Student publications in GigaByte
These papers are a part of a series of Data Releases crediting the outputs of a student-focused and community-driven manual annotation project for curating gene models and, if required, correcting anomalies in the genome assembly. With the aim of generating a high quality annotation for a better understanding of the biology of this important vector and pathogen-induced changes in gene regulation to aid the development of new strategies in fighting the disease. A total of eleven papers have been published as a part of this series. These will be included in the final Official Gene Set v3.0.

Official Gene Set beta v3.0 released (December 10 2019)
Diaci v3.0 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 v3.0 with 19,049 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, OGS v2.0, De novo transcriptome, 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. We also provide functional annotation of the proteins in Official Gene Set beta version 3 performed using Rapid Functional Annotation pipeline. Slides describing the results of the functional annotation are available online.

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.



Report and protein sequences Report and protein sequences Report and protein sequences Report and protein sequences Report and protein sequences Report