25 Genomes update. Yes, it’s been a while …

25 Genomes Project, Wellcome Sanger Institute

The project had been progressing at a steady-ish rate for a while, up until a few weeks ago and now we’ve run into some technical problems.

We’re using a number of different technologies to make the final genomes of our 25 species, they all serve slightly different purposes, with the aim that they all complement each other. Combined these technologies (and the clever people and computer programs that check the data) means that we can make very, very good quality genomes in a matter of months (possibly better than the human genome which took over 10 years with the old stuff).

So where are we now?

Pacbio complete for 13

Pacific Biosciences SEQUEL system. This is the main thing we use, you can get a pretty good genome with this technology alone, it uses long bits of DNA (about 50,000 letters). This works in a similar way to most other technologies as it labels the DNA with coloured dyes and takes photos of them as they are added to the bit in the well. The difference is the scale- this tech means you can ‘read’ 10s of thousands of letters of DNA per well (and there are 1 million of those), leading to a better genome. See the video below for a better explanation.

10X complete for 16

10X Genomics Chromium system. This is a clever new use of existing Illumina sequencing capabilities. This tech basically allows us to map smaller bits of DNA into a larger picture.

Hi-C complete for 2

This was invented by Erez Lieberman Aiden and gives an even bigger picture of how the bits of DNA fit together, allowing it to be put together in chromosome-sized chunks.

Bionano genomics SAPHYR.

Another way of fitting DNA together, this is especially useful to see large chunks of it that have moved around somewhat.

[basic] Genome assembly complete for 14

So not bad progress. We’re a little delayed, but ok for now.

The trouble with starfish

However, some species are proving to be rather problematic, most notably the starfish. We got [a lot] of sperm from one starfish* a few months ago thinking that as the sole purpose of sperm is to deliver DNA to an egg it would be a good place to start. Wrong.

For some, as yet unknown, reason the DNA in starfish sperm is oddly fragile- when we tried to extract it from the cells it broke up into bits only 200 letters long- WAAAAY shorter than the 150,000 aimed for.

You might wonder how we got starfish sperm. Apparently there’s a special chemical (called GSS- ‘gonad stimulating substance’) that you inject into the starfish that makes them- shall we say- ‘produce’ the sperm in surprisingly large quantities.

Flatworms aren’t too helpful, either

Working with flatworms hasn’t been straightforward either. Their sliminess is a problem, but not the only issue. The worms are essentially just a long gut surrounded by a bit of muscle and other anatomical odds and ends. This means they have a lot of nasty enzymes and other digestive juices inside that are specifically designed to break up long molecules (see below for a video)

When you combine sliminess and a large concentration of enzyme with the effects of freezing for storage, you end up with what was affectionately labelled ‘a zombie worm mush’ by our wormologists. Needless to say the DNA was not of a usable quality.

And as for truffles…

Truffles, too, seem not to like having their DNA extracted. After a few unsuccessful attempts we’re going to try a technique from 1992 that gave good results in the paper it came from and seems simple, so fingers crossed…