This week I wanted to discuss the use of model organisms in biological study, in particular those used in plant sciences. Model organisms are species that have been widely studied which help scientists understand biological processes. They are generally easier to maintain in the laboratory, have quick generation times and can easily be experimentally manipulated. Some model organisms also occupy a key position within evolutionary history. For example, there is increasing support for the use of the lycophyte, Selaginella moellendorffii for the study of plant evolution, especially to increase our understanding of the development of major plant features (e.g. stomata, complex leaf tissue) (Chang et al, 2016).
Below are listed some of the commonly used model species. Findings from the study of these organisms are then applied to non-model organisms.
Lessons from the A. thaliana genome
A genome contains a complete set of DNA of a species, including all of its genes. Each genome contains all of the information needed to build and maintain that organism. Studying this large set of DNA can reveal a great deal about the biology and function of genes.
Arabidopsis thaliana is in the mustard family, Brassicaceae and has been used as the major model species for all plants with applications to the fields of genetics, physiology, biochemistry and development. It was the first plant genome to be sequenced in 2000, a year before the human genome (The Arabidopsis Thaliana Initiative, 2000; Venter et al, 2001). The sequencing team came from institutes in the USA, Europe and Japan.
Nucleotide base pairs are the building blocks of DNA and the A. thaliana’s genome is estimated at 135 million base pairs in length. To put this into perspective, to date, the smallest plant genome analysed is Genlisea tuberosa, a carnivorous bladderwort (61 million base pairs (Mbp)) and the largest plant genome examined is Paris japonica, a species native to Japan, at a size of 150 billion base pairs (Gbp) in length (Fleischmann et al, 2014; Pellicer et al, 2010). Thale cress has a relatively small genome for a plant, meaning that it was both less expensive and technically challenging to sequence than other plants increasing the feasibility of study.
Within this genome is an estimated 35000 genes with approximately 26000 of these having been annotated. Gene and genome annotation is the process of identifying the location of genes and deciphering what their function is. By focusing efforts on studying one organism, the scientific community can gain a deeper understanding of plant biology. These findings and methodologies have then been applied to other organisms (e.g. analysing whether the function of the genes in Arabidopsis thaliana is the same or similar in a non-model species).
D. melanogaster and C. elegans were both sequenced prior to A. thaliana. From these sequences, there is a certain amount that can be learnt about the function of genes in plants. However with the sequencing of thale cress, there was an illumination of genes involved in plant specific functions such as defence, metabolism and transport. The implications of these discoveries in A. thaliana have had wide ranging impacts in the fields of evolutionary biology, bioinformatics and comparative genomics and have paved the way for the sequencing of over 200 plant genomes.
If you want to learn more:
- Chang, C. et al. (2016). Field Guide to Plant Model Systems. Cell, 167(2). 325 – 339.
- The Arabidopsis Genome Initiative. (2000). Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature. 408. 796 – 815.
- Venter, J. C. et al. (2001). The Sequence of the Human Genome. Science, 291(5507). 1304 – 1351.
- Fleischmann, A. et al. (2014). Evolution of genome size and chromosome number in the carnivorous plant genus Genlisea (Lentibulariaceae), with a new estimate of the minimum genome size in angiosperms. Annals of Botany, 114(8). 1651–1663.
- Pellicer et al. (2010). The largest eukaryotic genome of them all? Botanical Journal of the Linnean Society, 164(1). 10–15.