Gene discovery, annotation and orthology in the Asian citrus psyllid genome
The Asian citrus psyllid, Diaphorina citri, is the vector host to the citrus industry’s most threatening bacterial pathogen, Candidatus Liberibacter asiaticus. This bacterium is the causative agent of citrus greening disease and has cost the citrus industry more than $4 billion in revenue loss. The focus of my project this summer was to help find a solution to this devastating disease by working with the psyllid genome and looking for genes that might be involved in pathogen transmission or pathogen survival.
Not much is known about the genetics and genomics of the psyllid, so a literature search of related vector systems was conducted and a candidate gene list highlighting genes that play a role in immunity and gut-microbe homeostasis was compiled. The candidate genes that were successfully identified in the psyllid via BLAST were then manually annotated based on predicted gene models in Web Apollo. Additionally, an OrthoMCL analysis was done using the proteomes of 8 related hemipterans, including the psyllid, to identify conserved hemipteran proteins as well as proteins that are common to all sequenced hemipterans, but missing in the psyllid. This helped to evaluate the completeness of the psyllid genome assembly.
The results from this project will enable other researchers working on this problem to focus their efforts on finding ways to inhibit proteins/genes that have been identified and manually annotated in the psyllid and, therefore, help find a solution to citrus greening faster.
Working at BTI this summer was great. As someone who had never done research prior to this internship, I was excited and amazed to find out that the project I would be working on was of such high importance. To be given real responsibility and treated as an important member of the team was extremely rewarding. Everyone I worked with wanted me to succeed and gave me all of the support I needed to be able to do so. I really enjoyed being in an environment where learning about different aspects of plant biology, and science in general, was encouraged. Also, at the beginning of the summer I was totally new to bioinformatics research, but now I’m leaving with a skill set that I can use in many different fields. I feel lucky to have been exposed to so many areas of research and am eager to continue exploring plant science in future studies.