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EXCLUDED GENOMES A. Not of Bacterial Origin (Described As “Root

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EXCLUDED GENOMES A. Not of Bacterial Origin (Described As “Root 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 Cyanobacteria 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 “Oscillatoriales 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 Arthrospira 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
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