Improved annotation of the insect vector of citrus greening disease: Biocuration by a diverse genomics community
Date
2017Author
Saha, Surya
Hosmani, Prashant
Villalobos-Ayala, Krystal
Miller, Sherry
Shippy, Teresa
Flores, Mirella
Rosendale, Andrew
Cordola, Chris
Bell, Tracey
Mann, Hannah
DeAvila, Gabe
DeAvila, Daniel
Moore, Zachary
Buller, Kyle
Ciolkevich, Kathryn
Nandyal, Samantha
Mahoney, Robert
Joshua Van Voorhis
Dunlevy, Megan
Farrow, David
Hunter, David
Morgan, Taylar
Shore, Kayla
Guzman, Victoria
Izsak, Allison
Dixon, Danielle
Cridge, Andrew
Cano, Liliana
Cao, Xiaolong
Jiang, Haobo
Leng, Nan
Johnson, Shannon
Cantarel, Brandi L.
Richards, Stephen
English, Adam
Shatters, Robert G.
Childers, Chris
Chen, Mei-Ju
Hunter, Wayne
Cilia, Michelle
Mueller, Lukas A.
Munoz-Torres, Monica
Nelson, David
Poelchau, Monica F.
Benoit, Joshua B.
Wiersma-Koch, Helen
D'Elia, Tom
Brown, Susan J.
Metadata
Show full item recordAbstract
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 D. 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 D. citri biology and CLas interactions. 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. 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.
Citation
Saha, S., Hosmani, P., Villalobos-Ayala, K., Miller, S., Shippy, T., Flores, M., Rosendale, A., Cordola, C., Bell, T., Mann, H., DeAvila, G., DeAvila, D., Moore, Z., Buller, K., Ciolkevich, K., Nandyal, S., Mahoney, R., Dunlevy, M., Farrow, D., Hunter, D., Morgan, T., Shore, K., Guzman, V., Izsak, A., Dixon, D., Cridge, A., Cano, L., Cao, X., Jiang, H., Leng, N., Johnson, S., Cantarel, B. L., Richards, S., English, A., Shatters, R. G., Childers, C., Chen, M., Hunter, W., Cilia, M., Mueller, L. A., Munoz-Torres, M., Nelson, D., Poelchau, M. F., Benoit, J. B., Wiersma-Koch, H., D'Elia, T., & Brown, S. J. (2017). Improved annotation of the insect vector of citrus greening disease: Biocuration by a diverse genomics community. Database - The Journal of Biological Databases and Curation, 2017. https://doi.org/10.1093/database/bax032