Yannick's News

Oxford Nanopore sequencing – a revolution for non-model organisms?

admin — Sat, 18 Feb 2012 12:48:12 +0000

Exciting announcement of a new dirt-cheap machine-less DNA sequencing technology. If their promises hold true, this technology will be a game-changer for those of us working with “emerging” non-model organisms because:

it supposedly provide 100,000bp long reads. This will eliminate most scaffolding issues we have with assembling de novo genome sequence.
using the USB thumb-chip version, no machine is required. Thus when you are out in the field, you can sequence right then and there – a potential workaround for worrying about tissue sample export permits… at least until new regulations appear!

High error rates are problematic in short reads because they introduce ambiguity making it challenging to align and assemble these reads. However, this is much less of an issue with longer reads: A 100,000bp region will remain uniquely identifiable even with Oxford Nanopore’s currently high error rate of 4%. And because for assembly you will use multiple reads representing the same region, error rate of assembled sequence will be low: if two reads overlap, your consensus sequence for the overlapping region will have an error of 4% * 4% = 0.16% (supposing that the errors give lower quality scores than normal sequence). If you have 3x coverage or more, you can resolve most errors unambiguously…

New publications & New job

admin — Tue, 07 Feb 2012 12:24:20 +0000

New year, new country, new job: I am now a Lecturer at Queen Mary University of London. I will continue to use genomics and bioinformatics approaches to examine the interplay between social evolution and genome evolution. Get in touch if you’re interested in working with me in a great place.

And a few nice papers on which I am coauthor are now out.

PNAS: Relaxed selection is a precursor to the evolution of phenotypic plasticity. Led by Brendan Hunt at Georgia Tech
Bioinformatics: Visualization and quality assessment of de novo genome assemblies – led by Oksana Riba-Grognuz - Source code available.
Trends in Genetics: The genomic impact of 100 million years of social evolution in seven ant species. Reviews some of the findings from the ant genome projects & lays the foundation for coming analyses. Romain Libbrecht & I made the photo that was selected as cover image!

Genome analyses for emerging model organisms

admin — Wed, 21 Sep 2011 15:58:35 +0000

Using modern molecular tools on emerging (non-model) organism makes it possible to address exciting new questions. But the data aren’t as perfect they should be. In particular, genomes created from Roche 454, Illumina or ABI Solid sequence are fragmented: You wish you’d get a FASTA file with one long sequence per chromosome. Dream on! You get sequences for dozens to thousands of scaffolds. Each scaffold is a series of contigs, separated by stretches of unresolved NNNNNNNNN sequence (usually repetitive sequences). But the assembler knows these contigs are adjacent thanks to paired reads.

Genome fragmentation can make things challenging. Some tips from my experience with ant genomes:

How can you determine what is inside the unresolved poly-NNNNN sequence without genome walking or PCR and sequencing? Getting the whole thing will be difficult. But its easy to get a little:

Select resolved genomic sequence.
BLASTN against the raw unassembled reads (need help setting up a custom BLAST server?)
Among the reads that match your query, some will give you sequence that extends inside the unresolved NNNNNN region. If the sequence is known why wasn’t it shown? Because it’s repetitive nature made the sequence ambiguous for the assembly software.

Are two scaffolds adjacent?

Perhaps some paired reads do link them – but there were insufficient data for the assembler to be sure. With 454 assemblies, check newbler’s output in the 454Scaffolds.txt and 454PairStatus.txt files. These report where all paired reads map.
Or map independently obtained transcriptome or proteome data onto your genome. Oksana Riba-Grognuz developed an easy way of visualizing RNA mapped to genomes.
Or check a closely related species – perhaps the region is better assembled there.

How good is good enough? Some sequence/data/scaffolds/models are missing or mediocre! But no biological dataset is ever perfect. If you’re trying to make your emerging model organism’s data perfect… you’ll get nowhere fast. The 20% effort that bring you 80% of the way will probably be good enough to answer your exciting biological question.

Social insect genomics conference 2011

admin — Sun, 03 Jul 2011 04:00:57 +0000

Many interesting talks and stimulating discussions during Shenzhen’s Social Insect Genomics Conference which coincided with the release of Sanne Nygaard’s Acromyrmex echinatior leaf-cutter ant genome paper showing adaptations linked to fungal farming. More excitement is on its way with next generation sociogenetics projects bubbling up around the world & across the phylogeny!

May Taiwan Conf & June genome updates

admin — Thu, 09 Jun 2011 08:19:00 +0000

Had a great two weeks visiting John Wang’s lab at Academia Sinica, Taiwan, and join National Taiwan University’s International Symposium on Social Insects for wonderfully stimulating talks by Jo Billen, Lars Chittka, James Nieh, Kenji Matsuura & Bob Vander Meer. The symposium gave me the opportunity to share some thoughts about sequencing genomes with high throughput technologies in the journal of the Taiwan Entomological Society, Formosan Entomologist.

In genomic news, the Acromyrmex echinatior leafcutter ant genome, led by Sanne Nygaard & Koos Boosma is in press! The data are already on Fourmidable; and Fourmdiable’s ant genome BLAST interface was updated to the latest SequenceServer.

Fire ant genome published

admin — Mon, 21 Feb 2011 11:09:17 +0000

Two papers just out! Our Solenopsis invicta fire ant genome paper is out in PNAS. Win! And a study on fire ant Odorant Binding Proteins in PLoS ONE. Anurag Priyam and are developing a generic BLAST web interface in ruby. It’s already super useful for our fourmidable ant genome database, and I’m sure will be for others working with non-model organisms. (easy to use; less of a hassle to set up than gmod…). Using the server, you can blast ant genome sequences (and predicted genes).

Dengue Mosquito Fogging is Bad

admin — Wed, 01 Dec 2010 08:42:50 +0000

Jakartans use “fogger” chemical sprays to fight dengue-transmitting Aedes mosquitoes.

Whatever was meant to target the mosquitoes made cockroaches jumped into our swimming pool and drown themselves, and made “normal” ants frantically run in circles. This suggests that whatever they use for fogging is a generalist poison that screws up all insect brains and likely affects larger things as well. That is bad for controlling dengue, because many small animals compete with the mosquitos for food and reproductive space, or may even eat them (eg: larvae from other insects, or chick-chacks).

Probably for these reasons, fogging for dengue is not advised:

The World Health Organization’s (WHO) Indonesia Newsletter (2008) states “Fogging has been proven over 50 years of use to have no practical effect on dengue transmission”
A study in the Singapore Medical Journal (2005) concluded that “usual chemical fogging in natural environment was ineffective in breaking the reproductive lifecycle by eliminating gravid female Aedes mosquitoes“
The Philippino government’s Department of Health advises against fogging. [here] and [here].

So please stop fogging!

The best approach is to eliminate all possible breeding sites: getting rid of even small amounts of stagnant water (in containers, trash, leaves, flower pot dishes….)