Location: Temperate Tree Fruit and Vegetable Research
Project Number: 2092-22000-022-003-S
Project Type: Non-Assistance Cooperative Agreement
Start Date: Jun 1, 2020
End Date: May 31, 2023
Objective:
Objective 1: Sequence transcriptomes of multiple potato psyllid haplotypes with long read technology.
Objective 2: Establish a publicly available bioinformatics database for potato psyllid transcriptomes and genomes.
Approach:
Objective 1: RNA from Northwestern and Central potato psyllids with and without Liberibacter will be sequenced on the high throughput PacBio Sequel II instrument. The subreads will be clustered using the Circular Consensus Sequence (CCS) module and processed with the IsoSeq pipeline for each sample. The transcripts will be filtered and functionally annotated. This set will be clustered to remove redundancy and filtered for high quality transcripts representing complete insect genes. The consensus cluster sequences and singletons (unclustered reads) will make up the unigenes dataset. The annotation of unigenes will be run by the National Center for Biotechnology Information (NCBI) Basic Local Alignment Search Tool (BLAST) against a pooled database of non-redundant. Annotation of sequences will be performed using Blast2GO software that categorizes putative biological functions to genes by identifying similar sequences of known function within publicly available databases.
Objective 2: The transcriptome will be added to the AgriVectors database and made available to the community with user friendly tools for omics data. This database will be based on the Citrusgreening.org web portal (Fig 1) that has been developed in the Mueller lab. Metabolic pathway databases will provide organism specific pathways that can be used to mine metabolomics transcriptomics and proteomics results to identify pathways and regulatory mechanisms involved in disease response. All tools like the Apollo gene curation tool, JBrowse genome browser, Biocyc metabolic pathway databases, and Blast sequence analysis tools will connect to a central database containing gene models for plant host, insect vector, their endosymbionts and multiple Liberibacter pathogens. The portal will include user-friendly manual curation tools to allow the research community to continuously improve this knowledge base as more experimental research is published.
