Sequencing Larger Genomes

by Georgina Cornwall, PhD

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    00:01 we sequence genomes these days. Obviously in order to sequence a large genome, we have to have much larger chromosomes or plasmids. Plasmids can only carry so much information. They are small and they reside as accessories inside a bacterial cell. And so we have developed artificial chromosomes. The first ones were in yeast. The next ones were in bacteria and we are even working on human chromosomes now although at this point they are circular. We are working on getting them to be linear, but they still do seem to seggregate properly in culture, in vitro in a dish. We can stimulate mytosis of those cels to divide and reproduce the human artificial chromosome. Again we are working on getting them to be linear. But these artificial chromosomes can hold a lot more DNA, so it opens up a lot of potentials for us to sequence larger genomes. Again one of the tools that allow us to sequence our own genome. Looking at how we do manage the sequence such a large genome, we need to consider methods that have been used. They can basically be broken into two categories. We can do the clone-by-clone method or a shotgun method. The clone-by-clone method requires a little bit less lining up of fragments because there are less fragments or as more organization to the way that we get the fragments. It is called bac-to-bac or bacteria-to-bacteria also is another method or clone-by-clone because we have our initial set of clones and we will have fragments of DNA and then we further subdivide each of those fragments by putting them in another vector and into another whole set of bacteria.

    01:51 We almost have a sub-library or perhaps a shelf with a volume of encylopedias and another shelf with other volumes of encyclopedias, rather than just looking at the shelves. So we're more granular by putting them into a second vector and chopping up those pieces into shorter pieces. Then we can arrange all the pieces that are on one segment and then we can arrange all the pieces on the next segment. Once we have done that, we can arrange the whole linear chromosome by piecing it all back together. It is a sort of like a puzzle really. If you went online to look up DNA sequencing, you will find probably a lot of conflicting and confusing information, but basically, the clone-by-clone method goes by a number of different names also. Hierarchial sequencing or BAC to BAC because we are putting it from bacterial artificial chromosome or bacterial artificial chromosome.

    02:51 The next sequence or next method of sequencing is the shotgun method and this is only possible because of the higher levels of computing that are possible these days. Because what we are really doing is rather than doing bac-to-bac where we put a vector and then split that vector into smaller fragments, we just hack up the whole genome into milions of little pieces and so it is a shotgun method. Previously it was very computer consuming where we didn't necessarily have enough power to do it. But now with the advent of much more powerful computing, we can use this method and it is essentially doing the same thing lining up pieces. But if you have a million pieces that you don't know which larger fragment they came from and then which larger fragment, then we have a really tough time lining those pieces. But again computers do it all for us now, so were able to sequence more DNA more quickly with the shotgun method. Currently, both methods are still very readily used in genomic research. This shotgun sequencing could also be called whole genome shotgun sequencing just so that you are familiar with some of the names out there if you go and look into DNA sequencing. In this lecture, I have given you a quick introduction to variety of ways that we map the genome. We have physical mapping and we have genetic mapping. And then we have increasing levels of granularity using different tagging techniques and then finally actual genome sequencing. And so by now you should be able to distinguish between genetic and physical maps as well as describe the process of DNA sequencing, the Sanger dideoxy method of DNA sequencing. And you should be able to characterize both clone-by-clone sequencings as well as shotgun sequencing. Anyway, thank you so much for listening and I will look forward to taking you forward in our exploration of genomics in our next lecture.

    About the Lecture

    The lecture Sequencing Larger Genomes by Georgina Cornwall, PhD is from the course Genomics.

    Included Quiz Questions

    1. ...clone-by-clone sequencing.
    2. ...shotgun sequencing.
    3. ...consensus sequencing.
    4. ...STS Sequencing
    1. …the cloning of larger chromosomes and then subclone them into smaller pieces for sequencing.
    2. …the cloning of smaller DNA molecule into a plasmid for their sequencing.
    3. …the cloning of viral DNA molecule into a human chromosome for its sequencing.
    4. …the cloning of plasmid DNA molecule into a human chromosome for its sequencing.
    5. …the cloning of bacterial DNA molecule into a human chromosome for its sequencing.
    1. The shotgun method of sequencing goes well with highly repetitive type DNA molecules.
    2. The whole genome shotgun method involves the sequencing of overlapping DNA fragments in parallel and assembling of the small fragments into larger contigs and then chromosomes by using a computer programme.
    3. The whole genome shotgun method is rapid and straightforward as compared to clone to clone sequencing method.
    4. Any genome with lots of repetitive sequences leads to many difficulties during chromosome assembly.
    5. A genome with fewer repeated regions can easily be sequenced with whole genome shotgun method in lesser time.

    Author of lecture Sequencing Larger Genomes

     Georgina Cornwall, PhD

    Georgina Cornwall, PhD

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