HGNC branches out into plant gene naming
HGNC ·
Over the years HGNC has been approached several times with requests for help in naming genes in various species, including plant genes. While we always want to help, plants have been beyond the remit of our funding so we were limited to offering very general advice. However, the latest approach from the Oak Ridge National Laboratory (ORNL) in Tennessee asking for help naming genes in poplar trees also came with the offer of financial support. The timing couldn’t have been better for us as Susan was coming to the end of her existing funding and was looking for a new role.
So in March 2024 we started a collaboration with Dr Stanton Martin and his team in The Centre for Bioenergy Innovation (CBI) at ORNL to name genes in Populus trichocarpa. This tree model organism, also known as black cottonwood, western balsam-poplar or California poplar, is a member of the willow family and is economically important especially as a source of timber. The genome has been completely sequenced and is already on assembly version 4.1. Anyone trying to navigate a genome using only gene IDs as labels will understand why they are so keen to assign official gene symbols.
The first step is to review the nomenclature that has already been used for Populus trichocarpa genes, both in the literature and databases. This is helping us to understand things like how researchers have been describing poplar genes, what genes are of interest to the community, and which gene families have been studied in poplar.
The next step is to consult the user community and find out what they want from standardised gene naming. For example, does the case of the symbol matter, do they mind about punctuation in symbols? Currently a mixture of symbol styles are being used, e.g. EIN2.1, LIP1P-1, accD, rps11. If a gene has more than one symbol associated with it, how should we pick which one to “approve”? Should this be based on the information the symbol encapsulates, on which was published first, on which has been most used…?
To find out the answers to questions like these we have compiled a survey which we are sending to users - with help from our colleagues at ORNL who are aware of the wider user base. We will also attend the IUFRO Tree Biotech 2024 meeting in Annapolis this August, where we plan to talk with poplar researchers face to face, both to raise awareness of our efforts and ask for their help and advice.
Once we have feedback, we will then try to formulate some general naming guidelines for Populus trichocarpa, and start assigning gene symbols and names to an initial set of genes. This will also involve building a database and website for the poplar data, which will be based on our existing resources for human and vertebrate genes. So watch this space! If you, or any of your colleagues, have an interest in gene naming in trees, specific plant gene families or indeed in plants in general, please get in touch as we would love to hear from you.