Post on 03-Jul-2015
description
Increased rates of horizontal gene transfer in psychrophile genomes and potential links to the Phanerozoic climate record
Jeff S. Bowman, Eric Collins, Jody W. Deming
bowmanjs@ldeo.columbia.edu
• Why HGT might be elevated in psychrophile genomes • Introduce method for evaluating genomic plasticity in a
population • Application of this method, psychrophiles vs. mesophiles • Potential links between gene acquisition and the
Phanerozoic climate record
Why HGT might be elevated in cold environments
Junge et al. 2001
2
-15 °C
Wells and Deming, 2006
HGT may be elevated by phage-bacteria and bacteria-bacteria contact rates in ice environments
HGT may be elevated by phage-bacteria and bacteria-bacteria contact rates in ice environments
Infection rates and phage diversity may be higher in low temperature environments
3
Anesio and Bellas, 2011
Why HGT might be elevated in cold environments
Method for evaluating genomic plasticity in a population
Quantifying genomic plasticity
Are psychrophiles more genetically plastic than mesophiles?
Bowman et al., 2014, in prep 4
Genomic plasticity = gene loss + HGT + gene duplication
Method for evaluating genomic plasticity in a population
Maximum-likelihood tree of psychrophile and mesophile strains used in this analysis Bowman et al., 2014, in prep
5
Method for evaluating genomic plasticity in a population
Bowman et al., 2014, in prep
divG = abs(16S – CV) 16S: 16S distance CV: amino acid compositional vector distance (Qi et al., 2004) Values transformed • mean = 0 • variance = 1 • range between 0
and 1
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Method for evaluating genomic plasticity in a population
Bowman et al., 2014, in prep
divG = abs(16S – CV) 16S: 16S distance CV: amino acid compositional vector distance (Qi et al., 2004) Values transformed • mean = 0 • variance = 1 • range between 0
and 1
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Transposase (blue)
Integrase/ Recombinase (green)
Phage specific
Chapter 5 – Horizontal gene transfer (HGT) in psychrophile genomes
Bowman et al., 2014, in prep
divG = abs(16S – CV) 16S: 16S distance CV: amino acid compositional vector distance (Qi et al., 2004) Values transformed • mean = 0 • variance = 1 • range between 0
and 1
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Octadecabacter antarcticus divG = 0.09
Octadecabacter arcticus
divG = 0.25
Results, psychrophiles vs. mesophiles
Blue = psychrophiles, Orange = mesophiles • Distribution of 16S distances nearly identical between the two groups • Distribution of compositional vectors distances, divG, and divG are all
significantly different (p = 2.49 x 10-8, 3.5 x 10-6, 0.01) by the Mann-Whitney or Students T-tests
• Preliminary (limited sample size) evidence for enhanced plasticity in psychrophile genomes
Bowman et al., 2014, in prep 9
Estimating time since acquisition for probable HGT events
During glacial maximum… • Psychrophile range is expanded • More ice environments • More temperate phage?
Veizer et al., 2003
Temperature anomalies during Phanerozoic Eon
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Estimating time since acquisition for probable HGT events
Bowman et al., 2014, in prep
Distribution of HGT event probabilities
• Identify likely HGT events by anomalous GC content
• Estimate time since acquisition with GC amelioration method (Lawrence and Ochman, 1997)
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GC
anom
aly
Psychrophiles
Mesophiles
Estimating time since acquisition for probable HGT events
= period when Earth’s temp was below the current mean
= mass extinction event
= 10 My running mean
Psychrophiles
Mesophiles
Monte-Carlo analysis for psychrophiles
562.74
-757.61
Bowman et al., 2014, in prep 12
Conclusions + acknowledgements
• Developed a new method for evaluating genomic plasticity between populations
• Preliminary evidence for higher genomic plasticity among psychrophiles compared to mesophiles
• For psychrophiles, strong correlation between time since acquisition for putative HT genes and geologic cold periods
This presentation and code for methods linked from: www.ldeo.columbia.edu/~bowmanjs