In the 18 years since the completion of the Human Genome Project, the practicality of assembling full genomes for a wide range of taxa beyond ourselves has only improved. While model taxa systems have achieved genomes before many others, it is now possible for whole genomes to be assembled for a range of non-model organisms as well. But how do we assemble the genome of a species for the very first time (often de novo – literally “from the new”)? What can we do with this genome? Why is it so useful? Let’s delve into the process and outcomes of genome assembly a little more.
You’ve probably been exposed to one news headline or another in the recent past (let’s say the last 5 years) that reads something like “SCIENTISTS DISCOVER GENES THAT CAUSE (X).” X, of course, varies massively based on the study itself (and sometimes the bastardisation of said study by media): it can include describing medical conditions such as cancer, autism or congenital diseases; behavioural traits, such as sexual preferences; or broad physical traits, such as the classic problem of the inheritability of height. Unsurprisingly, you may think that trying to find the genes responsible for some traits should be either a) super easy, or b) super hard, depending on your own philosophical preference or the trait in question. So how do these studies come about, anyway?
If bigger is better, then biggest is best. Having the genome of a particular study species fully sequenced allows us to potentially look at all of the genetic variation in the entire gene pool: but how do we sequence the entirety of the genome? And what are the benefits of having a whole genome to refer to?
Well, assembling the whole genome of an organism for the first time is a very tricky process. It involves taking DNA sequence from only a few individuals, breaking them down into smaller fragments and multiplying these fragments into the billions (moreorless the same process used in other genomics technologies: the real difference is that we need the full breadth of the genome so that we don’t miss any spaces). From these fragments, we use a complex computer algorithm which builds up a consensus sequence like a Lego tower; by finding parts of sequences which overlap, the software figures out which pieces connect to one another. Hopefully, we eventually end up with one very long continuous sequence; the genome! Sometimes, we might end with a few very large blocks (called contigs), but this is also useful for analyses (correlated with how many/big blocks there are). With this full genome, we use information from other more completed genomes (such as those from model species like humans, mice or even worms) to figure out which sections of the genome relate to specific genes. We can then annotate these sections by labelling them as clear genes, complete with start and end point, and attach a particular physical function of that gene.
The benefits of whole genomes
Having an entire genome as a reference is an extremely helpful tool in conservation and evolutionary studies. The first, and perhaps most obvious benefit, is the sheer scale of the data we can use. By having the entirety of the genome available, we can use potentially billions of base pairs of sequence in our genetic analyses (for reference, the human genome is >3 billion base pairs long). Even if we don’t sequence the full genome for all of our samples, having a reference genome as basis for assembly our reduced datasets significantly improves the quantity and quality of sequences we can use.
Another very important benefit is the ability to prescribe function in our studies. Many of our processes for obtaining data, even for genomic technologies, use random and anonymous fragments of the genome. Although this is a cost-effective way to obtain a very large amount of data, it unfortunately means that we often have no idea which part of the genome our sequences came from. This means that we don’t know which sequences relate to specific genes, and even if we did we would have no idea what those genes are or do! But with an annotated genome, we can take even our fragmented sequence and check it against the genome and find out what genes are present.
Based on that, it seems pretty obvious about exactly how having an annotated genome can help us in studies of adaptation. Knowing the functional aspect of our genetic data allows us to more directly determine how evolution is happening in nature; instead of only being able to say that two species are evolving differently from one another, for example, we can explicitly look at how they are evolving. Is one evolving tolerance to hotter temperatures? Are they evolving different genes to handle different diets? Are they evolving in response to an external influence, like a viral outbreak or changing climate? What are the physiological consequences of these changes? These questions are critical in understanding past and future evolution, and full genome analysis allows us to delve into them much deeper.
This includes allowing us to better understand how adaptation actually works in nature. As we’ve discussed before, more traditional studies often assumed that single, or very few, genes were responsible for allowing a species to adapt and change, and that these genes had very strong effects on their physiology. But what we see far more often is polygenic adaptation; small changes in a very large number of genes which, combined together, allow the species to adapt and evolve. By having the entirety of the genome available, we are much more likely to capture all of the genes that are under natural selection in a particular population or species, painting a clearer picture of their evolutionary trajectory.
While many non-model species are still lacking in the available genomic information, whole genomes are progressively being sequenced for more and more species. As this astronomical dataset grows, our ability to investigate, discover and test theories about evolution, natural selection and conservation will also improve. Many projects already exist which aim specifically to increase the number of whole genomes available for certain taxonomic groups such as birds and bats: these will no doubt prove to be invaluable resources for future studies.