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.

DescriptionKOG No.C. merolae Gene IDC. reinhardtii Protein IDE-Value
Double membrane-bound organelles
    Nucleus
        Nucleolus
            Nucleolar protein NOL1/NOP2KOG1122CMP349C, CMT214C155441, 157957, 161814, 1635858.70E-33
            Ribosome biogenesis protein Nop56p/Sik1pKOG2573CMQ185C1545356.00E-114
            Ribosome biogenesis protein Nop58p/Nop5pKOG2572CMT605C1566391.00E-113
            60S ribosomal protein 15.5 kD/SNU13, NHP2/L7A familyKOG3387CMP335C1695501.40E-36
            H/ACA snRNP component GAR1KOG3262CMI184C1544596.30E-18
            Pseudouridine synthaseKOG2529CMM044C159827, 165705, 1717309.00E-152
            Box H/ACA snoRNP componentKOG3167CMN132C160832, 1683199.00E-28
            H/ACA snoRNP complex, subunit NOP10KOG3503CMH198C
            Nucleolar protein fibrillarin NOP77 (RRM superfamily)KOG0127CMR019C1624365.20E-28
            WD40 repeat nucleolar protein Bop1, involved in ribosome biogenesisKOG0650CMP117C168381, 1683823.60E-52
            Fibrillarin and related nucleolar RNA-binding proteinsKOG1596CMN074C1676741.90E-90
            Nucleolar RNA-associated protein (NRAP)KOG2054CMT453C1527562.40E-11
            Nucleolar protein involved in 40S ribosome biogenesisKOG2147159619
            Predicted nucleolar protein involved in ribosome biogenesisKOG2154CMP203C153823
            Cell growth-regulating nucleolar proteinKOG2186170784
            Proliferation-associated nucleolar protein (NOL1)KOG2360CMQ219C166986
        Chromatin
            Chromatin remodeling complex WSTF-ISWI, small subunitKOG0385CMJ200C, CMQ363C155935, 166121, 166985, 169081
            Chromatin remodeling complex SWI/SNFKOG0386CMH195C, CMM316C, CMJ053C, CMS028C155069, 158183, 165564
            Chromatin remodeling protein HARP/SMARCAL1KOG1000CMR070C154676, 155886, 162842, 1628437.40E-30
            Chromatin assembly complex 1 subunit B/CAC2KOG1009CMP030C1599823.40E-18
            Retinoblastoma pathway protein LIN-9/chromatin-associated protein AlyKOG1019171468
            Chromatin remodeling complex WSTF-ISWI, large subunitKOG1245CMJ244C
            Chromatin remodeling factor subunit and related transcription factorsKOG1279CML061C, CMM233C
            SWI-SNF chromatin remodeling complex, Snf5 subunitKOG1649CMT559C
            Chromatin remodeling protein, contains PHD zinc fingerKOG1973CMQ358C171356, 160490, 154083
        Chromosome maintenance
            Structural maintenance of chromosome protein 1 (SMC1)KOG0018CMI192C169433, 153089, 1552331.70E-54
            Structural maintenance of chromosome protein 2 (SMC2)KOG0933CMG189C164464, 1694333.00E-154
            Structural maintenance of chromosome protein 3 (SMC3)KOG0964CML027C162769, 167971
            Structural maintenance of chromosome protein 4 (SMC4)KOG0996CME029C156651, 169433
            DNA repair protein RAD18 (SMC family protein)KOG0250CMA066C154558, 1545328.70E-69
            DNA repair protein RAD50, ABC-type ATPase/SMC superfamilyKOG0962CMQ187C1647768.80E-13
            Structural maintenance of chromosome protein SMC5/Spr18KOG0979CMH246C156651, 156652
            Regulator of spindle pole body duplicationKOG1849CMD159C1649917.60E-09
            Conserved protein related to condensin complex subunit 1KOG0413CMQ236C
            Chromosome condensation complex condensin, subunit D2KOG0414CMR484C1553417.50E-15
            Chromosome condensation complex condensin, subunit GKOG2025CMS422C168195
            Chromosome condensation complex condensin, subunit HKOG2328CMF069C169845
        Histone
            Histone H1KOG4012CMN183C152784, 154462, 166540
            Histone H2AKOG1756CMN170C, CMN174C161746 + [26]2.10E-47
            Histone H2BKOG1744CMN145C, CMN173C153803 + [24]1.60E-31
            Histone H3KOG1745CMN165C, CMN176C, CME099C152775 + [35]4.10E-52
            Histone H4KOG3467CMN166C, CMN169C161832 + [32]5.00E-35
            CENP-AKOG1745CME099C
&        Transport
            Karyopherin (importin) αKOG0166CMT096C154475, 157323, 166294, 168625, 1710962.00E-136
            Karyopherin (importin) β1KOG1241CMO056C1612233.20E-82
            Karyopherin (importin) β3KOG2171CMI255C159427, 162988, 1657581.90E-15
            Nuclear architecture-related proteinKOG2439CML104C154604, 154613, 1634703.70E-25
            Nuclear pore complex, Nup155 componentKOG1900CMH179C1635041.00E-24
            Nuclear pore complex, Nup98 componentKOG0845CMB112C157262, 164460, 164461
            Nuclear pore complex, p54 componentKOG3091170132
            Nuclear pore complex, rNup107 componentKOG1964CMC129C171545
            Nuclear porinKOG2196167348
            Exportin 1 (Xpo1; CRM1/MSN5)KOG2020CMS276C1668380
            Nuclear transport receptor KAP120KOG1993164435, 167577
            Nuclear transport receptor Karyopherin-β2/TransportinKOG2023157342
            Nuclear transport receptor RanBP16KOG1410160790, 160794, 163343, 163345
        Nuclear transport receptor RANBP7/RANBP8KOG1991166497
        Nucleolar GTPase/ATPase p130KOG2992156312, 158268
        Predicted importin 9KOG2274154841
            Ran GTPase-activating proteinKOG1909CMG035C154033, 156666, 165921, 1719676.30E-19
        Small GTP-binding protein of RanKOG0096CMT257C1646225.60E-90
        Ran-binding protein RANBP1 and related RanBD domain proteinsKOG0864163501, 163502
        Spliceosomes
            U1 snRNP componentKOG3168157199, 166414
            Spliceosomal protein snRNP-U1A/U2BKOG4206159384, 167958
            U3 snoRNP componentKOG2781163262
KOG4655163626
KOG2600171407
            U4/U6 small nuclear ribonucleoprotein Prp4KOG0272158503, 168282, 168801
            U5 snRNP spliceosome subunitKOG1795162021
            U5 snRNP-specific proteinKOG0468CMK208C1719104.30E-43
            U6 snRNP-associated Sm-like proteinKOG1775166844
            Splicing factor 3b, subunit 4 (U2 snRNP)KOG0131CME063C158080
            Box C/D snoRNP and U4 snRNP component Snu13pKOG3387CMP335C1695501.40E-36
            Thioredoxin-like U5 snRNP component dim1KOG3414CMN033C, CMS018C1583624.70E-22
            snRNP core Sm-like protein SmX5KOG3448CMB130C156627, 1553381.80E-20
        Mitochondria
            Translocons
                Tom20171301
                Tom22CMG115C
                Tom40KOG3296CMF062C1615592.60E-41
                Tom70159288
                Tim8KOG3489CMI216C
                Tim9154330
                Tim10KOG3480CMG033C157296
                Tim13KOG1733CMB148C
                Tim17KOG1652CMS471C163245, 1583955.50E-41
                Tim22KOG3225CMS209C1638316.10E-15
                Tim23156509
                Tim44KOG2580CMJ253C1689381.10E-06
                Tim54KOG2832CMN179C1641809.30E-43
            Division
                Dynamin-related protein171301
                Organelle division protein FtsZCMG115C
        Plastid
            Translocons
                Toc34CMP284C153364, 1564835.80E-14
                Toc64KOG1211156765, 157654, 165871
                Toc75CMJ202C170954, 165731
                Toc159KOG1211153364
                Tic20155153
                Tic22CMC181C, CMJ105C162599
                Tic40KOG1308166119, 168128
                Tic62161722
                Tic110CMQ342C163303
            Division
                Dynamin-related proteinCMN262C1554462.00E-138
                Plastid division protein FtsZCMS004C, CMO089C1526721.10E-89
                MinE158874
                MinD157354
    Single membrane-bound organelles
        Endoplasmic reticulum
            ER lumen protein retaining receptorKOG3106CMR190C158379, 166543, 1720382.10E-57
            ER-to-Golgi transport protein/RAD50-interacting protein 1KOG2218169153
            ER vesicle integral membrane proteinKOG2729CME060C1612925.20E-14
            Membrane component of ER protein translocation complexKOG2927164494
            Membrane protein involved in ER to Golgi transportKOG2887157838, 169932
            Signal recognition particle receptor, α-subunitKOG0781CME016C1670878.60E-74
            Signal recognition particle receptor, β-subunitKOG0090CMM147C159090
            Signal recognition particle, subunit Srp54KOG0780CMC066C157035, 1659581.30E-49
            Signal recognition particle, subunit Srp54KOG0780CMO152C171457
            Signal recognition particle, subunit Srp68KOG2460CML086C161743
            Signal recognition particle, subunit Srp72KOG2376CMQ194C156546
            Signal recognition particle, subunit Srp19KOG3198CMR091C
            Vesicle coat complex AP-1, γ-subunitKOG1062CMF083C167317, 171947
            Vesicle coat complex AP-1/AP-2/AP-4, β-subunitKOG1061CMR021C155972, 159826, 163531, 170720
            Vesicle coat complex AP-2, α-subunitKOG1077168146
            Vesicle coat complex COPI, α-subunitKOG0292CMD156C157180
            Vesicle coat complex COPI, β-subunitKOG1058CMG048C1523461.00E-171
            Vesicle coat complex COPI, β-subunitKOG0276CMT617C168412
            Vesicle coat complex COPI, ε-subunitKOG3081CMD014C155710
            Vesicle coat complex COPI, γ-subunitKOG1078CMP053C1720549.00E-172
            Vesicle coat complex COPI, δ-subunitKOG2635CMO202C1616021.00E-74
            Vesicle coat complex COPI, ζ-subunitKOG3343CMN247C154191, 1550477.70E-10
            Vesicle coat complex COPII, GTPase subunit SAR1KOG0077CMT196C160753
            Vesicle coat complex COPII, subunit SEC13KOG1332CMJ112C1674158.80E-49
            Vesicle coat complex COPII, subunit SEC23KOG1986CMF170C159292, 1679910
            Vesicle coat complex COPII, subunit SEC24/subunit SFB2KOG1985CMQ471C168655, 1708726.00E-112
            Vesicle coat complex COPII, subunit SFB3KOG1984CMQ380C157030, 161297
&            Vesicle coat complex COPII, subunit SEC31KOG0307CMR203C157416
            Vesicle coat protein clathrin, heavy chainKOG0985CMF103C162480
            Vesicle coat protein clathrin, light chainKOG4031154013
            Vesicle trafficking protein Sec1KOG1300CMC019C165816, 171492
            Similar to COP-coated vesicle membrane protein p24KOG1692CMG098C158201
        Golgi apparatus
            Golgi proteins involved in ER retention (RER)KOG1688CMI263C1716237.00E-42
            Golgi SNAP receptor complex memberKOG3251CMS441C1716131.30E-09
            Golgi transport complex COD1 proteinKOG0412CMJ219C162230
            Golgi transport complex subunitKOG2069CMJ171C1567602.00E-11
            Predicted Golgi transport complex 1 proteinKOG2211159045
            Rab GTPase interacting factor, Golgi membrane proteinKOG3103CMQ462C1602183.40E-05
            Late Golgi protein sorting complex, subunit Vps53KOG2180CMR200C159541, 161878, 1621443.30E-13
            ER-to-Golgi transport protein/RAD50-interacting protein 1KOG2218169153
        Microbody (peroxisome)
            Peroxin-1 (Pex1)KOG0735CMI027C153527
            Pex2CMD105C
            Pex5KOG1125CMK124C1608891.30E-27
            Pex6KOG736CML252C
            Pex7KOG0277158976
            Pex10KOG0317CMT012C169232, 1692432.10E-08
            Pex11KOG4186159487
            Pex12KOG0826CMO084C1594835.80E-10
            Pex14KOG2629CMN043C163261
            Pex19KOG3133CMQ019C168404
            CatalaseKOG0047CMI050C1570741.00E-178
        Lysosome
            Vacuolar H+-ATPase V0 sector, subunit aKOG2189CMD095C[6]3.00E-167
            Vacuolar H+-ATPase V0 sector, subunit c″KOG0233CMS332C164229
            Vacuolar H+-ATPase V0 sector, subunit dKOG2957CMO274C1656894.40E-82
            Vacuolar H+-ATPase V0 sector, subunits c/c′KOG0232CMQ323C1595703.00E-40
            Vacuolar H+-ATPase V1 sector, subunit AKOG1352CMS342C1564350.00E+00
            Vacuolar H+-ATPase V1 sector, subunit BKOG1351CMP123C1676630
            Vacuolar H+-ATPase V1 sector, subunit CKOG2909CMC151C1695142.00E-35
            Vacuolar H+-ATPase V1 sector, subunit DKOG1647CMD007C1603281.90E-44
            Vacuolar H+-ATPase V1 sector, subunit EKOG1664CMQ010C1533412.20E-23
            Vacuolar H+-ATPase V1 sector, subunit FKOG3432CMQ237C1679838.20E-22
            Vacuolar H+-ATPase V1 sector, subunit GKOG1772CMH200C1561784.60E-05
            Vacuolar H+-ATPase V1 sector, subunit HKOG2759CMQ386C1649776.70E-26
            Vacuolar-type H+-translocating inorganic pyrophosphataseCMO102C1710948.00E-110
            Lysosomal and prostatic acid phosphatasesKOG3720CMM328C, CMT279C
        Autophagy
            Protein conjugation factor involved in autophagyKOG3439153015
            Ser/Thr-protein kinase involved in autophagyKOG0595152640, 160575, 171024
            Beclin-like protein (Apg6p)KOG2751163837
            Microtubule-associated anchor proteinKOG1654168349
            Cys protease required for autophagy, Apg4p/Aut2pKOG2674166084
            Protein involved in autophagocytosis during starvationKOG2981162469
        Cytosolic components
            ActinKOG0676CMM237C1548630
            Actin-related proteinsKOG0676CMS412C, CML073C156929, 161626, 169503, 169991
            Actin-related protein Arp4p/Act3pKOG0679CMR270C, CMJ223C169502
            Actin-related protein Arp6pKOG0680CMS185C
            λ-TubulinKOG1376CMT504C154911, 164620, 1657020
            β-TubulinKOG1375CMN263C169905, 170055, 158210, 1571940
            γ-TubulinKOG1374CMN304C158831, 1647243.00E-131
&            Dynein light chain type 1KOG3430CMT356C15928, 164296, 1647222.20E-30
            Dyneins, heavy chainKOG3595[24]
            Kinesin (KAR3 subfamily)KOG0239CMR497C152572, 154712, 166493, 1689836.00E-94
            Kinesin (KAR3 subfamily)KOG0239CMT097C1685583.70E-87
            Kinesin (SMY1 subfamily)KOG0240152501, 169875, 171909
            Kinesin light chainKOG1840[9]
            Kinesin-like proteinKOG0247169655
            Kinesin-like proteinKOG0246169327
            Kinesin-like proteinKOG0244154733, 158290, 161552, 163582, 167216
            Kinesin-like proteinKOG0243161485, 164385, 166682
            Kinesin-like proteinKOG0242CMQ429C[6]
            Kinesin-like proteinKOG4280CMO070C[13]
            Myosin class II heavy chainKOG0161[7]
            Myosin class V heavy chainKOG0160166295, 166465, 168960, 169141
        Cell wall
            AnkyrinKOG4177CME092C, CMQ294C, CMS172C163973 + [21]1.30E-21
            dTDP-Glc 4-6-dehydratase/UDP-GlcUA decarboxylaseKOG1429CME136C1636413.00E-116
            GDP-Man pyrophosphorylaseKOG1322CMF136C154457, 164593, 166665, 167020, 169713
            Glucosamine-6-P synthetasesKOG1268CMK166C1586405.20E-80
            Glucosamine-P N-acetyltransferaseKOG3396CMS020C, CMN031C1542034.30E-16
            Glucosidase II catalytic (alpha) subunitKOG1066CMM082C, CMM202C, CMF121C164756, 1647578.70E-59
            GlycosyltransferaseKOG1387CMI301C1537788.10E-16
            GlycosyltransferaseKOG0853CMT168C1561291.80E-28
            GPI transamidase complex, GPI16/PIG-T componentKOG2407156643
            GPI transamidase complex, GPI17/PIG-S componentKOG2459162068
            N-Acetylglucosaminyltransferase complex, subunit PIG-A/SPT14KOG1111CMR015C, CMR346C159722, 159723, 161264, 1683042.20E-77
            Phospholipid scramblaseKOG0621CMN259C1618382.50E-22
            UDP-Glc 4-epimerase/UDP-sulfoquinovose synthaseKOG1371CMA041C1604013.00E-105
            UDP-Glc 4-epimerase/UDP-sulfoquinovose synthaseKOG1371CMR012C1688721.20E-81
            UDP-Glc 4-epimerase/UDP-sulfoquinovose synthaseKOG1371CMR075C1526132.30E-80