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Old 06-03-2009, 12:54 PM   #1
bio-x
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Default advice for de novo assembly of plant genome using 454

I plant to de novo assemble one plant genome using 454, the size is about 1G. Has anyone experience in such way and give me some advice?

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Old 06-04-2009, 01:48 AM   #2
Melissa
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Just don't tell me you're gonna prepare the genomic DNA and sequence it!
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Old 07-23-2009, 11:59 PM   #3
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It will most likely be possible to sequence the genome, but the assembly process will be tricky since most plant genomes are extremely repetitive, so in the end you might end up with a very fragmented assembly with millions of short contigs. Perhaps paired end libraries might help a bit.
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Old 07-24-2009, 09:38 AM   #4
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University of Arizona recently published a paper using 454 to sequence rice. Their method is 454 Titanium + pooled BAC strategy. Some new school and some old school stuff. rice genome size is around 400 MB.

The paper title:
"De Novo Next Generation Sequencing of Plant Genomes"
It can be easily found over Google.
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Old 07-24-2009, 10:05 AM   #5
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Quote:
Originally Posted by rand View Post
It will most likely be possible to sequence the genome, but the assembly process will be tricky since most plant genomes are extremely repetitive, so in the end you might end up with a very fragmented assembly with millions of short contigs. Perhaps paired end libraries might help a bit.
A combination of pooled BACs + 454 Titanium is the way to go for draft assembly. Assembly is very challenging for big plants genome without BACs.

Plants have lots of repeat. Here long reads is important factor for good assembly.

Last edited by hlu; 07-29-2009 at 08:25 AM.
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