cyanobacterial phylogeny

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CHROMOSOMES EXCLUDED FROM THE
COMPLETE CHROMOSOME TREE



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%):






Markers

Candidatus Atelocyanobacterium thalassa


ALOHA=UCYN-A1

CP001842

76

Biont of Braarudosphaera bigelowii


CPSB-1

AP024987

77

Cyanobacterium sp.


uoEpiScrs1

OX373462

78

Desikacharya piscinale


CENA21

CP012036

78

Gloeomargarita ahousahtiae


VI4D9

CP088016

78

Gloeomargarita lithophora


D10

CP017675

78

Leptolyngbya sp.


7M

CP070897

72

Leptolyngbya sp.


15MV

CP071923

66

Limnospira fusiformis


KN01

CP091467

78

Microcoleus vaginatus


PCC 9802

CP146622

78

Nostoc carneum


NIES-2107

AP018180

75

Nostoc cf. commune


SO-36

AP025732

78

Nostoc linckia


NIES-25

AP018222

47

Synechocystis sp.


B12

CP101709

76

Thermosynechococcus sp.


KatS3mg067

AP024678

78






Chimeric (segments from two different cyanobacteria),

or poor sequences seriously disturbing tree topology:






Annamia dubia


NIES-4383

AP025630


Fischerella sp.


NIES-4106

AP018298


Halotia branconii


CENA392

CP124543


Hormoscilla sp.


8e647e88 chr. 3

OZ001295


Nostoc sp.


NIES-2111

AP018184


Nostoc commune


HK-02

AP018326


Planktothrix agardhii


976

LR882952


Raphidiopsis curvata


NIES-932

AP018317


Richelia sinica


FACHB-800

CP021056


Scytonema sp.


NIES-4073

AP018268


Sphaerospermopsis kisseleviana


NIES-73

AP018314


Tolypothrix tenuis


PCC 7101

AP018248


Trichocoleus desertorum


NBK24

CP116619







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


Halomicronema hongdechloris


C2206

CP021983


Microcoleus vaginatus


PCC 9802

JGI


Microcystis aeruginosa


PCC 7806

CP130696


Moorena producens


JHB

CP017708.1


Planktothrix agardhii


PCC 7805

LR882950


Synechococcus elongatus


PCC 6301

CP085785


Synechococcus sp.


WH 8101

CP047932


Synechocystis sp.


PCC 6803

CP003265


Synechocystis sp.


PCC 6803

BA000022




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





Strains of the OMF taxa:




A10-1-5-1 (CP096032), A15-127 (CP047948), A18-25c (CP047957), A15-24 (CP047960), A15-44 (CP047938),

A15-60 (CP047933), A15-62 (CP047950), A18-40 (CP047956), BIOS-U3-1 (CP047936)

BMK-MC-1 (CP047939), M16-1 (CP047954), M30B3 (CP073761), MEDNS5 (CP047952),

MVIR-18-1 (CP047942), NB0720_10 (CP090898),

NOUM97013 (CP047941), PROS-7-1 (CP047945), PROS-9-1 (CP047961),

PROS-U-1 (CP047951), ROS8604 (CP047946), RS9902 (CP047949), RS9907 (CP047944),

RS9909 (CP047943), SYN20 (CP047959), TAK9802 (CP047937), CCFWC 502 (CP114977),

KAC_102 (OY986434), KAC_105 (OY986432), KAC_106 (OY986433), KAC_114 (OY986430), KAC_108 (OY986431),

Prochlorococcus spp.:

MIT 0912 (CP114783), MIT 0913 (CP114782), MIT 0915 (CP114781), MIT 0917 (CP114784),

MIT 0918 (CP114780), MIT 0919 (CP114779), MIT 1013 (CP114778), MIT 1214 (CP114777),