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With modern sequencing, are a large quantity of 'DNA fragments' sufficient for full nuclear genome replication? edit: Make that two questions: one for 'full nu

by mapt 13y ago

With modern sequencing, are a large quantity of 'DNA fragments' sufficient for full nuclear genome replication? edit: Make that two questions: one for 'full nuclear genome replication' and one for 'full nuclear genome sequencing'.

Scriptor 13y ago
It actually is possible to recreate the full genome and sequence it from just fragments. In fact Craig Venter's strategy during the Human Genome Project used this idea. They made countless copies of the full genome, then fragmented each copy at different points. They then sequenced each fragment, since it's much faster to sequence short ones. After that they looked at all the overlaps in these fragments to create longer, continuos sequences.
akiselev 13y ago
When you sequence a new species (like when cannabis was sequenced last year) with a modern sequencing technique, you break up the large DNA strands into many small ones and then use a massive cluster to assemble the strands afterwards with statistical methods. It'll be more complicated here because you will have many varied samples with varying degrees of degeneration across different chromosomes, sequences, and samples but the basic concept is the same.
mapt 13y ago
So how about for replication? Have we developed the tech to go from mammal -> digital genome sequence -> physical replicated chromosome -> egg implanted with chromosome -> developmentally normal mammal -> fertile offspring, yet, or is that somewhere in the future?
- jamesjporter 13y ago
  No. That chain ends at the second step "digital genome sequence". In principle, we could synthesize a bunch of DNA strands corresponding to the genomic sequences and ligate them all together (although it would be absurdly expensive and laborious), but this would not constitute a chromosome. Eukaryotic chromosomes are organized in the nucleus by a huge variety of scaffolding and modifying factors (histones, etc.) into structures called chromatin. Recapturing this from sequence data is impossible, even in principle; the information is just not there. Indeed, understanding nuclear organization at a bunch of different leves is one of the big challenges of modern genetic research.

by mapt 13y ago

Scriptor 13y ago

It actually is possible to recreate the full genome and sequence it from just fragments. In fact Craig Venter's strategy during the Human Genome Project used this idea. They made countless copies of the full genome, then fragmented each copy at different points. They then sequenced each fragment, since it's much faster to sequence short ones. After that they looked at all the overlaps in these fragments to create longer, continuos sequences.

akiselev 13y ago

When you sequence a new species (like when cannabis was sequenced last year) with a modern sequencing technique, you break up the large DNA strands into many small ones and then use a massive cluster to assemble the strands afterwards with statistical methods. It'll be more complicated here because you will have many varied samples with varying degrees of degeneration across different chromosomes, sequences, and samples but the basic concept is the same.

mapt 13y ago

So how about for replication? Have we developed the tech to go from mammal -> digital genome sequence -> physical replicated chromosome -> egg implanted with chromosome -> developmentally normal mammal -> fertile offspring, yet, or is that somewhere in the future?

jamesjporter 13y ago
No. That chain ends at the second step "digital genome sequence". In principle, we could synthesize a bunch of DNA strands corresponding to the genomic sequences and ligate them all together (although it would be absurdly expensive and laborious), but this would not constitute a chromosome. Eukaryotic chromosomes are organized in the nucleus by a huge variety of scaffolding and modifying factors (histones, etc.) into structures called chromatin. Recapturing this from sequence data is impossible, even in principle; the information is just not there. Indeed, understanding nuclear organization at a bunch of different leves is one of the big challenges of modern genetic research.