ-subunit | KOG1062 | CMF083C | 167317, 171947 | |
| Vesicle coat complex AP-1/AP-2/AP-4, β-subunit | KOG1061 | CMR021C | 155972, 159826, 163531, 170720 | |
| Vesicle coat complex AP-2, α-subunit | KOG1077 | 168146 | ||
| Vesicle coat complex COPI, α-subunit | KOG0292 | CMD156C | 157180 | |
| Vesicle coat complex COPI, β-subunit | KOG1058 | CMG048C | 152346 | 1.00E-171 |
| Vesicle coat complex COPI, β-subunit | KOG0276 | CMT617C | 168412 | |
| Vesicle coat complex COPI, ɛ-subunit | KOG3081 | CMD014C | 155710 | |
| Vesicle coat complex COPI, γ-subunit | KOG1078 | CMP053C | 172054 | 9.00E-172 |
| Vesicle coat complex COPI, δ-subunit | KOG2635 | CMO202C | 161602 | 1.00E-74 |
| Vesicle coat complex COPI, ζ-subunit | KOG3343 | CMN247C | 154191, 155047 | 7.70E-10 |
| Vesicle coat complex COPII, GTPase subunit SAR1 | KOG0077 | CMT196C | 160753 | |
| Vesicle coat complex COPII, subunit SEC13 | KOG1332 | CMJ112C | 167415 | 8.80E-49 |
| Vesicle coat complex COPII, subunit SEC23 | KOG1986 | CMF170C | 159292, 167991 | 0 |
| Vesicle coat complex COPII, subunit SEC24/subunit SFB2 | KOG1985 | CMQ471C | 168655, 170872 | 6.00E-112 |
| Vesicle coat complex COPII, subunit SFB3 | KOG1984 | CMQ380C | 157030, 161297 | |
| & Vesicle coat complex COPII, subunit SEC31 | KOG0307 | CMR203C | 157416 | |
| Vesicle coat protein clathrin, heavy chain | KOG0985 | CMF103C | 162480 | |
| Vesicle coat protein clathrin, light chain | KOG4031 | 154013 | ||
| Vesicle trafficking protein Sec1 | KOG1300 | CMC019C | 165816, 171492 | |
| Similar to COP-coated vesicle membrane protein p24 | KOG1692 | CMG098C | 158201 | |
| Golgi apparatus | ||||
| Golgi proteins involved in ER retention (RER) | KOG1688 | CMI263C | 171623 | 7.00E-42 |
| Golgi SNAP receptor complex member | KOG3251 | CMS441C | 171613 | 1.30E-09 |
| Golgi transport complex COD1 protein | KOG0412 | CMJ219C | 162230 | |
| Golgi transport complex subunit | KOG2069 | CMJ171C | 156760 | 2.00E-11 |
| Predicted Golgi transport complex 1 protein | KOG2211 | 159045 | ||
| Rab GTPase interacting factor, Golgi membrane protein | KOG3103 | CMQ462C | 160218 | 3.40E-05 |
| Late Golgi protein sorting complex, subunit Vps53 | KOG2180 | CMR200C | 159541, 161878, 162144 | 3.30E-13 |
| ER-to-Golgi transport protein/RAD50-interacting protein 1 | KOG2218 | 169153 | ||
| Microbody (peroxisome) | ||||
| Peroxin-1 (Pex1) | KOG0735 | CMI027C | 153527 | |
| Pex2 | CMD105C | |||
| Pex5 | KOG1125 | CMK124C | 160889 | 1.30E-27 |
| Pex6 | KOG736 | CML252C | ||
| Pex7 | KOG0277 | 158976 | ||
| Pex10 | KOG0317 | CMT012C | 169232, 169243 | 2.10E-08 |
| Pex11 | KOG4186 | 159487 | ||
| Pex12 | KOG0826 | CMO084C | 159483 | 5.80E-10 |
| Pex14 | KOG2629 | CMN043C | 163261 | |
| Pex19 | KOG3133 | CMQ019C | 168404 | |
| Catalase | KOG0047 | CMI050C | 157074 | 1.00E-178 |
| Lysosome | ||||
| Vacuolar H+-ATPase V0 sector, subunit a | KOG2189 | CMD095C | [6] | 3.00E-167 |
| Vacuolar H+-ATPase V0 sector, subunit c″ | KOG0233 | CMS332C | 164229 | |
| Vacuolar H+-ATPase V0 sector, subunit d | KOG2957 | CMO274C | 165689 | 4.40E-82 |
| Vacuolar H+-ATPase V0 sector, subunits c/c′ | KOG0232 | CMQ323C | 159570 | 3.00E-40 |
| Vacuolar H+-ATPase V1 sector, subunit A | KOG1352 | CMS342C | 156435 | 0.00E+00 |
| Vacuolar H+-ATPase V1 sector, subunit B | KOG1351 | CMP123C | 167663 | 0 |
| Vacuolar H+-ATPase V1 sector, subunit C | KOG2909 | CMC151C | 169514 | 2.00E-35 |
| Vacuolar H+-ATPase V1 sector, subunit D | KOG1647 | CMD007C | 160328 | 1.90E-44 |
| Vacuolar H+-ATPase V1 sector, subunit E | KOG1664 | CMQ010C | 153341 | 2.20E-23 |
| Vacuolar H+-ATPase V1 sector, subunit F | KOG3432 | CMQ237C | 167983 | 8.20E-22 |
| Vacuolar H+-ATPase V1 sector, subunit G | KOG1772 | CMH200C | 156178 | 4.60E-05 |
| Vacuolar H+-ATPase V1 sector, subunit H | KOG2759 | CMQ386C | 164977 | 6.70E-26 |
| Vacuolar-type H+-translocating inorganic pyrophosphatase | CMO102C | 171094 | 8.00E-110 | |
| Lysosomal and prostatic acid phosphatases | KOG3720 | CMM328C, CMT279C | ||
| Autophagy | ||||
| Protein conjugation factor involved in autophagy | KOG3439 | 153015 | ||
| Ser/Thr-protein kinase involved in autophagy | KOG0595 | 152640, 160575, 171024 | ||
| Beclin-like protein (Apg6p) | KOG2751 | 163837 | ||
| Microtubule-associated anchor protein | KOG1654 | 168349 | ||
| Cys protease required for autophagy, Apg4p/Aut2p | KOG2674 | 166084 | ||
| Protein involved in autophagocytosis during starvation | KOG2981 | 162469 | ||
| Cytosolic components | ||||
| Actin | KOG0676 | CMM237C | 154863 | 0 |
| Actin-related proteins | KOG0676 | CMS412C, CML073C | 156929, 161626, 169503, 169991 | |
| Actin-related protein Arp4p/Act3p | KOG0679 | CMR270C, CMJ223C | 169502 | |
| Actin-related protein Arp6p | KOG0680 | CMS185C | ||
| λ-Tubulin | KOG1376 | CMT504C | 154911, 164620, 165702 | 0 |
| β-Tubulin | KOG1375 | CMN263C | 169905, 170055, 158210, 157194 | 0 |
| γ-Tubulin | KOG1374 | CMN304C | 158831, 164724 | 3.00E-131 |
| & Dynein light chain type 1 | KOG3430 | CMT356C | 15928, 164296, 164722 | 2.20E-30 |
| Dyneins, heavy chain | KOG3595 | [24] | ||
| Kinesin (KAR3 subfamily) | KOG0239 | CMR497C | 152572, 154712, 166493, 168983 | 6.00E-94 |
| Kinesin (KAR3 subfamily) | KOG0239 | CMT097C | 168558 | 3.70E-87 |
| Kinesin (SMY1 subfamily) | KOG0240 | 152501, 169875, 171909 | ||
| Kinesin light chain | KOG1840 | [9] | ||
| Kinesin-like protein | KOG0247 | 169655 | ||
| Kinesin-like protein | KOG0246 | 169327 | ||
| Kinesin-like protein | KOG0244 | 154733, 158290, 161552, 163582, 167216 | ||
| Kinesin-like protein | KOG0243 | 161485, 164385, 166682 | ||
| Kinesin-like protein | KOG0242 | CMQ429C | [6] | |
| Kinesin-like protein | KOG4280 | CMO070C | [13] | |
| Myosin class II heavy chain | KOG0161 | [7] | ||
| Myosin class V heavy chain | KOG0160 | 166295, 166465, 168960, 169141 | ||
| Cell wall | ||||
| Ankyrin | KOG4177 | CME092C, CMQ294C, CMS172C | 163973 + [21] | 1.30E-21 |
| dTDP-Glc 4-6-dehydratase/UDP-GlcUA decarboxylase | KOG1429 | CME136C | 163641 | 3.00E-116 |
| GDP-Man pyrophosphorylase | KOG1322 | CMF136C | 154457, 164593, 166665, 167020, 169713 | |
| Glucosamine-6-P synthetases | KOG1268 | CMK166C | 158640 | 5.20E-80 |
| Glucosamine-P N-acetyltransferase | KOG3396 | CMS020C, CMN031C | 154203 | 4.30E-16 |
| Glucosidase II catalytic (alpha) subunit | KOG1066 | CMM082C, CMM202C, CMF121C | 164756, 164757 | 8.70E-59 |
| Glycosyltransferase | KOG1387 | CMI301C | 153778 | 8.10E-16 |
| Glycosyltransferase | KOG0853 | CMT168C | 156129 | 1.80E-28 |
| GPI transamidase complex, GPI16/PIG-T component | KOG2407 | 156643 | ||
| GPI transamidase complex, GPI17/PIG-S component | KOG2459 | 162068 | ||
| N-Acetylglucosaminyltransferase complex, subunit PIG-A/SPT14 | KOG1111 | CMR015C, CMR346C | 159722, 159723, 161264, 168304 | 2.20E-77 |
| Phospholipid scramblase | KOG0621 | CMN259C | 161838 | 2.50E-22 |
| UDP-Glc 4-epimerase/UDP-sulfoquinovose synthase | KOG1371 | CMA041C | 160401 | 3.00E-105 |
| UDP-Glc 4-epimerase/UDP-sulfoquinovose synthase | KOG1371 | CMR012C | 168872 | 1.20E-81 |
| UDP-Glc 4-epimerase/UDP-sulfoquinovose synthase | KOG1371 | CMR075C | 152613 | 2.30E-80 |