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

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 usin...

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Autores principales: Saha, Surya, Hosmani, Prashant S, 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, Van Voorhis, Joshua, Dunlevy, Megan, Farrow, David, Hunter, David, Morgan, Taylar, Shore, Kayla, Guzman, Victoria, Izsak, Allison, Dixon, Danielle E, 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
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5502364/
https://www.ncbi.nlm.nih.gov/pubmed/29220441
http://dx.doi.org/10.1093/database/bax032
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author Saha, Surya
Hosmani, Prashant S
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
Van Voorhis, Joshua
Dunlevy, Megan
Farrow, David
Hunter, David
Morgan, Taylar
Shore, Kayla
Guzman, Victoria
Izsak, Allison
Dixon, Danielle E
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
author_facet Saha, Surya
Hosmani, Prashant S
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
Van Voorhis, Joshua
Dunlevy, Megan
Farrow, David
Hunter, David
Morgan, Taylar
Shore, Kayla
Guzman, Victoria
Izsak, Allison
Dixon, Danielle E
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
author_sort Saha, Surya
collection PubMed
description 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.
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spelling pubmed-55023642017-07-17 Improved annotation of the insect vector of citrus greening disease: biocuration by a diverse genomics community Saha, Surya Hosmani, Prashant S 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 Van Voorhis, Joshua Dunlevy, Megan Farrow, David Hunter, David Morgan, Taylar Shore, Kayla Guzman, Victoria Izsak, Allison Dixon, Danielle E 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 Database (Oxford) Original Article 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. Oxford University Press 2017-06-30 /pmc/articles/PMC5502364/ /pubmed/29220441 http://dx.doi.org/10.1093/database/bax032 Text en © The Author(s) 2017. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Original Article
Saha, Surya
Hosmani, Prashant S
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
Van Voorhis, Joshua
Dunlevy, Megan
Farrow, David
Hunter, David
Morgan, Taylar
Shore, Kayla
Guzman, Victoria
Izsak, Allison
Dixon, Danielle E
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
Improved annotation of the insect vector of citrus greening disease: biocuration by a diverse genomics community
title Improved annotation of the insect vector of citrus greening disease: biocuration by a diverse genomics community
title_full Improved annotation of the insect vector of citrus greening disease: biocuration by a diverse genomics community
title_fullStr Improved annotation of the insect vector of citrus greening disease: biocuration by a diverse genomics community
title_full_unstemmed Improved annotation of the insect vector of citrus greening disease: biocuration by a diverse genomics community
title_short Improved annotation of the insect vector of citrus greening disease: biocuration by a diverse genomics community
title_sort improved annotation of the insect vector of citrus greening disease: biocuration by a diverse genomics community
topic Original Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5502364/
https://www.ncbi.nlm.nih.gov/pubmed/29220441
http://dx.doi.org/10.1093/database/bax032
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