cyanobacterial phylogeny

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EXCLUDED CHROMOSOMES (COMPLETE)



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

Desikacharya piscinale


CENA21

CP012036

78

Gloeomargarita lithophora


D10

CP017675

78

Leptolyngbya sp.


7M

CP070897

72

Leptolyngbya sp.


15MV

CP071923

66

Limnospira fusiformis


KN01

CP091467

78

Nostoc cf. commune


SO-36

AP025732

78

Thermomargarita ahousahtiae


VI4D9

CP088016

78

Thermosynechococcus sp.


KatS3mg067

AP024678

78






Chimeric (segments from two different cyanobacteria),

or poor sequences seriously disturbing tree topology:






Richelia sinica


FACHB-800

CP021056


Woronichinia naegeliana


WA131

CP073041







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


Anabaena sp.


PCC 7122

AP018166


Microcoleus vaginatus


PCC 9802

JGI


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)