Genome complexity: variation within species (Introduction)

by David Turell , Friday, December 09, 2016, 18:51 (2693 days ago) @ David Turell

We had a discussion over an article BBella presented about E. coli learning to fight with antibiotics. I made the point that bacteria have alternative pathways, have variability within a species and can overcome the antibiotic if given time to make the adaptations or allow the résistance members of the species to survive and reproduce, and it was not new evolution but a use of available alternatives. This was her reference (Wednesday, October 05, 2016, 15:59) :

https://www.wired.com/2016/09/gorgeous-unsettling-video-evolution-action/

Now the scientific community is recognizing this genomic variability which comes in evolved organisms:

http://www.the-scientist.com/?articles.view/articleNo/47510/title/The-Pangenome--Are-Si...

"with genome sequencing becoming faster, cheaper, and more accessible all the time, it quickly became apparent that this attitude overlooked one very important aspect of biology—genomic variation among individuals. And for some species, such variation can be significant. In the early 2000s, for example, when Tettelin, then at the Institute for Genomic Research (TIGR), and his colleagues compared eight isolates of Streptococcus agalactiae (or group B Streptococcus, GBS), they found not only the small, within-gene variations predicted by conventional genetics, but an average of 33 completely new genes with every new genome sequenced. “It was a shock,” says Tettelin. “We saw there were many regions—relatively large regions—of diversity.”

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"Over the past 10 years, large-scale sequencing projects have revealed startling levels of individual genomic variation across the tree of life, challenging the value of the modern reference genome—as well as the very notion of a species. To better capture the genetic makeup of any given taxon, many researchers now argue that the field of genomics should adopt a pangenomic framework in which diversity is central, rather than incidental, to our view of species.

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"The pangenome concept has since been widely adopted by research groups trying to keep track of newly discovered diversity within and among bacterial taxa. In addition to high recombination rates and mobile genetic elements, which have long been known to be drivers of prokaryotic diversity, horizontal gene transfer—direct or indirect exchange of genetic material among even unrelated organisms—is proving to contribute to individual diversity across the bacterial domain and beyond.

"Bacteria have “access to a toolkit within species and across species,” Tettelin explains. For taxa with large, open pangenomes—often a reflection of high rates of gene transfer—that toolkit corresponds to a theoretically unlimited pool of easy-to-access new biological functions. “They’re essentially champions at versatility and adaptability,” he says.

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"To date, researchers have applied the pangenome framework to some 50 bacterial species, including model organisms, such as E. coli, and commercially significant microbes, such as the wine bacterium Oenococcus oeni. Scientists have used the same basic principles to consider shared and variable genes and gene families within larger groups such as genera, the human microbiome, and even the entire bacterial domain. Now, with the approach broadly accepted as a useful way to organize bacterial diversity, efforts are focusing on incorporating this more variation-centric view into metagenomics, phylogenetics, and even taxonomy itself.

“'We have learned a tremendous amount about the machinery of life from model organisms that have been studied in the lab, but we haven’t really confronted head-on the role of the diversity,” says Chisholm. “Now I think we’re learning that this diversity is part of what life is all about.”

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"Although variation in genomic content between two humans is minuscule in comparison with that of microbes or plants, the earliest attempt at building a human pangenome in 2009—based on the human reference genome and just two others—estimated that up to 40 megabases of sequence, including protein-coding regions, were absent from the reference genome. (my bold)

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"Even in the eukaryotic world, where genomic fluidity is far less pronounced, pangenomic analyses have cast new light on conventional taxonomies. Sequencing of multiple individuals in several groups of eukaryotic organisms, from marine phytoplankton to crop plants, have challenged traditional notions of within-species diversity and raised the question of what “species” even means. If the goal of classification is to create biologically useful groups of like organisms, then such questions are important to resolve—yet for now, at least, they’re still very much open."

Comment: Variability within species obviously common. That humans are not so variable supports my idea that we are the end of the evolution process. We have so much control of our lives we don't need the variability.