Download File

Playing with real data
Reference-guided assembly
(SNP calling)
Evolutionary & Ecological Genomics
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With dozens (or perhaps hundreds) of
genotypes from a range of habitats, we should
be able to associate ecology with genotype
Build phylogenies / haplotype networks to
understand relationships
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Infer evolutionary history
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Study the role of selection
The Short Read Archive (SRA)
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http://www.ncbi.nlm.nih.gov/sra
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Genomic data on many tens of thousands of
samples
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Search-able
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Download-able
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Not assembled
Genome resources at NCBI
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http://www.ncbi.nlm.nih.gov/genome/
Many hundreds of assembled genomes and
other resources
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Search-able
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Download-able
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A bit buggy / hard to find what you want
sometimes
Plastid genomes on NCBI
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http://www.ncbi.nlm.nih.gov/genomes/GenomesGroup.cgi
?taxid=2759&opt=plastid
599 plastid genomes
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427 'Viridiplantae' chloroplasts / plastids
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Viridiplantae
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Green algae
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Nonvasular plants
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Ferns, gymnosperms
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Flowering plants
279 eudicot plastid genomes
Expand on this dataset of plastid
genomes
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2 phases
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Variation within a species (Arabidopsis thaliana)
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SNP calling
Adding new species
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De novo assembly
Expand on this dataset of plastid
genomes
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2 phases
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Variation within a species (Arabidopsis thaliana)
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SNP calling
Adding new species
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De novo assembly
Chloroplast
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http://en.wikipedia.org/wiki/Chloroplast
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Why the chloroplast / plastid?
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Small, simple, well-studied genome
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Important (photosynthesis)
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High copy number
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Little repetitive 'junk'
Connecting climate to genotypes
1001 Arabidopsis genomes
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Actually 1049 in progress, but only a portion
completed
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Can order seeds from these inbred lines
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WGS data
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Excellent reference genome
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Not well genotyped at 'repetitive' sequences,
including the plastid
Chosen subset
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McKay et al. 2003
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Photosynthetic efficiency, Lat, Long, Elevation
Great genetic and phenotypic data, we just
have to put them together to see if anything
interesting is going on
Part of a larger dataset (automated SNP calls)
with interesting patterns
Ethics of SRA use
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Anyone can download the data
Courteous to allow the authors to write a paper
first
Toronto statement
http://signal.salk.edu/atg1001/Data_
Sharing_Policy.pdf
Homework
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By Thursday
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Read up on chloroplasts – wikipedia page
http://en.wikipedia.org/wiki/Chloroplast
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By next Monday
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D2L something interesting about chloroplasts
D2L a bash script for SNP genotyping your cp
By next Tuesday
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D2L a 'draft' SNP table for your ecotype
Bash scripting
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which bash
Bash scripting
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which bash
/bin/bash
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http://linuxconfig.org/bash-scripting-tutorial
Bash scripting
#!/bin/bash
Bash scripting
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#!/bin/bash
bwa index mt.fa
Bash scripting
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#!/bin/bash
bwa index mt.fa
bwa mem mt.fa sra_data.fastq > ler.sam
Bash scripting
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#!/bin/bash
bwa index mt.fa
bwa mem mt.fa sra_data.fastq > ler.sam
samtools view -b -o ler.bam -S ler.sam
samtools sort ler.bam ler.sorted
samtools index ler.sorted.bam
samtools faidx mt.fa
samtools mpileup -gf mt.fa ler.sorted.bam > mt.bcf
bcftools view -vc mt.bcf > snps_indels.vcf
Your chloroplast genomes
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Arabidopsis reference plastid sequence:
http://www.ncbi.nlm.nih.gov/nuccore/7525012?report=fasta
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Your fastq sequences – in the genomics2014
home folder, I will email you a link to yours