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Ecotypic diversity of marine
cyanobacteria: Tales from the
pangenome
Gabrielle Rocap
Unicellular marine cyanobacteria
ubiquitous
throughout the tropical and sub tropical oceans

extremely abundant (up to 4x105 cells/ml)

contribute significantly to primary productivity
Prochlorococcus


Small (0.6 x 0.8 mm)
divinyl chlorophylls a and b
Synechococcus


Larger (0.8 x 1.8 mm)
phycobilisomes
Images from http://ccmp.bigelow.org
Prochlorococcus and Synechococcus have differing
seasonal abundances in the Sargasso Sea
Durand et al., Deep Sea Research II 2001
2
1
0.8
MIT9312
Chl b/chl a2
Growth rate (day-1)
Prochlorococcus isolates differ in their photophysiology
0.6
0.4 MIT9313
MIT9312
MIT9313
1
0.2
0
0
1
10
100
1000
Growth irradiance (mmol Q m-2 s-1)
1
10
100
1000
Growth Irradiance (mmol Q m-2 s-1)
From Moore, Rocap & Chisholm 1998
rRNA phylogeny
corresponds to
physiological differences
—”ecotypes”
ENATL6
ENATL2
NATL2
ENATL5
SAR6
TATL1a
89
71
66
100
78
MED4
ENATL1
ENATL3
MIT9302
MIT9312
MIT9201
92
GP2
MIT9202
MIT9215
TATL1b
MIT9107
NATL2A
PAC1
ENATL7
ENATL4
97
SS120
MIT9211
MIT9303
72
MIT9313
SAR139
WH8112
84
I
WH8102
IV
SAR100
WH8101
WH8012
WH7805
II
I
II
III
Marine
Synechococcus
SAR7
Cyanobium PCC 6307
0.01
Adapted from Rocap et al 1999
Prochlorococcus ecotypes partition the water column
Ahlgren et al 2005 Env. Micro.
Prochlorococcus ecotypes have latitudinal gradients
Johnson et al.
Nature 2006
40°S
20°S
0°
20°N
40°N
ENATL6
ENATL2
NATL2
ENATL5
SAR6
TATL1a
Whole genome
sequences reveal large
differences among
strains
89
71
66
100
SS120
MIT9211
MIT9303
72
MIT9313
SAR139
WH8112
84
WH8102
SAR100
WH8101
WH8012
WH7805
SAR7
Cyanobium PCC 6307
0.01
1.66 Mbp, 31 %G+C
ENATL1
ENATL3
MIT9302
MIT9312
MIT9201
92
GP2
MIT9202
MIT9215
TATL1b
MIT9107
NATL2A
PAC1
ENATL7
ENATL4
97
78
MED4
1.75 Mbp, 36 %G+C
2.41 Mbp, 51 %G+C
2.43 Mbp, 60 %G+C
Protein Family domains in 3 Prochlorococcus genomes
MED4
(high
light)
11
30
24
SS120
(low
light)
865
35
21
119
MIT9313
(low
light)
21 domains in MED4 and MIT9313 but not SS120 include:
Urease_alpha
Urease_beta
Urease_gamma
UreD
UreE_C
UreF
ureC
Urease alpha-subunit, N-terminal domain
Urease beta subunit
Urease, gamma subunit
UreD urease accessory protein
UreE urease accessory protein, C-terminal domain
UreF
ureB ureA ureD ureE ureF ureG
urtA
urtB
urtC
urtD
urtE
30 domains in MED4 but not SS120 or MIT9313 include:
Cyanate lyase
Cyanate lyase-C-terminal domain
cynS
Cyanate ABC transporter
119 domains in MIT9313 but not SS120 or MED4 include:
Form_nir_trans
Formate/Nitrite transporter
Prochlorococcus MED4
deletion
Prochlorococcus MIT9313
Synechococcus WH8102
nirA
deletion
narB
nirA
Rocap et al 2003 Nature
Summary of N source utilization genes
NH4
NO2
NO3
MED4
+
-
-
SS120
+
-
MIT9313 +
+
urea
cyanate
N2
+
+
-
-
-
-
-
-
+
-
-
What is the interplay between “core” and “unique”
genes in determining ecotype fitness?
21 genomes now available
MIT9515
MED4
MIT9301
High light
AS9601
MIT9312
NATL1A
Prochlorococcus
NATL2A
Low light
SS120
MIT9303
MIT9313
CC9902
coastal
BL107
oligotrophic
CC9605
WH8102
WH7803
motile
oligotrophic
Synechococcus
WH7805
CC9311
RS9916
RS9917
coastal ?
coastal ?
coastal ?
RCC307
WH5701
0.1
coastal
Defining the marine cyanobacterial core:
Orthologs defined
by reciprocal best
blast hits
1082
Paralogs resolved
by a combination
of computational
and manual
curation
Core genes make up only 40-60% of each genome
3500
unilogs
core
2-20
orthologs
2500
2000
1500
1000
0
BL107
CC9902
MIT9313
MIT9303
SS120
NATL2A
NATL1A
MIT9301
AS9601
MIT9312
MIT9515
MED4
500
WH5701
RCC307
RS9917
RS9916
CC9311
WH7805
WH7803
WH8102
CC9605
Number of genes
3000
eMIT9313
eMIT9312
eMED4
clade 4
eNATL2A
Synechococcus
Low light Pro High light Pro
Ahlgren & Rocap
in prep
The pan genome is dominated by unilogs
COG categories
core
9%
27%
2-20 orthologs
64 %
unilogs
Ahlgren & Rocap
in prep
Colored pie portions:
assignable COG function
Unknown
function
Phylogenomics of core genes
Find tree for each gene set
Ask: Are there genes with evolutionary
distances that are greater than or
smaller than avergage?
Ask: Are there trees with conflicting
branching order suggesting horizontal
transfer of some genes?
consensus
Relative rates of evolution vary among core genes
Slow core genes
COG classification
1 Translation, ribosome
4 Replication, recombination, repair
15 Chaperones, protein modification
16 Energy product and conversion
20 Coenzyme transport and metabolism
25 Unknown function
25
All core genes
n=1082
1
23
22
21
20
17
1
25
3
4
6
9
16
3
4
5
89
10
14
15
15
24
0.14
23
22
21
frequency
0.12
20 19
0.1
18
1 3
16
17
4
6
10
18
19
0.08
20
22
25
0.06
24
0.04
Fast core genes
0.02
0
0
3
6
9
12
15
18
21
24
total protein tree distance
27
30
Ahlgren & Rocap
in prep
Phylogenetic mapping of gene gain/loss events
MIT9515
MED4
MIT9301
AS9601
MIT9312
MED4
MIT9515
MIT9301
AS9601
MIT9312
Genome reductions
NATL1A
NATL2A
NATL2A
NATL1A
SS120
MIT9303
MIT9313
CC9902
BL107
CC9605
WH8102
WH7803
WH7805
CC9311
RS9916
RS9917
RCC307
WH5701
0.1
Gene gains
(non-unilog)
Unilog gains
SS120
MIT9313
High
light
Pro
Low
light
Pro
MIT9303
CC9902
BL107
CC9605
WH8102
Cluster 1
Syn
RS9916
RS9917
WH7805
WH7803
CC9311
Cluster 2
Syn
RCC307
WH5701
Gene losses
Ahlgren & Rocap
in prep
Function of genes
gained
MIT9515
MED4
MIT9301
AS9601
MIT9312
NATL2A
NATL1A
SS120
MIT9313
MIT9303
CC9902
BL107
CC9605
WH8102
RS9916
RS9917
WH7805
WH7803
CC9311
RCC307
WH5701
Selected COG categories
Amino acid transport & metab.
Carbohydrate transport & metab.
Inorganic ion transport & metab.
Cell wall/membrane biogenesis
Replication
2’ metabolite transp. & metab.
Transduction
Defense mechanisms
Ahlgren & Rocap
All other functions
in prep
Insertions of cell surface gene clusters
MED4
13,648 bp
MIT 9313
56,445 bp
WH 8102
mutS
PMM1645
33 gene
insertion
cysE
gyrB
PMM1634
mutS
PMT0079
tRNA
Gly secA
gyrB
cysE PMT0121
mutS
WH0078
tRNA
Gly secA
gyrB
cysE WH0095
22,507 bp
67
MIT 9313
%G+C
tRNA
Gly secA
51
27
Function of genes
lost
MIT9515
MED4
MIT9301
AS9601
MIT9312
NATL2A
NATL1A
SS120
MIT9313
MIT9303
CC9902
BL107
CC9605
WH8102
RS9916
RS9917
WH7805
WH7803
CC9311
RCC307
WH5701
Selected COG categories
Amino acid transport & metab.
Carbohydrate transport & metab.
Inorganic ion transport & metab.
Cell wall/membrane biogenesis
Replication
2’ metabolite transp. & metab.
Transduction
Defense mechanisms
Ahlgren & Rocap
All other functions
in prep
Where do the unilogs come from?
Possible duplication events
phage: 0.15%
23%
Archaea: 0.3%
Bacteria: 9%
68%
ORFans
n = 7241
n = 963
Crenarchaeota
Firmicutes
Euryarchaeota
Planctomycetes
phage
Alphaproteobacteria
Acidobacteria
Betaproteobacteria
Actinobacteria
Deltaproteobacteria
Bacteroidetes
Epsilonproteobacteria
Chlamydiae
Gammaproteobacteria
Chlorobi
Magnetococcus
Cyanobacteria
Spirochaetes
Deinococcus-Thermus
Genomic islands
Coleman et al. 2006, Science
No genes have an
ortholog in subject
All genes have an
ortholog in subject
Found in all genomes (core)
Found only in query
(unilog)
Synechococcus
WH8102
Isl. 7
Isl. 4
Island 3, insertion of
capsular polysaccharide
synthesis.
Isl. 18
Islands 36: nitrate
operon deleted in
RS9917
Isl. 19
Isl. 37
% GC
tRNAs
Islands 33,34: urea
operon deleted in
WH7803
Inverted and
direct repeats
Genomic
island
RCC307
RS9917
RS9916
CC9311
WH7803
(query, WH8102)
CC9605
BL107
CC9902
Island 29: phycobilisome
genes deleted in RS9917
No genes have an ortholog
in subject
All genes have an ortholog in
subject
Found in all genomes (core)
Found only in query (unilog)
Ahlgren & Rocap
in prep
“close with a profound quote”
How’s your ma?
Not too good, she’s on her way out
We all are, act accordingly