EXCLUDED GENOMES (COMPLETE AND WGS)

A. not of bacterial origin (described as “Root” by CheckM, not placed in bacterial tree by pplacer) or bacterial but assigned to in the sequence flatfile

Candidatus Sericytochromatia bacterium JACYMC000000000 metagenome Hassallia byssoidea VB512170 JTCM00000000.1 Mastigocoleus testarum BC008 AXAQ00000000 “Mucilaginibacter” sp. G2-14 CP054139 “Phyllobacterium” sp BT25 JABUMX000000000 Prochlorococcus marinus HNLC1 GL947594 metagenome Prochlorococcus marinus HNLC2 GL947595 metagenome Synechococcus moorigangaii CMS01 VLTG00000000 Cyanobacteria bacterium 13-1-20CM MNIV00000000 metagenome Cyanobacteria bacterium CONCOCT.2.5kb 103 JAIEMQ00000000 metagenome Cyanobacteria_bacterium_CONCOCT.2.5kb_148_JAIEMW00000000_metagenome Cyanobacteria bacterium DASTOOL.1kb 042 JAIENO00000000 metagenome Cyanobacteria bacterium METABAT.1kb 096 JAIERL00000000 metagenome

B. from the complete-genomes dataset

Incomplete (contain fewer than 79 of 79 core marker genes, a gene being considered as present only if the query cover is greater than 40%): Marker genes Candidatus Atelocyanobacterium thalassa ALOHA CP001842 76 Desikacharya piscinale CENA21 CP012036 78 Gloeomargarita lithophora D10 CP017675 78 Leptolyngbya sp. 7M CP070897 72 Leptolyngbya sp. 15MV CP071923 66 “Prochloraceae cyanobacterium” LD05 CP073341 metagenome 78

Chimeric (segments from two different cyanobacteria), or poor sequences seriously disturbing tree topology:

Anabaenopsis elenkinii CCIBt3563 CP063311 Richelia sinica FACHB-800 CP021056

To prune the tree, removed genomes from clades that are over-represented:

Cyanobium sp. NS01 (CP047940), M30B3 (CP073761), Synechococcus sp. A15-127 (CP047948), A18-25c (CP047957), NOUM97013 (CP047941), A15-24 (CP047960) A15-44 (CP047938), A15-60 (CP047933), A15-62 (CP047950), A18-40 (CP047956), M16-1 (CP047954), BMK-MC-1 (CP047939), MEDNS5 (CP047952), Minos11 (CP047953), MVIR-18-1 (CP047942), PROS-7-1 (CP047945), PROS-9-1 (CP047961), PROS-U-1 (CP047951), ROS8604 (CP047946), RS9902 (CP047949), RS9907 (CP047944) RS9909 (CP047943), SYN20 (CP047959), TAK9802 (CP047937), BIOS-U3-1 (CP047936)

C. from the all-genomes dataset (the above were retained if more than 77 markers, except for non-cyanobacterial genomes):

Not cyanobacterial (described by CheckM as "bacterial" and not placed in the cyanobacterial clade by pplacer) or presumed chimers (described as "bacterial" by CheckM, but placed into the bacterial tree in unlikely positions by pplacer) having segments of both cyanobacterial and bacterial origin:

Aphanocapsa montana BDHKU210001 JTJD00000000.1 Fischerella ambigua UTEX 1903 R. Viswanathan Nodosilinea sp. LEGE 07088 JADEWX000000000 Nodularia sp. LEGE 06071 JADEWH000000000 Pleurocapsa sp. SU 196 0 JAAUUV000000000 metagenome Prochlorococcus sp. MED-G72 QOPO00000000 metagenome Prochlorococcus sp. MED-G73 QOPN00000000 metagenome Prochlorococcus sp. scB245a 518D8 JFNB00000000 Scytonema millei VB511283 JTJC00000000.1 Synechococcus sp. SB0666 bin 14 VXTW00000000 metagenome Synechococcus sp. SB0675 bin 6 VYDJ00000000 metagenome Synechococcus sp. SB0668 bin 13 VXWH00000000 metagenome Synechococcus sp. SB0668 bin 15 VXWJ00000000 metagenome Synechococcus sp. SB0662 bin 14 VXNS00000000 metagenome Synechococcus Bin 28 Ga0113640 Synechococcus Bin 27 Ga0113638 Cyanobacterium TDX16 NDGV00000000 “ cyanobacterium” MTP1 LNAA00000000 Incomplete (contain fewer than 79 of 79 core marker genes, a gene being considered as present only if the query cover is greater than 40%): Marker genes Acaryochloris sp. CRU 2 0 JAAUOM000000000 metagenome 74 Acaryochloris sp. RU 4 1 JAAURR000000000 metagenome 73 Acaryochloris sp. SU 5 25 JAAUVC000000000 metagenome 37 Aetokthonos hydrillicola CCALA 1050 JAAKGC000000000 75 Aetokthonos hydrillicola Thurmond2011 JAALHA00000000 60 Alkalinema sp. FL-bin-369 JACMPV000000000 metagenome 42 Alkalinema sp. RL 2 19 JAAUPX000000000 metagenome 29 Anabaena sp. 54 AM 0902 OMJF00000000 metagenome 59 Aphanizomenon flos-aquae 2012/KM1/D3 JSDP00000000 76 Aphanocapsa feldmannii 277cI SRMN00000000 metagenome 70 Aphanothece sp. CMT-3BRIN-NPC111 JAHHGU000000000 metagenome 76 maxima CS-328 ABYK00000000 73 Arthrospira sp. O9.13F PKGD00000000 72 Baaleninema simplex PCC 7105 ANFQ00000000 75 Brasilonema bromeliae SPC951 QMEB00000000 75 Brasilonema sp. CT11 JABXYX000000000 76 Calothrix sp. CSU 2 0 JAAUPE000000000 metagenome 76 Calothrix sp. SM1 5 4 JAAUTQ000000000 metagenome 40 Calothrix sp. SM1 7 51 JAAUTW000000000 metagenome 33 Candidatus Aurora vandensis MP9P1 JAAXLU000000000 metagenome 76 Candidatus Atelocyanobacterium thalassa MetaBAT-v2.12.1 CAJWSD000000000 metagenome 70 Candidatus Atelocyanobacterium thalassa UBA4158 DFVO00000000 metagenome 76 Candidatus Atelocyanobacterium thalassa ALOHA=UCYN-A1 CP001842 metagenome 76 Candidatus Synechococcus spongiarum isolate 1 FITM00000000 63 Candidatus Synechococcus spongiarum LMB bulk10D MWLG00000000 39 Candidatus Synechococcus spongiarum LMB bulk10E MWLF00000000 12 Candidatus Synechococcus spongiarum LMB bulk15M MWLD00000000 metagenome 71 Candidatus Synechococcus spongiarum LMB bulk15N MWLE00000000 metagenome 49 Candidatus Synechococcus spongiarum SH4 JENA00000000 metagenome 73 Chamaesiphon sp. CSU 1 12 JAAUOX000000000 metagenome 7 Chamaesiphon sp. isolate WC-16 JAGVCD000000000_metagenome 53 Chlorogloea purpurea SAG 13.99 JADQBB000000000 68 Coleofasciculus sp. Co-bin14 JACVRQ000000000 metagenome 56 Coleofasciculus sp. C3-bin4 JACVRI000000000 metagenome 47 Crocosphaera sp. DT 26 JABSPE000000000 metagenome 72 Chroococcales cyanobacterium metabat2.561 RPQW00000000 metagenome 34 Chroococcidiopsidaceae cyanobacterium CP BM ER R8 30 JAFASY000000000 metagenome 74 Chroococcidiopsidaceae cyanobacterium CP BM RX 35 JAFAVL000000000 metagenome 66 Chroococcus sp. CMT-3BRIN-NPC107 JAHHGY000000000 metagenome 75 Cyanobacteria bacterium 0813 bin36 JAHWKX000000000 metagenome 63 Cyanobacteria bacterium 13-1-20CM MNIV00000000 metagenome 9 Cyanobacteria bacterium AG-640-J16 JGI 32 Cyanobacteria bacterium bin 100 PROKKA JAFNEQ000000000 metagenome 43 Cyanobacteria bacterium bin.275 JABMNF000000000 metagenome 68 Cyanobacteria bacterium bin.51 JABMPN000000000 metagenome 84 Cyanobacteria bacterium Co-bin13 JACVRP000000000 metagenome 39 Cyanobacteria bacterium Co-bin8 JACVSF000000000 metagenome 49 Cyanobacteria bacterium CSSed11 75 PWXB00000000 metagenome 69 Cyanobacteria bacterium CYA N2 1 RHKP00000000 metagenome 69 Cyanobacteria bacterium DS2.008 PNLS00000000 metagenome 16 Cyanobacteria bacterium DS2.3.42 PNLN00000000 metagenome 54 Cyanobacteria bacterium DS3.002 PNLJ00000000 metagenome 22 Cyanobacteria bacterium isolate CG 2015-02 32 10 JAACPM00000000 74 Cyanobacteria bacterium isolate GSL.Bin21 JAAAOK00000000 metagenome 35 Cyanobacteria bacterium J003 RFFR00000000 75 Cyanobacteria bacterium J069 RFIF00000000 metagenome 70 Cyanobacteria bacterium J083 RFIT00000000 metagenome 74 Cyanobacteria bacterium J149 RFLH00000000 metagenome 60 Cyanobacteria bacterium MH1 Bin12 JAALKG000000000 metagenome 59 Cyanobacteria bacterium NC groundwater 1444 JACQUT000000000 metagenome 56 Cyanobacteria bacterium PMG 004 SEBC00000000 metagenome 14 Cyanobacteria bacterium PMG 004 SEBC00000000 metagenome 14 Cyanobacteria bacterium PMG 012 SEBD00000000 metagenome 15 Cyanobacteria bacterium PR.023 PNKA00000000 metagenome 60 Cyanobacteria bacterium PR.3.49 PNKB00000000 metagenome 49 Cyanobacteria bacterium REEB417 JAGWVJ000000000 49 Cyanobacteria bacterium REEB446 JAGWWP000000000 70 Cyanobacteria bacterium REEB498 JAGWYU000000000 46 Cyanobacteria bacterium REEB65 JAGWZZ000000000 55 Cyanobacteria bacterium REEB67 JAGXAB000000000 75 Cyanobacteria bacterium SCGC 014-E08 JGI 17 Cyanobacteria bacterium SCGC AG-490-B05 JGI metagenome 38 Cyanobacteria bacterium SCGC AG-650-H12 JGI metagenome 41 Cyanobacteria bacterium SCGC AG-650-K04 JGI metagenome 38 Cyanobacteria bacterium SIG26 SUTS00000000 metagenome 68 Cyanobacteria bacterium SIG27 SUTT00000000 metagenome 66 Cyanobacteria bacterium SIG28 SUTU00000000 metagenome 70 Cyanobacteria bacterium SIG29 SUTV00000000 metagenome 65 Cyanobacteria bacterium SIG30 SUTW00000000 metagenome 70 Cyanobacteria bacterium SIG31 SUTX00000000 metagenome 67 Cyanobacteria bacterium SIG32 SUTY00000000 metagenome 53 Cyanobacteria bacterium SW 4 48 29 PXQI00000000 metagenome 76 Cyanobacteria bacterium SW 9 47 5 PXQF00000000 metagenome 11 Cyanobacteria bacterium T3Sed10 304 PXCV00000000 metagenome 72 Cyanobacteria bacterium T3Sed10 36R1 PXEF00000000 metagenome 62 Cyanobacteria bacterium TMED177 NHIA00000000 metagenome 27 Cyanobacteria bacterium TMED188 NHIL00000000 metagenome 33 Cyanobacteria bacterium TMED229 NHKA00000000 metagenome 35 Cyanobacteria bacterium UBA10660 DMXX00000000 metagenome 64 Cyanobacteria bacterium UBA10660 DMXX00000000 metagenome 64 Cyanobacteria bacterium UBA11049 DPEI00000000 metagenom 73 Cyanobacteria bacterium UBA11148 DORG00000000 metagenome 60 Cyanobacteria bacterium UBA11149 DORF00000000 metagenome 74 Cyanobacteria bacterium UBA11153 DOIX00000000 metagenome 74 Cyanobacteria bacterium UBA11159 DOJB00000000 metagenome 74 Cyanobacteria bacterium UBA11162 DNZA00000000 metagenome 58 Cyanobacteria bacterium UBA11166 DNYY00000000 metagenome 69 Cyanobacteria bacterium UBA11367 DNOY00000000 metagenome 68 Cyanobacteria bacterium UBA11368 DNOW00000000 metagenome 71 Cyanobacteria bacterium UBA11369 DNOV00000000 metagenome 71 Cyanobacteria bacterium UBA11370 DNGI00000000 metagenome 70 Cyanobacteria bacterium UBA11371 DNGJ00000000 metagenome 76 Cyanobacteria bacterium UBA11440 DOQK00000000 metagenome 69 Cyanobacteria bacterium UBA11440 DOQK00000000 metagenome 69 Cyanobacteria bacterium UBA11691 DOHO00000000 metagenome 72 Cyanobacteria bacterium UBA1186 DBYM00000000 metagenome 68 Cyanobacteria bacterium UBA11991 DOWB00000000 metagenome 58 Cyanobacteria bacterium UBA11991 DOWB00000000 metagenome 58 Cyanobacteria bacterium UBA1221 DBXD00000000 metagenome 68 Cyanobacteria bacterium UBA12227 DMEQ00000000 metagenome 58 Cyanobacteria bacterium UBA2320 DDVE00000000 metagenome 75 Cyanobacteria bacterium UBA2813 DEGZ00000000 metagenome 68 Cyanobacteria bacterium UBA2819 DEGT00000000 metagenome 69 Cyanobacteria bacterium UBA2855 DEFJ00000000 metagenome 64 Cyanobacteria bacterium UBA2877 DEEN00000000 metagenome 69 Cyanobacteria bacterium UBA2883 DEEH00000000 metagenome 68 Cyanobacteria bacterium UBA2892 DEDY00000000 metagenome 68 Cyanobacteria bacterium UBA3301 DESZ00000000 metagenome 69 Cyanobacteria bacterium UBA3803 DFEL00000000 metagenome 49 Cyanobacteria bacterium UBA4093 DFYB00000000 metagenome 70 Cyanobacteria bacterium UBA4641 DHMN00000000 metagenome 47 Cyanobacteria bacterium UBA6393 DJQF00000000 metagenome 62 Cyanobacteria bacterium UBA6446 DJOE00000000 metagenome 70 Cyanobacteria bacterium UBA791 DBIX00000000 metagenome 70 Cyanobacteria bacterium UBA8156 DMPD00000000 metagenome 71 Cyanobacteria bacterium UBA8530 DOBT00000000 metagenome 66 Cyanobacteria bacterium UBA8543 DMJW00000000 76 Cyanobacteria bacterium UBA8553 DLUV00000000 metagenome 74 Cyanobacteria bacterium UBA8803 DNXU00000000 metagenome 74 Cyanobacteria bacterium UBA9226 DOVO00000000 metagenome 73 Cyanobacteria bacterium UBA9273 DNME00000000 metagenome 68 Cyanobacteria bacterium UBA947 DBCX00000000 metagenome 70 Cyanobacteria bacterium UBA9579 DNSU00000000 metagenome 61 Cyanobacteria bacterium UBA9971 DNRP00000000 metagenome 67 Cyanobacteria/Melainabacteria group GL2-53 DAZW00000000 metagenome 66 Cyanobacteria/Melainabacteria group S15B-MN24 DAZV00000000 metagenome 70 Unidentified cyanobacterium 13 1 40CM 2 61 4 MNHI00000000 metagenome 18 Cyanobacterium BACL30 MAG-120619 LICO00000000 69 Cyanobacterium BACL30 MAG-120619-bin27 LICO00000000 65 Cyanobacterium Cyano1 PKDN00000000 metagenome 62 Cyanobacterium Cyano2 PKDM00000000 metagenome 71 Cyanobacterium G8-9 PYVJ00000000 27 Cyanobacterium sp. Zagget 111 MP Ga0015049 70 Cyanobiont of Ornithocercus magnificus OmCyn01 BIMP00000000 76 Cyanobium sp. 16 1 VMCY00000000 metagenome 71 Cyanobium sp. CSSed162cmA 499R1 SKRX00000000 metagenome 70 Cyanobium sp. M30B57 JAGYKC000000000 metagenome 70 Cyanobium sp. M55B138 JAGYNF000000000 metagenome 64 Cyanobium sp. PLM2.Bin73 REEV00000000 metagenome 76 Cyanobium sp. RS427 42782 PBVK00000000 33 Cyanobium sp. SAT1300 23347 PAXG00000000 metagenome 28 Cyanothece sp. UBA12306 DLXW00000000 metagenome 69 Dolichospermum circinale Clear-D4 JACVZX000000000 metagenome 75 Dolichospermum sp. SB001 JAEMTT000000000 metagenome 74 Filamentous cyanobacterium CCP1 PVWE00000000 58 Filamentous cyanobacterium CCP5 PYEQ00000000 73 Filamentous cyanobacterium Phorm 46 PVWH00000000 67 Fischerella sp. SpSt-362 DSPK00000000 metagenome 72 Fischerella thermalis WC217 NHAJ00000000 71 Fischerella thermalis CCMEE 5319 NMQD00000000 74 Geminocystis sp. M7585 C2015 104 DVEF00000000 76 Gloeobacter violaceus SpSt-379 DSQC00000000 metagenome 62 Gloeobacterales cyanobacterium ES-bin-141 JACMIX000000000 metagenome 75 Gloeobacteraceae cyanobacterium ES-bin-144 JACMIY000000000 metagenome 60 Gloeobacteraceae cyanobacterium ES-bin-316 JACMLO000000000 metagenome 50 Gloeocapsa sp. UFS-A4-WI-NPMV-4B04 JAHHHE000000000 metagenome 74 Gomphosphaeria aponina SAG 52.96=DSM 107014 JADQBC000000000 59 Halothece sp. BinSanityLC-kmean-bin 24 JAHEOB000000000 metagenome 75 Halothece sp. KZN 001 MDVL00000000 ALSO AS Euhalothece 76 Halothece sp. SG1 65 4 JGI 62 Hassallia sp. WJT32-NPBG1 JAHHHG000000000 metagenome 73 Hydrococcus sp. CSU 1 8 JAAUPD000000000 metagenome 38 Hydrococcus sp. RM1 1 31 JAAUQM000000000 metagenome 15 Hydrococcus sp. SU 1 0 JAAUUS000000000 metagenome 26 Hydrocoleum sp. CS-953 LGSU00000000 76 Jacksonvillea sp. ISTCYN1 VLNZ00000000 67 Leptolyngbya valderiana BDU 20041 LSYZ00000000 71 Leptolyngbya sp. 2LT21S03 JGI 75 Leptolyngbya sp. 7M CP070897 72 Leptolyngbya sp. 15MV CP071923 66 Leptolyngbya sp. CYN1 QUBX00000000 metagenome 58 Leptolyngbya sp. DLM2.Bin27 RECJ00000000 metagenome 73 Leptolyngbya sp. isolate ES-bin-223 JACMKL000000000 metagenome 66 Leptolyngbya sp. RL 3 1 JAAUQE000000000 metagenome 67 Leptolyngbya sp. SIO1E4 JAAHFU00000000 metagenome 75 Leptolyngbyaceae cyanobacterium CSSed162cmA 214 SKLP00000000 metagenome 51 Leptolyngbyaceae cyanobacterium CSSed162cmB 428R1 SLAZ00000000 metagenome 48 Leptolyngbyaceae cyanobacterium CSSed165cm 216 SLIY00000000 metagenome 62 Leptolyngbyaceae cyanobacterium MAG.088 JAHQVZ000000000 metagenome 76 Leptolyngbyaceae cyanobacterium M65 K2018 010 DVEE00000000 metagenome 75 Leptothoe spongobia TAU-MAC 1115 JADOES000000000 66 Leptothoe kymatousa TAU-MAC 1615 JADOER000000000 58 Mastigocladus laminosus UU774 MNPM00000000 (version 1) 72 Mastigocladus laminosus UU774 JXIJ00000000 71 Mastigocladus laminosus WC112 NGJL00000000 60 cyanobacterium S07.Bin061 JAABRK000000000 metagenome 42 Microcoleaceae bacterium UBA10368 DNYC00000000 metagenome 59 Microcoleaceae bacterium UBA11344 DMYK00000000 metagenome 65 Microcoleaceae bacterium UBA9251 DPLL00000000 metagenome 70 Microcoleus sp. C1-bin4 JACVRF000000000 metagenome 59 Microcoleus sp. Co-bin12 JACVRO000000000 metagenome 44 Microcoleus sp. CSU 2 2 JAAUPI000000000 metagenome 75 Microcoleus sp. SM1 3 4 JAAUTI000000000 metagenome 71 Microcoleus sp. SU 5 3 JAAUVD000000000 metagenome 73 Microcoleus sp. SU 5 6 JAAUVE000000000 metagenome 55 Microcoleus sp. T1-bin1 JACVSI000000000 metagenome 62 Microcoleus sp. T3-bin5 JACVSO000000000 metagenome 57 Microcystis flos-aquae DF17 QQWB00000000 metagenome 74 Microcystis sp. LSC13-02 MTBT00000000 73 Moorea sp. SIO4A5 JAAHHZ000000000 metagenome 76 Nodosilinea sp. CSSed162cmB 84 SLGH00000000 metagenome 30 Nodularia sp. CSSed162cmB 296 SKYQ00000000 metagenome 33 Nostocales cyanobacterium PH2015 08D 39 10 RDYJ00000000 metagenome 71 Nostocales cyanobacterium PH2015 08D 37 15 RDYK00000000 metagenome 64 Nostocales cyanobacterium W4 JAAXUI00000000 metagenome 76 Nostoc cf. edaphicum LEGE 07299 JADEXF000000000 60 Nostoc sp. 3336mG QHKA00000000 71 Nostoc sp. C3-bin3 JACVRH000000000 metagenome 59 Nostoc sp. 'Peltigera malacea cyanobiont' DB3992 NSHF00000000 76 Nostoc linckia NIES-25 AP018222 66 Nostoc carneum NIES-2107 AP018180 75 Nostoc commune herbarium specimen S1-bin1 70 Nostoc flagelliforme herbarium specimen S2-bin1 72 Nostoc sp. RI 552 WGNO00000000 metagenome 76 Nostocaceae cyanobacterium CSSed10 463m PWQB00000000 metagenome 59 Nostocaceae cyanobacterium isolate MGR bin409 JACDGJ000000000 metagenome 51 Okeania sp. KiyG1 BLZO00000000 74 Oscillatoria sp. S11.Bin022 JAABSJ000000000 metagenome 75 Oscillatoriales cyanobacterium LEGE 11467 JADEXN000000000 44 Oscillatoriales cyanobacterium PH2015 14S 45 132 RDXC00000000 metagenome 76 Oscillatoriales cyanobacterium PH2015 10S 46 199 RDXU00000000 metagenome 70 Oscillatoriales cyanobacterium PH2015 07D 46 1245 RDYR00000000 metagenome 76 Oscillatoriales cyanobacterium PH2015 07D 45 11 RDYS00000000 metagenome 64 Oscillatoriales cyanobacterium PH2015 06S 54 30 RDYZ00000000 metagenome 73 Oscillatoriales cyanobacterium PH2015 06S 46 2585 RDZA00000000 metagenome 74 Oscillatoriales cyanobacterium PH2015 06S 45 83 RDZB00000000 metagenome 66 Oscillatoriales cyanobacterium PH2015 02D 45 1038 REAK00000000 metagenome 64 Oscillatoriales cyanobacterium PH2015 01D 46 31 REAX00000000 metagenome 67 Oscillatoriales cyanobacterium SpSt-402 DSRD0000000 metagenome 39 Oscillatoriales cyanobacterium USR001 MBRE00000000 31 Phormidesmis sp. FL-bin-119 JACMMV000000000 metagenome 39 Cf. Phormidesmis sp. LEGE 11477 JADEXO000000000 38 Phormidesmis priestleyi ULC027 QGMP00000000 75 Phormidium pseudopriestleyi FRX01 JAFLQW000000000 71 Phormidium tanganyikae FI6-MK23 JAHHHU000000000 metagenome 76 Phormidium willei BDU 130791 LSZA00000000 73 Phormidium sp. Bin_1 JAIFKK000000000 metagenome 55 Phormidium sp. CSSed162cmB 426 SLAY00000000 metagenome 63 Phormidium sp. CSSed165cm 523 SLQG00000000 metagenome 69 Phormidium sp. GEM2.Bin31 REDN00000000 metagenome 73 Phormidium sp. S10.Bin050 JAABSD000000000 metagenome 75 Pleurocapsa minor GSE-CHR-MK-17-07R JAHHHY000000000 metagenome 71 Plectolyngbya sp. WJT66-NPBG17 JAHHHX000000000 metagenome 76 agardhii Bin4 JACDQL000000000 metagenome 58 CCAP 1459/11A BJCD00000000 12 Planktothrix rubescens PCC 7821 LR812491 64 Planktothrix sp. bin-235-243 JAIFLY000000000 metagenome 70 Planktothrix sp. FACHB-1355 JACJUP000000000 63 Planktothrix sp. UBA8402 DMPJ00000000 metagenome 49 Planktothrix sp. UBA8407 DMPE00000000 metagenome 53 Planktothrix sp. UBA10369 DNYD00000000 metagenome 57 Prochlorococcus marinus F1-20-MAGs057 SXXM00000000 metagenome 69 Prochlorococcus marinus F1-20-MAGs142 SYAQ00000000 metagenome 43 Prochlorococcus marinus SCGC AAA795-F05 CVSV00000000 67 Prochlorococcus marinus SCGC AAA795-I06 CVSW00000000 71 Prochlorococcus marinus SCGC AAA795-I15 CVSY00000000 71 Prochlorococcus marinus SCGC AAA795-J16 CVSX00000000 71 Prochlorococcus marinus SCGC AAA795-M23 CVSZ00000000 70 Prochlorococcus sp. HOT 208 60 MVOP00000000 44 Prochlorococcus sp. HOT208 60m 805A16 MWPA00000000 33 Prochlorococcus sp. HOT208 60m 808A10 MWOZ00000000 46 Prochlorococcus sp. HOT208 60m 808G21 MWOY00000000 47 Prochlorococcus sp. HOT208 60m 808M21 MWOX00000000 73 Prochlorococcus sp. HOT208 60m 810B23 MWOW00000000 69 Prochlorococcus sp. HOT208 60m 810P02 MWOV00000000 72 Prochlorococcus sp. HOT208 60m 810P02 MWOV00000000 74 Prochlorococcus sp. HOT208 60m 813B04 MWOU00000000 41 Prochlorococcus sp. HOT208 60m 813E23 MWOT00000000 16 Prochlorococcus sp. HOT208 60m 813G15 MWOS00000000 49 Prochlorococcus sp. HOT208 60m 813I02 MWOR00000000 71 Prochlorococcus sp. HOT208 60m 813L03 MWOQ00000000 35 Prochlorococcus sp. HOT208 60m 813O04 MWOP00000000 55 Prochlorococcus sp. HOT208 60m 813O14 MWOO00000000 73 Prochlorococcus sp. HOT212 60m 823D04 MWPG00000000 16 Prochlorococcus sp. HOT212 60m 824C06 MWPF00000000 44 Prochlorococcus sp. HOT212 60m 824E10 MWPE00000000 42 Prochlorococcus sp. HOT212 60m 824O11 MWPD00000000 47 Prochlorococcus sp. HOT212 60m 826P21 MWPC00000000 66 Prochlorococcus sp. REDSEA-S17 B1 LUPS00000000 metagenome 56 Prochlorococcus sp. REDSEA-S22 B1 LUPT00000000 metagenome 47 Prochlorococcus sp. REDSEA-S23 B1 LUPU00000000 metagenome 56 Prochlorococcus sp. REDSEA-S28 B1 LUPV00000000 metagenome 46 Prochlorococcus sp. SP3034 67481 PBHJ00000000 metagenome 32 Prochlorococcus sp. TMED223 NHJU00000000 metagenome 55 Prochlorococcus sp. UBA1269 DBVH00000000 metagenome 46 Prochlorococcus sp. UBA1273 DBVD00000000 metagenome 45 Prochlorococcus sp. UBA1528 DCQC00000000 metagenome 74 Prochlorococcus sp. UBA3467 DFRI00000000 metagenome 45 Prochlorococcus sp. UBA3999 DGBR00000000 metagenome 71 Prochlorococcus sp. UBA7854 DLSU00000000 metagenome 43 Prochlorococcus sp. W10 ALPH00000000 22 Prochlorococcus sp. W11 ALPI00000000 39 Prochlorococcus sp. W12 ALPJ00000000 12 Prochlorococcus sp. W2 ALPB00000000 64 Prochlorococcus sp. W3 ALPC00000000 29 Prochlorococcus sp. W4 ALPD00000000 28 Prochlorococcus sp. W5 ALPL00000000 4 Prochlorococcus sp. W6 ALPK00000000 28 Prochlorococcus sp. W7 ALPE00000000 50 Prochlorococcus sp. W8 ALPF00000000 63 Prochlorococcus sp. W9 ALPG00000000 12 Prochloron didemni P1 JGI 75 Prochloron sp. SP5CPC1 JACONB000000000 metagenome 65 Prochlorothrix hollandica CALU 1027=PCC 9006 AJTX00000000 75 Pseudanabaena sp. bin-143 JAIFKZ000000000 metagenome 75 Pseudanabaena sp. CRU 2 10 JAAUOO000000000 metagenome 46 Pseudanabaena sp. RU 4 16 JAAURW000000000000 metagenome 39 Pseudanabaena sp. UBA10436 DNLA00000000 76 Pseudanabaena sp. ULC068 QBMK00000000 75 Raphidiopsis raciborskii CS-506 A VDFG00000000 76 Raphidiopsis raciborskii LB2897 VOIM00000000 58 Richelia sp. CSU 2 1 JAAUPF000000000 metagenome 76 Richelia intracellularis HM01 CAIS00000000 63 Richelia intracellularis RC01 CBZS00000000 76 Richelia sp. SL 2 1 JAAUSO000000000 metagenome 76 Richelia sp. SM2 1 7 JAAUUF000000000 metagenome 61 Richelia intracellularis UBA3481 DFQU00000000 metagenome 71 Richelia sp. UBA11571 DLZW00000000 metagenome 67 Roseofilum sp. Cyano bin5 Ga0079927 64 Roseofilum sp. LKpool bin4 Ga0079931 37 Scytonema sp. CRU 2 7 JAAUOR000000000 metagenome 63 Scytonema hyalinum WJT4-NPBG1 JAHHIB000000000 metagenome 72 Scytonema millei VB511283 JTJC00000000.2 (regression from 79 in v. 1) 41 Spirulina sp. bin-256 JAIFME000000000 metagenome 21 Spirulina sp. DLM2.Bin59 RECT00000000 metagenome 69 Spirulina sp. S17.Bin059 JAABSU000000000 metagenome 75 Synechococcales cyanobacterium bin2 JAAFJH000000000 metagenome 71 Synechococcales cyanobacterium bin59 JAAFHZ000000000 metagenome 76 Synechococcales cyanobacterium MH2 Bin29 JAALKT000000000 metagenome 73 Synechococcales cyanobacterium T60 A2020 003 JACYMB000000000 metagenome 75 Synechococcales bacterium UBA12195 DPNP00000000 metagenome 56 Synechococcales bacterium UBA8647 DOVM00000000 metagenome 68 Synechococcus Bin 27 JGI 74 Synechococcus Bin 28 JGI 29 Synechococcus sp. BS30m-G30 JADHRT000000000 metagenome 67 Synechococcus sp. BS301-5m-G53 JADHMX000000000 metagenome 63 Synechococcus sp. CO36406bin 26 WTHF000000000 metagenome 50 Synechococcus sp. CO36386bin 29 WTFZ000000000 metagenome 62 Synechococcus sp. CO36386bin 37 WTGE000000000 metagenome 64 Synechococcus sp. HW C51 JAAZUZ000000000 metagenome 72 Synechococcus sp. HW C201 JAAZVJ000000000 metagenome 45 Synechococcus sp. KhW C443 JAAZWA000000000 metagenome 42 Synechococcus sp. PL34863bin 39 WTHL000000000 metagenome 78 Synechococcus sp. MED-G67 QOPT00000000 metagenome 68 Synechococcus sp. MED-G68 QOPS00000000 metagenome 74 Synechococcus sp. MED-G69 QOPR00000000 metagenome 66 Synechococcus sp. MED-G70 QOPQ00000000 metagenome 66 Synechococcus sp. MED-G71 QOPP00000000 metagenome 72 Synechococcus sp. SB0664 bin 36 VXRQ00000000 metagenome 53 Synechococcus sp. SB0662 bin 45 VXPA00000000 metagenome 56 Synechococcus sp. SB0663 bin 10 VXQA00000000 metagenome 66 Synechococcus sp. SB0672 bin 10 VYAE00000000 metagenome 69 Synechococcus sp. SB0665 bin 28 VXSZ00000000 metagenome 73 Synechococcus sp. SB0663 bin 10 VXQA00000000 metagenome 74 Synechococcus sp. SB0672 bin 6 VYAY00000000 metagenome 73 Synechococcus sp. SB0669 bin 7 VXYH00000000 metagenome 75 Synechococcus sp. SB0669 bin 8 VXYI00000000 metagenome 73 Synechococcus sp. SB0673 bin 10 VYBD00000000 metagenome 75 Synechococcus sp. SB0675 bin 7 VYDK00000000 metagenome 76 Synechococcus sp. SB0677 bin 5 VYFS00000000 metagenome 76 Synechococcus sp. SB0678 bin 12 VYGA00000000 metagenome 75 Synechococcus sp. SB0667 bin 8 VXWB00000000 metagenome 76 Synechococcus sp. SB0670 bin 20 VXYW00000000 metagenome 75 Synechococcus sp. 16 2 VMCZ00000000 metagenome 47 Synechococcus sp. GFB01 LFEK00000000 75 Synechococcus sp. Lanier MWMJ00000000 metagenome 32 Synechococcus sp. NP17 2133 PBYZ00000000 metagenome 74 Synechococcus sp. REDSEA-S02 B4 LURK00000000 metagenome 74 Synechococcus sp. RS344 3044 PBPY00000000 metagenome 48 Synechococcus sp. SupBloom Metag 053 JAEMSK000000000 metagenome 73 Synechococcus sp. SAT82 31040 PAJY00000000 metagenome 42 Synechococcus sp. TMED20 NHBZ00000000 metagenome 71 Synechococcus sp. TMED66 NHDT00000000 metagenome 72 Synechococcus sp. TMED155 NHHE00000000 metagenome 69 Synechococcus sp. TMED169 NHHS00000000 metagenome 46 Synechococcus sp. TMED185 NHII00000000 metagenome 56 Synechococcus sp. TMED187 NHIK00000000 metagenome 37 Synechococcus sp. TMED19 NHBY00000000 metagenome 74 Synechococcus sp. TMED205 NHJC00000000 metagenome 42 Synechococcus sp. TMED90 NHER00000000 metagenome 52 Synechococcus sp. Tous MRUD00000000 metagenome 74 Synechococcus sp. UBA8638 DOFR00000000 metagenome 66 Synechococcus sp. UBA9887 DPOG00000000 metagenome 70 Synechococcus sp. isolate NIOZ-UU94 JACNLY000000000 metagenome 72 Synechococcus sp. isolate NIOZ-UU175 JACNIM000000000 metagenome 5 Thermosynechococcus sp. M55 K2018 012 DVEC00000000 metagenome 76 Thermosynechococcus sp. OHK43 JACOMP000000000 metagenome 70 Thermosynechococcus sp. WC-1 JAGVDA000000000 metagenome 57 Tolypothrix sp. Co-bin9 JACVSG000000000 metagenome 52 Tolypothrix sp. T3-bin4 JACVSN000000000 metagenome 32 thiebautii H9-4 LAMW00000000 44 uncultured Aliterella sp. 10 20180511 Bin MAXBIN 075 CAJQOK000000000 metagenome 58 uncultured cyanobacterium B12 bin-1940 CAIYEC000000000 50 uncultured cyanobacterium LaPlata-1m-b bin-276 CAITZL000000000 metagenome 75 uncultured cyanobacterium LaPlata-1m-b bin-676 CAIOXF000000000 metagenome 76 uncultured cyanobacterium Erken-D3 bin-1049 CAIRWM000000000 metagenome 76 uncultured cyanobacterium MGYG-HGUT-02235 CABMDG000000000 metagenome 70 uncultured cyanobacterium MGYG-HGUT-03890 CABOOI000000000 metagenome 70 uncultured cyanobacterium MGYG-HGUT-04459 CABPKF000000000 metagenome 60 uncultured cyanobacterium T7-5 bin-036 CAIMSC000000000 75 uncultured cyanobacterium T7 bin-034 CAIWLC000000000 76 uncultured cyanobacterium B12 bin-0982 CAIVAU000000000 76 uncultured cyanobacterium I3-5 bin-680 CAIJEA000000000 75 uncultured cyanobacterium Ki2-D1 bin-0219 CAIWSY000000000 metagenome 60 uncultured cyanobacterium Ki2-D2 bin-1184 CAIWIR000000000 metagenome 60 uncultured cyanobacterium Umea1p3 bin-620 CAIJJB000000000 metagenome 73 uncultured cyanobacterium Umea1p1 bin-912 CAIYEE000000000 metagenome 66 uncultured Snowella sp. Erken-D5 bin-0612 CAIRRO000000000 metagenome 29 uncultured Microcoleus sp. AVDCRST MAG84 CADCTZ000000000 72 uncultured Leptolyngbya sp. AVDCRST MAG94 CADCTY000000000 39 uncultured Nodularia sp. LaPlata-1m-b bin-688 CAIVJC000000000 57 uncultured Synechococcus sp. 3 20180319 Bin 161 1 CAJQPG000000000 metagenome 46 uncultured Synechococcus sp. 3 20180319 Bin 305 1 CAJQPQ000000000 metagenome 64 Vulcanococcus sp. Con-13 JAHUZR000000000 metagenome 70 Vulcanococcus sp. CPBay Sum27G08 21 JAFMGK000000000 metagenome 67 Vulcanococcus sp. CPBay Sum20G08 28 JAFMGD000000000 metagenome 63 Vulcanococcus sp. CPBay Sum15G08 31 JAFMFG000000000 metagenome 66 Vulcanococcus sp. DEBay Sum29DG08 32 JAFMMN000000000 metagenome 74 Vulcanococcus sp. DEBay Sum22NG08 44 JAFMLP000000000 metagenome 70 Vulcanococcus sp. DEBay Sum22DG08 74 JAFMKL000000000 metagenome 74 Vulcanococcus sp. DEBay Sum29NG08 81 JAFMNC000000000 metagenome 66 Vulcanococcus sp. CPBay Sum27L08 19 JAFMGO000000000 metagenome 75 Vulcanococcus sp. CPBay Sum15L08 68 JAFMFX000000000 metagenome 75

Greater than 10% contaminated (many of these are also listed above): Contamination

Aphanocapsa montana BDHKU210001 JTJD00000000 32.76 Chrysosporum ovalisporum UAM-MAO CDHJ00000000 22.19 Fischerella ambigua UTEX 1903 JGI 38.8 Fischerella thermalis CCMEE 5319 NMQD00000000 22.73 Hassallia byssoidea VB512170 JTCM00000000 104.63 Halothece sp. KZN 001 MDVL00000000 (also as Euhalothece) 12.42 Leptolyngbya valderiana BDU 20041 LSYZ00000000 54.29 Limnoraphis robusta CS-951 LATL00000000 11.79 Lyngbya confervoides BDU141951 JTHE00000000.1 23.11 Microcystis aeruginosa SPC777 ASZQ00000000 16.52 Mastigocoleus testarum BC008 LMTZ00000000 41.11 Mastigocoleus testarum BC008 AXAQ00000000 200 Prochlorococcus sp. scB245a 518D8 JFNB00000000 11.96 Prochlorococcus marinus HNLC1 GL947594 metagenome 250.33 Prochlorococcus marinus HNLC2 GL947595 metagenome 250.33 Synechococcus sp. TMED20 NHBZ00000000 41.38 Synechococcus sp. TMED66 NHDT00000000 19.89 Scytonema millei VB511283 JTJC00000000.1 44.54 Cyanobacterium TDX16 NDGV00000000 156.41 Cyanobacteria bacterium SCGC AG-650-H12 JGI metagenome 12.96 Oscillatoriales cyanobacterium MTP1 LNAA00000000 80.53

Chimeric (segments from two different cyanobacteria), or poor sequences seriously disturbing tree topology:

Anabaenopsis elenkinii CCIBt3563 CP063311 Aphanocapsa sp. GSE-SYN-MK-11-07L JAHHGS000000000 metagenome Alkalinema sp. RU 4 3 JAAUSA000000000 metagenome Aphanizomenon flos-aquae CCAP 1446/1C=PCC 7938 heterocyst JAAMUW000000000 Aphanizomenon flos-aquae CCAP 1446/1C=PCC 7938 vegetative JAAMUX000000000 Aphanizomenon flos-aquae UKL13-PB LTEC00000000.2 metagenome Brasilonema octagenarum HA4186-MV1 JAHHGW000000000 metagenome Calothrix sp. C42 A2020 038 JACYLQ000000000 metagenome Calothrix sp. PCC 7716 AP025018 Calothrix sp. XPORK 5E (JGI, no longer available) Chroococcus sp. FPU101 BLJI00000000 Coleofasciculus sp. FACHB-1120 JACJTV000000000 Coleofasciculus sp. FACHB-125 JACJOI000000000 Coleofasciculus sp. FACHB-129 JACJOH000000000 Coleofasciculus sp. FACHB-64 JACJOW000000000 Coleofasciculus sp. FACHB-64 JACJOW000000000 Coleofasciculus sp. FACHB-SPT36 JACJSL000000000 Coleofasciculus sp. FACHB-SPT9 JACJOJ000000000 Coleofasciculus sp. FACHB-T130 JACJOG000000000 "Cyanobacteria bacterium" WB6 1B 304 RGDS00000000 metagenome "Cyanobacteria bacterium" (27 metagenomes): PXPI00000000-PXPZ00000000, PXQA00000000-PXQI00000000 Cyanomargarita calcarea GSE-NOS-MK-12-04C JAHHGZ000000000 metagenome Cyanosarcina radialis HA8281-LM2 JAHHHA000000000 metagenome Desmonostoc muscorum CCALA 125 JACERF000000000 Desmonostoc muscorum LEGE 12446 JADEXS000000000 "Filamentous cyanobacterium" LEGE 11480 JADEXQ000000000 Fischerella thermalis M66 A2018 004 JACYMA000000000 metagenome Fischerella thermalis M58 A2018 009 JACYLY000000000 metagenome Geminocystis sp. GBBB08 VRZC00000000 metagenome Gloeocapsa sp. DLM2.Bin57 RECR00000000 metagenome Gloeocapsopsis crepidinum LEGE 06123 JADEWN000000000 "Gloeomargaritaceae cyanobacterium" C42 A2020 066 JACYLR000000000 metagenome Halomicronema hongdechloris C2206 (LAZT00000000 and CP021983.1), Iningainema sp. BLCCT55 JACXAE000000000 Kaiparowitsia implicata GSE-PSE-MK54-09C JAHHHI000000000 metagenome Kastovskya adunca ATA6-11-RM4 JAHHHJ000000000 metagenome Kovacikia sp. CCNU0001 CP083582 complete Leptolyngbya sp. PKUAC-SCTE412 CP072600 complete Leptolyngbya sp. SIO3F4 JAAHHO000000000 metagenome Leptolyngbya sp. SIOISBB JAAHII000000000 metagenome Leptolyngbya sp. UWPOB LEPTO1 JAFLCJ000000000 metagenome Lyngbya sp. HA4199-MV5 JAHHHL000000000 metagenome Merismopedia glauca CCAP 1448/3 PVWJ00000000 Microcoleus sp. FACHB-45 JACJPE000000000 Microcoleus sp. FACHB-68 JACJOT000000000 Microcoleus sp. FACHB-84 JACJOL000000000 Microcoleus sp. FACHB-SPT15 JACJNU000000000 Microcoleus vaginatus WJT46-NPBG5 JAHHHM000000000 metagenome Moorea sp. SS36440bin 2 WTKN00000000 metagenome Nostoc indistinguendum CM1-VF10 JAHHHS000000000 metagenome Nostoc desertorum CM1-VF14 JAHHHR000000000 metagenome "Nostocales cyanobacterium" PH2015 10S 36 12 RDXV00000000 metagenome Oculatella sp. FACHB-28 JACJPJ000000000 Oculatella sp. LEGE 06141 JADEWO000000000 Oscillatoria princeps RMCB-10 JAHHHT000000000 metagenome Oscillatoria salina IIICB1 JAAHBQ000000000 " cyanobacterium" M7585 C2015 266 DVEG00000000 metagenome "Oscillatoriales cyanobacterium" PH2015 11S 45 847 RDXR00000000 metagenome "Oscillatoriales cyanobacterium" PH2015 07U 46 236 RDYN00000000 metagenome "Oscillatoriales cyanobacterium" PH2015 03U 45 708 REAA00000000 metagenome "Oscillatoriales cyanobacterium" PH2015 02U 45 393 REAI00000000 metagenome "Oscillatoriales cyanobacterium" PH2015 14S 56 116 RDXB00000000 metagenome Oxynema sp. CENA135 JAEOXH000000000 Pegethrix bostrychoides GSE-TBD4-15B JAHHHV000000000 metagenome “Prochloraceae cyanobacterium” LD05 CP073341 metagenome Raphidiopsis raciborskii KL1 JADQCS000000000 metagenome Richelia sinica FACHB-800 CP021056 Rivularia sp. IAM M-261 BPQA00000000 Rivularia sp. T60 A2020 040 JACYMD000000000 metagenome Romeria aff. gracilis LEGE 07310 JADEXG000000000 Scytolyngbya sp. HA4215-MV1 JAHHIA000000000 metagenome Sphaerospermopsis torques-reginae ITEP-024 CP080598 Spirirestis rafaelensis WJT71-NPBG6 JAHHID000000000 metagenome Stenomitos rutilans HA7619-LM2 JAHHIE000000000 metagenome Symplocastrum torsivum CPER-KK1 JAHHIF000000000 metagenome “Synechococcales cyanobacterium” M55 K2018 004 DVEB00000000 metagenome “Synechococcales cyanobacterium” S06.Bin197 JAABRE000000000 metagenome Timaviella obliquedivisa GSE-PSE-MK23-08B JAHHII000000000 metagenome Trichocoleus desertorum ATA4-8-CV12 JAHHIL000000000 metagenome Trichocoleus sp. FACHB-90 JACJOK000000000 Tychonema sp. LEGE 07196 JADEXB000000000 uncultured cyanobacterium B-1 bin-000 CAIZKS000000000 metagenome uncultured cyanobacterium A5 bin-0177 CAIRPA000000000 metagenome uncultured Nodularia sp. LaPlata bin-0263 CAISZL000000000 metagenome uncultured Nodularia sp. LaPlata-1m-a bin-391 CAIPYS000000000 metagenome uncultured Nodularia sp. LaPlata-b bin-1655 CAIVSM000000000 metagenome uncultured Nodularia sp. LaPlata-a bin-2690 CAIWDD000000000 metagenome uncultured Synechococcales cyanobacterium AVDCRST MAG81 CADCWO000000000 metagenome

Duplicate (re-assembled or re-sequenced) genomes:

Aetokthonos hydrillicola CCALA 1050 (JAHHGQ00000000) (metagenome) Anabaena sp. PCC 7122 (AP018166), Arthrospira sp. PCC 8005 (CAFN00000000), Brasilonema sp. UFV-L1 (QMEA00000000), Calothrix desertica PCC 7102 (VLKB00000000) Chlorogloeopsis fritschii PCC 6912 (RSCJ00000000), Chroococcales cyanobacterium CENA595 (JGI), Chroococcidiopsis sp. PCC 6712 (Gp0005064), Crocosphaera watsonii WH 0003 (JGI), Geminocystis herdmanii PCC 6308 (ALVO00000000), Gloeocapsopsis sp. AAB1 (PTJN00000000), Halomicronema hongdechloris C2206 (LAZT00000000 and CP021983.1), Hormoscilla sp. GUM202 (RFFC00000000.2) (metagenome), Limnothrix sp. CACIAM 69d (MKGP00000000), Lyngbya sp. CCY 8106(=PCC 8106) (JGI), Microcystis aeruginosa NIES-88 (JXYX00000000), Microcystis aeruginosa NIES-298 (BEIU00000000, BEYQ00000000), Moorea producens 3L (AEPQ00000000), Nodularia spumigena CCY9414 (AAVW00000000), Nostoc sp. PCC 7120 (RSCN00000000), Nostoc sp. PCC 7120 (FACHB-418) (JACJQQ000000000), Oscillatoriales cyanobacterium JSC-12 (AJUB00000000), Phormidesmis priestleyi ULC007 (PVWG00000000, QBMQ00000000), Picosynechococcus sp. PCC 7002 (FXWN00000000, JAHHPT000000000, JAHHPU000000000), Planktothrix rubescens PCC 7821 LR812491 (regression), Planktothrix serta PCC 8927 (CZCU00000000.1), Planktothrix paucivesiculata PCC 9631 (CZCS00000000.1), Raphidiopsis raciborskii CS-505 (LYXA00000000), Raphidiopsis raciborskii CS-506 B (VDFF00000000), Raphidiopsis raciborskii CS-506 C (VDFE00000000), Raphidiopsis raciborskii CS-506 D (VDFD00000000), Richelia intracellularis HH01 AM 2804 (OMJX00000000), Richelia sinica FACHB-800 (JACJTT000000000), Scytonema millei VB511283 (JTJC00000000.1, JTJC00000000.2, JTJC00000000.3), Scytonema tolypothrichoides VB-61278 (JXCA02000000), Scytonema sp. HK-05 (MRCF00000000), Sphaerospermopsis aphanizomenoides BCCUSP55 (LUFH00000000.2) Spirulina major PCC 6313 (ALVQ00000000), Synechococcus sp. CB0101 (ADXL00000000), Synechococcus elongatus FACHB-242 (UTEX 625, PCC 6301) (JACJSY000000000), Synechococcus elongatus FACHB-805 (PCC 7942) (JACJTX000000000), Synechococcus sp. P1 UW179A (UCNJ00000000), Synechococcus sp. WH 8101 (CP047932), Synechocystis sp. PCC 6803 (CP003265), Synechocystis sp. PCC 6803 (JAABOT000000000), Synechocystis sp. PCC 6803 (BA000022), Thermosynechococcus vestitus PKUAC-SCTE542 (CP032152.1), Tolypothrix campylonemoides VB511288 (JXCB00000000.2): 16S rRNA high similarity to Rhodopseudomonas, from JGI: Calothrix desertica PCC 7102, Nostoc punctiforme PCC 73102, Synechococcus sp. PCC 73109

Genomes with more than 4000 contigs:

Chrysosporum ovalisporum UAM-MAO (CDHJ00000000); Phormidium sp. Bin_1 JAIFKK000000000 metagenome Unidentified cyanobacterium 13 1 40CM 2 61 4 (MNHI00000000); Cyanobacterium TDX16 (NDGV00000000)

To prune the tree , removed genomes from clades that are over-represented:

Prochlorococcus: omitted all (hundreds) genomes derived from single cells; omitted all metagenomes, 13 strains of P. marinus with accession numbers JAAORC000000000-JAAORO000000000. MU1414 (PGOQ00000000), MU1412 (PGOR00000000), MU1411 (PGOS00000000), MU1410 (PGOT00000000), MU1406 (PGOU00000000), MU1405 (PGOV00000000), MU1404 (PGOW00000000), MU1403 (PGOX00000000), MU1402 (PGOY00000000), Metagenomes of the sister OMF taxa of the "Synechococcus”/”Vulcanococcus”" cluster and of isolates Synechococcus sp. 8F6 (NQKZ00000000), Ace-Pa (VITZ00000000), BS55D (PHQT00000000), BS56D (PHQU00000000), HB1133 (SDBW0000000), P1 UW179A (UCNJ00000000), BIOS-E4-1 (CP047935), BOUM118 (CP047947), RS9915 (CP047934), A15-127 (CP047948), A18-25c (CP047957), NOUM97013 (CP047941), A15-24 (CP047960), A15-28 (CP047931), A15-44 (CP047938), A15-60 (CP047933), A15-62 (CP047950), A18-40 (CP047956), M16-1 (CP047954), BMK-MC-1 (CP047939), MEDNS5 (CP047952), Minos11 (CP047953), MVIR-18-1 (CP047942), PROS-7-1 (CP047945), PROS-9-1 (CP047961), PROS-U-1 (CP047951), ROS8604 (CP047946), RS9902 (CP047949), RS9907 (CP047944) RS9909 (CP047943), SYN20 (CP047959), TAK9802 (CP047937), BIOS-U3-1 (CP047936), WH5701 (AANO00000000), LA31 (CP075523), CCY0621 (JAFKRH000000000), CCY9618 (JAFKRG000000000), CP7909 (JAFKRK000000000), CP7910 (JAFKRJ000000000), CP7913 (JAFKRI000000000), HK05 (JAHRXJ000000000) approx. 500 isolates of S. lacustris, Cyanobium spp. LEGE 06113 (JADEWM000000000), LEGE 06143 (JADEWP000000000), NS01 (CP047940), Tous (PXXO00000000)

Microcystis: unused sequences are the metagenomes: M. aeruginosa CACIAM 03 (MCIH00000000), M. aeruginosa DA14 (QQWE00000000), M. flos-aquae DF17 (QQWB00000000), M. aeruginosa TA09 (QQWA00000000), M. flos-aquae TF09 (QQWC00000000), M. wesenbergii TW10 (QQWD00000000), 52 with accession numbers SFAA-SFCA00000000 M. aeruginosa PMC 728.11 (JADCRC000000000) and the isolates: Microcystis spp. strains LE3 (MTBS00000000), FCY-26 (AJHB00000000), FCY-27 (AJUS00000000), FCY-28 (AJUT00000000), NaRes975 (MOLN00000000), CHAOHU (MOLZ00000000), 46 isolates (JAADAC00000000-JAADBY00000000), BLCCF108 (JACEGB000000000), BLCCF158 (JACEGC000000000), KW (MVGR00000000), FACHB-1317 (JACJQV00000000, FACHB-1342 (JACJSV000000000), FACHB-1344 (JACJSW000000000), FACHB-917 (JACJSZ000000000), LEGE 11464 (JADEXM000000000), LEGE 00239 (JADEVY000000000), LEGE 00066 (JADEVX000000000), LEGE 08355 (JADEXI000000000), LEGE 91341 (JADEXY000000000)

Five metagenomes of the ADA clade: Anabaena spp. WA113 (LJOS00000000), MDT14b (LJOV00000000), Dolichospermum spp. OL01 (JACGCQ000000000), BR01 (JACGCP000000000), WA123 (JACGCS000000000)

Nine of the almost identical genomes of the Nostoc linckia strain Z series: LAGY00000000, LAGZ00000000, LAHB00000000, LAHC00000000, LAHD00000000, LAHE00000000, LAHH00000000, LAHI00000000, LAHJ00000000 and Nostoc spp. CCNP1411 (CP054698) FACHB-87 (JACJRX00000000) FACHB-110 (JACJRU00000000) FACHB-130 (JACJTB00000000) FACHB-159 (JACJTU00000000) FACHB-252 (JACJTC00000000) FACHB-395 (JACJSF00000000) FACHB-857 (JACJTK00000000) FACHB-888 (JACJQM00000000) FACHB-973 (JACJSJ00000000) MG11 (JACXXN000000000) WHI (WBKM00000000)

Removed 17 almost identical Fischerella isolates from White Creek, Yellowstone NP, USA: NGZS00000000-NGZZ0000000 and NHAA0000000-NHAK0000000, retaining only strains WC439 (NHAE00000000) and WC441 (NHAD00000000)

60 metagenomes in the series JAAUON00000000 to JAAUUY000000000

24 metagenomes (not excluded above) PXPJ00000000 to PXQH00000000

Over 100 genomes, of a variety of genera, with FACHB strain numbers with accession numbers JACJNU000000000 to JACJUP000000000; 39 metagenomes with a SIO designation

Others:

Over 30 genomes with a SIO designation, containing many mismatches in the 16S rRNA gene (if this gene is representative of the entire genome, we can have little confidence in the placement of the latter in the tree).