2/3/2015
Outline
• Importance of peat bogs
• Sphagnum fallax
• Mutualistic relationship with cyanobacteria
• High quality JGI sequencing
Metabolic Modeling of PlantMicrobe Interactions in KBase
Sam Seaver
Jan. 13th 2015
Sphagnum fallux: Bog moss
Sphagnum dominates peatlands, cover ~36% of the earth’s surface and store ~1/3 of
the earth’s terrestrial carbon.
• Functional annotation of genomes in KBase
• Metabolic reconstructions in KBase
• Merging of two species
• Metabolic interaction (N2 fixation)
Nitrogen fixation via cyanobacteria
Tollund man (Denmark: died 350 BC)
JGI Community Science Project (S. magellanicum, S.
fallax) with J. Schmutz, K. Barry, J. Tuskan, D.
Weston and J. Shaw
Initial results from genome sequencing
S. fallax (v0.5)
Assembly (from Illumina MiSeq 49x coverage of 400, 500 bp,
3.3kb, 6.4kb):
Science Driver: Approximately 30% of terrestrial carbon
is stored in Sphagnum spp. dominated peatlands
What is proposed:
• High-quality genome sequence and assembly of
Sphagnum magellanicum & S. fallax
• RNASeq from diverse developmental and experimental
samples
• SNP identification from resequencing 20 sporelings
• Construction of a high-resolution genetic map
• Resequencing of 9 Sphagnum species
Expected outcome:
• Provide a critical link in the early evolution of
embryophytes from algal ancestors and comparative
assessment of other sequenced mosses
• Enable genome association studies for key traits
governing carbon cycle dynamics (e.g., productivity and
mortality, photosynthesis, decomposition rates)
Scaffold number: 1,228
L50/N50:
61/1.8
Contig number: 7,689
L50/N50: 998/121.2 KB
Total scaffold size : 396.4 MB
Total contig size: 395.0 MB (-> 0.4% gap)
Annotation (based on 2B RNA-seq from 8 tissue/conditions &
available homology):
Primary transcripts (loci)
26,939
Alternative transcripts 5,359
Total transcripts
32,298
Average number of exons 5.9
Median exon length
175
Median intron length 245
Focus now is on building a genetic map for chromosome
reconstruction
HIGH QUALITY SUBSTRATE FOR MODEL PREDICTION
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2/3/2015
Genome-scale in silico modeling
Annotation and Reconstruction Workflow
Flux-balance
analysis approach:
• What
Kinetic
canapproach:
we model:
Structural/stoichiometric
constraint-based
approach
a number
of parameters
enzymes
• –
In aRequires
given metabolic
network,
what isfor
themany
possible
range of metabolic
phenotypes?
Fast computation
–
Requires
computational power
• Example: must be able to generate a compound given a certain medium
(particularly carbon-limited growth)
Genome
Annotated
Genome
Integration of
specialized
plant
biochemistry
Curation of
plant primary
metabolism
Sphagnum and Cyanobacteria Genomes in KBase
Annotation
Computation
isofunctional
protein
families
Curation of
plant primary
metabolism
Draft model
Reconstruction
Working
model
Metabolic Annotation in KBase (Cyanobacteria)
https://narrative.kbase.us/functional-site/#/ws/objects/Cyanobacteria_Sphagnum_Interaction
Metabolic Annotation in KBase (Sphagnum)
Metabolic Reconstruction in KBase (Cyanobacteria)
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2/3/2015
Metabolic Reconstruction in KBase (Sphagnum)
Metabolic Interactions in KBase
• Plant-Microbe Metabolic Interaction:
• The nitrogen provided for the biomass of a Sphagnum moss is fixed by a
cyanobacteria
N2
NH3
3