The following appendix accompanies the article

Genetic diversity of picoeukaryotes in a semi-enclosed harbour in the subtropical western Pacific Ocean

Man Kit Cheung, Ka Hou Chu, Chi Pang Li, Hoi Shan Kwan, Chong Kim Wong*

Department of Biology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China

*Corresponding author. Email: [email protected]

Aquatic Microbial Ecology 53:295–305 (2008)

Table A1. List of all the operational taxonomic units (OTUs) recovered in the current study. For each OTU, its GenBank closest relative with accession number, the sequence percent similarity, BLAST score, Query/Subject ratio and frequency from each clone library are provided. The remaining columns indicate the OTU frequency from each clone library

OTUs OTU frequency Library Clone Closest relative GenBank % similarity BLAST Query/ MB01 MB04 MB07 MB10 TH01 TH04 TH07 TH10 Accession # score Subject

Alveolates group II MB01 3 Uncultured marine alveolate group II clone DH147-EKD16 AF290071 94.9 1210 751/791 25 1 7 11 Amoebophrya sp. AF239260 97.6 1279 730/748 1 6 16 Uncultured marine picoplankton AP-picoclone15 DQ386751 94.8 1232 754/795 5 2 4 15 19 Uncultured alveolate clone RA010613.44 AY295708 96.1 861 522/543 1 42 Amoebophrya sp. ex Scrippsiella sp. AF472555 91.9 1096 733/798 2 1 52 Uncultured marine eukaryote clone UEPACAFp5 AY129057 96.6 1319 770/797 8 3 TH01 1 Uncultured marine eukaryote clone UEPACCp3 AY129036 98.9 1317 745/753 4 4 1 8 8 Uncultured marine eukaryote clone UEPACBp4 AY129045 98.8 1330 738/747 3 35 Uncultured eukaryote clone ENI40076.00788 AY937888 94.1 678 430/457 2 2 37 Amoebophrya sp. ex Gymnodinium instriatum AF472554 94.2 1003 629/668 16 42 Uncultured marine picoplankton clone He000803_31 AJ965140 96.3 660 388/403 1 1 MB04 24 Uncultured marine eukaryote clone ENVP10203.00015 DQ917938 99.4 965 528/531 2 25 Amoebophrya sp. ex Scrippsiella sp. AF472555 97.8 1199 680/695 3 TH04 14 Amoebophrya sp. ex Karlodinium micrum AF472553 95 1194 727/765 5 18 Uncultured marine eukaryote clone NOR26.14r DQ119913 99.7 1280 697/699 2 26 Uncultured marine eukaryote clone NOR50.19 DQ119916 90.5 839 589/651 2 MB07 9 Uncultured marine eukaryote clone UEPAC41p3 AY129042 99.6 1400 765/768 1 17 4 21 15 Uncultured eukaryote clone SCM37C36 AY664989 93.2 1031 662/711 1 21 Eukaryote clone OLI11009 AJ402348 98.2 1323 765/779 4 29 Uncultured marine picoplankton AP-picoclone20 DQ386756 98.8 1345 747/756 2 42 Uncultured marine eukaryote clone UEPACEp3 AY129038 98.9 1434 796/805 3 1 Table A1 (continued)

OTUs OTU frequency Library Clone Closest relative GenBank % similarity BLAST Query/ MB01 MB04 MB07 MB10 TH01 TH04 TH07 TH10 Accession # score Subject

TH07 2 Uncultured marine eukaryote clone NW414.31 DQ119928 92.6 1051 689/744 2 5 Uncultured alveolate clone RA010613.20 DQ186535 93.3 1079 691/741 5 10 6 Uncultured eukaryote clone SCM37C21 AY664990 93.8 1101 695/741 2 9 Uncultured marine eukaryote clone ENVP36162.00243 DQ918787 94.9 459 279/294 3 12 Uncultured eukaryote clone SCM37C21 AY664990 90.8 987 689/759 5 5 18 Uncultured marine picoplankton clone He000327_39 AJ965089 99.4 647 355/357 1 26 Uncultured marine eukaryote clone BL001221.40 AY426886 90.6 983 681/752 2 3 27 Uncultured marine eukaryote clone UEPACAPp3 AY129041 99.6 1301 710/713 3 32 Uncultured alveolate clone RA010613.126 DQ186534 95.7 1182 709/741 1 42 Amoebophrya sp. ex Karlodinium micrum AF472553 97.4 1227 702/721 1 1 1 43 Amoebophrya sp. ex Karlodinium micrum AF472553 96.5 1123 656/680 1 MB10 27 Uncultured alveolate clone RA010412.70 DQ186533 98.2 1127 646/658 1 30 Amoebophrya sp. ex Ceratium tripos AY208892 99.3 1293 712/717 2 46 Amoebophrya sp. ex Ceratium tripos AY208892 100 1260 682/682 1 3 1 51 Uncultured marine picoplankton AP-picoclone8 DQ386744 92.4 1090 720/779 1 TH10 1 Eukaryote clone OLI11012 AJ402330 95.7 1240 749/783 4 4 Uncultured eukaryote clone BB01_83 AY885027 93.7 798 508/542 8 7 Uncultured marine alveolate group II clone DH147-EKD16 AF290071 95.7 1201 718/750 3 12 Amoebophrya sp. ‘Dinophysis’ AF239260 96.5 1219 714/740 2 19 Amoebophrya sp. AY775284 93 1149 742/798 2 22 Amoebophrya sp. ex Karlodinium micrum AF472553 92.2 1110 734/796 1 25 Uncultured alveolate clone RA000907.2 AY295491 95.6 682 409/428 1 27 Uncultured eukaryote clone Q2A03 EF173006 95.8 1194 715/746 2 46 Uncultured marine picoplankton AP-picoclone8 DQ386744 98.4 1179 660/671 1 49 Uncultured marine alveolate group II clone DH147-EKD6 AF290068 91.5 1070 720/787 1 Alveolates group I MB04 17 Uncultured marine eukaryote clone ENVP21819.00079 DQ918313 98.6 1105 616/625 2 MB07 2 Uncultured marine eukaryote clone BL001221.41 AY426887 98.9 1332 739/747 1 11 10 5 5 2 40 Uncultured eukaryote isolate CAR_E214 AY256282 98.1 1301 736/750 1 TH07 0 Uncultured eukaryote isolate A3_E031 AY046773 89.4 806 579/648 1 4 Uncultured marine alveolate isolate 65 DQ916410 88.1 881 667/757 23 TH10 8 Uncultured eukaryote clone SCM37C30 AY665056 97 1345 781/805 1 45 Uncultured eukaryote clone TAGIRI-10 AB191418 99.4 1297 711/715 1 1 57 Uncultured eukaryote clone SCM38C41 AY664995 99.1 1367 755/762 1 Alveolata; Ciliophora MB01 7 Strombidium sp. AY143564 99.3 1208 665/670 2 3 12 Uncultured marine eukaryote clone CD8.16 DQ647517 97.8 1347 763/780 2 1 1 3 1 3 13 Uncultured marine eukaryote clone CD8.16 DQ647517 99.6 1273 696/699 1 1 18 Strombidium sp. AY143564 98.9 1421 789/798 1 21 Uncultured marine eukaryote clone MD65.05 DQ119933 97.6 1347 771/790 5 1 1 26 Uncultured marine eukaryote clone NW414.24 DQ120009 99.1 1421 785/792 1 2 1 35 Uncultured eukaryote clone ENI40076.00328 AY937624 95.5 1068 640/670 1 36 Uncultured eukaryote clone ENI42482.00244 AY938119 99.8 948 515/516 1 1 37 Uncultured eukaryote clone ENI40076.00328 AY937624 99.1 1201 661/667 1 3 1 Table A1 (continued)

OTUs OTU frequency Library Clone Closest relative GenBank % similarity BLAST Query/ MB01 MB04 MB07 MB10 TH01 TH04 TH07 TH10 Accession # score Subject

Alveolata; Ciliophora TH01 13 Ciliate sp. NCMS0601 AM412525 94.8 1138 698/736 4 MB04 2 Uncultured eukaryote clone ENI40076.00749 AY937854 99.6 953 520/522 3 7 Uncultured eukaryote clone ENI40076.00328 AY937624 99.1 1201 661/667 1 TH04 2 Uncultured marine eukaryote clone NW414.24 DQ120009 97.1 1210 700/721 1 16 Uncultured marine eukaryote clone MD65.18 DQ119937 97.6 1256 718/736 1 21 Uncultured marine eukaryote clone UEPACAIp5 AY129053 98.9 1290 715/723 7 4 37 Uncultured marine eukaryote clone MD65.18 DQ119937 97.9 1321 748/764 1 39 Uncultured eukaryote clone ENI47296.00059 AY938245 97.2 1098 632/650 8 4 42 Uncultured marine eukaryote clone UEPACAIp5 AY129053 98.4 880 494/502 2 1 2 MB07 25 Uncultured eukaryote clone D3P05C08 EF100279 93.8 1062 675/720 2 30 Strombidium sp. AY143564 95.3 1166 707/742 1 38 Cryptocaryon irritans AF351579 93.6 1129 714/763 1 MB10 16 Strobilidium caudatum AY143573 94.9 1110 682/719 1 31 Tintinnopsis dadayi AY143562 95.5 1240 748/783 2 33 Strobilidium caudatum AY143573 94.4 1092 678/718 1 36 Strombidinopsis sp. AM412524 95.8 688 408/426 2 40 Parastrombidinopsis shimi AJ786648 93.8 989 623/664 1 TH10 18 Uncultured eukaryote clone SCM15C2 AY665093 94.5 1229 761/805 1 20 Uncultured eukaryote clone SCM28C124 AY665085 99.5 1423 780/784 2 24 Uncultured eukaryote clone ENI42482.00186 AY938072 98.6 913 508/515 1 33 Strobilidium caudatum AY143573 93 1075 692/743 7 2 2 34 Strombidium sp. AY143564 99.5 1356 743/747 1 6 1 1 4 1 3 37 Strombidium sp. AY143565 93.4 1146 736/788 1 53 Uncultured marine colpodean ciliate clone DH147-EKD23 AF290076 88.9 941 706/794 1 1 1 58 Eutintinnus pectinis AF399170 93.9 1105 694/739 2 1 Alveolata; Dinophyceae MB01 6 Uncultured eukaryote clone SCM37C24 AY664894 98.7 1395 777/787 8 4 27 Uncultured marine eukaryote clone BL001221.15 AY426867 99.1 1421 785/792 1 2 33 Uncultured eukaryote clone SCM15C23 AY664993 99 1413 783/791 2 1 40 Uncultured eukaryote clone SCM37C27 AY664962 99.4 1432 786/791 1 1 2 TH01 22 Uncultured marine eukaryote clone BL001221.42 AY426888 99.1 1238 682/688 1 MB04 15 Uncultured eukaryote clone SCM28C60 AY664961 95.8 1255 749/782 3 34 Pyrodinium bahamense var. compressum DQ500120 96.1 1199 709/738 1 39 Uncultured eukaryote clone SCM27C15 AY664924 98.5 1297 724/735 1 1 TH07 15 Uncultured marine eukaryote clone CD8.10 DQ647514 100 1295 701/701 2 1 MB10 3 Ceratium longipes DQ388462 99.6 1291 705/708 2 3 1 2 10 Ceratium longipes DQ388462 99.3 981 539/543 1 23 Noctiluca scintillans DQ388461 97.1 1158 667/687 1 29 Pentapharsodinium sp. AF274270 96.7 1240 722/747 3 52 Noctiluca scintillans DQ388461 99.6 1459 797/800 1 5 TH10 6 Uncultured eukaryote clone SCM37C27 AY664962 99.8 1016 552/553 1 10 Uncultured marine picoplankton AP-picoclone12 DQ386748 98.5 1301 729/740 1 Table A1 (continued)

OTUs OTU frequency Library Clone Closest relative GenBank % similarity BLAST Query/ MB01 MB04 MB07 MB10 TH01 TH04 TH07 TH10 Accession # score Subject

Chlorophyta; Prasinophyceae MB01 5 Micromonas pusilla AY425316 99.5 1430 783/787 4 22 Micromonas pusilla AB183589 99.7 1454 792/794 3 1 2 30 Uncultured prasinophyte clone NW414.32 DQ055165 99.7 1437 782/784 2 1 3 31 Micromonas pusilla AB183589 97.5 1351 775/795 1 38 Micromonas pusilla AB183589 98 1040 589/601 1 TH01 40 Ostreococcus sp. AY425310 99.6 913 498/500 1 1 MB04 46 Micromonas pusilla AY425316 99.7 1376 749/751 1 MB07 17 Pycnococcus sp. AB058359 98.4 1347 755/767 3 1 31 Coccoid prasinophyte MBIC10622 AB058375 95.8 1186 709/740 4 2 1 TH07 44 Uncultured prasinophyte clone NW414.29 DQ055172 99.4 848 465/468 1 TH10 5 Micromonas pusilla AY425316 98.6 1393 777/788 5 1 2 Stramenopiles MB01 25 Uncultured eukaryote clone BL010625.35 AY381219 99.7 1264 688/690 2 1 2 34 Eukaryote marine clone ME1-24 AF363207 93.4 1116 713/763 1 2 TH01 2 Uncultured marine eukaryote clone IND60.8 DQ234593 99.6 1447 790/793 1 5 Uncultured marine eukaryote clone CD8.06 DQ647511 95.3 1109 671/704 1 6 Uncultured marine eukaryote clone UEPACCp4 AY129066 100 1435 793/793 2 2 3 14 Labyrinthuloides minuta AF265339 98.1 821 462/471 2 19 Uncultured marine picoplankton clone He000803_6 AJ965030 95.1 636 387/407 1 20 Uncultured marine eukaryote clone BL001221.14 AY426866 99.6 983 536/538 7 1 24 Uncultured marine eukaryote clone UEPACLp5 AY129067 99.9 1424 773/774 1 31 Uncultured marine eukaryote clone FV18_3H10 DQ310211 99.4 1208 663/667 3 3 38 Uncultured marine eukaryote clone FV23_1D5 DQ310262 99.5 1456 795/799 5 2 43 Uncultured marine picoplancton clone He010218_6 AJ965071 99 1050 580/586 1 44 Uncultured eukaryote isolate CAR_D107 AY256317 94.3 1206 754/800 1 MB04 3 Uncultured marine eukaryote clone MD65.32 DQ062487 98.1 1343 757/772 14 18 Uncultured marine eukaryote clone NW617.17 DQ062467 99.1 1002 552/557 2 21 Uncultured eukaryote isolate C3_E035 AY046863 99 1391 767/775 2 23 Uncultured marine picoplancton clone He000803_4 AJ965031 98.9 957 530/536 4 36 Uncultured marine stramenopile clone DH148-5-EKD53 AF290083 98.9 1275 708/716 1 1 TH04 3 Uncultured marine eukaryote clone UEPACRp5 AY129069 99 1310 724/731 2 32 Uncultured eukaryote clone BL010320.17 AY381209 98.7 1345 749/759 1 36 Pseudobodo tremulans AF315604 98.7 989 550/557 1 MB07 19 Uncultured eukaryote clone BL000921.26 AY381196 99 1279 708/715 1 TH07 3 Leptocylindrus danicus AJ535175 99.7 1223 667/669 1 16 Uncultured marine picoplankton clone He001005_47 AJ965040 99.2 904 498/502 1 21 Uncultured eukaryote clone ME1-28 AY116221 98.4 1199 675/686 1 36 Uncultured eukaryote clone BL010320.6 AY381207 98.1 1258 709/723 1 MB10 48 Uncultured eukaryote clone BL010320.17 AY381209 93.3 1092 705/756 1 TH10 39 Uncultured marine eukaryote clone ENVP10203.00002 DQ917930 97.3 985 569/585 1 43 Uncultured marine eukaryote clone CD8.09 DQ121426 97.7 1277 726/743 1 47 Pseudo-nitzschia multiseries AY221947 98.1 1354 766/781 1 51 Eukaryote marine clone ME1-24 AF363207 89.4 926 681/762 1 Table A1 (continued) OTUs OTU frequency Library Clone Closest relative GenBank % similarity BLAST Query/ MB01 MB04 MB07 MB10 TH01 TH04 TH07 TH10 Accession # score Subject

Cercozoa TH01 15 Cryothecomonas aestivalis AF290539 98.7 1236 703/712 1 1 1 1 1 MB04 43 Uncultured marine eukaryote clone NOR26.21 DQ314817 98.5 1299 734/745 1 1 4 TH04 43 Uncultured cercozoan clone 10-4Fu21 AY360723 91.9 909 599/652 1 MB07 4 Uncultured marine eukaryote clone NOR46.27 DQ314814 98.8 1360 755/764 1 6 Uncultured eukaryote clone TAGIRI-3 AB191411 91.5 822 560/612 3 8 Uncultured plasmodiophorid clone RD010517.43 AY295738 90.2 689 489/542 4 1 22 Uncultured eukaryote clone NAMAKO-13 AB252753 99.4 1122 615/619 1 23 Uncultured eukaryote clone SCM27C7 AY665094 92.4 1003 669/724 1 45 Uncultured plasmodiophorid clone RD010517.43 AY295738 89.1 656 484/543 1 50 Uncultured cercozoan clone C1 AY620329 97.8 922 524/536 1 TH07 17 Uncultured cercozoan clone 10-4Fu21 AY360723 92.9 1003 642/691 2 MB10 13 Uncultured cercozoan clone 9-1.7 AY620309 90.6 457 317/350 1 21 Uncultured eukaryote clone NAMAKO-6 AB252746 98.5 961 536/544 1 TH10 54 Uncultured eukaryote clone SCM27C7 AY665094 96.8 1038 606/626 2 Haptophyceae TH01 17 Chrysochromulina scutellum AJ246274 99 1199 664/671 1 23 Unidentified prymesiophyte clone OLI16029 AF107080 99 715 395/399 1 MB07 26 Uncultured marine eukaryote clone BL010625.10 AY426921 97.4 1284 735/755 1 32 Uncultured marine eukaryote clone BL010625.10 AY426921 98.6 1371 765/776 2 1 1 Cryptophyta MB04 26 Teleaulax acuta AF508275 99.6 1243 679/682 1 1 TH04 10 Plagioselmis prolonga AF508272 99 1267 701/708 3 1 Cryptophyta (Nucleomorph) MB01 32 Uncultured marine picoplancton clone He001005_108 AJ965235 99.4 976 534/537 1 TH04 31 Teleaulax amphioxeia AJ421146 99.8 963 523/524 1 2 Katablepharidophyta TH01 39 Leucocryptos marina AB193602 99.8 983 533/534 1 1 Telonemia TH01 26 Uncultured eukaryote clone RA000907.3 AY295501 99.3 813 446/449 1 MB04 38 Uncultured eukaryote clone SCM38C20 AY665037 98.2 1227 692/705 1 Picobiliphytes MB04 45 Uncultured phototrophic eukaryote clone RA000907.33 DQ222876 99.2 1367 753/759 2 1 1 1 5 2 2 TH07 20 Uncultured phototrophic eukaryote clone He000803.72 DQ222873 99.3 726 399/402 5 TH10 11 Uncultured phototrophic eukaryote clone RA000907.18 DQ222879 99.4 1301 712/716 1 1 4 59 Uncultured phototrophic eukaryote clone RA001219.38 DQ222878 98.5 1426 797/809 1 Fungi MB01 14 Uncultured eukaryote clone TAGIRI-23 AB191431 95.9 998 588/613 2 1 MB10 47 Uncultured eukaryote clone NAMAKO-37 AB252777 99.4 1420 770/775 1 Choanoflagellida TH01 41 Uncultured eukaryotic picoplankton clone B360 EF196793 97.8 641 363/371 1 Radiolaria MB10 6 Amphibelone anomala AB178582 98.5 1173 655/665 1 TH10 26 Pseudocubus obeliscus AB246692 98.9 1419 788/797 1 48 Uncultured eukaryote clone ENI42482.00307 AY938166 97.2 361 207/213 1 Table A1 (continued)

OTUs OTU frequency Library Clone Closest relative GenBank % similarity BLAST Query/ MB01 MB04 MB07 MB10 TH01 TH04 TH07 TH10 Accession # score Subject

Chlorarachniophyte (Nucleomorph) MB07 10 Lotharella sp. AF076177 89.7 717 515/574 1 Mesomycetozoea MB04 9 Triparticalcar arcticum DQ536480 91.2 1016 695/762 1 Eimeriidae environmental sample clone Elev_18S_1414a EF024885 90 2.230 1593/1771 TH10 32 Triparticalcar arcticum DQ536480 91.1 1051 724/795 1 Ellobiopsids MB07 44 Thalassomyces sp. JDS-2003 EF539155 90 610 432/480 1 1 MB10 44 Ceratium tenuea AF022192 89.5 1118 815/911 1 Unknown group MB07 52 Uncultured marine eukaryote clone PD6.12 DQ647530 97.8 1266 720/736 1 1 Uncultured Chytridiomycete clone WS 10-E14a AJ867630 86.7 1803 1470/1696 Metazoa TH01 34 Garveia sp. AY920766 99.3 1266 696/701 1 1 MB04 12 Junceella aquamata AY962535 94.7 1195 735/776 8 31 Uncultured marine eukaryote clone MD65.36 DQ344788 98.7 1301 754/764 1 2 12 5 42 Bolinopsis infundibulum AF293687 99.9 1322 717/718 3 MB10 1 Uncultured eukaryote clone SCM38C38 AY665127 90.6 318 221/244 25 8 Uncultured copepod isolate MENSA3 AY437861 94.8 1168 716/755 7 15 Uncultured eukaryote clone ENI40076.00862 AY937955 92.3 274 179/194 3 25 Uncultured marine eukaryote clone NOR50.21 DQ344797 97.4 1149 676/694 11 26 Uncultured eukaryote clone ENI40076.00443 AY937695 96.5 514 300/311 3 32 Uncultured copepod clone 73 AY491394 95.1 1000 607/638 1 39 Uncultured eukaryote clone SCM38C38 AY665127 95.5 1144 687/719 37 11 42 Uncultured eukaryote clone SCM27C52 AY665125 96.1 1255 745/775 1 6 1 45 Uncultured marine eukaryote clone ENVP36162.00349 DQ918849 94.1 562 352/374 1 TH10 2 Uncultured eukaryote clone ENI42482.00368 AY938215 99.2 1092 601/606 2 35 Uncultured marine eukaryote clone MD65.36 DQ344788 95.5 712 428/448 1 aResults from full length sequences