Download - Vibrio genome analysis
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Vibrio genome analysis
ChristinaIsabellaRolandSarahi
Veronica
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General protocol
Isolation of vibrios DNA extraction
Illumina sequencingAssembly and annotation
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Quality of data
40 60 80 100 120 140 160 180 200 2200
50100150200250300350400450
2012 2011 2010 2009
Number of contigs
N50
Year
HS0A 2012HS0B 2012HS0C 2012*HA8H 2012PA2D 2011PA2G 2011PA1E 2010PA16E 2009HA7E 2009
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General genomic featuresHS0A HS0B HS0C HA8H
Genome size(Mbp)
5.30 5.37 4.91 5.52
# Contigs 75 63 75 104
# Coding sequences
4668 4654 4283 5076
# RNAs 85 96 97 86
% GC content 44.07 44.09 43.61 43.93
N50 (Kbp) 236 385 235 165
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Whole genome tree using Kr method
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0 10 20 30 40 50 60 70 800
500100015002000250030003500400045005000
Vibrio genomes compared
Cons
erve
d ge
nes
Vibrio core genome analysis
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Gene Number % of TotalTotal number of genes 834 100
COG (clusters of orthologous groups)
811 97.2
Enzymes 333 39.3KEGG 400 47.9
Core genus genome
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Core genus genome
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Whole genome tree using Kr method
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Whole genome tree recA tree
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What makes the clusters different
• PA2G contains a bioluminescent operon
•HA8H contains Siderophore Biosyn Pathway
•What about HS0A, HS0B and HS0C?
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Vibrio 2012-HA8H Vibrio 2012-HS0C
Vibrio HS0A
Vibrio HS0B
Sequence comparison to V. Splendidus
Genome similarity to V. Splendidus
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Comparison to HS0A
HSOB
HS0C
How does HS0A compare to …
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How does HS0A compare to …
Percent identity
Num
ber o
f hom
olog
ous g
enes
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Metabolic Pathways of Vibrio HS0A-2012
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Metabolic comparison using Pathway Tools:Differences between HS0A and HS0B are highlighted in red
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Metabolic Comparison using KEGG
• Compares the “functioning parts” of two organisms
• A functioning part is indicated as present if all of the genes to carry out a given subsystem are found in a given genome
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Metabolic Functional Comparison of Vibrios using KEGG
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# of Subsystems
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Metabolic Comparison using RAST database
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Looking for homologyALFY
Comparing HS0A to HS0B & HS0C
A – B 87%
A – C 5%A – non homologous 8%
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Is homology reflected in the DNA signatures?
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Is homology reflected in the DNA signatures?
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PCoA plot of Codon Usage in HS0A
21.9%
5.6%
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PCoA plot of Codon Usage in HS0A
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PCoA plot of Dinucleotide Frequencies in HS0A
30.9%
15.0%
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PCoA plot of Dinucleotide Frequencies in HS0A
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A gene transect … ?
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And the molecular biology producing the patterns?
• Phage receptors – strong positive selection• Integrons
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Maltoporin
• membrane protein• lamda phage receptor• found in HA0A, neither HA0B or HA0C have it
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What are integrons?
• Selfish genetic elements– In circular form– Integrated in the genome– Carrying and expressing a variety of “useful” genes
• Integrases originate from phages• Conserved recognition site to direct
recombination• Transmission via conjugation
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acquiring gene cassettes
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Inversion of the integrase neighborhood
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Alignment A,B,C, V. splendidus, anguillarium, furnissii
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diguanylate cyclase• 2 Guanosine triphosphate ↔ 2 diphosphate + cyclic di-3',5'-guanylate
(cyclic-di-GMP)
• a bacterial second messenger involved in…
http://tts.imtranslator.net/LgOh