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I want to study the properties of Pyrococcus Furiosus in surving to gamma irradiation by exploiting the analysis of DNA sequencing data as a bioinformatics study. Before learning how to analyse this kind of data, I wanted to have a look at some work that was already done. I found this interesting article: Genome Sequencing of a Genetically Tractable Pyrococcus furiosus Strain Reveals a Highly Dynamic Genome.

I think that it could be a good starting point. However, it is not easy to understand the whole article for me and I suspect that the source of this difficulty is mainly due to the fact that I do not know what "Genetically Tractable Pyrococcus Furiosus Strain" means.

Searching in Google I found this article: Systematic evasion of the restriction-modification barrier in bacteria, that explains:

Bacteria that are recalcitrant to genetic manipulation using modern in vitro techniques are termed genetically intractable. Genetic intractability is a fundamental barrier to progress that hinders basic, synthetic, and translational microbiology research and development beyond a few model organisms. The most common underlying causes of genetic intractability are restriction modification (RM) systems, ubiquitous defense mechanisms against xenogeneic DNA that hinder the use of genetic approaches in the vast majority of bacteria and exhibit strain-level variation. Here, we describe a systematic approach to overcome RM systems.

Then it tells also that:

A strain that is not amenable to alterations of its genome or to the introduction of new genetic information during genetic engineering is termed genetically intractable.

Therefore, from this short explanations, I have an idea of what genetically intractable means. But, I still wonder why in the first article that I mentioned, the scientists should have been interested in sequencing such a genome (genetically tractable) and in comparing it with the one that was firstly sequenced (the so called reference strain) ? Moreover, what does genetically tractable mean?

Indeed, in the case of the first article, the following description is reported:

The best characterized of the Pyrococcus species is P. furiosus, the first to be isolated (19) and the first to have its genome sequenced (49). This organism has been studied by numerous “-omics”-based approaches, including transcriptomics by tiling (59) and DNA microarrays (14, 35, 51, 54, 57), comparative genomics (8, 33, 60), proteomics (32, 42), metallomics (11), and structural genomics (25). In many ways, it has become one of the model hyperthermophiles, a status recently sustained by the development of a genetic system for the organism (37). This was based on isolation of a variant in a lab strain population, designated COM1, which was highly efficient in taking up and recombining exogenous DNA in both circular and linear forms. The COM1 strain was obtained by targeted gene disruption of the pyrF. locus (PF1114) using a plasmid designed for double-crossover recombination (37).

Then what they do is:

The genome sequence of COM1 has now been determined, and comparison with the published sequence of the P. furiosus reference strain (49) (NC_003413) revealed a surprisingly large number of changes.

Thus, I do not understand (both in the case of this article and also in general case) what genetically tractable means (the description given by the article is not sufficient for me to understand) and why are we interested in doing the alignment between the reference genome sequence and the genome of genetically tractable strain ?

Sorry if my question could be trivial but my biological backgrounds are really poor. I reported the extracts of the articles because they give me an idea of the answer but, to be honest, I do not have fully understood them. Therefore, if you can explain me also those extracts, it would be great. Thank you in advance.

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You've already basically got the idea of "genetically tractable": if we can readily modify an organism's genome using known techniques, then it's genetically tractable.

That's a moving target, of course, because the set of available techniques is constantly expanding, so this is more of a pragmatic definition than a taxonomic definition. It's a notion that's quite important, however, because it's far harder to study an organism or to develop applications if you can't manipulate its genome. If you can manipulate genetics, then you can make knock-out strains, introduce new functionality, and apply many, many other powerful and useful biological techniques.

So now to the last part of the question: assuming you've now got a tractable strain, why compare it with the reference strain? Well, if you're working on engineered applications, you probably really don't need to (other than from curiosity). If you want to use the tractable strain to study things about the original, reference form of the organism, however, then you need to know their differences in detail, in order to have some idea of how much your results obtained by manipulation of the tractable strain are likely to inform your understanding of the reference form.

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  • $\begingroup$ Thank you @jakebeal . I have a last question: so, for example, if they destroy a gene (PF1114) and then they compare the "modified" genome with the reference and they see (by DNA sequencing) that the tractable genome has two large chromosomal segments that have inverted order with respect to the reference order and that, despite this, there are no apparent consequence for proper metabolic function, is this a sort of assessment of the fact that they are resistant to distruptions (that maybe caused by gamma irradiation) ? $\endgroup$ – Manuela Feb 21 at 18:33
  • $\begingroup$ @Manuela I think this is really a separate question about how to interpret the relationships between genomes. Destroying a gene and rearranging chromosomal segments are quite different types of activities, and I'm not really sure how you're trying to put the pieces together here. $\endgroup$ – jakebeal Feb 21 at 18:52
  • $\begingroup$ Ok thank you again . $\endgroup$ – Manuela Feb 21 at 19:13

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