Teresa D Shippy, Prashant S Hosmani, Mirella Flores-Gonzalez, Marina Mann, Sherry Miller, Matthew T Weirauch, Chad Vosberg, Crissy Massimino, Will Tank, Lucas de Oliveira, Chang Chen, Stephanie Hoyt, Rebekah Adams, Samuel Adkins, Samuel T Bailey, Xiaoting Chen, Nina Davis, Yesmarie DeLaFlor, Michelle Espino, Kylie Gervais, Rebecca Grace, Douglas Harper, Denisse L Hasan, Maria Hoang, Rachel Holcomb, Margaryta R Jernigan, Melissa Kemp, Bailey Kennedy, Kyle Kercher, Stefan Klaessan, Angela Kruse, Sophia Licata, Andrea Lu, Ron Masse, Anuja Mathew, Sarah Michels, Elizabeth Michels, Alan Neiman, Seantel Norman, Jordan Norus, Yasmin Ortiz, Naftali Panitz, Thomson Paris, Kitty M R Perentesis, Michael Perry, Max Reynolds, Madison M Sena, Blessy Tamayo, Amanda Thate, Sara Vandervoort, Jessica Ventura, Nicholas Weis, Tanner Wise, Robert G Shatters, Michelle Heck, Joshua B Benoit, Wayne B Hunter, Lukas A Mueller, Susan J Brown, Tom D'Elia, Surya Saha
{"title":"Diaci v3.0:黄龙病的昆虫载体--柑橘蛙的染色体组组装、全新转录组和人工注释。","authors":"Teresa D Shippy, Prashant S Hosmani, Mirella Flores-Gonzalez, Marina Mann, Sherry Miller, Matthew T Weirauch, Chad Vosberg, Crissy Massimino, Will Tank, Lucas de Oliveira, Chang Chen, Stephanie Hoyt, Rebekah Adams, Samuel Adkins, Samuel T Bailey, Xiaoting Chen, Nina Davis, Yesmarie DeLaFlor, Michelle Espino, Kylie Gervais, Rebecca Grace, Douglas Harper, Denisse L Hasan, Maria Hoang, Rachel Holcomb, Margaryta R Jernigan, Melissa Kemp, Bailey Kennedy, Kyle Kercher, Stefan Klaessan, Angela Kruse, Sophia Licata, Andrea Lu, Ron Masse, Anuja Mathew, Sarah Michels, Elizabeth Michels, Alan Neiman, Seantel Norman, Jordan Norus, Yasmin Ortiz, Naftali Panitz, Thomson Paris, Kitty M R Perentesis, Michael Perry, Max Reynolds, Madison M Sena, Blessy Tamayo, Amanda Thate, Sara Vandervoort, Jessica Ventura, Nicholas Weis, Tanner Wise, Robert G Shatters, Michelle Heck, Joshua B Benoit, Wayne B Hunter, Lukas A Mueller, Susan J Brown, Tom D'Elia, Surya Saha","doi":"10.1093/gigascience/giae109","DOIUrl":null,"url":null,"abstract":"<p><strong>Background: </strong>Diaphorina citri is an insect vector of \"Candidatus Liberibacter asiaticus\" (CLas), the gram-negative bacterial pathogen associated with citrus greening disease. Control measures rely on pesticides with negative impacts on the environment, natural ecosystems, and human and animal health. In contrast, gene-targeting methods have the potential to specifically target the vector species and/or reduce pathogen transmission.</p><p><strong>Results: </strong>To improve the genomic resources needed for targeted pest control, we assembled a D. citri genome based on PacBio long reads followed by proximity ligation-based scaffolding. The 474-Mb genome has 13 chromosomal-length scaffolds. In total, 1,036 genes were manually curated as part of a community annotation project, composed primarily of undergraduate students. We also computationally identified a total of 1,015 putative transcription factors (TFs) and were able to infer motifs for 337 TFs (33%). In addition, we produced a genome-independent transcriptome and genomes for D. citri endosymbionts.</p><p><strong>Conclusions: </strong>Manual annotation provided more accurate gene models for use by researchers and provided an excellent training opportunity for students from multiple institutions. All resources are available on CitrusGreening.org and NCBI. The chromosomal-length D. citri genome assembly serves as a blueprint for the development of collaborative genomics projects for other medically and agriculturally significant insect vectors.</p>","PeriodicalId":12581,"journal":{"name":"GigaScience","volume":"13 ","pages":""},"PeriodicalIF":11.8000,"publicationDate":"2024-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Diaci v3.0: chromosome-level assembly, de novo transcriptome, and manual annotation of Diaphorina citri, insect vector of Huanglongbing.\",\"authors\":\"Teresa D Shippy, Prashant S Hosmani, Mirella Flores-Gonzalez, Marina Mann, Sherry Miller, Matthew T Weirauch, Chad Vosberg, Crissy Massimino, Will Tank, Lucas de Oliveira, Chang Chen, Stephanie Hoyt, Rebekah Adams, Samuel Adkins, Samuel T Bailey, Xiaoting Chen, Nina Davis, Yesmarie DeLaFlor, Michelle Espino, Kylie Gervais, Rebecca Grace, Douglas Harper, Denisse L Hasan, Maria Hoang, Rachel Holcomb, Margaryta R Jernigan, Melissa Kemp, Bailey Kennedy, Kyle Kercher, Stefan Klaessan, Angela Kruse, Sophia Licata, Andrea Lu, Ron Masse, Anuja Mathew, Sarah Michels, Elizabeth Michels, Alan Neiman, Seantel Norman, Jordan Norus, Yasmin Ortiz, Naftali Panitz, Thomson Paris, Kitty M R Perentesis, Michael Perry, Max Reynolds, Madison M Sena, Blessy Tamayo, Amanda Thate, Sara Vandervoort, Jessica Ventura, Nicholas Weis, Tanner Wise, Robert G Shatters, Michelle Heck, Joshua B Benoit, Wayne B Hunter, Lukas A Mueller, Susan J Brown, Tom D'Elia, Surya Saha\",\"doi\":\"10.1093/gigascience/giae109\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><strong>Background: </strong>Diaphorina citri is an insect vector of \\\"Candidatus Liberibacter asiaticus\\\" (CLas), the gram-negative bacterial pathogen associated with citrus greening disease. Control measures rely on pesticides with negative impacts on the environment, natural ecosystems, and human and animal health. In contrast, gene-targeting methods have the potential to specifically target the vector species and/or reduce pathogen transmission.</p><p><strong>Results: </strong>To improve the genomic resources needed for targeted pest control, we assembled a D. citri genome based on PacBio long reads followed by proximity ligation-based scaffolding. The 474-Mb genome has 13 chromosomal-length scaffolds. In total, 1,036 genes were manually curated as part of a community annotation project, composed primarily of undergraduate students. We also computationally identified a total of 1,015 putative transcription factors (TFs) and were able to infer motifs for 337 TFs (33%). In addition, we produced a genome-independent transcriptome and genomes for D. citri endosymbionts.</p><p><strong>Conclusions: </strong>Manual annotation provided more accurate gene models for use by researchers and provided an excellent training opportunity for students from multiple institutions. All resources are available on CitrusGreening.org and NCBI. The chromosomal-length D. citri genome assembly serves as a blueprint for the development of collaborative genomics projects for other medically and agriculturally significant insect vectors.</p>\",\"PeriodicalId\":12581,\"journal\":{\"name\":\"GigaScience\",\"volume\":\"13 \",\"pages\":\"\"},\"PeriodicalIF\":11.8000,\"publicationDate\":\"2024-01-02\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"GigaScience\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1093/gigascience/giae109\",\"RegionNum\":2,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"MULTIDISCIPLINARY SCIENCES\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"GigaScience","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1093/gigascience/giae109","RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"MULTIDISCIPLINARY SCIENCES","Score":null,"Total":0}
Diaci v3.0: chromosome-level assembly, de novo transcriptome, and manual annotation of Diaphorina citri, insect vector of Huanglongbing.
Background: Diaphorina citri is an insect vector of "Candidatus Liberibacter asiaticus" (CLas), the gram-negative bacterial pathogen associated with citrus greening disease. Control measures rely on pesticides with negative impacts on the environment, natural ecosystems, and human and animal health. In contrast, gene-targeting methods have the potential to specifically target the vector species and/or reduce pathogen transmission.
Results: To improve the genomic resources needed for targeted pest control, we assembled a D. citri genome based on PacBio long reads followed by proximity ligation-based scaffolding. The 474-Mb genome has 13 chromosomal-length scaffolds. In total, 1,036 genes were manually curated as part of a community annotation project, composed primarily of undergraduate students. We also computationally identified a total of 1,015 putative transcription factors (TFs) and were able to infer motifs for 337 TFs (33%). In addition, we produced a genome-independent transcriptome and genomes for D. citri endosymbionts.
Conclusions: Manual annotation provided more accurate gene models for use by researchers and provided an excellent training opportunity for students from multiple institutions. All resources are available on CitrusGreening.org and NCBI. The chromosomal-length D. citri genome assembly serves as a blueprint for the development of collaborative genomics projects for other medically and agriculturally significant insect vectors.
期刊介绍:
GigaScience seeks to transform data dissemination and utilization in the life and biomedical sciences. As an online open-access open-data journal, it specializes in publishing "big-data" studies encompassing various fields. Its scope includes not only "omic" type data and the fields of high-throughput biology currently serviced by large public repositories, but also the growing range of more difficult-to-access data, such as imaging, neuroscience, ecology, cohort data, systems biology and other new types of large-scale shareable data.