Improved annotation of the insect vector of citrus greening disease: biocuration by a diverse genomics community

Authors: SAHA, SURYA - Boyce Thompson Institute; HOSMANI, PRASHANT - Boyce Thompson Institute; VILLALOBOS-AYALA, KRYSTAL - Indian River State College; MILLER, SHERRY - Kansas State University; SHIPPY, TERESA - Kansas State University; FLORES, MIRELLA - Boyce Thompson Institute; ROSENDALE, ANDREW - University Of Cincinnati; Shatters, Robert - Bob; D'ELIA, TOM - Indian River State College; BROWN, SUSAN - Kansas State University; Hunter, Wayne; Heck, Michelle

Submitted to: Database: The Journal of Biological Databases and Curation
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/25/2017
Publication Date: 3/1/2019
Citation: Saha, S., Hosmani, P.S., Villalobos-Ayala, K., Miller, S., Shippy, T., Flores, M., Rosendale, A., Shatters, R.G., D'Elia, T.D., Brown, S.J., Hunter, W.B., Heck, M.L. 2019. Improved annotation of the insect vector of citrus greening disease: biocuration by a diverse genomics community. Database: The Journal of Biological Databases and Curation. 2019. https://doi.org/10.1093/database/baz035.
DOI: https://doi.org/10.1093/database/baz035

Interpretive Summary: The Asian citrus psyllid (Diaphorina citri Kuwayama) is the insect vector of the bacterium Candidatus Liberibacter asiaticus (CLas), the pathogen associated with citrus Huanglongbing (HLB, citrus greening). HLB threatens citrus production worldwide. Suppression or reduction of the insect vector using chemical insecticides has been the primary method to inhibit the spread of citrus greening disease. Accurate structural and functional annotation of the Asian citrus psyllid genome, as well as a clear understanding of the interactions between the insect and CLas, are required for development of new molecular-based HLB control methods. A draft assembly of the Diaphorina citri genome has been generated and annotated with automated pipelines. However, knowledge transfer from well-curated reference genomes such as that of Drosophila melanogaster to newly sequenced ones is challenging due to the complexity and diversity of insect genomes. To identify and improve gene models as potential targets for pest control, we manually curated several gene families with a focus on genes that have key functional roles in Diaphorina citri biology and CLas interactions. This community effort produced 530 manually curated gene models across developmental, physiological, Ribonucleic acid interference (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. A comprehensive 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.

Technical Abstract: The Asian citrus psyllid (Diaphorina citri Kuwayama) is the insect vector of the bacterium Candidatus Liberibacter asiaticus (CLas), the pathogen associated with citrus Huanglongbing (HLB, citrus greening). HLB threatens citrus production worldwide. Suppression or reduction of the insect vector using chemical insecticides has been the primary method to inhibit the spread of citrus greening disease. Accurate structural and functional annotation of the Asian citrus psyllid genome, as well as a clear understanding of the interactions between the insect and CLas, are required for development of new molecular-based HLB control methods. A draft assembly of the Diaphorina citri genome has been generated and annotated with automated pipelines. However, knowledge transfer from well-curated reference genomes such as that of Drosophila melanogaster to newly sequenced ones is challenging due to the complexity and diversity of insect genomes. To identify and improve gene models as potential targets for pest control, we manually curated several gene families with a focus on genes that have key functional roles in Diaphorina citri biology and CLas interactions. This community effort produced 530 manually curated gene models across developmental, physiological, Ribonucleic acid interference (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. A comprehensive 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.