Tag Archives: sequencing

Naked Mole Rat, another day, another genome

The latest genome to be completed is the naked mole rat (Heterocephalus glaber). Now, could there be a cooler (if ugly) mammal on the planet? It’s one of only two truly eusocial mammals in the world, it lives up to 28 long years (my daughter’s rat, no relation, lived only 3 years) and is surprisingly resistant to a lot of diseases.

So, no wonder the genome was sequenced. Maybe we can learn some things about social behavior and longevity.

Of course there is a resource for it at http://www.naked-mole-rat.org/ though it’s basically just a blast server and some downloads. I’m counting down to the day it’s available at UCSC or Ensembl :D. I have some genes I’m interested in comparing.

Bulk sequence pricing

Illumina announces that they are slicing their price of whole-genome sequence to 19,500 . This is half what they were charging before. Hey, you can get it at 14,5000 per genome if you do it in bulk, 5 or more people. Perhaps you and your family for a cool 72,500?

As I mentioned before, the price of personal genome sequencing has been plummeting and I predicted 1,000 by the end of a year’s time. Admittedly, that is a bit (understatement) of an optimistic prediction, but the trajectory definitely is headed that way.

SEQanswers

I’ve been perusing the latest supplement of Nature Methods on “Visualizing Biological Data” (and will blog about it sometime this week, interesting stuff), when I came across a reference to SEQanswers, an online discussion group for the Next Generation Sequencing community. It seems to be a quite well used discussion group, with lots of interesting and useful discussion.

If you are at all interested in NG sequencing, or genomics for that matter, you might want to check it out.

10,000 Vertebrate Genomes

genome10kvia The Long Now and the projects new publication in the Journal of Heredity,  the Genome 10K project aims:

to assemble a genomic zoo—a collection of DNA sequences representing the genomes of 10,000 vertebrate species, approximately one for every vertebrate genus. The trajectory of cost reduction in DNA sequencing suggests that this project will be feasible within a few years. Capturing the genetic diversity of vertebrate species would create an unprecedented resource for the life sciences and for worldwide conservation efforts.

10,000 vertebrate genomes. That’s a lot. In fact, that’s 50 fold greater number than is currently in progress (that list is chordata, at 208, including multiple genomes form one species, humans), and nearly 500 fold the number of complete vertebrate genomes available. An ambitious goal to say the least. The participants are multitude including the coordinators David Haussler (Howard Hughs Medical Institute, UCSC), Stephen O’Brien (Laboratory of Genomic Diversity, National Cancer Institute) and Oliver Ryder (Institute of Conservation Research, San Diego Zoo).

The three coordinators’ institutes suggest some of particular benefits that they hope to get out of this project: medical data, evolutionary data, conservation efforts. I do believe such a project will indeed bring many of those benefits. I remember 20 years ago the arguments about the Human Genome Project (too expensive, too ambitious, benefits won’t be commiserate, big science pushing out basic research). I think it’s arguable that the worst fears were not realized and that there have been a number of benefits already and soon to come. 10k vertebrate genomes now seems feasible and beneficial.

Of course, one could hope there’d be a plant project and an invertebrate project down the pike?

And, it goes without saying, if you thought there were database funding, accessibility, usability, etc issues now…

Where bollworms lead you

bollwormWell, I was reading this press item about a team of scientists from the University of Melbourne and Baylor College of Medicine who are sequencing the genome of Helicoverpa armigera aka cotton bollworm, corn earworm, tobacco budworm.. you get the picture, it’s a major agricultural pest. One thing caught my eye, they expect it to be completed in four months. These projects are getting shorter and shorter.

Anyway, I did a search on that species (which brings me to a question, why can I find it in the NCBI taxonomy browser and Wikipedia, but not the Encyclopedia of Life?) which lead me to an interesting database I’d never seen before: Pherobase, a database of pheromones. It appears to be a one-man operation (El-Sayed, AM) but extensive nonetheless. I don’t know enough about this field to review it for scientific merit (though there does seem to be a decent amount of info), but thought I’d put it out there. Amazing where internet searches can semi-randomly lead you.

Future of genome sequencing

We’ve written before about the feel of ‘a genome a day’ around here. RPM at Evolgen points to a paper that suggests his prediction (from last year) that “de novo sequencing of whole eukaryotic genomes may be a thing of the past.” Perhaps he is correct, though we do have quite a large number of de novo sequencing projects for eukaryotic genomes in the pipeline for the moment. He suggests that, as this paper has done, sequencing projects will “use 454 to sequence cDNA libraries.” Though there is loss of data in not sequencing the non-transcriptome part of the genome, as the abstract in the paper he points to says:

We conclude that 454 sequencing, when performed to provide sufficient coverage depth, allows de novo transcriptome assembly and a fast, cost-effective, and reliable method for development of functional genomic tools for nonmodel species. This development narrows the gap between approaches based on model organisms with rich genetic resources vs. species that are most tractable for ecological and evolutionary studies.

There is a lot of interesting discussion in the comments to his post.

Miscanthus genome will "fuel" advances

miscanthusI am still digesting (so to speak) the conference I went to the last couple days at JGI. The thrust of the conference was the sequencing and study of genomes (both biomass fuelstock and bacteria/fungus digesters :)) to help create a liquid fuel source for our energy needs. I found it to be a fascinating conference and will definitely write more about it early next week.

For now, I’d like to point you to the work being done on the Miscanthus genome. This is a fascinating plant and possibility for a fuel source. It’s more productive than Switchgrass (and corn and sugar), it has no known diseases or pests (though that will change when/if it becomes a major crop), it is perennial needing much less fertilizer/pesticide input, it grows by rhizomes and sequesters carbon in the ground, it would take much less land to supply liquid fuel needs, it is drought resistant and it can cure cancer. Ok, so the last is not true. Yet, it is a very promising plant. The genome is being sequenced to help scientists and growers determine ways to domesticate it better and to solve the “big” problem… the expense of converting the cellulose to fuel (which is also the topic of metagenomic and genomic research on bacteria at JGI).

A genome a day

I want to say ‘keeps the ? away” but can’t think of anything. This is just a quick post. Mary’s first line on the corn genome post, “sometimes it feels like ‘another day, another genome‘ round here got me to thinking”, it isn’t so far off the mark. According to GOLD there are 905 ongoing eukaryotic genomes (according to Entrez Genome Project,  it’s 225, but those are only ones reported to NCBI). The cost of sequencing and completing a genome has drastically decreased. For example, Illumnia recently reported sequencing a human genome in 1 month for $100,000.

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