I’m interested in plant biology and I was wondering if there was any way I could integrate plant sciences using a plant model organism such as Arabidopsis Thaliana in my genomics project. I know that plants having varying responses to stimuli from their environment and that many proteins encoded by specific genes play a large role in this. I remember learning about how plant cells change their internal ion composition and that this creates electrical potentials throughout the cells and tissue and helps the plant circumnutate. There are also genes the code receptor proteins for specific plant hormones like ethylene in response to their environment to induce ripening of fruit or senescence and many other ways that plants respond to changes in their environment. I was wondering if there are any orthologs of A. Thaliana’s genes that play a role in response to stimuli and environmental changes in any of the other model organisms and if those ortholog genes are expressed in the nervous system, because they ways that plants respond to changes in their environment, to me, seem to resemble them having a sort of “nervous system” which I find very interesting. Also, how could I go about finding information on plant gene expression and orthologs in model organisms? Many of the databases we were given so far (e.g. FlyBase, Human Protein Atlas, Cellxgene) all focus on “non-plant” organisms. So far, I found that FlyBase does has an option to search for orthologs between A. Thaliana and other model organisms.
@mmccoy. how about plant neurons or neuron-like genes?
I found this cool paper, wonder if there are some of the features of neurons in these genes.
Fun to think about!!
https://www.nature.com/articles/s41467-022-28483-6.pdf
Gramene/Ensemble Plants is a great resource for finding information on orthologs and gene expression across plants, and can also be helpful for cross kingdom comparisons. You can search for a particular gene at https://plants.ensembl.org. For example, I just searched for rec8 in rice and found OsRad21-3 (Os08g0266700). The gene gain/loss tree associated with this gene includes some animals, as you can see in the attached image.
Ensembl has similar tools for other eukaryotes too (metazoa.ensembl.org, fungi.ensembl.org, protists.ensembl.org, and then just ensembl.org for vertebrates and a few model organisms in other clades). I use these frequently!
Here is another paper about a highly conserved gene in animals and plants.
Is there any way to put this dataset into R studio so that I can analyze gene expression like we do with cellxgene and the mice genes in R studio with the UMAP and Violin plots?
https://www.zmbp-resources.uni-tuebingen.de/timmermans/plant-single-cell-browser-root-atlas/
https://www.zmbp-resources.uni-tuebingen.de/timmermans/plant-single-cell-browser-leaf-atlas/
paper that has an overview of the browser