Hasta la VISA, genomes!

By: Dan Mead, Project coordinator for the 25 Genomes Project at the Wellcome Sanger Institute

Date: 18.12.18

Greetings and salutations,

After another long period of inactivity due to me being busy/lazy/forgetful [delete as appropriate] I thought it was about time I wrote another one of these updates.

The more observant of you might have noticed that this is now an ‘official’ Sanger blog so all of the [removed due to inappropriate language] sweary bits that you usually find scattered through this [removed due to inappropriate language] little blog will be absent from here on in.

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So we’ve actually managed to sequence 25 genomes!

In fact we did 26 due to the incident of the mis-identified ragwort, which does admittedly sound like an Agatha Christie novel, where we ended up doing the common ragwort* instead of the Oxford ragwort, before realising our mistake.


*The common ragwort (Senecio jacobaea), aka ‘stinking willie’, has a much bigger (3Gb) and more complex (hexaploid) genome than the Oxford ragwort. This had us worried (!) and led us to explore what was going on


For regular readers you may also be interested in findingout how we got around the tricky truffle problem; well we didn’t. In a fudge ofepic proportions we switched out this species for one of our ‘backup’ species,the Broad-bordered Bee Hawk-moth (Hemarisfuciformis).

This is not to say I’m not trying to do the truffle as well, in fact I’ve done a little research on it. With a little help [ok, a lot, I basically did nothing] from Yang I now have a microscope image of the cells in the truffle.

A bit of reading and it seems that the spores have a grand total of four (yes FOUR!) cell walls (1, 2), which may or may not explain the difficulty. Next up on the list of things to try is Metapolyzyme (3), a six enzyme cocktail that has (at least in theory) all the stuff needed to digest those pesky walls so we’ll see how that goes.

What else has been going on?

Quite a bit, as it turns out. We had a visit from Arina Omer of the Aiden lab who, in conjunction with the Sanger Institute R&D and pipeline teams, prepped 18 samples for Hi-C sequencing which will really help the assembly of the genomes. This is obviously great but unfortunately to finish these off we need to send the prepared DNA samples to Baylor College of Medicine in the US. But why would that be a problem, surely with today’s logistics, sending some frozen DNA across the Atlantic is a breeze right?

It would be if it weren’t for the fact that these samples are from plants, birds and other things. They therefore need a bunch of permits/letters that would normally accompany *the actual intact material* such as leaves, whole organisms etc. Now I get the need for biosecurity, however you’d find it very difficult to damage an ecosystem by spilling a tube of purified DNA! Government agencies really need to get on this, months have been lost so far figuring this nonsense out.

Anyway, regardless of the kerfuffle, there are a number of decent genomes now in various states of assembly that will only get better with additional data (we now have a Bionano Saphyr as well 🙂 ), here are the highlights (green is good, yellow ok, red is bleugh):

Name contig N50 length (Mb) [bits of DNA without any gaps] scaffold N50 length (Mb) [the bits to the left stuck together]
European Golden Eagle
23.81
44.95
European Robin
3.71
10.64
European Turtle Dove
3.43
15.56
Giant Hogweed
0.12
0.22
Indian Balsam
0.82
1.83
Brown Trout
1.69
52.21
Ringlet Butterfly
1.05
1.27
Broad-bordered Bee Hawk-moth
6.77
8.01
Red Mason Bee
7.04
8.53
Asian Hornet
1.27
2.95
European Water Vole
2.23
8.4
Eurasian Otter
30.4
53.73
Common Pipistrelle
3.19
4.7
Grey Squirrel
9.35
11.46
Red Squirrel
11.89
116.63
Fen Raft Spider
0.4
0.65
Smaller Spotted Catshark
0.49
24.31
King Scallop
0.67
1.05

Getting out of the office

I gave a talk at Genome Science in Nottingham and another atthe PacBio user group meeting in Lisbon – where, at the latter, we got the ‘official’ word on the Illumina takeover of the company – essentially nothing will happen until the middle of 2019 (for some thoughts on this see this excellent piece by @OmicsOmicsBlog).

I also went to the National Biodiversity Network conference (Nottingham again) and had a great and random chat with an entomologist from Buglife (apologies if you reading this, I’m terrible with names) where we discussed:

  1. using a vacutainer to preserve small insects
  2. wrapping spindly legged critters in fabric off-cuts so they don’t break
  3. cutting up blankets to stop collection pots rattling around

Also that there doesn’t appear to be a useful tips and tricks for working in the field book/guide for collecting stuff (someone should definitely do this).

I’m also currently working on helping to get the Darwin Tree of Life Project off the ground (see hereherehereand here)which is keeping me super busy.

And that, as they say, is all folks!

About the Author

Dan Mead is the project coordinator for the 25 Genomes Project at the Wellcome Sanger Institute

References

  1. Briza P, Ellinger A, Winkler G, Breitenbach M. Chemical composition of the yeast ascospore wall. The second outer layer consists of chitosan. The Journal of biological chemistry. 1988; 263(23): 11569-74.
  2. Piepkorn M, Hovingh P, Linker A. Glycosaminoglycan free chains. External plasma membrane components distinct from the membrane proteoglycans. The Journal of biological chemistry. 1989; 264(15): 8662-9.
  3. Tighe S, Afshinnekoo E, Rock TM, McGrath K, Alexander N,McIntyre A, et al. Genomic Methods and Microbiological Technologies for Profiling Novel and Extreme Environments for the Extreme Microbiome Project (XMP). Journal of biomolecular techniques : JBT. 2017; 28(1): 31-9.