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The nightmarishly complex wheat genome finally yields to scientists
- skookumchuck 8y agoIt's necessary to sequence all these so presumably they can be recreated if/when they go extinct.
- schoen 8y agoThere's a drastically cheaper option for that: https://en.wikipedia.org/wiki/Gene_bank https://en.wikipedia.org/wiki/Gene_bank e.g. https://en.wikipedia.org/wiki/Seed_bank https://en.wikipedia.org/wiki/Seed_bank
- skookumchuck 8y agoBut less reliable. Wasn't one of the seed banks in the arctic destroyed by flooding recently? Digital versions can be replicated and distributed at 0 cost.
- xvedejas 8y agoAssuming you're referring to the Svalbard Global Seed Vault, the Wikipedia page answers your question: > In October 2016, the seed vault experienced an unusually large degree of water intrusion due to higher than average temperatures and heavy rainfall .... The vault was designed for water intrusion and as such the seeds were not at risk. The article's source: https://www.popsci.com/seed-vault-flooding https://www.popsci.com/seed-vault-flooding
- skookumchuck 8y agoThanks for the reference. We should indeed continue with seed vaults. But I'd feel better with a backup for that in the form of digital data.
- maxander 8y agoIf things go far enough downhill that the Svalbard vault is lost and its contents just allowed to rot, I’d be surprised if we retained the technological capacity to do things like synthesizing a complex genome from data. (I’m not sure we could do that with present technology either, for that matter.)
- skookumchuck 8y agoLibraries and museums burn down all the time, or get destroyed in wars. Consider the recent fire at the Hewlett-Packard museum, where all the paper history was lost. Nobody made a backup, even though paper lasts longer term than data on a hard drive. Frankly, I think storing data as ASCII in pits on a substrate is a great long term solution, as it can be read with a simple optical microscope, and ASCII is forever. One of the cool things about digital data is it can be copied forward limitlessly. Make the seed genomes public domain and put them on a server - people will make copies, like they make copies of wikipedia to store in their prepper bunkers.
- XorNot 8y agoI think UTF-8 is fine in this case since it's ASCII until it's not so you can write the UTF-8 spec out first. Human knowledge is more then English alphabet characters and not all concepts translate properly.
- roywiggins 8y agoEven with the digital copy of the genome, you have to synthesize the entire genome, the cell it belongs in, and the rest of the seed to get a plant. That seems... possible, but hard enough that it doesn't make sense to call the sequenced genome a "backup".
- skookumchuck 8y agoIt's infinitely better than having a photo of a wheat stalk.
- panic 8y agoIs it possible to recreate a wheat plant from just its genome?
- captain_perl 8y agoToday? No. Likely the so-called "junk DNA" was skipped over and we are still learning what the impact of environment and hormones is on gene expression. What we can do today is to manipulate DNA and re-inject into an egg. Although not nothing, this is not "just its genome." In 100 years? Probably.
- bohadi 8y agoA decent analogy might be: is it possible to recreate a running program from just it's source? (lacking a compiler, development and production environments, and perhaps user inputs) so my feeling is, not really, to an approximation
- skookumchuck 8y agoSure it's possible. (I've recreated programs from source despite lacking the compiler, etc., originally used on it. The trick is to adapt something else to the task.) The source contains instructions on how it works, and those instructions can be used elsewhere.
- eggie 8y agoNo. You need a wheat cell as well. Then you might be in business. And, no, it is not possible (today) to rebuild a multi gigabase hexaploid genome. The best that's been done so far is mycoplasma (500kb genome, which is many orders of magnitude smaller). Also, the "genome sequence" presented here is not really complete. Thus far only the simplest organisms have had their genomes synthesized from a digital template and resulted in a viable cell. We rarely can produce a "complete" genome for anything other than bacteria and viruses. And for those, the diversity in the population makes the idea of establishing a single genome sequence somewhat limiting.
- code_duck 8y agoSeems like many other dire circumstances would have to befall the earth before any of the global top 3 crops become extinct.
- skookumchuck 8y agoThere are many, many varieties of wheat. They all need to preserved, because they have many different strengths/weaknesses. Having a monoculture of crops is a terrible vulnerability. Look at what is happening with our current monoculture of bananas.
- code_duck 8y agoAs a longtime celiac sufferer, it would be in my best interest and that of my descendants for all of those varieties to be eradicated, like smallpox. There’s nothing especially beneficial about wheat as a food, and it has drawbacks, such as how it is the only food I can think of with its own autoimmune disease.
- madengr 8y agoThe article says wheat has 5x the human genome. I assume that means it’s very high in protein. Isn’t that what most of the world needs, as opposed to mostly carbohydrates?
- code_duck 8y agoHigh in protein compared to what? Is wheat better than millet, sorghum, quinoa, teff, oats, corn, and rice, or is it just a European tradition to base cuisine on wheat? I’m not an agricultural or genetic expert and I have no idea what relation genome complexity has to proteins or how that makes it useful to humans. Overall wheat is not very high in protein... it’s a crop grown for carbohydrates. If you were trying to fulfill your daily protein needs from wheat, you’d fall quite short. I suppose it complements more adequate sources. The protein it does have - gluten - isn’t especially digestible compared to alternatives like corn or rice, though it does have a texture that people find pleasant or useful in baking. Crops like lentils and soy are what you grow if you want to grow protein.
- cabaalis 8y agoI've been seeing "Genome of X has been fully sequenced" articles over the course of some years. Can someone who understands it explain to a layman like myself how exactly this benefits us?
- grey413 8y agoGenomes are used as a reference point for all sorts of genetic analysis. It's comparable to having the source code to a binary. Plant breeding in particular benefits from having better analytical tools on hand, since it's such a critical field with such a gargantuan and diverse pool of organisms to study.
- Old_Thrashbarg 8y agoIn that analogy, perhaps it's more like having successfully read out every byte of a binary that was encoded onto a medium that is extremely to read off of. Having the source code... I'm not sure what that would be analogous to, but it would probably quite a long way off.
- toasterlovin 8y agoI think the best big picture explanation of why this is important is this: our ability to feed and care for humanity is dependent on biology. Genomes are the source code for biology. Reading the source code is the first step to understanding the source code. Understanding the source code will allow us to build better expressions of biology (those being both ourselves and the animals and plants we depend on).
- adrian_mrd 8y agoGreat explanation, thanks.
- Pica_soO 8y agoTry to see the anti-gene-modification initiatives as a security by obscurity approach. Seeing the horrors of info-security (drm, attacks, cheap-hacks) today unfolding, and imagining a nature, where wild gene drives are on the loose, this approach seems misguided but at its core valid. The one time loss of half the biosphere that will occur with the source code being readable is greater then any gain. A great book to get more into the dangers of genetic editing and proprietary genes: https://en.wikipedia.org/wiki/The_Windup_Girl https://en.wikipedia.org/wiki/The_Windup_Girl
- avip 8y agoIsraeli press gives lots of credit to Bioinformatics company NRGene.
- a_bonobo 8y agoYes, NRGene is an Israeli company, so that would make sense. NRGene has a proprietary algorithm that uses a large amount of Illumina sequences to build a pretty good genome assembly. This technology has been used in a few organisms with large genomes, as it has been used in v1.0 of this assembly. However there have been previous, less high quality wheat genome assemblies based on Bacterial Artificial Chromosomes (BACs), and that information has made its way into this assembly too, along with long-distance information from HiC and genetic maps and Bionano technology.
- avip 8y agoYep I’m not qualified to tell facts from PR on this one (which is why I made that comment)
- Alex3917 8y ago> For example, about 26 genes are differentially active in wheat varieties with solid stems and those with hollow stems If it has a solid stem, wouldn’t it no longer be in the grass family by definition?
- grey413 8y agoNope. Phylogenetic families are based on the degree of shared ancestry, not the presence or absence of any given trait. I mean, don't get me wrong, you CAN develop phylogenetic trees based on traits. That's how Linnaeus and all subsequent taxonomists did it before they could just look directly at DNA. But it takes a lot of traits, and has been preempted by DNA based methods anyway.
- Alex3917 8y ago> Phylogenetic families are based on the degree of shared ancestry, not the presence or absence of any given trait. What about the rhyme “Sedges have edges, rushes are round, and grasses are hollow right down to the ground?” You’re telling me scientists are now saying that DNA testing is more accurate than just using the rhyme?
- bostonpete 8y agoSeems like they're just bending the facts to conform to their observations.
- ufo 8y agoIt is not about DNA vs phenotypes. The issue is that biologists are more interested in building an universal classification, a single tree of life for all species, than they are in building single-phenotype-based classifications that dont nest particularly well. For example, if you looked at just the ability to fly, you would group birds and bats on a same group. But that would be wrong because bats are clearly more closely related to flightless mammals than they are to birds. This becomes obvious if you account for more characteristics of the animal (presence of fur, bone shape, pregnancy, etc) or if you examine the DNA.