In the third of our series of blog posts Celebrating Basic Plant Science, Catherine Kidner from Edinburgh’s Royal Botanic Garden explains how she pinpoints what makes a species a species. This sheds light onto what drove that species’ evolution. Catherine spoke about her research at a conference earlier in the year – you can see her talk in this video.
There are likely to be about 9 million species on Earth (not counting bacteria). Each species has traits which define it and allow it to thrive in its niche. My research group at the Royal Botanic Garden in Edinburgh is trying to understand the diversity around us, so we need to know what these traits are and how they contribute to the success, or otherwise, of the species.
There are difficulties with this approach to understanding diversity. For a start, traits we think are important may not be that important to the species concerned. Also, some traits critical to a species’ success might be difficult to measure, for example phosphate uptake by roots; or be seen only on very specific occasions, like response to a particular pathogen.
Using genetics to define differences between species
We get around these problems by looking at genetic differences between species. New sequencing technologies make it relatively quick and easy to sequence the genome of an individual.
In a typical genome, around 25 000-50 000 genes code for proteins. If we want to know how two species differ we can compare sequences of these protein coding genes and see which types of gene differ the most between species. These changes in gene sequences mean the proteins work differently.
Not all genes are expressed, that is translated into proteins, all the time, and we can see which sets of genes are expressed at particular times and in different organs, like petal or leaf. So when looking at how species differ, we can also look at which genes show the biggest changes in expression level, which would mean one species having more of a particular protein than the other.
Having a list of which genes show sequence changes and which show expression changes is not much help if it’s just a list of genes xzy, abc and rst. What really makes this a useful technique are the huge databases which have been built up over the past 20 years. Work in model species such as yeast, Arabidopsis, mouse and Drosophila have determined functions for many genes in typical genomes. We can match the genes in our ‘interesting genes’ lists to sequences from these model organisms to find out that, for example, gene xzy looks like a disease resistance gene, or gene abc looks like a gene that controls root growth rates.
A typical comparative study might highlight hundreds of genes which differ between species, so even with good descriptions of function we still have a lot of data to sift though to find patterns. We can simplify the lists by using GO (Gene Ontology) terms. This is a way of describing what genes do in a very defined way.