CyanoLyase

Genomes

This page lists publicly available genomes of cyanobacteria, red algae and cryptophytes or organelles containing one or more phycobilin lyases and related proteins.

Details on the phylogeny (phylum, order, genus, species) are indicated for all strains, but lower taxon levels (subcluster, clade, subclade) are specified only for marine picocyanobacteria, as determined by comparing whole genomes (Kettler et al., 2007; Dufresne et al., 2008), 16S rDNA genes (Fuller et al., 2003) and petB genes (Mazard et al., 2012), respectively.

Pigment type, as defined notably by Six et al., (2007) for marine Synechococcus spp. and by Moore & Chisholm (1999) for Prochlorococcus spp., is also specified whenever applicable.

Strains in which at least one phycobilin lyase has been biochemically characterized are called "model strains" and indicated by stars.

Abbreviations : FLI, Friedrich Loeffler Institute, JCVI, J. Craig Venter Institute; JGI, Joint Genome Institute; PBP, phycobiliprotein; PC, phycocyanin; PEC, phycoerythrocyanin; PEI, phycoerythrin I; PEII, phycoerythrin II; PEIII, phycoerythrin III

Id Phylum Order Species Strain Subcluster Clade/Ecotype Subclade PBP in rods Habitat Pigment type Sequencing center Genome status Remark                                                                      
2 Cyanobacteria Chroococcales Synechococcus sp. CC9311 5.1 I Ia PC+PEI+PEII marine 3d/CA4 JGI complete
3 Cyanobacteria Chroococcales Synechococcus sp. CC9605 5.1 II IIc PC+PEI+PEII marine 3c JGI complete
4 Cyanobacteria Chroococcales Synechococcus sp. WH8109 5.1 II IIa PC+PEI+PEII marine 3b JCVI assembled contigs
5 Cyanobacteria Chroococcales Synechococcus sp. WH8102 5.1 III IIIa PC+PEI+PEII marine 3c JGI complete Strain in which RpcG has been characterized (Blot et al., 2009)
6 Cyanobacteria Chroococcales Synechococcus sp. CC9902 5.1 IV IVa PC+PEI+PEII marine 3d/CA4 JGI complete
7 Cyanobacteria Chroococcales Synechococcus sp. BL107 5.1 IV IVa PC+PEI+PEII marine 3d/CA4 JCVI complete
8 Cyanobacteria Chroococcales Synechococcus sp. WH7803 5.1 V V PC+PEI+PEII marine 3a Genoscope complete
9 Cyanobacteria Chroococcales Synechococcus sp. WH7805 5.1 VI VIa PC+PEI marine 2 JCVI assembled contigs
10 Cyanobacteria Chroococcales Synechococcus sp. RS9917 5.1 VIII VIII PC marine 1 JCVI assembled contigs halotolerant
11 Cyanobacteria Chroococcales Synechococcus sp. RS9916 5.1 IX IX PC+PEI+PEII marine 3d/CA4 JCVI assembled contigs Strain in which RpcG (Blot et al. 2009) and MpeZ (Shukla et al. 2012) have been characterized
12 Cyanobacteria Chroococcales Synechococcus sp. WH5701 5.2 PC marine 1 JCVI assembled contigs halotolerant
13 Cyanobacteria Chroococcales Synechococcus sp. RCC307 5.3 5.3-I PC+PEI+PEII marine 3b Genoscope complete
14 Cyanobacteria Chroococcales Synechococcus sp. CB0101 5.2 CB4 PC marine 1 JCVI contigs
15 Cyanobacteria Chroococcales Synechococcus sp. CB0205 5.2 CB5 PC+PEI marine 2 JCVI contigs
16 Cyanobacteria Chroococcales Synechococcus sp. PCC7335 4 PC+PEI marine CA3 JCVI assembled contigs
17 Cyanobacteria Chroococcales Synechococcus sp. PCC7002 3 PC marine halotolerant 1 Penn State University complete Strain in which CpcE/F (Zhou et al,1992; Fairchild et al., 1992; Fairchild & Glazer 1994), CpcT (Shen et al, 2006), CpcS-I and CpcU (Saunée et al, 2008, Shen et al, 2008) have been characterized.
18 Cyanobacteria Chroococcales Cyanobium sp. PCC7001 Cbm 2 PC marine 1 JCVI
19 Cyanobacteria Chroococcales Synechococcus sp. WH8016 5.1 I Ib PC+PEI+PEII marine 3a JGI draft - assembled contigs
20 Cyanobacteria Chroococcales Prochlorococcus marinus MED4 (CCMP1986/CCMP1378) Pro HLI HLI beta-PEIII marine low b/a JGI complete Strain in which CpeS has been characterized (Wiethaus et al., 2010b). Strain likely co-identical to PCC9511.
21 Cyanobacteria Chroococcales Prochlorococcus marinus MIT9515 Pro HLI HLI beta-PEIII marine low b/a JCVI complete
22 Cyanobacteria Chroococcales Prochlorococcus marinus MIT9301 Pro HLII HLII beta-PEIII marine low b/a JCVI assembled contigs
23 Cyanobacteria Chroococcales Prochlorococcus marinus AS9601 Pro HLII HLII beta-PEIII marine low b/a JCVI complete
24 Cyanobacteria Chroococcales Prochlorococcus marinus MIT9215 Pro HLII HLII beta-PEIII marine low b/a JGI complete
25 Cyanobacteria Chroococcales Prochlorococcus marinus MIT9312 Pro HLII HLII beta-PEIII marine low b/a JGI complete
26 Cyanobacteria Chroococcales Prochlorococcus marinus MIT9202 Pro HLII HLII beta-PEIII marine low b/a JGI complete
27 Cyanobacteria Chroococcales Prochlorococcus marinus NATL1A Pro LLI LLI PEIII marine high b/a JCVI complete
28 Cyanobacteria Chroococcales Prochlorococcus marinus NATL2A Pro LLI LLI PEIII marine high b/a JGI complete
29 Cyanobacteria Chroococcales Prochlorococcus marinus SS120 (CCMP1375) Pro LLII LLII PEIII marine high b/a Genoscope complete
30 Cyanobacteria Chroococcales Prochlorococcus marinus MIT9211 Pro LLIII LLIII PEIII marine High b/a JCVI complete
31 Cyanobacteria Chroococcales Prochlorococcus marinus UH18301 Pro HLII HLII beta-PEIII marine low b/a JCVI assembled contigs
32 Cyanobacteria Chroococcales Prochlorococcus sp. MIT9303 Pro LLIV LLIV PEIII marine high b/a JCVI complete
33 Cyanobacteria Chroococcales Prochlorococcus sp. MIT9313 Pro LLIV LLIV PEIII marine high b/a JGI complete
34 Cyanobacteria Chroococcales Synechocystis sp. PCC6803 (ATCC27184) PC freshwater 1 Kazusa complete Strain in which CpcT (Bolte et al, 2008), CpcE/F (Alvey et al, 2011) and NblB (Li & Sherman, 2002) have been characterized
35 Cyanobacteria Chroococcales Acaryochloris marina MBIC11017 (AM1) PC marine 1 TGen Sequencing Center complete Chlorophyll d-producing cyanobacterium with phycobiliprotein aggregates but no phycobilisome. Close to CCMEE5410 strain.
36 Cyanobacteria Nostocales Anabaena (Nostoc) sp. PCC7120 PC+PEC freshwater Kazusa complete Strain in which CpcS-III (Zhao et al 2006), PecE/F (Jung et al. 1995, Blot et al. 2009) and CpcT (Zhao et al. 2007, Zhang et al. 2012) have been characterized
37 Cyanobacteria Nostocales Anabaena variabilis ATCC29413 (PCC7937) PC+PEC freshwater JGI complete
38 Cyanobacteria Nostocales Anabaena (Nostoc) azollae 0708 PC+PEC intracellular JGI complete Cyanobiont of the aquatic fern Azolla filiculoides
39 Cyanobacteria Oscillatoriales Arthrospira (Spirulina) maxima CS-328 PC freshwater 1 JGI incomplete (129 scaffolds)
40 Cyanobacteria Chroococcales Crocosphaera watsonii WH8501 PC+PEI marine JGI unassembled contigs
41 Cyanobacteria Chroococcales Cyanothece sp. ATCC51142 PC marine 1 Washington University complete
42 Cyanobacteria Chroococcales Cyanothece sp. PCC7424 PC+PEI freshwater 2 JGI complete
43 Cyanobacteria Chroococcales Cyanothece sp. PCC7425 PC freshwater 1 JGI complete
44 Cyanobacteria Chroococcales Cyanothece sp. PCC8801 PC+PEI freshwater 2 JGI complete
45 Cyanobacteria Chroococcales Cyanothece sp. PCC8802 PC freshwater 1 JGI complete
46 Cyanobacteria Chroococcales Cyanothece sp. CCY0110 PC marine 1 JCVI incomplete
47 Cyanobacteria Chroococcales Cyanothece sp. PCC7822 PC+PEI freshwater 2 JGI complete
48 Cyanobacteria Nostocales Fremyella diplosiphon (Tolypothrix sp. / Calothrix sp.) Fd33 (UTEX481/PCC7601) PC+PEI freshwater CA3 Human Genome Sequencing Center Houston incomplete Genome sequenced but not yet accessible. So the lyase gene set is incomplete yet. Sequences reported here come from sequencing of individual genes. Fd33 is a short filament mutant of F. diplosiphon strain UTEX 481.
49 Cyanobacteria Stigonematales Fischerella sp. (Mastigocladus laminosus) JSC-11 PC+PEC freshwater JGI incomplete (34 scaffolds) Close to Fischerella sp. PCC 7603 in which CpcE/F (Zhao et al, 2006) as well as PecE and/or PecF (Storf et al. 2001, Zhao et al., 2005, Bohm et al, 2007) have been characterized
50 Cyanobacteria Chroococcales Gloeobacter violaceus PCC7421 PC+PEI Rock 2 Kazusa complete The chromophorylation of the PE of this strain is controversial. Indeed Bryant et al. (1981) reported that the alpha subunit would bind 3 PEB and the beta subunit 3 PEB and one PUB, whereas CpeA and CpeB sequences have no additional binding sites as other PEs. No obvious candidate for a lyase-isomerase was found in this genome.
51 Cyanobacteria Chroococcales Gloeothece sp. PCC6909/1 PC+PEI freshwater 2 JCVI incomplete (23 scaffolds)
53 Cyanobacteria Oscillatoriales Lyngbya aestuarii CCY9616 (PCC8106/CCY8106) PC marine 1 JCVI incomplete (20 scaffolds)
54 Cyanobacteria Oscillatoriales Microcoleus chthonoplastes PCC7420 PC+PEC halotolerant JCVI incomplete (142 scaffolds)
55 Cyanobacteria Chroococcales Microcystis aeruginosa NIES-843 PC freshwater 1 Kazusa complete
56 Cyanobacteria Nostocales Nodularia spumigena CCY9414 PC marine 1 JCVI incomplete (204 scaffolds)
57 Cyanobacteria Nostocales Nostoc punctiforme ATCC29133 (PCC73102) PC+PEI Soil 2 JGI complete
58 Cyanobacteria Chroococcales Synechococcus elongatus PCC7942 1.1 PC freshwater 1 JGI complete Strain in which cpcE/F (Bhalerao et al, 1994) and NblB (Dolganov & Grossman, 1999) have been characterized.
59 Cyanobacteria Chroococcales Synechococcus elongatus PCC6301 (ATCC 27144) 1.1 PC freshwater 1 Nagoya University co-identical with PCC7942 except for a 186 bp inversion (Sugita et al, 2007)
60 Cyanobacteria Chroococcales Synechococcus sp. JA-2-3B'a(2-13) PC Hot spring 1 TIGR complete
61 Cyanobacteria Chroococcales Synechococcus sp. JA-3-3Ab PC Hot spring 1 TIGR complete
62 Cyanobacteria Chroococcales Thermosynechococcus elongatus BP-1 PC Hot spring 1 Kazusa complete
63 Cyanobacteria Oscillatoriales Trichodesmium erythraeum IMS101 PC+PEI marine JGI complete
65 Rhodophyta Cyanidioschyzon merolae 10D PC thermophile 1 National Institute of Genetics, Japan incomplete
67 Cryptophyta Pyrenomonadales Guillardia theta CCMP2712 Cr-PE 545 marine n.a. JGI draft assembly Only the nucleomorph genome is available, so the phycobilin lyase set is only partial.
70 Cyanobacteria Chroococcales Microcystis aeruginosa PCC7806 PC freshwater, soil 1 Institut Pasteur
71 Cyanobacteria Oscillatoriales Arthrospira (Spirulina) platensis NIES-39 PC freshwater 1 National Institute of Technology and Evaluation (Tokyo) incomplete (19 scaffolds)
72 Cyanobacteria Oscillatoriales Microcoleus vaginatus FGP-2 PC desert soil crust 1 JGI complete
73 Cyanobacteria Oscillatoriales Lyngbya majuscula 3L PC+PEI marine 2 Scripps Institution of Oceanography draft
74 Cyanobacteria Oscillatoriales Oscillatoria sp. PCC6506 (PCC9029/ATCC29081 /UTEX 1547) PC unknown 1 genoscope draft
75 Cyanobacteria Nostocales Cylindrospermopsis raciborskii CS-505 PC freshwater 1 FLI Jena draft
76 Cyanobacteria Nostocales Raphidiopsis brookii D9 PC freshwater 1 FLI Jena draft
78 Rhizaria Cercozoa Paulinella chromatophora M0880 PC endosymbiont of amoeba 1 Leibniz Institute for Age Research complete Photosynthetic endosymbiont (chromatophore) of a freshwater filose amoeba. It is genetically closest from Synechococcus sp. WH5701. Massive gene reduction (1 Mbp)
80 Cyanobacteria Chroococcales Cyanothece sp. ATCC51472 PC marine 1 JGI draft
81 Cyanobacteria Chroococcales Acaryochloris sp. CCMEE5410 APC only salted lake JCVI 511 contigs Chlorophyll d-producing cyanobacterium with no phycobilisome. Close to MBIC11017 strain.
82 Cyanobacteria Oscillatoriales Arthrospira (Spirulina) platensis Paraca PC freshwater 1 University of Applied Sciences of Western Switzerland draft (1820 scaffolds)
83 Cryptophyta Cryptomonadales Hemiselmis andersenii CCMP644 Cr-PE 555 marine n.a. Canadian Institute for Advanced Research complete Only the nucleomorph genome is available, so the phycobilin lyase set is only partial.
84 Cyanobacteria Chroococcales Crocosphaera watsonii WH0003 PC+PEI marine University of California at Santa Cruz unassembled contigs Unlike WH8501, this strain seemingly does not possess a rpcG-like gene, So Cys-82 alpha-PC likely binds PCB (or PEB?).
85 Cyanobacteria Chroococcales Microcystis aeruginosa PCC9701 PC freshwater 1 Genoscope incomplete
86 Cyanobacteria Chroococcales Microcystis aeruginosa PCC9808 PC freshwater 1 Genoscope incomplete
87 Cyanobacteria Chroococcales Microcystis aeruginosa PCC7941 PC freshwater 1 Genoscope incomplete
89 Cyanobacteria Chroococcales Microcystis aeruginosa PCC9443 PC freshwater 1 Genoscope incomplete
90 Cyanobacteria Chroococcales Microcystis aeruginosa PCC9717 PC freshwater 1 Genoscope incomplete
91 Cyanobacteria Chroococcales Microcystis aeruginosa PCC9432 PC freshwater 1 Genoscope incomplete
92 Cyanobacteria Chroococcales Microcystis sp. T1-4 PC+PEI freshwater 2 Genoscope incomplete
93 Cyanobacteria Chroococcales Synechococcus sp. WH8020 5.1 I Ia PC+PEI+PEII marine 3d/CA4 preliminary, incomplete draft Genome sequenced but not yet public (A.F. Post, pers. comm.). Sequences reported here come either from the sequencing of a large part of the PBS gene region (Wilbanks et al. 1993) or extracted from the preliminary genome assemblage (but set still incomplete).
94 Cyanobacteria Oscillatoriales Oscillatoria nigro-viridis PCC7112 PC+PEI soil in orchid house 2 JGI complete
95 Cyanobacteria Nostocales Scytonema hofmanni PCC7110 PC+PEC limestone Heinrich-Heine-University Duesseldorf contigs refseq not yet available
Bioproject: PRJNA157363
protein datafile available at http://www.molevol.de/resources/012cyano/PCC7110_cds_aa.fas
96 Cyanobacteria Stigonematales Fischerella muscicola PCC73103 (SAG 1427-1) PC+PEC Soil, rice field Heinrich-Heine-University Duesseldorf contigs Not available in refseq yet
Bioproject: PRJNA104965
Data available at: http://www.molevol.de/resources/012cyano/PCC73103_cds_aa.fas
97 Cyanobacteria Stigonematales Fischerella muscicola PCC7414 PC+PEC hot spring Heinrich-Heine-University Duesseldorf contigs Not available in refseq yet
Bioproject: PRJNA104967
Genbank: AJLK00000000
98 Cyanobacteriales Stigonematales Fischerella thermalis PCC7521 PC+PEC hot spring Heinrich-Heine-University Duesseldorf contigs Refseq not avialable yet
Bioproject: PRJNA104969
Genbank: AJLL00000000
99 Cyanobacteria Stigonematales Chlorogloeopsis sp. PCC9212 PC+PEC thermal spring Heinrich-Heine-University Duesseldorf contigs refseq not available yet
Bioproject: PRJNA104963
Genbank: AJLM00000000
100 Cyanobacteria Stigonematales Chlorogloeopsis fritschii PCC6912 PC+PEC soil Heinrich-Heine-University Duesseldorf contigs Refseq not available yet
Bioproject: PRJNA104961
Genbank: AJLN00000000
101 Cyanobacteria Nostocales Calothrix sp. PCC6303 PC+PEI freshwater 2 JGI complete possesses 3 plasmids
102 Cyanobacteria Nostocales Calothrix sp. PCC7507 PC+PEC sphagnum bog JGI complete
105 Cynaobacteria Oscillatorialles Oscillatoria sp. PCC10802 PC+PEI unknown (Thailand) JGI contigs Not in refseq
Bioproject: PRJNA158815
Genbank: ANKO00000000
106 Cyanobacteria Oscillatorialles Oscillatoria acuminata PCC6304 (SAG 1449-3) PC unknown JGI complete contains two plasmids
107 Cyanobacteria Stigonematales Fischerella sp. PCC9605 PC+PEC Limestone with cryptoendolithic growth JGI contigs Not yet in refseq
Bioproject: PRJNA158819
108 Cyanobacteria Stigonematales Fischerella sp. PCC9431 PC+PEC unknown JGI Not yet in refseq nor Genbank
Bioproject: PRJNA158821
109 Cyanobacteria Stigonematales Fischerella sp. PCC9339 PC+PEC JGI Not yet in refseq
Bioproject: PRJNA159505
Genbank; ALVS00000000
112 Cyanobacteria Nostocales Nostoc sp. PCC7524 PC+PEC moderate hot spring JGI complete contains two plasmids
113 Cyanobacteria Nostocales Nostoc sp. PCC7107 PC+PEC shallow pond (saline?) JGI complete Isolated in a pond at Point Reyes Peninsula, California (near the Pacific Ocean)
114 Cyanobacteria Nostocales Cylindrospermum stagnale PCC7417 PC+PEC soil (greenhouse) JGI Contains three plasmids
115 Cyanobacteria Nostocales Anabaena cylindrica PCC7122 PC+PEC freshwater pond JGI complete Contains six plasmids
116 Cyanobacteria Nostocales Anabaena sp. PCC7108 PC+PEC intertidal zone JGI contigs not yet in refseq
Bioproject: PRJNA158737
Genbank: AJWF00000000
120 Cyanobacteria Nostocales Rivularia sp. PCC7116 PC+PEC unknown JGI complete contains two plasmids
121 Cyanobacteria Chroococcales Synechocystis sp. PCC7509 PC rock JGI contigs (174)
122 Cyanobacteria Chroococcales Gloeocapsa sp. PCC7428 PC moderate hot spring JGI complete contains 4 plasmids
123 Cyanobacteria Pleurocapsales Chroococcidiopsis thermalis PCC7203 PC+PEC soil JGI complete contains 2 plasmids
124 Cyanobacteria Chroococcales Dactylococcopsis salina PCC8305 saline lake JGI complete
125 Cyanobacteria Chroococcales Halothece sp. PCC7418 PC saline lake JGI complet
128 Cyanobacteria Pleurocapsales Pleurocapsa sp. PCC7327 PC+PEI hot Spring JGI complete
129 Cyanobacteriales Chroococcales Gloeocapsa sp. PCC73106 PC+PEI sphagnum bog JGI contigs
130 Cyanobacteria Oscillatoriales Leptolyngbya sp. PCC7376 PC+PEI marine JGI complete
131 Cyanobacteria Chroococcales Cyanobacterium stanieri PCC7202 PC alkaline pond JGI complete
133 Cyanobacteria Chroococcales Cyanobacterium aponimum PCC10605 JGI complete contains 1 plasmid
134 Cyanobacteria Pleurocapsales Stanieria cyanosphaera PCC7437 PC+PEI freshwater (pool) JGI complete contains 5 plasmids
136 Cyanobacteria Pleurocapsales Xenococcus sp. PCC7305 PC+PEI marine JGI contigs (235)
137 Cyanobacteria Oscillatoriales Microcoleus sp. PCC7113 PC+PEI soil, orchid house 2 JGI complete contains 8 plasmids
138 Cyanobacteria Oscillatoriales Crinalium epipsammum PCC9333 PC sandy crust JGI complete contains 8 plasmids
139 Cyanobacteria Chroococcales Chamaesiphon minutus PCC6605 PC+PEI freshwater JGI complete contains 2 plasmids
141 Cyanobacteria Chroococcales Cyanobium gracile PCC6307 PC freshwater (lake) JGI complete
143 Cyanobacteria Oscillatoriales Leptolyngbya sp. PCC6406 PC+PEC freshwater JGI contigs (378)
145 Cyanobacteria Oscillatoriales Leptolyngbya sp. PCC7375 PC+PEI marine? 2 JGI contigs (six)
146 Cyanobacteria Oscillatoriales Geitlerinema sp. PCC7407 PC unknown JGI complete
147 Cyanobacteria Oscillatoriales Leptolyngbya boryana PCC6306 PC freshwater JGI contigs not yet in refseq nor Genbank
148 Cyanobacteria Chroococcales Synechococcus sp. PCC6312 PC freshwater JGI complete contains 1 plasmid
149 Cyanobacteria Chroococcales Synechococcus sp. PCC7502 PC sphagnum bog JGI complete contains 2 plasmids
151 Cyanobacteria Oscillatoriales Pseudanabaena sp. (biceps) PCC7429 PC sphagnum bog JGI contigs (465)
152 Cyanobacteria Oscillatoriales Pseudanabaena sp. PCC7367 PC+PEI Snail shell. Intertidal zone JGI complete
154 Cyanobacteria Chroococcales Microcystis aeruginosa TAIHU98 PC freshwater 1

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