Chromosome Purification Before De Novo Assembly

Question

[Jeremy Leipzig]

How difficult it is to use flow cytometry to purify or isolate genomic dna by individual chromosome?

Why isn't this done as a first step before the de novo assembly of novel organisms like the naked mole rat?

[Manu Prestat]

Publish it before it's too late!!

[Jeremy Leipzig]

i see some mention of this approach during the human genome project - probably in combination with BACs

[jinych2bgi]

What is the progress

Answer 1

[lh3]

I would like to see their comparison to WGS. Frankly, I am not sure how much this strategy helps. Repeats present genome-wide are also repetitive in each chromosome, which still prevents us from getting long contigs. Assembling per chromosome does help to reduce memory, but I do not see this is a major problem nowadays. Flow sorting chromosomes and then constructing barcode libraries add efforts and costs. The contamination rate from other chromosomes is like 10-20% as I remember. These efforts seem not paid off well.

Anyway just my guess. Could be wrong.

Answer 2

[SES]

This approach is being used to sequence the wheat genome. See the Vitulo et al. 2011 paper in PLoS One, for example.

Answer 3

[Yannick Wurm]

Major hurdles:

• you need to be able to get the right kinds of cells (metaphase?) in sufficient quantities that let you separate individual chromosomes
• you need to be able to identify chromosomes (size, fluorescence, probes?)
• you need to care (why does it matter?)
• you need to have the relevant manpower (previously genome projects were run by molecular biologists; emerging model organisms sequencing is often run by evolutionary biologists or ecologists who haven't ever even seen a PCR machine)

I think the general attitude is "we'll get what we can with the current technology"... because 2 more years of improvements in sequencing technology will make things automagically better.