Mitochondrial and Chloroplast
DNA in Scaffolds
Goal
• Determine which scaffolds have mitochondrial
or chloroplast DNA
– Grape and Arabidopsis reference sets
• Ideally somehow annotate scaffolds/Contigs
Process
• A lot of blast results
• Program
– Splits up blast results
– Counts the number of times a specific scaffold
appears
• Store data in format that is editable in excel
454
Top 454 Mitochondria Hits
9
8
7
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2
1
0
scaffold18185 scaffold02014 scaffold14997 scaffold22747 scaffold12638 scaffold23105 scaffold14449 scaffold19050
454
Top 454 Chloroplast Hits
8
7
6
5
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2
1
0
scaffold07344
scaffold00103
scaffold15425
scaffold00515
Illumina
Top Illumina Mitochondria Hits
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8
7
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5
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2
1
0
Illumina
Top Illumina Chloroplast Hits
10
9
8
7
6
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3
2
1
0
ConsensusfromContig26966 ConsensusfromContig27000
ConsensusfromContig9008
ConsensusfromContig19940 ConsensusfromContig27060
Why I used the Top Most Frequent hits
8
7
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2
1
0
What Next?
• Possible additional feature is to pull out scaffolding
sequences that give x hits
• Annotation issues with geneious
What we can do in Geneious
• Scaffolds identified through blast and counting
hits re-Blasted as queries against grape and
Arabidopsis mitochondria DNA
– Just took one of the scaffolds with the most hits
and re-blasted
• Some alignment with ORFs
1 scaffold against all mitochondrial genes for grape and Arabidopsis
Notice 14 total hits… Different e-value? Program wrong?
Scaffold/contig
Mitochondial
Gene
How Accurate is Geneious ORF?
Questions…
• How do we want to use geneious?
• Is further work really helpful?
• Or good enough know these scaffolds as flagged?