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> we're working with so many species that we can't sequence all their genomes Are you talking about sequencing enough to get adequate coverage for reconstructi

> we're working with so many species that we can't sequence all their genomes Are you talking about sequencing enough to get adequate coverage for reconstruction? Also, what do you think of the criticism that it is difficult to know the potential effects of GMO on their ecosystems in the wild?

csirac2 12y ago
It's been a few years, but the plant geneticists I used to work with until 2012 seemed to have to solve a lot of problems to get reliable full-genome sequences of de novo species (these have no reference assemblies to go by). Including what I had until then assumed was the simple act of just sampling DNA material: multiple consistent sites on the plants were sampled and this context was important not just for gene expression, but overall sanity checking of final assemblies (speaking of sanity checks: flow cytometry as well). Then there was setting up Illumina and 454 sequencing experiments, which seemed to involve quite a few iterations/experimentation in developing primers, choosing bead configuration, amplification procedures and a whole lot of other stuff I don't understand... And still, after all that, the literature did have a bunch of species that had already had a few genes sequenced using earlier methods and traditional PCRs, so the whole sample set was given this treatment as well, again as a sanity check and to get a strong reference to earlier results (1000+ of species, thousands of individual plants, each with multiple samples as I mentioned). And still, after all that... the evolutionary history of this group of plants still looks slightly different depending on which genes you looked at. And so now I know what a consensus tree is... and how much fun it is to see researchers have their software doing MCMC tree building run in just a few days on HPC compute clusters when they'd previously waited months :-)
Blahah 12y ago
> Are you talking about sequencing enough to get adequate coverage for reconstruction? Yes. Assembling a genome requires a lot of sequencing data or different kinds, and is expensive. Genomes (especially in plants) can be huge. We're only interested, at least in this specific example, in the things that are expressed. These make up a small proportion of the genome, and so we sequence only those things. > Also, what do you think of the criticism that it is difficult to know the potential effects of GMO on their ecosystems in the wild? Agriculture in general has a vast impact on the environment. This is true across the board - including organic, GMOs, 'conventional', etc. By its very nature agriculture is about shaping the environment so we can control a piece of it to optimise it for food production. Our responsibility is to try to predict and minimise the effects that might cause problems. So far, GMOs have proven to have relatively little effect on the environment (compared to other drivers of agricultural productivity, like pesticide and herbicide use, for example). In the case of C4 rice we can predict what the major potential issue might be: C4 rice plants might perform so well that they outcompete wild plants outside the field setting. `There are some technological tricks we can use to try to ensure plants don't do well outside the field.
- ptaipale 12y ago
  When you say "relatively little", what does that mean? I can't see why there would be any difference at all that comes from some (plant) being GMO in itself. Some plants developed with GMO technology might of course behave differently from other variants of same species; for instance if some GMO variantg grows up faster than previous seeds and is harvested faster and you can grow another crop in the same season and get a better yield, then there is of course more need for fertilizing etc. But that in itself does not come from something being GMO.
  - Blahah 12y ago
    Well, with first-generation GMOs, a single gene was inserted into a crop. This is totally unlike all previous crop breeding, where changes were complex and no single gene was likely to control the trait. So before GMOs, there was basically no chance that a trait bred into crops could escape into the wild by gene flow, but with first-gen GMOs that became a real possibility. It has indeed been recorded happening a bunch of times, leading to, for example, herbicide resistance in weeds. I should point out that herbicide resistance in weeds was widespread before GMOs by other mechanisms, and in fact the switch to glyphosate has been a great thing because we've massively reduced the application of harmful chemicals, while glyphosate is benign. But the fact remains that GMOs do carry their own specific risks that are a result of the technology and methodology, rather than the specific application.

csirac2 12y ago

It's been a few years, but the plant geneticists I used to work with until 2012 seemed to have to solve a lot of problems to get reliable full-genome sequences of de novo species (these have no reference assemblies to go by). Including what I had until then assumed was the simple act of just sampling DNA material: multiple consistent sites on the plants were sampled and this context was important not just for gene expression, but overall sanity checking of final assemblies (speaking of sanity checks: flow cytometry as well). Then there was setting up Illumina and 454 sequencing experiments, which seemed to involve quite a few iterations/experimentation in developing primers, choosing bead configuration, amplification procedures and a whole lot of other stuff I don't understand... And still, after all that, the literature did have a bunch of species that had already had a few genes sequenced using earlier methods and traditional PCRs, so the whole sample set was given this treatment as well, again as a sanity check and to get a strong reference to earlier results (1000+ of species, thousands of individual plants, each with multiple samples as I mentioned). And still, after all that... the evolutionary history of this group of plants still looks slightly different depending on which genes you looked at. And so now I know what a consensus tree is... and how much fun it is to see researchers have their software doing MCMC tree building run in just a few days on HPC compute clusters when they'd previously waited months :-)

Blahah 12y ago

> Are you talking about sequencing enough to get adequate coverage for reconstruction? Yes. Assembling a genome requires a lot of sequencing data or different kinds, and is expensive. Genomes (especially in plants) can be huge. We're only interested, at least in this specific example, in the things that are expressed. These make up a small proportion of the genome, and so we sequence only those things. > Also, what do you think of the criticism that it is difficult to know the potential effects of GMO on their ecosystems in the wild? Agriculture in general has a vast impact on the environment. This is true across the board - including organic, GMOs, 'conventional', etc. By its very nature agriculture is about shaping the environment so we can control a piece of it to optimise it for food production. Our responsibility is to try to predict and minimise the effects that might cause problems. So far, GMOs have proven to have relatively little effect on the environment (compared to other drivers of agricultural productivity, like pesticide and herbicide use, for example). In the case of C4 rice we can predict what the major potential issue might be: C4 rice plants might perform so well that they outcompete wild plants outside the field setting. `There are some technological tricks we can use to try to ensure plants don't do well outside the field.

ptaipale 12y ago
When you say "relatively little", what does that mean? I can't see why there would be any difference at all that comes from some (plant) being GMO in itself. Some plants developed with GMO technology might of course behave differently from other variants of same species; for instance if some GMO variantg grows up faster than previous seeds and is harvested faster and you can grow another crop in the same season and get a better yield, then there is of course more need for fertilizing etc. But that in itself does not come from something being GMO.
- Blahah 12y ago
  Well, with first-generation GMOs, a single gene was inserted into a crop. This is totally unlike all previous crop breeding, where changes were complex and no single gene was likely to control the trait. So before GMOs, there was basically no chance that a trait bred into crops could escape into the wild by gene flow, but with first-gen GMOs that became a real possibility. It has indeed been recorded happening a bunch of times, leading to, for example, herbicide resistance in weeds. I should point out that herbicide resistance in weeds was widespread before GMOs by other mechanisms, and in fact the switch to glyphosate has been a great thing because we've massively reduced the application of harmful chemicals, while glyphosate is benign. But the fact remains that GMOs do carry their own specific risks that are a result of the technology and methodology, rather than the specific application.