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posted by chromas on Thursday April 26 2018, @08:54AM   Printer-friendly
from the encyclopods dept.

A project to sequence the genomes of all complex/eukaryotic species on Earth is moving forward:

The central goal of the Earth BioGenome Project is to understand the evolution and organization of life on our planet by sequencing and functionally annotating the genomes of 1.5 million known species of eukaryotes, a massive group that includes plants, animals, fungi and other organisms whose cells have a nucleus that houses their chromosomal DNA. To date, the genomes of less than 0.2 percent of eukaryotic species have been sequenced.

The project also seeks to reveal some of the estimated 10 million to 15 million unknown species of eukaryotes, most of which are single cell organisms, insects and small animals in the oceans. The genomic data will be a freely available resource for scientific discovery and the resulting benefits shared with countries and indigenous communities where biodiversity is sourced. Researchers estimate the proposed initiative will take 10 years and cost approximately $4.7 billion.

In a perspective paper [DOI: 10.1073/pnas.1720115115] [DX] published today (April 23) in the Proceedings of the National Academy of Sciences (PNAS), 24 interdisciplinary experts comprising the Earth BioGenome Project Working Group, provide a compelling rationale for why the project should go forward and outline a roadmap for how it can be achieved.

The Smithsonian Institution is on board:

Assembling the species will be a massive undertaking, which is why partnerships with institutions that procure and preserve the Earth's biodiversity, such as natural history museums, botanical gardens, zoos and aquaria, will be crucial for success. The Smithsonian herbarium, for example, contains around 300,000 species.

"Many scientists at the Smithsonian Institution with its 19 museums and nine research institutes are applying genomics technologies in their research to increase our understanding of the natural world. The strength of biodiversity genomics at the Smithsonian is a good indicator of the vital role the institution will play in furthering the goals of the Earth BioGenome Project," Kress said.

Also at the Smithsonian Institution and GEN.

Previously: Earth BioGenome Project Aims to Sequence the Genomes of All Species on Earth
Scientists Plan to Sequence 10,000 Plant and Eukaryotic Microbe Genomes


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  • (Score: 2) by leftover on Thursday April 26 2018, @04:10PM (5 children)

    by leftover (2448) on Thursday April 26 2018, @04:10PM (#672191)

    It seems to me that a sensible approach in such a large scale project would be to identify subgroups of particular interest. My first candidate would be enteral bacteria. They keep turning up as possible contributors to many ailments but we don't seem to know much about most of them. This doesn't diminish the world-wide vision of the project and it could have nearly immediate benefits. Sequencing all the varieties of wombats, not so much.

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  • (Score: 2) by takyon on Thursday April 26 2018, @06:23PM (2 children)

    by takyon (881) <reversethis-{gro ... s} {ta} {noykat}> on Thursday April 26 2018, @06:23PM (#672249) Journal

    It already exists: https://hmpdacc.org [hmpdacc.org]

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    • (Score: 2) by leftover on Thursday April 26 2018, @08:30PM (1 child)

      by leftover (2448) on Thursday April 26 2018, @08:30PM (#672303)

      16S rRNA sequencing was performed to characterize the complexity of microbial communities

      Only enough to count the species of critters, not enough to catalog the proteins they encode for. Every mention of microbiome effect on health seems to stop after the "complexity is good" meme. If a big well-funded study could do the heavy lifting to completely sequence all of the known gut bugs and publish the data, it could unleash a swarm of small-funding projects. Even secondary school students could get in on that. Undergrads in computational biology would have real data to chew on, xxx-at-home projects could see results in human lifetimes, all the bitcoin mining rigs to be abandoned after that bubble pops could have a new use. Lots of potential.

      Yikes. That sounded like realDonaldTrump. I should stop now.

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      • (Score: 0) by Anonymous Coward on Thursday April 26 2018, @09:21PM

        by Anonymous Coward on Thursday April 26 2018, @09:21PM (#672325)

        Undergrads in computational biology would have real data to chew on,

        There is enough data available already that hasn't been chewed on yet.

        xxx-at-home projects could see results in human lifetimes,

        Why are they not getting any results yet? Even with the present data. Hell, I even spend months a year ago analysing sequence data from a kinesin family over multiple plant species, manually. Got some interesting results from that. That could easily be automated (which is still on my todo list) for other gene families.

        all the bitcoin mining rigs to be abandoned after that bubble pops could have a new use. Lots of potential.

        Problem is that bitcoin mining rigs can't do much more than calculating SHA256D hashes... very efficiently. Not very useful in computational biology.

  • (Score: 2) by HiThere on Thursday April 26 2018, @06:44PM (1 child)

    by HiThere (866) Subscriber Badge on Thursday April 26 2018, @06:44PM (#672257) Journal

    Tackyon said "complex/eukaryotic species". That doesn't include bacteria. It would get your tapeworms, though, and possibly a few others. Some amoeba, perhaps.

    I didn't read the original proposal, but it makes sense to limit it to "complex/eukaryotic species", because that's an order of magnitude (or so) reduction in the number of species that they propose to handle. I still don't think they can get everything. We're still finding new species every year or so...often only once. Just this year there was a photo of a new kind of deep sea squid. How're you going to sequence that?

    It a worthwhile project, but the stated goals are overly ambitious. They probably have to be for political reasons, but don't believe they can be accomplished. And that's without worrying about bacteria, etc. (Sorry, I still think of prokaryotes, and that's no longer the accepted division. I don't remember the current one.)

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    • (Score: 0) by Anonymous Coward on Thursday April 26 2018, @09:26PM

      by Anonymous Coward on Thursday April 26 2018, @09:26PM (#672328)

      Just this year there was a photo of a new kind of deep sea squid. How're you going to sequence that?

      1) Go back to deep see spot.
      2) Find deep sea squid.
      3) Catch the squid.
      4) Get back to the lab.
      5) Extract DNA from the squid.
      6) Sequence squid DNA
      7) Collect sequence data from now extinct deep sea squid.