ecotypic diversity of marine cyanobacteria: tales from the pangenome
DESCRIPTION
Ecotypic diversity of marine cyanobacteria: Tales from the pangenome. Gabrielle Rocap. Small (0.6 x 0.8 m m) divinyl chlorophylls a and b. Larger (0.8 x 1.8 m m) phycobilisomes. Unicellular marine cyanobacteria. ubiquitous throughout the tropical and sub tropical oceans - PowerPoint PPT PresentationTRANSCRIPT
Ecotypic diversity of marine cyanobacteria: Tales from the
pangenome
Gabrielle Rocap
Small (0.6 x 0.8 m) divinyl chlorophylls a and b
Larger (0.8 x 1.8 m) phycobilisomes
Prochlorococcus Synechococcus
ubiquitous throughout the tropical and sub tropical oceans
extremely abundant (up to 4x105 cells/ml)
contribute significantly to primary productivity
Unicellular marine cyanobacteria
Images from http://ccmp.bigelow.org
Durand et al., Deep Sea Research II 2001
Prochlorococcus and Synechococcus have differing seasonal abundances in the Sargasso Sea
Prochlorococcus isolates differ in their photophysiology
0
0.2
0.4
0.6
0.8
1
1 10 100 1000
Growth irradiance (mol Q m-2 s-1)
MIT9312
MIT9313
Gro
wth
ra
te (
da
y-1)
MIT9313MIT9312
0
1
2
Growth Irradiance (mol Q m-2 s-1)
Ch
l b/c
hl a
2
1 10 100 1000
From Moore, Rocap & Chisholm 1998
MED4
MIT9313
WH8102
ENATL2
MIT9201GP2
MIT9107
ENATL6
NATL2ENATL5
SAR6
ENATL1ENATL3
MIT9302MIT9312
MIT9202MIT9215
NATL2A
ENATL7ENATL4
SS120MIT9211
MIT9303
SAR139WH8112
SAR100WH8101
WH8012WH7805
SAR7
Cyanobium PCC 6307
0.01
89
97
92
72
71
10078
66
84
Marine Synechococcus
I
IPAC1
TATL1b
TATL1a
rRNA phylogeny corresponds to physiological differences —”ecotypes”
Adapted from Rocap et al 1999
II
IIIII
IV
Ahlgren et al 2005 Env. Micro.
Prochlorococcus ecotypes partition the water column
Johnson et al. Nature 2006
40°S 20°S 20°N 40°N0°
Prochlorococcus ecotypes have latitudinal gradients
MED4
MIT9313
WH8102
ENATL2
MIT9201GP2
MIT9107
ENATL6
NATL2ENATL5
SAR6
ENATL1ENATL3
MIT9302MIT9312
MIT9202MIT9215
NATL2A
ENATL7ENATL4
SS120MIT9211
MIT9303
SAR139WH8112
SAR100WH8101
WH8012WH7805
SAR7
Cyanobium PCC 6307
0.01
89
97
92
72
71
10078
66
84
Whole genome sequences reveal large
differences among strains
PAC1
TATL1b
TATL1a1.66 Mbp, 31 %G+C
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
SS120 (low light)
MED4 (high light)
2430
865
MIT9313 (low light)
119
11
3521
21 domains in MED4 and MIT9313 but not SS120 include:
Urease_alpha Urease alpha-subunit, N-terminal domainUrease_beta Urease beta subunitUrease_gamma Urease, gamma subunitUreD UreD urease accessory proteinUreE_C UreE urease accessory protein, C-terminal domainUreF UreF
ureC 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
deletion
deletion
Prochlorococcus MED4
Synechococcus WH8102narB nirA
Prochlorococcus MIT9313nirA
Rocap et al 2003 Nature
Summary of N source utilization genes
NH4 NO2 NO3 urea cyanate N2
MED4
SS120
MIT9313
+
-+
+
+
+
+
-
-
-
-
-
-
-
+
-
-
-
What is the interplay between “core” and “unique” genes in determining ecotype fitness?
0.1
MIT9301
AS9601
MIT9312
MIT9515
MED4
NATL1A
NATL2A
SS120
MIT9303
MIT9313
WH7803
WH7805
CC9311
RS9916
RS9917
CC9902
BL107
CC9605
WH8102
RCC307
WH5701
21 genomes now available
Low light
Synechococcus
coastal
coastal ?
coastal ?coastal ?
coastal
oligotrophic
oligotrophicmotile
High light
Prochlorococcus
1082
Orthologs defined by reciprocal best blast hits
Paralogs resolved by a combination of computational and manual curation
Defining the marine cyanobacterial core:
High light Pro
eMED4eMIT9312eMIT9313
eNATL2Aclade 4
Low light ProSynechococcus
0
500
1000
1500
2000
2500
3000
3500
WH
5701
RC
C30
7R
S99
17R
S99
16C
C93
11W
H78
05W
H78
03W
H81
02
CC
9605
BL
107
CC
9902
MIT
9313
MIT
9303
SS
120
NA
TL
2AN
AT
L1A
MIT
9301
AS
9601
MIT
9312
MIT
9515
ME
D4
unilogs
core
2-20 orthologs
Nu
mb
er o
f g
enes
Core genes make up only 40-60% of each genome
Ahlgren & Rocap in prep
unilogs
core
2-20 orthologs
9%
27%
64 %
COG categories
Unknown function
Colored pie portions: assignable COG function
The pan genome is dominated by unilogs
Ahlgren & Rocap in prep
Phylogenomics of core genes
consensus
Find tree for each gene set
Ask: Are there trees with conflicting branching order suggesting horizontal transfer of some genes?
Ask: Are there genes with evolutionary distances that are greater than or smaller than avergage?
total protein tree distance
Slow core genes
Fast core genes
All core genesn=1082
1 Translation, ribosome
15 Chaperones, protein modification16 Energy product and conversion
25 Unknown function
Relative rates of evolution vary among core genes
1
346
915
16
1720
2122
23
25
13
45
8 910
1415
1617
18192021
2223
24
25
1 34
6101819
2022
24
25
20 Coenzyme transport and metabolism
0
0.02
0.04
0.06
0.08
0.1
0.12
0.14
0 3 6 9 12 15 18 21 24 27 30
fre
qu
en
cy
4 Replication, recombination, repair
COG classification
Ahlgren & Rocap in prep
WH5701
RCC307
MIT9303MIT9313
AS9601
MED4
MIT9301
MIT9312
MIT9515
NATL1A NATL2A
SS120
RS9917 RS9916
CC9311 WH7803
WH7805
BL107 CC9605
CC9902
WH8102 0.1
MIT9301AS9601
MIT9312
MIT9515MED4
NATL1A
NATL2A
SS120MIT9303
MIT9313
WH7803WH7805
CC9311RS9916RS9917
CC9902
BL107CC9605
WH8102
RCC307
WH5701
Genome reductions
Gene losses
Unilog gains
Gene gains (non-unilog)
Cluster 1 Syn
Cluster 2 Syn
High light Pro
Low light Pro
Phylogenetic mapping of gene gain/loss events
Ahlgren & Rocap in prep
WH5701 WH5701
RCC307 RCC307
MIT9303MIT9313
MIT9303MIT9313
AS9601
MED4 MIT9301
MIT9312
MIT9515
AS9601
MED4 MIT9301
MIT9312
MIT9515
NATL1A NATL2A
NATL1A NATL2A
SS120
RS9917 RS9916
CC9311 WH7803 WH7805
RS9917 RS9916
CC9311 WH7803 WH7805
BL107 CC9605
CC9902
WH8102
BL107 CC9605
CC9902
WH8102
All other functions
Replication
Cell wall/membrane biogenesis
Amino acid transport & metab.
Carbohydrate transport & metab.Inorganic ion transport & metab.
2’ metabolite transp. & metab.TransductionDefense mechanisms
Selected COG categories
Function of genes gained
Ahlgren & Rocap in prep
Insertions of cell surface gene clusters
%G+C
67
27
51MIT 9313
MED4
13,648 bp
tRNA Gly secA cysE
gyrBmutSPMM1645 PMM1634
MIT 9313
56,445 bpsecA cysE
gyrBmutS tRNA GlyPMT0079 PMT0121
33 gene insertion
WH 8102
22,507 bp
secA cysEgyrBmutS tRNA
GlyWH0078 WH0095
WH5701 WH5701
RCC307 RCC307
MIT9303MIT9313
MIT9303MIT9313
AS9601
MED4 MIT9301
MIT9312
MIT9515
AS9601
MED4 MIT9301
MIT9312
MIT9515
NATL1A NATL2A
NATL1A NATL2A
SS120
RS9917 RS9916
CC9311 WH7803 WH7805
RS9917 RS9916
CC9311 WH7803 WH7805
BL107 CC9605
CC9902
WH8102
BL107 CC9605
CC9902
WH8102
All other functions
Replication
Cell wall/membrane biogenesis
Amino acid transport & metab.
Carbohydrate transport & metab.Inorganic ion transport & metab.
2’ metabolite transp. & metab.TransductionDefense mechanisms
Selected COG categories
Function of genes lost
Ahlgren & Rocap in prep
Archaea: 0.3%
phage: 0.15%
Bacteria: 9% ORFans
n = 963
n = 7241
23%
68%
Possible duplication events
Crenarchaeota
Euryarchaeota
phage
Acidobacteria
Actinobacteria
Bacteroidetes
Chlamydiae
Chlorobi
Cyanobacteria
Deinococcus-Thermus
Firmicutes
Planctomycetes
Alphaproteobacteria
Betaproteobacteria
Deltaproteobacteria
Epsilonproteobacteria
Gammaproteobacteria
Magnetococcus
Spirochaetes
Where do the unilogs come from?
Genomic islands
Coleman et al. 2006, Science
Found in all genomes (core)
Found only in query (unilog)
All genes have an ortholog in subject
No genes have an ortholog in subject
% GC
tRNAs
Inverted and direct repeats
Island 29: phycobilisome genes deleted in RS9917
Genomic island
All genes have an ortholog in subject
No genes have an ortholog in subject
Found in all genomes (core)
Found only in query (unilog)
Island 3, insertion of capsular polysaccharide synthesis.
Islands 33,34: urea operon deleted in WH7803
Islands 36: nitrate operon deleted in RS9917
Isl. 4Isl. 7
Isl. 37
Isl. 18
Isl. 19
Synechococcus
WH8102
RCC307RS9917RS9916CC9311WH7803
BL107CC9902
(query, WH8102)CC9605
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