What makes one species different from another?

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Published on: December 10, 2013

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

Catherine Kidner uses genomic data to understand why Begonia like these have evolved into different species

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 xzyabc 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. 

Pinpointing what drives evolution

Say we have the gene sequences and expression levels of a large chunk of the genomes of two plant species. One of the genes that differ in sequence is similar to a gene from the well studied plant Arabidopsis thaliana: gene At1g67260, called TCP1.

These are the GO-terms attached to TCP1:

  • GO:0009908 – flower development
  • GO:0005634 – nucleus
  • GO:003677 – DNA binding
  • GO:0003700 – sequence specific DNA binding-transcription factor activity

These four GO-terms tell us that the protein is found in the nucleus, where it  binds to DNA sequences and regulates the expression of other genes, ultimately affecting flower development.

To find out if this is significant in distinguishing two species, we then look through the GO terms for the rest of our list of genes that differ between the species to see if there are other genes in it with an effect on flower development. We need to find out which GO terms are most common in the lists of genes variable between the two species. 

What causes evolution of tropical Begonia species?

Begonia teysmanniana

Recently, my research group has been working on Begonia, a group of plants that live in the dim understorey of tropical forests. One of the GO terms highly represented in lists of variable genes is ‘chloroplast,’ suggesting that adapting photosynthetic machinery in chloroplasts to these dim light conditions has driven many changes between Begonia species. Without the genomic technology and computing resources that let us ‘scroll’ through the genes expressed in Begonias and quickly determine which types of gene are most variable, we would have missed this aspect of variation between species as it is far more difficult to measure than leaf shape, flower form or plant height.

We’re now looking in detail at the changes between species in specific chloroplast proteins to see how they might change photosynthetic activity, and hopefully test this in the lab.

 

 

Image credits: Top images, from left: Begonia sp. by Pauline EcclesBegonia bowerae by Wildfeuer; Begonia deliciosa by SalixBegonia Corallina by Simon EugsterBegonia teysmanniana c/o Catherine Kidner.

 



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