Calothrix sp. PCC 7507 Microchaete sp. PCC 7126 Nostoc punctiforme PCC 73102

Cylindrospermum stagnale PCC 7417 Nodularia spumigena CCY 9414

Nostoc sp. PCC 7107 Nostoc sp. PCC 7524

Anabaena variabilis ATCC 29413 Nostoc sp. PCC 7120

Cylindrospermopsis raciborskii CS-509 Cylindrospermopsis raciborskii CS-505 Raphidiopsis brookii D9

Anabaena sp. PCC 7108 Anabaena cylindrica PCC 7122

Nostoc azollae 0708 Anabaena sp. 90 Anabaena circinalis AWQC131C Anabaena circinalis AWQC310F

Tolypothrix sp. PCC 9009 Mastigocladopsis repens PCC 10914

Chlorogloeopsis fritschii PCC 9212 Chlorogloeopsis fritschii PCC 6912

Unidentified cyanobacterium PCC 7702 Fischerella sp. PCC 9605

Fischerella sp. JSC-11 Fischerella thermalis PCC 7521

Fischerella sp. PCC 9431 Fischerella muscicola PCC 73103

Fischerella sp. PCC 9339 Calothrix sp. PCC 6303

Calothrix desertica PCC 7102 Calothrix sp. PCC 7103

Mastigocoleus testarum BC008 Rivularia sp. PCC 7116

Richelia intracellularis HH01 Synechocystis sp. PCC 7509

Chroococcidiopsis thermalis PCC 7203 Gloeocapsa sp. PCC 7428 Crinalium epipsammum PCC 9333

Chamaesiphon minutus PCC 6605 Microcoleus chthonoplastes PCC 7420

Microcoleus sp. PCC 7113 Spirulina major PCC 6313

Spirulina subsalsa PCC 9445 Cyanobacterium sp. ESFC-1

Dactylococcopsis salina PCC 8305 Halothece sp. PCC 7418 Gloeocapsa sp. PCC 73106

Geminocystis herdmanii PCC 6308 Cyanobacterium aponimum PCC 10605

Cyanobacterium stanieri PCC 7202 Synechococcus sp. PCC 7002

Leptolyngbya sp. PCC 7376 Stanieria cyanosphaera PCC 7437

Pleurocapsa sp. PCC 7319 Chroococcidiopsis sp. PCC 6712 Xenococcus sp. PCC 7305

Synechocystis sp. PCC 6803 Microcystis aeruginosa NIES-843

Cyanothece sp. PCC 7424 Cyanothece sp. PCC 7822

Pleurocapsa sp. PCC 7327 Cyanothece sp. PCC 8801 Cyanothece sp. PCC 8802

Cyanobacterium sp. UCYN-A Crocosphaera watsonii WH 8501

Cyanothece sp. CCY 0110 Cyanothece sp. ATCC 51142 Cyanothece sp. ATCC 51472

Geitlerinema sp. PCC 7105 Oscillatoria acuminata PCC 6304

Oscillatoria sp. PCC 10802 Microcoleus vaginatus PCC 9802 Microcoleus vaginatus FGP-2 Oscillatoria nigro-viridis PCC 7112

Oscillatoria sp. PCC 6506 Oscillatoria formosa PCC 6407

Trichodesmium erythraeum IMS101 Arthrospira platensis Paraca Arthrospira platensis NIES-39 Arthrospira sp. PCC 8005

Arthrospira maxima CS-328 Arthrospira platensis C1

Geitlerinema sp. PCC 7407 Oscillatoriales sp. JSC-1

Leptolyngbya boryana PCC 6306 Oscillatoriales sp. JSC-12

Acaryochloris sp. CCMEE 5410 Acaryochloris marina MBIC11017

Cyanothece sp. PCC 7425 Synechococcus sp. PCC 6312

Thermosynechococcus elongatus BP-1 Synechococcus sp. PCC 7335

Leptolyngbya sp. PCC 7375 Nodosilinea nodulosa PCC 7104

Leptolyngbya sp. PCC 6406 Prochlorothrix hollandica PCC 9006

Synechococcus elongatus PCC 7942 Synechococcus elongatus PCC 6301

Synechococcus sp. CB 0205 Synechococcus sp. CB 0101

Cyanobium sp. PCC 7001 Cyanobium sp. PCC 6307

Synechococcus sp. WH 5701 Synechococcus sp. RCC307

Prochlorococcus marinus MIT 9301 Prochlorococcus marinus AS 9601 Prochlorococcus marinus MIT 9312 Prochlorococcus marinus MIT 9215

Prochlorococcus marinus MIT 9202 Prochlorococcus marinus MIT 9515 Prochlorococcus marinus, subsp. pastoris CCMP 1986

Prochlorococcus marinus MIT 9211 Prochlorococcus marinus, subsp. marinus CCMP 1375

Prochlorococcus marinus NATL 1A Prochlorococcus marinus NATL 2A

Prochlorococcus marinus MIT 9313 Prochlorococcus marinus MIT 9303

Synechococcus sp. WH 8109 Synechococcus sp. CC 9605 Synechococcus sp. WH 8102

Synechococcus sp. CC9616 Synechococcus sp. CC 9902 Synechococcus sp. BL 107

Synechococcus sp. RS 9917 Synechococcus sp. RS 9916

Synechococcus sp. WH 7805 Synechococcus sp. WH 7803

Synechococcus sp. CC 9311 Synechococcus sp. WH 8016

Pseudanabaena sp. PCC 7367 Pseudanabaena sp. PCC 7429

Synechococcus sp. PCC 7502 Pseudanabaena sp. PCC 6802

Synechococcus sp. PCC 7336 Synechococcus sp. JA-2-3B Synechococcus sp. JA-3-3Ab

Gloeobacter violaceus PCC 7421

100 54

87 78

100 100 100 81

100 100

100 95

100 100 100

81

100

93

100 97

100

99 100 100

100 100

97

99

100 100

67

74

58

100

66 100

100

100

100

100 100

100 100

100 100

100 100

100 100 100

92

100 89

100

100 100 100 100 100

51 67

100

73

100

76 100

92

72

100 100

100 100

100

99 100 100

100 99

53 74

100

100 99 56

73

100

100 99 100

68

100

100 100

100 100

93

84 100

55

100 80

100 100

100 100

100

100 100

100 100

97 96

100 100

99 100

100 97 100

100

100

75

100

97

95

58

95

81 94 100

100

100 100

100

0.05

Supplementary Figure 1

1A

Heterocystous

1B

1C

2

3

4

5

6

7

8

9

393 437

Nostoc sp. PCC 7120 17231510 CSETGGCMRMETHGGAQ A AGLFQQVSSLSEQKAEALLSQQVQRWG

Anabaena variabilis ATCC 29413 75907904 ----------------- - ---------------------------

Nostoc punctiforme PCC 73102 186684152 ----------------- S -------T-------------------

'Nostoc azollae' 0708 298490390 ----------------- S ---------------------------

Nodularia spumigena CCY9414 119511492 ----------------- - -------G-------------------

Raphidiopsis brookii D9 282897264 -T----------Q---- S -------N--A---P-F----------

Cylindrospermopsis raciborskii CS-505 282899816 -T----------Q---- S -------N--A---P-F----------

Fischerella sp. JSC-11 354568217 -T----------Q---- S T------T--------V----------

Anabaena sp. 90 414078165 ----------------- S S------T-------------------

Anabaena cylindrica PCC 7122 2504130653 ----------------- S ----------------V----------

Anabaena sp. PCC 7108 2506489905 ----------------- S ----------------V----------

Calothrix desertica PCC 7102 2510027306 ------------Q---- S T------T-------------------

Calothrix sp. PCC 6303 2504094737 ------------Q---- S T--------------------------

Calothrix sp. PCC 7103 2507480228 ------------Q---- S T------T-------------------

Calothrix sp. PCC 7507 2505802851 -T--------------- S ---------------------------

Cylindrospermum stagnale PCC 7417 2509770253 ----------------- S ---Y------------V----------

Fischerella sp. PCC 9339 2517062478 -T----------Q---- S -------T--------V----------

Fischerella sp. PCC 9431 2512977690 -T----------Q---- S -------T--------V----------

Fischerella sp. PCC 9605 2516145506 ------------Q---- S V------T--------V----------

Nostoc sp. PCC 7107 2503741400 ----------------- S ---------------------------

Nostoc sp. PCC 7524 2509808890 ----------------- S ---------------------------

Rivularia sp. PCC 7116 2510086386 ------------Q---- S --V---IT-------------------

Tolypothrix sp. PCC 9009 2507331957 ------------Q---- S S----H-T--------V----------

Mastigocladopsis repens PCC 10914 2517239059 ------------Q---- S T-V---------------V--------

Synechocystis sp. PCC 7509 2517698676 ----S------SG---- SCR-------AD----L---E-L----

Chroococcidiopsis thermalis PCC 7203 2503611005 ----S------A----- --IVN--T--AD-S--E-----L----

Gloeocapsa sp. PCC 7428 2503794189 -----------VG---- -CR-------AD----I-----L--V-

Crinalium epipsammum PCC 9333 2504686063 ----S------AG-R-- SCRIL--AP-TD--P-Q-----LR---

Oscillatoriales cyanobacterium JSC-12 410710805 ----A------SG---- S TIRTE--TAT-D----L--T--L----

Oscillatoria sp. PCC 6506 300866082 -----------S----- T-RIN--TP-FD-QT-Q----HL----

Microcoleus chthonoplastes PCC 7420 254413372 --Q-T------A----- -CRI---TPMFD--T-Q-----L---S

Microcoleus vaginatus FGP-2 334118083 ---V--------K---- TDR-N---P-FD-VT-H--G-HL-S--

Arthrospira platensis Paraca 284052912 ----T------AG-S-- SCQTE--T-VTD----Y-MA--L----

Arthrospira platensis NIES-39 291565751 ----T------AG-T-- SCQTE--T-VTD----Y-MA--L----

Arthrospira maxima CS-328 209528064 ----T------AG-S-- SCQTE--T-VTD----Y-MA--L----

Arthrospira sp. PCC 8005 376004853 ----T------AG-S-- SCQTE--T-VTD----Y-MA--L----

Trichodesmium erythraeum IMS101 113474534 ----T----L-AG-S-- SCRTE---A--D----Y-MA--L----

Cyanothece sp. PCC 7424 218438479 ----T------AS---- SCRI---T--AD-NT-Q--G--LR---

Cyanothece sp. PCC 8802 257061610 --G-T------AS---- -CRIE--T--AD-NT-Y--GR-L----

cyanobacterium UCYN-A 284929726 --G-T------AS---- -CRIE--T--AD--TDN-IQR-L----

Crocosphaera watsonii WH 8501 67922964 --G-T------AS---- -CRIE--T--AD-QTDQ-IQK-L----

Cyanothece sp. ATCC 51142 172037448 --G-T------AS---- -CRIE--T--AD--TDQ-IEK-L----

Cyanothece sp. PCC 7425 220908800 ----K------AG---- SC-TY---P-A--RS-V----EL----

Cyanothece sp. CCY0110 126659462 --G-T------AS---- -CRIE--TP-GD--T-H-IEK-L----

Cyanothece sp. PCC 7822 307153983 ----K------AS---- SCRIE--T--AD-NT-Q--G--LR---

Microcystis aeruginosa NIES-843 166367106 --G-T------AS---- SCRVE---H-ED--T-T--GK-L----

Synechocystis sp. PCC 6803 16330360 --G-V------AG---- NYRV---TA-DD-NT-Q--GR-L----

Microcystis aeruginosa PCC 7806 159027869 --G-T------AS---- SCRIE---H-ED--T-T--GK-L----

Synechococcus elongatus PCC 6301 56751778 ----T------AG---- SCRTE--APP-NETS-S--AM-M----

Synechococcus sp. PCC 7002 170078067 ----S---H--SG---- SCRIE--TP-AD-AT-H--G--L----

Thermosynechococcus elongatus BP-1 22298082 ----R------AG-S-- LCRTYH-TP--D-T--I----EL----

Acaryochloris marina MBIC11017 158336019 ----R------AG---- SCRI-H-TP-QD-SS-T-----L---D

Acaryochloris sp. CCMEE 5410 359460906 ----R------AG---- SCRI-H-TP-QD-SS-T-----L---D

Synechococcus sp. JA-3-3Ab 86605107 ----T------AR---- RCVVR--AP-EQESL-T--AAEL--P-

Synechococcus sp. JA-2-3B'a(2-13) 86610338 ---IT------AM---- RCVVR--AP-EQDSLDT--AAEL--L-

Supplementary Figure 2

Partial sequence alignment for an outer membrane adhesion protein (OpcA), showing a 1 aa insert that is specific for all heterocystous cyanobacteria.

Other

Cyanobacteria

Heterocystous

Clade 1A

(35/35)

Clade 1B

Clade 1C

12 58

Nostoc sp. PCC 7120 17227740 YQEAKNAYTQPQAVIVLGGST RNL EREKFTASFARKHPNLPIWISGG

Anabaena variabilis ATCC 29413 75908946 --------------------- --- -----------Q-----------

Nostoc punctiforme PCC 73102 186685641 -K-VQ-QFV-----V------ -R- -------E-V-Q---I----T--

'Nostoc azollae' 0708 298492064 -K-VQ-QLLH----L------ -R- -------N--N----I-------

Nodularia spumigena CCY9414 119512189 ---S-IEELP----L------ SH- -------N---Q--S--------

Raphidiopsis brookii D9 282897433 -R-VQ-QFSI----L-----S KH- ---R-A-N--K----I----T--

Cylindrospermopsis raciborskii CS-505 282900742 -R-VQ-QFSI----L-----S KR- ---R-A-N--K----I----T--

Fischerella sp. JSC-11 354565955 -K-IQGQF-----IL------ KK- -------D---------------

Anabaena sp. 90 414076403 KAVQ-QFV----IL------ -L- -------KL-HQY--I-------

Anabaena cylindrical PCC 7122 2504134854 -K-VQ-RIVH---ML------ -R- -------D--KD--DI----T--

Anabaena sp. PCC 7108 2506491282 -K-VQTQFV----ML------ -R- -------D-------I----T--

Calothrix desertica PCC 7102 2510024772 -R-VQ-TFI--E-IL------ KS- -------Q--K---SI-------

Calothrix sp. PCC 6303 2504097749 -K-VASQFKH-E-IL------ QK- ---Q---K-----Q-M-------

Calothrix sp. PCC 7103 2507478722 -R-VQ-TFI--E-IL------ KS- -------K--K---SI-------

Calothrix sp. PCC 7507 2505801542 -K-V-SQFV-----V------ KY- -------D------D--------

Cylindrospermum stagnale PCC 7417 2509771849 -K-VQ-QFSH---ML------ -R- -------D---E---I----T--

Fischerella sp. PCC 9339 2517061082 -K-IQGQF-----IL------ KK- -------D---------------

Fischerella sp. PCC 9431 2512978662 -K-IQGQF-----IL------ KK- -------D---------------

Fischerella sp. PCC 9605 2516144190 -K-IQGQLV----IL------ -K- -------D-----SD--------

Mastigocladopsis repens PCC 10914 2517240349 -K-IQSQFV----IL------ SK- -------D--H-Y----------

Nostoc sp. PCC 7107 2503740398 -K-FQQQTK--E--L------ KK- -------E-V-------------

Nostoc sp. PCC 7524 2509811009 ------ND-----I------- K-- -------K---Q------L----

Rivularia sp. PCC 7116 2510085245 -KKVQTVFV----IL------ KS- -------K--K------------

Tolypothrix sp. PCC 9009 2507333918 -K-V-SQVV-----L------ AR- -------D----N-------T--

Synechocystis sp. PCC 7509 497320292 SAI-LKIAPF---ILT---DI Y--ISA-N--KMY---DL---S-

Chroococcidiopsis thermalis PCC 7203 2503615841 ---V-SQLEPY--IL-----V Q----AIE--QNK-D----V---

Gloeocapsa sp. PCC 7428 2503796048 -K-I-SQLEP---IL-----T K----A-Q------DI---V---

Crinalium epipsammum PCC 9333 2504685048 -K-I-SYFV---VIF----EP L--Q-A-K---Q---I---V---

Chamaesiphon minutus PCC 6605 2510440289 -R-LE-NWI----IF----EE ---L-A-K--HQ-----V-----

Microcoleus vaginatus FGP-2 334119335 --QV-SEFQR----L----A- ---V-A-K---DY-E----V-S-

Oscillatoria sp. PCC 6506 300867952 FNQI-SYWE----LF----AA ---V-A-K---E--Q----V-S-

Trichodesmium erythraeum IMS101 113475490 --QISGTIKP---LL----AI ---A-A-E---Q----D--V-S-

Microcoleus chthonoplastes PCC 7420 254409604 -KQIQSYLI--E-IL----EE ---L-A-D--QQ--D-H--V-S-

Moorea producta 3L 332709823 -KRIESYLV--KVAL-----E S--RYA-K--I---D-N--V-S-

Crocosphaera watsonii WH 0003 357262463 -KQLQSHFV--E-IF----HE D--R-A-QL-L---D----V-S-

Cyanothece sp. CCY0110 126654814 -KQLQSYFA--E-IF----HE D--R-A-KL-LE-------V-S-

Crocosphaera watsonii WH 8501 67923734 -KQLQSHFV--E-IF----HK D--S-A-QL-L---D----V-S-

Cyanothece sp. ATCC 51142 172037429 -KQLQAYFV--E-IF----HE D--R-A-KL-LE--D----V-S-

Cyanothece sp. PCC 8801 218246780 -KQVQSYRVK-E-IF----HE ---R-A-QL-KD--T----V-S-

Microcystis aeruginosa NIES-843 166368105 -HDLRQQWLK-E-IF----HA D--R-A-KL-KEY-D----V-S-

Cyanothece sp. PCC 7424 218440733 -KQIQSYLVK-E-IL----HE ---R-A-HL-A-N-Q----V-S-

Cyanothece sp. PCC 7822 307151691 -N-IQSYLVK-E-IV----HE ---RYA-HL-S-N-T----V-S-

Microcystis aeruginosa PCC 7806 159027601 -LDLRQQWLK-E-IF----HA D--R-A-KL-KEY-D----V-S-

Synechococcus sp. PCC 7002 170078552 --RIQG-LRPAK-IF----HE ---R-A-Q--QE--D-KV-V-S-

Synechococcus sp. PCC 7335 254423350 -TRYQQQFLT-PVAL----AP ---R-A-Q--KT--TVE----S-

Supplementary Figure 3

Partial sequence alignment for the hypothetical protein Npun_R5589, showing a 3 aa insert that is specific for all heterocystous cyanobacteria.

Other

Cyanobacteria

Heterocystous

Clade 1A

(35/35)

Clade 1B

Clade 1C

15 49

Raphidiopsis brookii D9 282896270 EVQEILNLAIARQ SK DLSQEFSYQQILEIAKELQI

Cylindrospermopsis raciborskii CS-505 282901647 ------------- -- --------------------

'Nostoc azollae' 0708 298492349 ---Q--Q------ TD -GA--------I---A----

Nostoc punctiforme PCC 73102 186682283 D--Q--H------ AN -KNT----E------A--E-

Nodularia spumigena CCY9414 119513508 D--R--Q------ AD -QDK------L-------D-

Anabaena variabilis ATCC 29413 75910215 D--R--Q------ AD -QDK----E-L----T--E-

Nostoc sp. PCC 7120 17228870 D--R--Q------ AD -QDKD---E-L----T--E-

Fischerella sp. JSC-11 354564846 DI-K--H------ A- -QEK----E-L----T--E-

Anabaena sp. 90 414076514 D--Q--Q------ VD -ND--------V---T----

Anabaena cylindrical PCC 7122 2504134472 ---Q--Q------ TN -RD--------I---A----

Anabaena sp. PCC 7108 2506493475 ---Q--Q------ TH -HN--------I---A----

Calothrix desertica PCC 7102 2510029456 DI-Q--H---T-- AS -QEK----E-LR---R--E-

Calothrix sp. PCC 6303 2504096913 DI-Q--QI---H- V- -DNK------LA---G--E-

Calothrix sp. PCC 7103 2507475919 DI-Q--H---T-- AS -QEK----E-LR---S--E-

Calothrix sp. PCC 7507 2505802223 ---Q--H------ AA -PDR----KEL----A--E-

Cylindrospermum stagnale PCC 7417 2509768490 D--K--QF----- AD -QNK----E------A--E-

Fischerella sp. PCC 9339 2517061191 DI-K--H------ A- -QEK----E-L----G--E-

Fischerella sp. PCC 9431 2512978111 DI-K--H------ A- -QEK----E-L----G--E-

Fischerella sp. PCC 9605 2516145318 D--K--Q------ AR -QEK----E-L----A--E-

Mastigocladopsis repens PCC 10914 2517240588 DI-Q-------TE AD -KDK----E-L----A--E-

Nostoc sp. PCC 7107 2503739014 D--R--Q------ AD -QDK----ELL----G--D-

Nostoc sp. PCC 7524 2509810010 DI-R--Q------ AD -QDK----E------Q--E-

Tolypothrix sp. PCC 9009 2507333762 D--Q--H------ AD -KEK----E-L----A--E-

Rivularia sp. PCC 7116 427733945 D--Q--Q------ V D-DK---HEVL----A--D-

Synechocystis sp. PCC 7509 2517699426 DI-Q--SI----- -D-T------LV---E--E-

Chroococcidiopsis thermalis PCC 7203 428207657 DI-Q--QI----- AYEG---R--L----A--E-

Gloeocapsa sp. PCC 7428 434395444 DI-Q--QI--S-- AHEG--TRE-LV---A--E-

Moorea producta 3L 332711211 DI-Q-----L--- EMVE---RE-LV---S--G-

Microcoleus chthonoplastes PCC 7420 254410564 -L-Q------V-- ANGG---RT-LV---A--G-

Trichodesmium erythraeum IMS101 113477975 D--Q--Q--LVNR SEGG--TKV-L----Q-MGV

Oscillatoria sp. PCC 6506 300864692 DA-Q--Q-----R EETG-M-RT-LF-V-S--G-

Lyngbya sp. PCC 8106 119488066 DA----KI-F-KK -ENG-LTRP-LM---I--G-

Arthrospira maxima CS-328 209527444 DA----QI-M--G QETG-LTRT-LE-M-M--G-

Arthrospira sp. PCC 8005 376003370 DA----QI-M--G QETG-LTRT-LE-M-I--G-

Cyanothece sp. PCC 7822 307154767 DI-Q--H--L--R NDQE-L-RE-LW---A--E-

Cyanothece sp. PCC 7424 218441995 DI-Q--Q------ TDKE-L-RE-LW---A--E-

Synechococcus elongatus PCC 6301 56752424 D-----QR----S TAQD---A--LQ-M-A--G-

Cyanothece sp. PCC 7425 220906465 D--Q---I---HD TDKE---RT-L----A--G-

Acaryochloris marina MBIC11017 158339009 Q--Q-------Q- -YEG---HA-L----E--A-

Acaryochloris sp. CCMEE 5410 359461391 Q--Q-------Q- -YEG---HA-L----E--A-

Cyanothece sp. PCC 8802 257061346 D-----H-----K TDVE-L-RA-LW---A--D-

Cyanothece sp. PCC 8801 218247319 D-----H-----K TDVE-L-RA-LW---A--D-

Synechococcus sp. PCC 7335 254421339 -A-Q--QI---KE TE-G-LTRL-LS---A--N-

Crocosphaera watsonii WH 8501 67921458 ------H-----K TEVE-L-RT-LW---A--D-

Microcystis aeruginosa NIES-843 166364903 D-----Y---S-- GDKG-ITR--L----DD-A-

Microcystis aeruginosa PCC 7806 159030188 D-----Y---S-- GDRG-ITR--L----DD-A-

Cyanothece sp. ATCC 51142 172035381 ------H-----K TEVE-L-RT-LW---A--D-

Cyanothece sp. CCY0110 126660395 ------H-----K TEVE-L-RT-LW---A--D-

Synechococcus sp. JA-2-3B'a(2-13) 86609907 D--Q--QR----- PRLG--TRS-LQ-M-A--G-

Supplementary Figure 4

Partial sequence alignment for the hypothetical protein Aazo_3898, showing a 2 aa insert that is specific for all heterocystous cyanobacteria.

Other

Cyanobacteria

Heterocystous

Clade 1A

(35/35)

Clade 1B

138 166

Cylindrospermopsis raciborskii cs-505 282900401 LRLINPNTVETLVV EGTLKPANTKVLDTS

Raphidiopsis brookii D9 282896777 -------------- ---------------

Nostoc punctiforme PCC 73102 186681617 --F-------SM-- ---------------

Anabaena variabilis ATCC 29413 75908439 --F--------M-A ---------------

Nostoc sp. PCC 7120 17232449 --F--------M-A ---------------

'Nostoc azollae' 0708 298492588 -----------M-- ---------------

Nodularia spumigena CCY9414 119512057 --F--------M-- -------H-------

Fischerella sp. JSC-11 354566808 -----------M-- -------S-------

Anabaena sp. 90 414079171 ----------SM-- ---------------

Anabaena cylindrical PCC 7122 2504134966 -------------- ---------------

Anabaena sp. PCC 7108 2506492599 -------------- ---------------

Calothrix desertica PCC 7102 2510031380 I-F----S-GA--- -------G-------

Calothrix sp. PCC 6303 2504093044 ------S---SML- ---------------

Calothrix sp. PCC 7103 2507482394 I-F----S-GA--- -------G-------

Calothrix sp. PCC 7507 2505804306 --F--------M-- ---------------

Cylindrospermum stagnale PCC 7417 2509766399 -----------M-- ---------------

Fischerella sp. PCC 9339 2517063661 -------------- -------S-------

Fischerella sp. PCC 9431 2512980373 ------------L- -------S-------

Fischerella sp. PCC 9605 2516144991 -----------M-- -------S-------

Mastigocladopsis repens PCC 10914 2517242224 -----------M-- -------S-------

Nostoc sp. PCC 7107 2503741797 -----------M-A ---------------

Nostoc sp. PCC 7524 2509810941 --F--------M-A -------R-------

Rivularia sp. PCC 7116 2510088452 -----------M-A -------T-------

Tolypothrix sp. PCC 9009 2507336664 -----------M-- ---------------

Fischerella muscicola PCC 7414 428160144 -----------M-- -------S-------

Fischerella thermalis PCC 7521 428159493 -----------M-- -------S-------

Mastigocoleus testarum BC008 548699197 --------L-SM-- -------S-------

Synechocystis sp. PCC 7509 2517697026 --I-------SML- A ------SI-------

Chroococcidiopsis thermalis PCC 7203 2503613126 -------S---ML- A -------A-------

Gloeocapsa sp. PCC 7428 2503795020 -----F-N--SVLL A -----A-A---V---

Oscillatoria sp. PCC 6506 300866347 -------SLD-VL- A ---F---P-------

Trichodesmium erythraeum IMS101 113474964 -------SLDAVL- A ------ST--I----

Lyngbya sp. PCC 8106 119486128 ---L---SL-SMLI A -------SS-I----

Microcoleus vaginatus FGP-2 334119393 ------KSFD-VL- A ---F---SA--V---

Arthrospira platensis Paraca 284050004 -Q-----SL--TLL A -----S-H-------

Arthrospira platensis NIES-39 291571392 -Q-----SL--TLL A -----S-H-------

Arthrospira maxima CS-328 209523296 -Q-----SL--TLL A -----S-H-------

Moorea producta 3L 332709826 -Q-----SL-SVL- A -----S-SS-II---

Microcoleus chthonoplastes PCC 7420 254414739 -------SLD-ML- A -------TS------

Cyanothece sp. PCC 8801 218247389 -------SI---L- A ----Q--S--I----

Cyanothece sp. PCC 7424 218441363 -------SI-SML- A Q---Q--S--II---

Cyanothece sp. PCC 7822 307153453 -------SI-SML- A Q---Q--A--II---

Cyanothece sp. ATCC 51142 172037003 -------SI---L- A ----QA-S---V---

Cyanothece sp. CCY0110 126657580 -------SI---L- A ----QA-S--IV---

Crocosphaera watsonii WH 8501 67921336 -------SI---L- A ----QA-S---V---

Synechococcus sp. PCC 7335 254422819 F------SY---LI S ------SKS------

Cyanothece sp. PCC 7425 220907268 ---V---S----LL A -------AA------

Microcystis aeruginosa PCC 7806 159030191 -------SM-SIL- A ----QA-A---V---

Microcystis aeruginosa NIES-843 166364900 -------SM-SIL- A ----QA-A---V---

Synechocystis sp. PCC 6803 16330795 M------SI--MLL A ------IPP--V---

Synechococcus elongatus PCC 7942 81301192 I--V--GS--SALL A -------IS--I---

Synechococcus elongatus PCC 6301 56751731 I--V--GS--SALL A -------IS--I---

Synechococcus sp. PCC 7002 170079416 -------SLD--L- A ----R-SP--II---

Acaryochloris marina MBIC11017 158334463 -------SI--MLL A ----Q-SP-------

Synechococcus sp. CB0101 318040430 ---F---ST-A-L- A D-V-M--SA-I----

Synechococcus sp. CB0205 317970579 ---F---ST-A-L- A D-V-M--SA-I----

Synechococcus sp. JA-3-3Ab 86605617 ---F---Y ALQAA A --SVVA-SP------

Cyanobium sp. PCC 7001 254432606 ---FS-G-T-A-L- A --V-R--SA-I----

Synechococcus sp. WH 5701 87302967 ---F--SST-A-L- A D-V-Q--TA-I----

Synechococcus sp. RCC307 148241696 ---F--SST-A-L- A D-V-Q--SP-IV---

Synechococcus sp. CC9902 78185114 ---F--AST-A-L- A D-V-T--TA-I----

Synechococcus sp. CC9311 113954728 ---F--TST-A-L- A D-V-T--TP-I----

Synechococcus sp. WH 8109 260434968 ---F--AST-A-L- A D-V-T--TA-I----

Synechococcus sp. CC9605 78212386 ---F--AST-A-L- A D-V-T--TA-I----

Synechococcus sp. WH 7805 88809168 ---F--TST-A-L- A D-V-T--TA-I----

Gloeobacter violaceus PCC 7421 37522655 --RF-L-SLNAGSE S GQFRGD-RP-IV---

Prochlorococcus marinus NATL1A 124026438 ---F---ST-S-L- A D-V-T--SA------

Prochlorococcus marinus MIT 9211 159903901 ---L---ST-A-LI A --I-T--SG-I----

Prochlorococcus marinus CCMP1375 33240835 ---L---SA-A-L- A --I-T--SA-II---

Supplementary Figure 5

Partial sequence alignment for a PilT domain-containing protein, showing a 1 aa deletion that is specific for all heterocystous cyanobacteria.

Other

Cyanobacteria

Heterocystous

Clade 1A

(35/35)

Clade 1B

150 188

Anabaena variabilis ATCC 29413 75909548 WYVRRFRQLFVNSDLGKTI AE SPLIQPLISSFFNVNWTA

Nostoc sp. PCC 7120 17231973 ------------------- -- ------------------

Nodularia spumigena CCY9414 119510108 ------Q------------ -- ------------------

Nostoc punctiforme PCC 73102 186684639 ------------------- T- -------------I----

'Nostoc azollae' 0708 298489626 ------------------- S- -----SV-T--------V

Cylindrospermopsis raciborskii 282899262 --I------LA------A- S- ------V-T-L-------

Raphidiopsis brookii D9 282897934 --I------LA------A- S- ------V-T-L-------

Fischerella sp. JSC-11 354564838 -----------------A- S- ---------T---I---S

Anabaena sp. 90 414077181 --M---------------- T- ----------L--I----

Anabaena cylindrical PCC 7122 2504134583 ------------------- T- --------T---------

Anabaena sp. PCC 7108 2506494235 ------------------- T- ----------LV---GN-

Calothrix desertica PCC 7102 2510029004 -----------------A- S- ---------T---I---S

Calothrix sp. PCC 6303 2504098517 ----------A-----RS- S- -------V-T---I---S

Calothrix sp. PCC 7103 2507476256 --------V--------A- S- ---------T---I---S

Calothrix sp. PCC 7507 2505803562 -----------S-----A- -- --F----------I----

Cylindrospermum stagnale PCC 7417 2509767434 ----------I-------- -- ------------------

Fischerella sp. PCC 9339 2517061650 ------QK----------- S- -------------I---S

Fischerella sp. PCC 9431 2512978140 ------QK---------A- S- ----------L--I---S

Fischerella sp. PCC 9605 2516145094 --------------F--A- S- ---------T--------

Mastigocladopsis repens PCC 10914 2517243856 ----------I-------- S- ---------T-------S

Nostoc sp. PCC 7107 2503739419 ------------------- T- ------------------

Nostoc sp. PCC 7524 2509810080 ---------I--------- -- --------T----I----

Rivularia sp. PCC 7116 2510091050 ----------I------A- SD --F------T-L---P--

Tolypothrix sp. PCC 9009 2507333152 --L--------------A- S- --F----V-T---I----

Synechocystis sp. PCC 7509 2517696510 --S---GK-ITE---V--V --FL----ATV---S--G

Chroococcidiopsis thermalis PCC 7203 2503615542 --A---GK-ITD----R-V --FL---LA-I---S--G

Gloeocapsa sp. PCC 7428 2503796761 ----------T------A- -D --F---------------

Oscillatoria sp. PCC 6506 300867643 --I-----V-AD-----SL --FV--VV-TVL--D-SG

Microcoleus chthonoplastes PCC 254414832 --F-----I-TE-----A- --F---VT-AIL--T--P

Trichodesmium erythraeum IMS10 113474690 --I-----VILD---Y-A- --FV--VSNAIL--D--G

Arthrospira sp. PCC 8005 376003701 --I-----V-LD-----AL --FV--IA-TVLS-DISG

Arthrospira maxima CS-328 209523873 --I-----V-LD-----AL --FV--IA-TVLS-DISG

Arthrospira platensis Paraca 284053117 --I-----V-LD-----AL --FV--IA-TVLS-DISG

Lyngbya sp. PCC 8106 119486305 --------V-LD--FW-A- --FA--VS-AVLS-DLS-

Moorea producta 3L 332710553 --S-----VMAD-----AL --F---VT-AIL--S--S

Microcoleus vaginatus FGP-2 334121333 --I-----AL-D-----AL --F---VV-TVLT-DLSG

Cyanothece sp. PCC 7425 220908177 --------V-AD-----AL A-F---IT-TVL----S-

Acaryochloris sp. CCMEE 5410 359459621 --A-----VIAD-----AL --FV--VTAAV-T--LAG

Acaryochloris marina MBIC11017 158339106 --A-----VIAD-----AL --FV--VTAAV-T--LAG

Synechococcus sp. PCC 7002 170077619 --I----EV-QA----RAV --F---VT-AIL--S--F

Cyanothece sp. PCC 7822 307152899 --I-----VLTE--I--IL --F---IT-AIL--S---

Cyanothece sp. PCC 7424 218438224 --A-----V-TD--I--VL --FV--ITAAI--MS---

cyanobacterium UCYN-A 284929490 --LE----I-AE------L V-F------TIL-TS--L

Cyanothece sp. PCC 8802 257059735 --L---G-ILQE--I--AL --F---IT-AIL--S-S-

Cyanothece sp. PCC 8801 218246693 --L---G-ILQE--I--AL --F---IT-AIL--S-S-

Cyanothece sp. CCY0110 126656655 -------EVLTE--V---L A-FV--IT-AIL--S-S-

Crocosphaera watsonii WH 0003 357263608 ------QKVLTE--V---L A-FV--IT-AIL--S-S-

Crocosphaera watsonii WH 8501 67922712 ------QKVLTE--V---L A-FV--IT-AIL--S-S-

Cyanothece sp. ATCC 51142 172036145 -------EVLTE--V--AL A-FV--IT-AIL--S-S-

Microcystis aeruginosa PCC 980 389788061 --S-----V-SD-EI-R-L --FF--IAAAVL-FSFNP

Microcystis sp. T1-4 390437842 --S-----V-SD-EI-R-L --FF--IAAAVL-FSFNP

Microcystis aeruginosa NIES-843 166364942 --L-----V-SD-EI-R-L --FF--IAAAVL-FSFNP

Synechocystis sp. PCC 6803 16329406 --W---QKVLAD-EVVQ-L --FV--VA-AVLS---SP

Synechococcus sp. PCC 7335 254423462 --Y---K-V-QD-QFYRS- --F-G-VTGAV-SSGLSG

Synechococcus sp. JA-3-3Ab 86606917 --W--ASKA-LG---A--L R-FVE--LR-VST-EFSS

Cyanothece sp. PCC 7425 220908387 --F-----AME-L-IA-IA AS-GG-IA-ALLSA-IDS

Synechococcus sp. JA-2-3B'a(2- 86607941 --W--AS-A-LG---A--L R-FAE--LR-VST-EFSS

Gloeobacter violaceus PCC 7421 37520796 --T--LGEA-QK-AI-QVL --FLE-IARAILT--IST

Supplementary Figure 6

Partial sequence alignment for the protein arsenite efflux ATP-binding protein (ArsA), showing a 2 aa insert that is specific for all heterocystous cyanobacteria.

Other

Cyanobacteria

Heterocystous

Clade 1A

(35/35)

Clade 1B

271 308

Cylindrospermopsis raciborskii CS-505 282901375 LKIAIAENYQSLG PQNPS LLQPALNSYQEAYIIAWQLQ

Raphidiopsis brookii D9 282895320 I-----------V ----- F-------------------

'Nostoc azollae' 0708 298492846 ------Q-----A RE--N ---E-F-K-----VT---S-

Anabaena variabilis ATCC 29413 75908794 -QL---A--ET-A RE--A -IEA-FKN------T-----

Nostoc sp. PCC 7120 17232832 -QL---A--ET-A RE--A --EA-FKN------T-----

Nostoc punctiforme PCC 73102 186683811 --L---A--E--A KKD-N --LE-FQN-----TT----R

Nodularia spumigena CCY9414 119513457 --L--GA--E--A QE-S- --TQ-F-N-----MM-VRSR

Fischerella sp. JSC-11 354566601 --L---SD-E--A KE--N -I-E-F-N--Q--T------

Anabaena sp. 90 414076365 --L---A--E--A QKD-N -K-Q-FDN--A--TG----E

Anabaena cylindrical PCC 7122 2504134063 ------------T -E--N ---E-F-K-----VT-----

Anabaena sp. PCC 7108 2506491940 ------S-----S QE--N ---A-F-N-----T------

Calothrix desertica PCC 7102 2510023380 -T--M---NS-EA -AK-D --Q-EN-FQN--Q--T---E

Calothrix sp. PCC 6303 2504094719 V-GI-----SD-E L-VKS --E--PEVFKN-----Q---

Calothrix sp. PCC 7103 2507477005 -T--M---NS-EA -AK-D --Q-EN-FQN--Q--T---E

Calothrix sp. PCC 7507 2505803000 --L---S--E--A KE--T ---E-FKY-----ST----E

Cylindrospermum stagnale PCC 7417 2509768583 ------T--ET-- QE--- -R-E-F-N-----TT-----

Fischerella sp. PCC 9339 2517059366 --L---SD-E--A KK--N ---E-F-N--Q--T----S-

Fischerella sp. PCC 9431 2512978868 --L--GSD-E--A KK--N ---E-F-N--Q--TM---S-

Fischerella sp. PCC 9605 2516144267 --L--GSD-E--A RE--N ---E-F-N--Q--TT-----

Mastigocladopsis repens PCC 10914 2517242537 --Q--GSD-E--A RK--- ---E-FKN-----TT----E

Nostoc sp. PCC 7107 2503741932 --L---A--E--A KE--N -I-E-F-N--Q--TT--ES-

Nostoc sp. PCC 7524 2509813079 -QL---A--EI-A KD-AD --LE-FKH-----TT-----

Rivularia sp. PCC 7116 2510090014 --L--GAD-EV-A KE-SN -VDE-FKN-----TM--DF-

Tolypothrix sp. PCC 9009 2507332845 -E--L--GSD--- -AKE- -T--PE-FKN-----TT---

Gloeocapsa sp. PCC 7428 434392354 IRL---AD--A-- QT-Q-FQN-----AS--S--

Moorea producta 3L 332710739 ------SD-N--N QPEK-SQT-----SL--S--

Microcoleus vaginatus FGP-2 334118683 I-M---SD--TI- QINL-AQY-----NL-VPI-

Oscillatoria sp. PCC 6506 300864500 --ME--S--EV-- Q-NL-NQY-----AS-LVV-

Microcoleus chthonoplastes PCC 7420 254409564 ---G-GAD-EA-N QPEK-SQ------AL--SS-

Lyngbya sp. PCC 8106 119486370 --LS-GLD-EK-- Q--Q-SQN-----TV-TTI-

Trichodesmium erythraeum IMS101 113475114 I--S-----EE-- R-NL-SQY-----S--QSI-

Arthrospira platensis NIES-39 291570022 Q-----T-HEQ-- QF-Q-GEA--Q--QF-INI-

Arthrospira platensis Paraca 284050571 Q-----T-HEQ-- QF-Q-GEA--Q--QF-INI-

Arthrospira maxima CS-328 209527005 ------T-HEQ-- QF-Q-GQA--Q--QF-INI-

Arthrospira sp. PCC 8005 376005648 ------T-HEQ-- QF-Q-GQA--Q--QF-INI-

Microcystis aeruginosa NIES-843 166368640 ---Q-GLD--A-K DANK-SQNF----SL-FA--

Microcystis aeruginosa PCC 7806 159030405 ---Q-GLD--A-K DVNK-SQNF----SL-FA--

Cyanothece sp. CCY0110 126657841 ---D-GKD-ET-D QPEL-SQN-----AL--S--

Crocosphaera watsonii WH 0003 357261708 ---E-GQD----D QPEL-SQN-----AL--S--

Crocosphaera watsonii WH 8501 67924390 ---E-GQD----D QPEL-SQN-----AL--S--

Cyanothece sp. PCC 7822 307150085 I--L-GQD-DT-N QPEK-SQNF---FSL--A--

Cyanothece sp. PCC 7424 218439980 I-VL-GLD-DA-N QPEK-SQNF---FSL--S--

Cyanothece sp. ATCC 51472 354556658 ---D-GKD-ET-D QPEL-SQN-----AL--S--

Cyanothece sp. ATCC 51142 172037896 ---D-GKD-ET-D QPEL-SQN-----AL--S--

Cyanothece sp. PCC 8802 257060454 ---S-GQD-EA-N QPEM-SKN-----SLS-S--

Cyanothece sp. PCC 8801 218248221 ---S-GQD-EA-N QPEM-SKN-----SLS-S--

cyanobacterium UCYN-A 284929663 --VD-GQD--L-D QPEI-SKN-----TL--K-K

Synechocystis sp. PCC 6803 16329967 IQ---GDH-LE-E QPEN-SQA--K--TL--SIK

Synechococcus sp. PCC 7335 254424809 -LVV--Q---AIN QPNN-ITY-RS--VT-QK-G

Supplementary Figure 7

Partial sequence alignment for a TPR repeat protein, showing a 5 aa insert that is specific for all heterocystous cyanobacteria.

Other

Cyanobacteria

Heterocystous

Clade 1A

(33/35)

Clade 1B

215 246

Nostoc sp. PCC 7120 17227812 ALIAFTKSGGYTAFR F KQLAEIMSPTLILWGD

Anabaena variabilis ATCC 29413 75910904 --------------- - ------I---------

Nostoc punctiforme PCC 73102 186683027 -----------S--- - -KISQ-LQQ-------

Nodularia spumigena CCY9414 119511478 -----------S--K A ---S--VQ--------

'Nostoc azollae' 0708 298492243 -----------S--K - N---Q-RQ--------

Raphidiopsis brookii D9 282896104 S--T--Q----Q--K L Q--GK-GQ--------

Cylindrospermopsis raciborskii CS-505 282898677 S--T--Q----Q--K L EE-GK-GQ--------

Fischerella sp. JSC-11 354565585 --------------- - -K-G--QQ--------

Anabaena sp. 90 414079767 Q-----------G—K - P---K-AQ--------

Anabaena cylindrical PCC 7122 2504133143 --------------K L Q---Q-GQ--------

Calothrix desertica PCC 7102 2510030745 -----------G--- - TK-S--QQ--------

Calothrix sp. PCC 6303 2504097127 -----------N--K G ER-SQ-KQQ-------

Calothrix sp. PCC 7103 2507482909 -----------G--- - TK-S--KQ--------

Calothrix sp. PCC 7507 2505799986 -----------RS-S M QK-SQ-VQ--------

Cylindrospermum stagnale PCC 7417 2509766433 -----------G--- L D---R-KQ--------

Fischerella sp. PCC 9339 2517061242 --------------- - -K-G--QP--------

Fischerella sp. PCC 9431 2512976424 --------------- - -K-G--QP--------

Fischerella sp. PCC 9605 2516146682 --------------- - -K-G--QQ--------

Mastigocladopsis repens PCC 10914 2517241138 -----------S--- - -NIGQ-VQ--------

Nostoc sp. PCC 7107 2503742243 -----------S--- - ----Q-LQ--------

Nostoc sp. PCC 7524 2509810474 -----------S--- - -K----NQ--------

Rivularia sp. PCC 7116 2510088358 -----------QP-K A N--V--EPE-------

Tolypothrix sp. PCC 9009 2507331558 -----------SG-K L N--SQ-KQ--------

Synechocystis sp. PCC 7509 2517696465 ------------S-K - -DK--Q-KPK------

Chroococcidiopsis thermalis PCC 7203 2503613649 -----------SS-K - -NR-NQ-QP-------

Gloeocapsa sp. PCC 7428 2503794595 ------------S-K - EK--Q-EQ-------E

Microcoleus vaginatus FGP-2 334119253 -----------GG-G EK-SQ-QQ-------K

Microcoleus chthonoplastes PCC 7420 254410223 ---S-------PP-G QK-TQ-QQ-------K

Arthrospira platensis NIES-39 291570622 G--E-------G--G DR-NT-QQ-------K

Arthrospira platensis Paraca 284050533 G--E-------G--G DR-NT-QQ-------K

Arthrospira maxima CS-328 209523662 G--E-------G--G DR-NT-QQ-------N

Trichodesmium erythraeum IMS101 113476588 ---S-------GS-K QK-HL-QQQ------E

Cyanothece sp. PCC 7424 218440099 ---S-------GS-V A---QLIQ-------E

Cyanothece sp. PCC 7425 220907352 --VY--Q----GS-A Q---HLQA-------R

Microcystis aeruginosa NIES-843 166368955 ---S-------GS-L P--SQ-DRE---I--E

Cyanothece sp. PCC 8802 257059639 -----------GS-K R--PQLKPE---I--Q

Cyanothece sp. PCC 8801 218246596 -----------GS-K R--PQLNPE---I--Q

Microcystis aeruginosa PCC 7806 159030698 ---S-------G--L QK-SQ-NRE---I--E

Crocosphaera watsonii WH 0003 357263214 ---S-------GS-K QEIINLKQE-IVI--E

Acaryochloris sp. CCMEE 5410 359462238 --VG-------NFLY DTIKD-PH-------E

Acaryochloris marina MBIC11017 158338347 --VG-------NFLY DTIKD-PH-------K

Cyanothece sp. PCC 7822 307151502 ---S-------GC-S E--PK-KQ-------E

Cyanothece sp. ATCC 51142 172037253 S--S-------GS-K EEMVN-KQE---I--E

Synechococcus sp. PCC 7002 170077488 ---Q---G---GS-Y PK-KQ-QQ-------E

Synechococcus elongatus PCC 7942 81301093 G-RR--R----GSM- SR-P-LRQ--QL---R

Synechocystis sp. PCC 6803 16330122 G----S-----GS-A E--GQ-TL-S--I--K

Synechococcus elongatus PCC 6301 56751825 G-RR--R----GSM- SR-P-LRQ--QLV--R

Synechococcus sp. RCC307 148241885 --AC-AR---FAGVG APLPAA-IHV---A

Synechococcus sp. RS9916 116073047 S-A--AR---FA-CG APLPSQTLQV---N

Synechococcus sp. CC9311 113953479 S-A--AR---FAGCG SPLPSQ-LHV---E

Synechococcus sp. BL107 116072471 --A--AR---FAGSG IPLPSQ-LHVI--A

Synechococcus sp. WH 7805 88808915 --A--AR---FSGSG HPLPQQ-MHV---N

Synechococcus sp. WH 7803 148239873 --A--AR---FSGSG HPLPQQ-LHV---N

Synechococcus sp. CC9902 78184960 --A--ARG--FAGSG SPLPSQ-LHVI--A

Synechococcus sp. WH 8016 352093664 S-A--AR---FAGCG DPLPPQ-LHV---E

Synechococcus sp. CB0101 318040238 --G--AR---FAGCG DPLPPQ-LQV---Q

Cyanobium sp. PCC 7001 254430710 --RR-AR---FAGCG QPLPPL-IQV---A

Prochlorococcus marinus AS9601 123968725 S-AS-A----FAGTQ KYIQNI-IKT-C-E

Gloeobacter violaceus PCC 7421 37522627 -I----R----APLG EK-PALSP-------E

Supplementary Figure 8

Partial sequence alignment for the protein 2-hydroxy-6-oxohepta-2,4-dienoate hydrolase, showing a 1 aa insert that is specific for heterocystous and Clade 1B cyanobacteria.

Other

Cyanobacteria

Heterocystous

Clade 1A

(34/35)

Clade 1B

177 237

Cylindrospermopsis raciborskii CS-505 282901218 DRQRLDALEKYATL VADIIRMGVNSESL VRNYPPPGPVLETMNMLGRSATPPAALQLLVDL

Raphidiopsis brookii D9 282895501 ------------I- --------I----- ------------------------------I--

'Nostoc azollae' 0708 298493171 -----E------S- ----V-T----D-- A-A----A------------G--L--F---I--

Nodularia spumigena CCY9414 119509770 -----E------A- L--VV-----YDT- A-A----A-----------P----G-F---I--

Nostoc sp. PCC 7120 17231942 -----EG----G-- L---VKV-L-YD-- A-A----A-----------P---QG-F------

Anabaena variabilis ATCC 29413 75907545 -----EG----G-- L---VKV-L-YD-- A-A----AL----------P---QG-F------

Nostoc punctiforme PCC 73102 186685031 -----EG-----A- L--TV-T---YD-- A-A---SA------T----PT--QG-F------

Fischerella sp. JSC-11 354564734 --H--E------A- L---V-V-L-YD-- A-A----A---------------QG--------

Anabaena sp. 90 414079583 -------------- L--VVMLK--YD-- A-AC---AS--------------Q--F---I--

Anabaena cylindrical PCC 7122 2504134902 -----ET-----A- M---V-----FD-- A-A----A---------------Q--F---I--

Anabaena sp. PCC 7108 2506493148 -----E------V- L---V-T---FD-- A-A---GV---------------Q--F---I--

Calothrix desertica PCC 7102 2510025980 --H-IE------A- L--TTKA--TY-TV A-A---SA-------L---P---Q--F---I--

Calothrix sp. PCC 6303 2504092983 --H--E-------- L--VGKP---YDQV S-A----AT----------P---QG-F------

Calothrix sp. PCC 7103 2507477633 --H-IE------A- L--TTKA--TY-TV A-A---SA-------L---P---Q--F---I--

Calothrix sp. PCC 7507 2505801696 -----EG-----A- M---V-T---YD-- S-A----AT-----T--------QG-F------

Cylindrospermum stagnale PCC 7417 2509772192 -----EG-----A- M---V-----YD-- A-A---GA------T--------Q--F---I--

Fischerella sp. PCC 9339 2517059235 --H--E------A- L---V-V-LSYD-- A-A----A---------------QG--------

Fischerella sp. PCC 9431 2512975787 --H--E------A- L---V-L-L-YD-- A-A----A---------------QG--------

Fischerella sp. PCC 9605 2516145385 --H--E------A- L--TV-V-L-YD-- A-A----A--Q---S--------QG-F------

Mastigocladopsis repens PCC 10914 2517240263 --H--E------A- L--V--V-LSYD-- A-A----AL----------T---QG-F------

Nostoc sp. PCC 7107 2503738855 --H--E------A- M-N-V-E--KYDA- A-A----A-----------P---QG-F---I--

Nostoc sp. PCC 7524 2509809935 -----E------A- L---V-A---YD-- A-A----A-----------H---QG-F------

Rivularia sp. PCC 7116 2510085161 --H--E------A- L--VT-G--KY--- AQA----AQ-----T----T---QG-FE-----

Tolypothrix sp. PCC 9009 2507333391 E-H-IE-V----A- L---V-G--TYDT- G-A----A-----IT----P---QG-F---I--

Synechocystis sp. PCC 7509 2517699259 -----E-I-RF-LT MVETG-S-GMQDP -RN--ALL--I--H---T---Q-VM---I--

Chroococcidiopsis thermalis PCC 7203 2503612348 -------IA---I- LVEGT-Q-L-PDA- --A----AI-T---ST---N---VT-F------

Gloeocapsa sp. PCC 7428 2503795344 ----IE-------- LVEGV-S--TPD-- A-T-A--AS-V----T---P---Q--F------

Microcoleus vaginatus FGP-2 334116976 --T------RF--- GEEATHRT-A---LAS-E--EN-E--F------

Oscillatoria sp. PCC 6506 300869627 --T------RF-L- GEEATHRT-A---LAS----E--E--F------

Trichodesmium erythraeum IMS101 113477198 -YN---II--F--H GEETSHRSQAM--LAT-KVPE-SE--FK-----

Arthrospira platensis NIES-39 291568149 --A------RF-LY GEEASHT--A---LSS-N-PQ--S-SF------

Arthrospira maxima CS-328 209528143 --T------RF-LY GEEASHT--A---LSS-N-PQ--S-SF------

Lyngbya sp. PCC 8106 119488090 --P------RL-LN GEEASHATSAF--LAT-E-PQ-ASG--E-----

Microcoleus chthonoplastes PCC 7420 254417643 --T-FEL--RFVLY PENTSRAAQDILAT-D-PQ--Q--FD--I--

Moorea producta 3L 332712186 --T-F----RFVSE PDK-SRA-Q--LEA-K-PQN-EN-FD--IN-

Cyanothece sp. PCC 7822 307150006 --T--E----FILQ PEQKHSSAQDIL-AVD--Q--E---E--IS-

Microcystis sp. T1-4 390439312 --I--ES---FILQ PEQKYPAAMDILSL----Q--E--FE-----

Microcystis aeruginosa NIES-843 166367429 --I--ES---FILQ PEQKYPAAMDILSL----Q--E--FE-----

Cyanothece sp. PCC 7424 218438216 --P--E----LVLQ PEQKNQAAQDLLSS----T--E---E--IE-

Cyanothece sp. CCY0110 126660660 --T---S---FVLH PEQNHRNAQDLLKE--QAT-AE--FE---A-

Cyanothece sp. PCC 8801 218246504 --N--ES--RLILQ PEQTHRNAQ-LLSEI---Q--E--FE---E-

Cyanothece sp. PCC 8802 257059537 --N--ES--RLILQ PEQTHRNAQ-LLSEI---Q--E--FE---E-

Cyanothece sp. ATCC 51142 172038259 --T--EL---FVLQ PEQNHRNAQDLLKE--QGT-AE--FD---A-

Cyanothece sp. PCC 7425 220906337 --L--ET--RF-VF GEDSNQRVQAQ-LLASA--GS-SQD-FR-----

Synechococcus sp. PCC 7002 170077199 ----FES---FVLY PEQSARAAHDLLE-----P-TEQ-FR---S-

Acaryochloris marina MBIC11017 158337924 --TY-Q----F-A- GDEATTRSTAT-VLST-K-GTS-D--F-----V

Thermosynechococcus elongatus BP-1 22298194 --K--EQ--R--IA IESSAQHQAAIDLLSE-K-PTQ-LG-F------

Synechocystis sp. PCC 6803 16329795 --L--E----FILF PEQNHRQA-DILQT--KPGRTDETQN--IE-

Acaryochloris sp. CCMEE 5410 359463693 --TY-Q----F-A- GDEATTRSTAT-VLST-K-GTS-D--F-----V

Synechococcus elongatus PCC 6301 56750434 --PW-K---QW-LF SEDGNNTRAAT-VLTA---Q-SAQ--HD---A-

Synechococcus sp. PCC 7335 254423969 --P--EIV-R--L- GDESSQKSAAQ-LLTE-NQDKS-E--FDF--A-

Crocosphaera watsonii WH 8501 67924092 --S--ES---FVLQ PEQSHRNAQDLLKE--HKTI-DS-FE---A-

Gloeobacter violaceus PCC 7421 37521185 --L------R--LW GDEASDRASAQDVLSQ--HTTRSED-IA---A-

Supplementary Figure 9

Partial sequence alignment for the protein Ribonuclease II, showing a 14 aa insert that is specific for all heterocystous and Clade 1B cyanobacteria.

Other

Cyanobacteria

Heterocystous

Clade 1A

(35/35)

Clade 1B

36 80

Nostoc sp. PCC 7120 17232530 GHAPLLTALDTGVLRVRTSK SQ NWQAIALLGGFAEVEEDEVTILV

Anabaena variabilis ATCC 29413 75908514 -------------------- -- -----------------------

Nodularia spumigena CCY9414 119509844 ----M--------M---A-- NE D----------------------

'Nostoc azollae' 0708 298490973 ----M-S------M---AT- NS -----------------------

Raphidiopsis brookii D9 282896619 ----M-----I--M---AE- NA ---S-------------------

Fischerella sp. JSC-11 354564801 -------------M---P-- N- G-TP---M---------------

Anabaena sp. PCC 7108 2506490110 ------S---I--M---AN- N- D------A------D--------

Calothrix sp. PCC 7507 2505800918 -----------------AA- N- E-K-------------N------

Cylindrospermum stagnale PCC 7417 2509770535 -------------M---A-- N- D-------------DQ-------

Fischerella sp. PCC 9605 2516145128 -------------M---AA- N- A-TP---M-------A-------

Mastigocladopsis repens PCC 10914 2517244237 -------------M---S-- N- D-V----S-------Q-------

Rivularia sp. PCC 7116 2510087609 ----M-S------M---ADN N- --V----S---------------

Tolypothrix sp. PCC 9009 2507332446 -------------M----N- N- --T----M-------DN-I----

Fischerella muscicola PCC 7414 428160030 -------------M---P-- N- G-TP---M---------------

Fischerella thermalis PCC 7521 428159540 -------------M---P-- N- G-TP---M---------------

Chlorogloeopsis fritschii PCC 9212 428159827 -------------M---P-- N- Q-IP-----------Q-------

Mastigocoleus testarum BC008 548700003 ------S---A--M---S-A N- D-V----M--------N------

Anabaena sp. 90 414078065 ----M-----I--M---A-- NA P-------------DQ-------

Synechocystis sp. PCC 7509 2517697913 -----------A-M---PNS NR E-I----M-------NN------

Gloeocapsa sp. PCC 7428 2503797447 -------------M---P-S NE D-V----M-------S-------

Chroococcidiopsis thermalis PCC 7203 2503612037 -----------A-M---PE- G- S-V----M-------S-------

Crinalium epipsammum PCC 9333 2504684574 ------S------M---DG- --V----M-----I-NND-----

Chamaesiphon minutus PCC 6605 2510439501 ---A-------A-M--KAG- D K-TP---M------DNN---V--

Trichodesmium erythraeum IMS101 113476899 -------------M---AEN D-I----M-----I-A---S---

Arthrospira platensis Paraca 284053203 D---------P--M---AKN E-MS---ME-----QNN-I-V--

Acaryochloris marina MBIC11017 158338427 ------S---V--M---PG- D-VS---M---V---N---V---

Cyanothece sp. PCC 7425 220910364 ---------E---M---SG- E-LP---M-------NN------

Thermosynechococcus elongatus BP-1 22298069 N--------E---M---QDR E-V----M-------NN------

Synechococcus elongatus PCC 6301 56751795 ------S----------AD- E-L---V--------NN---V--

Synechococcus sp. CC9311 113952887 --VS--A---V-------NS ---S---M-------S-D--V--

Microcystis aeruginosa NIES-843 166362834 ---------NI--M-I-PG- D-EN--V--------NN-IKV--

Synechocystis sp. PCC 6803 161344760 N--------EI--M---PG- D--N--VM-------NN--KV--

Synechococcus sp. RS9917 87123625 --VS--A---V------DTN G--S---M-------A----V--

Synechococcus sp. JA-2-3B'a(2-13) 86609666 --------IGN--M--KADG K-L---VM-------NN---V--

Cyanothece sp. PCC 8801 218248403 S------N--I--M---LD- D-KSLVVM--I----Q-ILQV--

Prochlorococcus marinus CCMP1986 33861995 --IS-V--I-I----L-MNS K-KS---M-----I-S---IV--

Supplementary Figure 10

Partial sequence alignment for the ATP synthase epsilon subunit, showing a 2 aa insert that is specific to all heterocystous and Clade 1B

cyanobacteria.

Other

Cyanobacteria

Heterocystous

Clade 1A

(35/35)

Clade 1B

Clade 1C

150 191

Nostoc sp. PCC 7120 17232408 KSTTDFTPLDQDGKVGLLNVSE D NVSIYALDGQHRLMGVQGL

Anabaena variabilis ATCC 29413 75908425 ---------------------- - -------------------

Nostoc punctiforme PCC 73102 186684604 ------I---K--------I-- - D-T----------------

Nodularia spumigena CCY9414 119510075 ----------K--------I-- E --T-----------S----

Cylindrospermopsis raciborskii CS-505 282898769 -A--------AN-HI-----A- E D-N----------------

Raphidiopsis brookii D9 282895759 -A----I-S-ANSHI-----A- E DT---V-------------

Anabaena sp. 90 414077230 -A----I---K-S------I-- E --T----------------

Anabaena cylindrical PCC 7122 2504134542 -A----I---K--------I-- E --T----------------

Anabaena sp. PCC 7108 2506494376 -A----I---K--------I-- E --T----------------

Calothrix desertica PCC 7102 2510029039 R-AIE-----SKN-F----I-D E D-T----------------

Calothrix sp. PCC 6303 2504098002 ---IE-----SE--L----LT V E-IT-H-------------

Calothrix sp. PCC 7103 2507476220 R-AIE-----SGK-F----I-D E D-T----------------

Calothrix sp. PCC 7507 2505802822 ------I---K-A------I-- - DIT----------------

Cylindrospermum stagnale PCC 7417 2509767393 ----------K--------I-- - DIT----------------

Fischerella sp. PCC 9339 2517060815 Q---A--A---E---------- E D-T----------------

Fischerella sp. PCC 9431 2512979193 Q------A--KE---------- E D-T----------------

Fischerella sp. PCC 9605 2516143914 ----V-----HE-------I-- - --T----------------

Mastigocladopsis repens PCC 10914 2517240453 ----E-----K-D------L-- E --T----------------

Nostoc sp. PCC 7107 2503744024 ----------K-A--------- E --T----------------

Nostoc sp. PCC 7524 2509810176 ---N-----K----------- E --T----------------

Rivularia sp. PCC 7116 2510087541 ----E--NF-DE--F---DI-Q E --T-----------A----

Tolypothrix sp. PCC 9009 2507335032 ---I------K----------Q E D------------------

Fischerella muscicola PCC 7414 428160168 ----------KE-------I-- E --T----------------

Mastigocoleus testarum BC008 548697743 ----Q----GK--NF------- - D-T----------------

Chroococcidiopsis thermalis PCC 7203 2503612942 -----IT--RE--------A- A D-T------------A---

Gloeocapsa sp. PCC 7428 2503794502 ---I--R---R--S-----FAP E-T----------------

Crinalium epipsammum PCC 9333 2504683944 QPAAE-----K--N----DI-A D-T-F--------------

Chamaesiphon minutus PCC 6605 2510439303 E-AAI-M---GNNSF---D-G- S-R----------------

Microcoleus chthonoplastes PCC 7420 254412761 Q-AA--I----NQT----D--P S---F--------------

Trichodesmium erythraeum IMS101 113475600 --A---FS--SQ------DLRL E-AVF----------I---

Microcoleus vaginatus FGP-2 334118575 --A-E--SF-KNENL------K EL--F--------------

Moorea producta 3L 332711306 Q-AAE--S--K--T----D--D H---F----------I-A-

Oscillatoria sp. PCC 6506 300864427 --SA--LAI-KNET--F--IKD --VF----------I---

Arthrospira platensis Paraca 284054012 C-AAEYI---EH--I-I-DL-S P--VF----------I--V

Arthrospira sp. PCC 8005 376003672 C-VAQYI---EH--I-I-DL-S S--VF----------I--V

Arthrospira maxima CS-328 209526890 C-AAQYI---EH--I-I-DL-S S--VF----------I--V

Lyngbya sp. PCC 8106 119491185 E-AIA-EG--SQ-QL---HLTS D-AVF----------I---

Cyanothece sp. PCC 8802 257060278 RTVA-------QNRL----IG- -F--F----------I---

Cyanothece sp. PCC 8801 218247201 RTVA-------QNRL----IG- -F--FV---------I---

Cyanothece sp. CCY0110 126656075 V-VDE--S---NDS-----IGK -Y--F----------I---

Cyanothece sp. ATCC 51142 172035450 V-VDN--S--KNDSI----IG- -Y--F----------I---

Crocosphaera watsonii WH 0003 357261885 V-VD---S--KNDSI----IGK -Y--F----------I---

Cyanothece sp. PCC 7822 307154544 IPAVN-----PQQNL---D--- -F--F----------I---

Cyanothece sp. PCC 7424 218441732 T-AVN-----PQ-NL---DI-D -Y--F----------I---

Supplementary Figure 11

Partial sequence alignment for hypothetical protein Npun_R4490, showing a 1 aa insert that is specific for heterocystous and Clade 1B cyanobacteria.

Other

Cyanobacteria

Heterocystous

Clade 1A

(35/35)

Clade 1B

Clade 1C

484 531

Nostoc sp. PCC 7120 17231417 RYSCETIERYLKE RLEKL RYEFPKTLVVNSHTTNTPGHAAVDFVAAIN

Anabaena variabilis ATCC 29413 75907993 ------------- ----- ------------------------------

Nostoc punctiforme PCC 73102 186685021 ------------- --Q-- -RQ-------S---------E----I----

'Nostoc azollae' 0708 298492899 S-------H---- --L-- -K---N----S--------------IT---

Nodularia spumigena CCY9414 119509214 --------S---- ----- -QQ---S--IS-R--S----------GD--

Raphidiopsis brookii D9 282897691 --------D--QN --Y-- KRQ--HS---S-Q-----A-P-IECLS---

Cylindrospermopsis raciborskii CS-505 282900956 --------D--QD --Y-- KRQ--HS---S-Q-----A-P-IECLS---

Fischerella sp. JSC-11 354568775 -------AD---- --Q-- QKR-A-----S-L-------E-A--ITS--

Anabaena cylindrica PCC 7122 2504131986 --------S---Q --Q-- -KQ--E----S--------------IG---

Anabaena sp. PCC 7108 2506492357 --------G--RQ --Q-- -K---N----S--------------IG---

Calothrix desertica PCC 7102 2510026813 -----------R- ---R- YRIS--S--IS-S------------A-E--

Calothrix sp. PCC 6303 2504097196 -------DK---- ----I YRL------IS-S-------Q-----NE--

Calothrix sp. PCC 7103 2507479824 -----------R- ---R- YRIS--S--IS-S------------A-E--

Calothrix sp. PCC 7507 2505802998 ------------- --A-- -RQ--H---IS-------------------

Cylindrospermum stagnale PCC 7417 2509766094 --------S---- --Q-- -R---N----S--------------I----

Fischerella sp. PCC 9339 2517062065 -------AS--Q- --QR- QKQ-S-----S-L-------E----ITS--

Fischerella sp. PCC 9431 2512979265 -------AS--Q- --QR- QKQ-S-----S-L-------E----ITS--

Fischerella sp. PCC 9605 2516143099 -------AG---- --QR- LTQ-------S-L-------E-A--I-T--

Mastigocladopsis repens PCC 10914 2517243550 ------------- ---R- QQQ------IS---------E---------

Nostoc sp. PCC 7107 2503741105 --------N---- ----- --Q---S--IS-R-----D-P-A----T--

Nostoc sp. PCC 7524 2509812369 --------S---- --A-- --Q------I--Q--------------D--

Rivularia sp. PCC 7116 2510090525 ---S--------- --D-- -HLY----I-S---------E------S--

Tolypothrix sp. PCC 009 2507336334 ------------- ---R- QK--------S------L--K------E--

Crinalium epipsammum PCC 9333 2504684029 ---S-A--Q-I-Q ---QF QKKY------S-Q--S-HK-E-L--IKD--

Chamaesiphon minutus PCC 6605 2510436756 --GSD--D--IQQ A-KQ- EDSYT-----C------T--P-----SS--

Cyanothece sp. PCC 7425 219883216 KW-SKNL-T--QT --PDKRI-RID-ESVAD-Q-P-YGI-EQL-

Cyanothece sp. PCC 8802 257059993 NWGTQ-L-S---K QFPDA-I-RID-ESLTD-N---YQCIKQL-

Cyanothece sp. PCC 8801 218246932 NWGTQ-L-S---K QFPDA-I-RID-ESLTD-N---YQCISQL-

Microcystis aeruginosa NIES-843 166367098 KWGTI-L-S--RK QFPQK-I-RID-ESLPDY----YQAIGNL-

cyanobacterium UCYN-A 284929649 KWGTQ-L-L--QQ QFPEA-I-RID-ESLID-N-S-YKCIDHLD

Cyanothece sp. CCY0110 126660034 KWGTQ-L-S---K QFPDA-I-RID-QSLTN-N-D-YQCITQL-

Synechococcus sp. PCC 7002 170076845 QW-TS-L-I---N QFPDR-I-RLDAESLAD-E-P-YGAMGQ--

Crocosphaera watsonii WH 0003 357262293 KWGTQ-L-L---K QFPTANI-RID-QSLTD-N-P-YQCITKL-

Crocosphaera watsonii WH 8501 67923848 KWGTQ-L-L---K QFPTANI-RID-QSLTD-N-P-YQCITKL-

Microcystis aeruginosa PCC 9443 389730945 KWGTI-L-Y--RK QFPQK-I-RID-ESLQDYS-D-YEAIGNL-

Cyanothece sp. PCC 7424 218439140 QWGTL-L-A--NK LFPDL-I-RLD-ESLAD-H-P-YNCITRL-

Cyanothece sp. PCC 7822 307151280 QWGTLSL-A---K QFPTL-I-RLD-ESLAD-TQ--YNCITHLD

Cyanothece sp. ATCC 51142 172036781 KWGTQ-L-S--NK LFPDA-I-RID-QSLTD-H-D-YQCITQL-

Cyanothece sp. ATCC 51472 354554593 KWGTQ-L-S--NK LFPDA-I-RID-QSLTD-H-D-YQCITQL-

Synechocystis sp. PCC 6803 16332075 AWGTRNL-A---K QFPDRRI-RIDAESLSD-H-P-HGSLTNL-

Lyngbya sp. PCC 8106 119484516 QWGTC-L-T---T QFPNL-I-RID-ESLSD-S-P-YGCINQL-

Arthrospira platensis NIES-39 291568873 KWGTS-L-A-F-T QFPQL-I-RID-QSLAD-H-P-YGCINRL-

Arthrospira platensis Paraca 284050328 KWGTS-L-A-F-T QFPQL-I-RID-QSLAD-H-P-YGCINRL-

Microcoleus chthonoplastes PCC 7420 254411821 QWGTC-L-A--RS -FPEA-I-RID-ESLTE-T-P-YGCMRDLD

Arthrospira sp. PCC 8005 376002382 KWGTS-L-A-F-A QFPQL-I-RID-QSLAD-H-P-YGCINRL-

Arthrospira maxima CS-328 209526706 KWGTS-L-A-F-A QFPQL-I-RID-QSLAD-H-P-YGCINRL-

Trichodesmium erythraeum IMS101 113474847 KWGTRAL-A---K QFPKL-I-RID-ESLAEVN-P-YGCIKSL-

Moorea producta 3L 332705148 QWGTC-L-A---K QFPHLRI-RID-ESLGETN-P-MGCINNL-

Supplementary Figure 12

Partial sequence alignment for the hypothetical protein Npun_R4929, showing a 5 aa insert that is specific for all heterocystous and Clade 1C cyanobacteria.

Heterocystous

Clade 1A

(35/35)

Other

Cyanobacteria

Clade 1C

Supplementary Table 1: Highly Conserved Proteins Used for the Construction of Maximum-Likelihood and Neighbor-Joining Trees.

Protein Gene Name Length (Amino Acids) Alanyl-tRNA synthetase AlaRS 880 Phosphatidate cytidylyltransferase CdsA 294 Elongation factor P EF-P 185 Glycine/serine hydroxymethyltransferase GlyA 427 Cell division transporter substrate-binding protein FtsY 546 DNA gyrase subunit A GyrA 872 DNA gyrase subunit B GyrB 645 Translation initiation factor 2 IF-2 1039 Isoleucyl-tRNA synthetase IleRS 960 Dimethyladenosine transferase KsgA 271 Leucyl-tRNA synthetase LeuRS 872 Phenylalanyl-tRNA synthetase alpha chain PheRS 330 DNA polymerase I PolA 977 DNA recombination protein A RecA 357 50S ribosomal protein L2* RibProtL2 287 50S ribosomal protein L4* RibProtL4 210 50S ribosomal protein L5* RibProtL5 182 50S ribosomal protein L6* RibProtL6 182 30S ribosomal protein S2* RibS2 265 30S ribosomal protein S3* RibS3 260 30S ribosomal protein S5* RibS5 174 30S ribosomal protein S8 RibS8 133 30S ribosomal protein S11* RibS11 131 30S ribosomal protein S15 RibS15 89 RNA polymerase alpha subunit RpoA 315 RNA polymerase beta prime subunit RpoC1 1350 Preprotein translocase SecA subunit SecA 930 Seryl-tRNA synthetase SerRS 426 Tryptophanyl-tRNA synthetase TrpS 335 Tyrosyl-tRNA synthetase TyrRS 398 ATP-dependent DNA helicase UvrD 772 GTP-binding protein YchF 363

Protein lengths are associated with Nostoc sp. PCC 7120 *Protein sequences are also present in the concatenated tree dataset used by Shih et al., (2013).

Supplementary Table 2: Sequence Characteristics of Featured Cyanobacterial Genomes. Organisms NCBI Assembly No. Clade Size (Mpb) No. of proteins References Acaryochloris marina MBIC11017 ASM1810v1 B 8.36 8383 Washington University Acaryochloris sp. CCMEE 5410 ASM23877v2 N/D 7.88 7,512 JCVI Anabaena circinalis AWQC131C Acir310F B 4.45 - BGI Anabaena circinalis AWQC310F Dcir131C B 4.41 - BGI Anabaena cylindrica PCC 7122 ASM31769v1 B 7.06 5,838 DOE JGI Anabaena sp. 90 ASM31270v1 B 5.15 4,511 Univ of Helsinki Anabaena sp. PCC 7108 ASM33213v1 B 5.89 - DOE JGI Anabaena variabilis ATCC 29413 ASM20407v1 B 7.11 5710 DOE JGI

Arthrospira maxima CS-328 ASM17355v1 B 6 5,690 DOE JGI Arthrospira platensis C1 ASM30791v1 B 6.01 6,108 KMUTT Arthrospira platensis NIES-39 AP011615.1 B 6.79 6630 (Fujisawa et al., 2010) Arthrospira platensis Paraca ASM17541v2 B 5 4,674 Univ of Applied Sciences Arthrospira sp. PCC 8005 ASM17689v2 B 6.15 5,951 Genoscope Calothrix desertica PCC 7102 - B 11.42 10334 DOE JGI Calothrix sp. PCC 6303 ASM31743v1 B 6.96 5,535 DOE JGI Calothrix sp. PCC 7103 ASM33130v1 B 11.58 - DOE JGI Calothrix sp. PCC 7507 ASM31657v1 B 7.02 5,950 DOE JGI Chamaesiphon minutus PCC 6605 ASM31714v1 B 6.76 5,945 DOE JGI Chlorogloeopsis fritschii PCC 6912 ChlPCC6912_1.0 B 7.75 6,851 HHU Duesseldorf Chlorogloeopsis fritschii PCC 9212 ChlPCC9212_1.0 B 7.65 6,688 HHU Duesseldorf Chroococcidiopsis sp. PCC 6712 - B 5.72 5116 DOE JGI Chroococcidiopsis thermalis PCC 7203 ASM31712v1 B 6.69 5,752 DOE JGI Crinalium epipsammum PCC 9333 ASM31749v1 B 5.62 5002 DOE JGI Crocosphaera watsonii WH 8501 ASM16719v1 B 6.24 5958 DOE JGI b Cyanobacterium aponinum PCC 10605 ASM31767v1 B 4.18 3,431 DOE JGI cyanobacterium PCC 7702 - B 4.89 4283 DOE JGI Cyanobacterium sp. ESFC-1 - B 5.63 4914 DOE JGI Cyanobacterium sp. UCYN-A - B 1.44 1199 UC Santa Cruz Cyanobacterium stanieri PCC 7202 ASM31765v1 B 3.16 2,837 DOE JGI Cyanobium gracile PCC 6307 ASM31651v1 C 3.34 3,280 DOE JGI Cyanobium sp. PCC 7001 ASM15563v1 C 2.83 2,771 JCVI Cyanothece sp. ATCC 51142 ASM1784v1 B 5.46 5304 (Welsh et al., 2008) Cyanothece sp. ATCC 51472 ASM23142v1 B 5.46 - DOE JGI Cyanothece sp. CCY 0110 ASM16933v1 B 5.88 6475 JCVI Cyanothece sp. PCC 7424 ASM2182v1 B 6.55 5710 DOE JGI b Cyanothece sp. PCC 7425 ASM2204v1 N/D 5.79 5327 DOE JGI b Cyanothece sp. PCC 7822 ASM14733v1 B 7.84 6642 DOE JGI b Cyanothece sp. PCC 8801 ASM2180v1 B 4.79 4367 DOE JGI b Cyanothece sp. PCC 8802 ASM2404v1 B 4.8 4444 DOE JGI b Cylindrospermopsis raciborskii CS-505 ASM17583v1 B 3.88 3449 FLI Jena c Cylindrospermopsis raciborskii CS-509 - B 4.03 5215 Univ of New South Wales Cylindrospermum stagnale PCC 7417 ASM31753v1 B 7.61 6229 DOE JGI Dactylococcopsis salina PCC 8305 ASM31761v1 B 3.78 3,337 DOE JGI Fischerella muscicola PCC 7414 FisPCC7414_1.0 B 6.90 6,057 HHU Duesseldorf Fischerella sp. JSC-11 ASM23136v1 B 5.38 4627 DOE JGI b Fischerella sp. PCC 9339 ASM31558v1 B 8.01 6720 DOE JGI Fischerella sp. PCC 9431 ASM44729v1 B 7.18 6104 DOE JGI Fischerella sp. PCC 9605 - B 8.08 7060 DOE JGI Fischerella thermalis PCC 7521 FisPCC7521_1.0 B 5.44 4,629 HHU Duesseldorf Geitlerinema sp. PCC 7105 ASM33235v1 B 6.15 5338 DOE JGI Geitlerinema sp. PCC 7407 ASM31704v1 N/D 4.68 3,912 DOE JGI Geminocystis herdmanii PCC 6308 ASM33223v1 B 4.26 4,146 DOE JGI Gloeobacter violaceus PCC 7421 ASM1138v1 A 4.66 4430 (Nakamura et al., 2003) Gloeocapsa sp. PCC 73106 ASM33203v1 B 4.03 4,087 DOE JGI Gloeocapsa sp. PCC 7428 ASM31755v1 B 5.88 5,011 DOE JGI Halothece sp. PCC 7418 ASM31763v1 B 4.18 3,708 DOE JGI Leptolyngbya boryana PCC 6306 ASM35328v1 N/D 7.26 6827 DOE JGI Leptolyngbya sp. PCC 6406 ASM33209v1 N/D 5.78 5,190 DOE JGI Leptolyngbya sp. PCC 7375 ASM31611v1 N/D 9.42 7,828 DOE JGI Leptolyngbya sp. PCC 7376 ASM31660v1 B 5.13 4,228 DOE JGI Mastigocladopsis repens PCC 10914 ASM31556v1 B 6.47 5846 DOE JGI Mastigocoleus testarum BC008 - B 15.87 13458 DOE JGI Microchaete sp. PCC 7126 ASM33229v1 B 5.74 5192 DOE JGI Microcoleus chthonoplastes PCC 7420 ASM15555v1 B 8.68 8,294 JCVI, Institut Pasteur Microcoleus sp. PCC 7113 ASM31751v1 B 7.97 6,441 DOE JGI Microcoleus vaginatus FGP-2 ASM21407v1 B 6.7 5574 DOE JGI Microcoleus vaginatus PCC 9802 - B 6.59 5500 - Microcystis aeruginosa NIES-843 ASM1062v1 B 5.84 6312 (Kaneko et al., 2007) Nodosilinea nodulosa PCC 7104 ASM30938v1 N/D 6.89 6414 DOE JGI Nodularia spumigena CCY 9414 ASM16913v1 B 5.32 4860 GBM Foundation

Nostoc azollae' 0708 ASM19651v1 B 5.49 3,651 (Ran et al., 2010) Nostoc punctiforme PCC 73102 ASM2002v1 B 9.06 6689 DOE JGI Nostoc sp. PCC 7107 ASM31662v1 B 6.33 5,237 DOE JGI

Supplementary Table 2 Continued: Sequence Characteristics of Featured Cyanobacterial Genomes. Organisms NCBI Assembly No. Clade Size (Mpb) No. of proteins References Nostoc sp. PCC 7120 ASM970v1 B 7.21 6129 (Kaneko et al., 2001) Nostoc sp. PCC 7524 ASM31664v1 B 6.79 5,449 DOE JGI Oscillatoria formosa PCC 6407 ASM33215v1 B 6.89 5693 DOE JGI Oscillatoria nigro-viridis PCC 7112 ASM31747v1 B 8.27 6,360 DOE JGI Oscillatoria sp. PCC 10802 ASM33233v1 B 8.59 7012 DOE JGI Oscillatoria sp. PCC 6506 ASM18045v1 B 6.68 5,822 Institut Curie Oscillatoriales sp. JSC-1 - B 7.87 6942 DOE JGI Oscillatoriales sp. JSC-12 - B 5.53 5024 DOE JGI Pleurocapsa sp. PCC 7319 ASM33219v1 B 7.39 6690 DOE JGI Pleurocapsa sp. PCC 7327 ASM31702v1 B 4.99 4,268 DOE JGI Prochlorococcus marinus AS 9601 ASM1564v1 C 1.67 1920 GBM Foundation

Prochlorococcus marinus CCMP1375 ASM792v1 C 1.75 1883 (Dufresne et al., 2003) Prochlorococcus marinus CCMP1986 ASM1146v1 C 1.66 1717 (Rocap et al., 2003) Prochlorococcus marinus MIT 9211 ASM1858v1 C 1.69 1854 GBM Foundation Prochlorococcus marinus MIT 9215 ASM1806v1 C 1.74 1982 DOE JGI

Prochlorococcus marinus MIT 9301 ASM1596v1 C 1.64 1906 GBM Foundation Prochlorococcus marinus MIT 9303 ASM1570v1 C 2.68 2997 GBM Foundation Prochlorococcus marinus MIT 9312 ASM1264v1 C 1.71 1810 DOE JGI Prochlorococcus marinus MIT 9313 ASM1148v1 C 2.41 2269 DOE JGI Prochlorococcus marinus MIT 9515 ASM1566v1 C 1.7 1905 GBM Foundation

Prochlorococcus marinus MIT9202 ASM15859v1 C 1.69 1,890 JCVI Prochlorococcus marinus NATL1A ASM1568v1 C 1.86 2193 GBM Foundation Prochlorococcus marinus NATL2A ASM1246v1 C 1.84 2162 DOE JGI Prochlorothrix hollandica PCC 9006 ASM33231v1 N/D 5.65 4770 DOE JGI Pseudanabaena sp. PCC 7367 ASM31706v1 N/D 4.89 3,854 DOE JGI Pseudanabaena sp. PCC 7429 ASM33221v1 N/D 5.48 4,757 DOE JGI Raphidiopsis brookii D9 ASM17585v1 B 3.19 3007 DOE JGI b Richelia intracellularis HH01 ASM35012v1 B 2.21 1,674 UC-Santa Cruz Rivularia sp. PCC 7116 ASM31666v1 B 8.73 6,644 DOE JGI Scytonema hofmanni UTEX 2349 - B 8.13 7302 DOE JGI Spirulina major PCC 6313 ASM31400v1 B 5.05 4408 DOE JGI Spirulina subsalsa PCC 9445 ASM31400v1 B 5.32 4580 DOE JGI Stanieria cyanosphaera PCC 7437 ASM31757v1 B 5.54 4,781 DOE JGI Synechococcus elongatus PCC 6301 ASM1006v1 N/D 2.7 2523 (Sugita et al., 2007) Synechococcus elongatus PCC 7942 ASM1252v1 N/D 2.74 2662 DOE JGI Synechococcus sp. BL107 ASM15380v1 C 2.28 2,507 JCVI Synechococcus sp. CB0101 ASM17923v1 C 2.69 3010 JCVI Synechococcus sp. CB0205 ASM17925v1 C 2.43 2719 JCVI Synechococcus sp. CC9311 ASM1458v1 C 2.61 2892 (Palenik et al., 2006) Synechococcus sp. CC9605 ASM1262v1 C 2.51 2645 DOE JGI Synechococcus sp. CC9616 - C 2.65 2892 DOE JGI Synechococcus sp. CC9902 ASM1250v1 C 2.23 2306 DOE JGI Synechococcus sp. JA-2-3B'a(2-13) ASM1322v1 N/D 3.05 2862 TIGR Synechococcus sp. JA-3-3Ab ASM1320v1 N/D 2.93 2760 TIGR Synechococcus sp. PCC 6312 ASM31668v1 N/D 3.72 3,545 DOE JGI Synechococcus sp. PCC 7002 ASM1948v1 B 3.41 3187 Penn. State University Synechococcus sp. PCC 7335 ASM15559v1 N/D 5.97 5,586 Institut Pasteur, JCVI Synechococcus sp. PCC 7336 ASM33227v1 N/D 5.14 4,634 DOE JGI Synechococcus sp. PCC 7502 ASM31708v1 N/D 3.58 3,318 DOE JGI Synechococcus sp. RCC307 ASM6352v1 C 2.22 2534 Institut Pasteur Synechococcus sp. RS9916 ASM15382v1 C 2.66 2,961 JCVI Synechococcus sp. RS9917 ASM15306v1 C 2.58 2770 GBM Foundation

Synechococcus sp. WH 5701 ASM15304v1 C 3.04 3346 GBM Foundation Synechococcus sp. WH 7803 ASM6350v1 C 2.37 2533 Institut Pasteur Synechococcus sp. WH 7805 ASM15328v1 C 2.62 2883 GBM Foundation Synechococcus sp. WH 8016 ASM23067v1 C 2.71 2990 DOE JGI Synechococcus sp. WH 8102 ASM19597v1 C 2.43 2519 (Palenik et al., 2003) Synechococcus sp. WH 8109 ASM16179v1 C 2.19 2,577 JCVI Synechocystis sp. PCC 6803 ASM34078v1 B 3.95 3575 (Kaneko et al., 1996) Synechocystis sp. PCC 7509 ASM33207v1 B 4.91 4,703 DOE JGI Thermosynechococcus elongatus BP-1 ASM1134v1 N/D 2.59 2476 (Nakamura et al., 2002) Trichodesmium erythraeum IMS101 ASM1426v1 B 7.75 4,451 DOE JGI Xenococcus sp. PCC 7305 ASM33205v1 B 5.93 5,373 DOE JGI

DOE JGI - Department of Energy Joint Genome Institute

FLI - Fritz-Lipmann-Institute

GBM - The Gordon and Betty Moore Foundation

TIGR - The Institute of Genome Research

JCVI - J. Craig Venter Institute

KMUTT - King Mongkut's University of Technology Thonburi

N/D - Not Determined

HHU-Heinrich-Heine-Universität

Reference List

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