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Advancing Science with DNA Sequence

A Genome Analysis Case Study with the Integrated Microbial Genome Expert Review (IMG/ER) SystemIntegrated Microbial Genome Expert Review (IMG/ER) System

Konstantinos Mavrommatis

Genome Biology ProgramJoint Genome Institute

Advancing Science with DNA Sequence

Access to your genome+ public genomes

http://img.jgi.doe.gov/erhttp://img.jgi.doe.gov/er

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Advancing Science with DNA Sequence

Advancing Science with DNA Sequence

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Advancing Science with DNA Sequence

Advancing Science with DNA SequenceOrganism page

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Advancing Science with DNA Sequence

Advancing Science with DNA Sequence

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Advancing Science with DNA Sequence

Advancing Science with DNA Sequence

IMGcurationcuration

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Advancing Science with DNA Sequence

Gene annotation curation

Advancing Science with DNA SequenceGene page

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Advancing Science with DNA Sequence

Advancing Science with DNA Sequence

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Advancing Science with DNA Sequence

Curation check

Advancing Science with DNA Sequence

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Advancing Science with DNA Sequence

Advancing Science with DNA Sequence

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Advancing Science with DNA Sequence

Advancing Science with DNA Sequence

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Advancing Science with DNA Sequence

Advancing Science with DNA Sequence

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Advancing Science with DNA SequenceCuration check

Advancing Science with DNA Sequence

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Advancing Science with DNA Sequence

Advancing Science with DNA Sequence

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Advancing Science with DNA Sequence

IMGdirected searchesdirected searches

Advancing Science with DNA Sequence

Gene searches

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Advancing Science with DNA Sequence

Gene searchby key words

Advancing Science with DNA Sequence

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Advancing Science with DNA Sequence

Advancing Science with DNA Sequence

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Advancing Science with DNA Sequence

IMGdiscovery

Advancing Science with DNA Sequence

user

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Advancing Science with DNA Sequence

Genes with homologs in Gram + (Firmicutes) absent in Gram -

Unknown:sporulation notobserved inobserved inHalothermothrix

Advancing Science with DNA Sequence

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Advancing Science with DNA Sequence

Advancing Science with DNA SequenceSearch for Halothermothrix genes, absent in Gram + (Firmicutes)

known:from cell envelopecharacterization,

RESULT: Halothermothrix genes, absent in Gram +ves (Firmicutes) but present in Gram -ves

consistent with Gram –ultrastructure

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Advancing Science with DNA Sequence

Abundance comparison

•Highest density of carbohydrate ABC transporters except for members of the p pRhizobiaceae, 3% the genome •The phosphotransferase system appears to be in the process of being removed from the genome.

•Enzyme I (Hore_20150) has a frameshift that does not occur at a slippery site,•IIA subunit •IIC subunit •NO IIB subunit

Adaptation to low nutrient environment

Advancing Science with DNA Sequence

Horizontally transferred genes.