Annotation of Psyllid Genome

We are annotating the genome of Diaphorina citri using the Apollo system that is hosted at Boyce Thompson Institute. Prashant Hosmani, Mirella Flores and Surya Saha from the Mueller lab at Boyce Thompson Institute are leading this initiative. Monica Munoz-Torres conducted the initial training. Teresa Shippy and Sherry Miller from Kansas State University Bioinformatics Center are the consulting expert annotators.

This project includes annotators across multiple sites including Kansas State University, Indian River State College and Cornell University. We are using a Basecamp project to organize our activities. We have training webinars and regular online lab meetings. You are welcome to join us. Please let us know if you are interested using the contact form. Please include information about your annotation experience and genes of interest, if any. We will add you to the Basecamp project and invite you to the next annotation video conference.




A screenshot of the WebApollo genome annotation platform


State of Psyllid Annotation


Official Gene Set v2.0 released (March 2018)
Diaci v2.0 is the current genome version and is being used for annotation on Apollo. Please get in touch using the contact form for write access. The Official Gene Set v2.0 with 20,793 genes is based on Pacbio Isoseq and Illumina RNAseq evidence. All public RNAseq data has been mapped to this genome. We have also mapped Pacbio Isoseq and Illumina RNAseq reads to assist in identification of correct splice sites. Gene models from OGS v1.0, MCOT v1, NCBI Gnomon (100 and 101) and other insect genomes have also been made available as evidence tracks. You can download the data from our FTP site.

Diaci1.1 is the previous official version of the Diaphorina citri genome. The contig N50 for this assembly is 38 kb. It was submitted to NCBI and called NCBI-diaci1.1. You can access it here. It was annotated with the NCBI Gnomon pipeline.

The Maker annotations from the Diaci1.0 version of the genome have also been mapped to the current version. The mapping program looked for exact matches between the two assemblies, accounting for stretches of the assembly that were converted to N's. It created an 'alignment file', which was used to perform the re-mapping of features in gff3 format. Maker annotations that mapped to sequence that did not exist in Diaci1.1 or only contained N's in the NCBI-approved assembly were discarded. The Maker annotations that were on retained sequence were preserved in their original format, except for their location (scaffold name, coordinates, and strand if appropriate). 37 Maker gene models from Diaci1.0 did not map to Diaci1.1. Both the Maker annotations and NCBI annotations are available as evidence in Web Apollo.

Official Gene Set v1.0 published (March 2017)
The manual annotation paper describes the workflow for the curation of genes and specific gene families in developmental, physiological, RNAi regulatory, and immunity-related pathways in this gene set. This community effort produced 530 manually curated gene models across developmental, physiological, RNAi regulatory, and immunity-related pathways. As previously shown in the pea aphid, RNAi machinery genes putatively involved in the microRNA pathway have been specifically duplicated. The comprehensive MCOT transcriptome enabled us to identify a number of gene families that are either missing or misassembled in the draft genome. In order to develop biocuration as a training experience, we included undergraduate and graduate students from multiple institutions, as well as experienced annotators from the insect genomics research community. The resulting gene set (OGS v1.0) combines both automatically predicted and manually curated gene models. Please see the supplementary notes and annotation updates for individual gene reports and protein sequences.

Training
There are many training resources available. Monica Munoz-Torres has put together a comprehensive guide on the manual curation process. A recent version of her training slides can be found here. Monica Poelchau at NAL created a tutorial for the new BLAST interface.

Annotation Links
  • WebApollo
  • The genome page for Diaphorina citri is available here.
  • The organism page for Diaphorina citri at i5k is available here.
  • New annotators can register to annotate here.
  • The data files for annotation are available on the FTP site.

We are using annotation rules adapted from the i5k pilot. The annotators will use the replaced models field to state what model they are replacing with each annotation. Monica Poelchau at the NAL created the following guide to explain the rationale and details of this process.

The Diaphorina citri data that National Agricultural Library hosts can be downloaded from here. The Maker annotations re-mapped to the NCBI-diaci1.1 assembly are available here.



Annotation Updates


The annotation updates are currently unavailable due to a server problem. We apologize for any inconvenience. Please check back later.