All past CitrusGreening news items
These eleven 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. 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.
We present an improved and highly contiguous de novo Diaci version 3.0 assembly based on proximity ligation-based (Hi-C) scaffolding of a non-redundant unitigs from the previous Diaci version 2 genome assembly. The genome and associated annotation were released and first described in a preprint on December 10, 2019.
USDA National Institute of Food and Agriculture (NIFA) recently awarded 12 grants totaling over $45 million for research to combat Huanglongbing (HLB). There are more details at the CRIS site about projects funded in FY2020. Press release for the NMC led project can be found at the Texas A&M Kingsville website.
The most dramatic differences between the transcriptome and proteome of CLas-infected and control plants were observed at 10 wpg, including coordinated increases in transcripts and proteins of citrus orthologs of known plant defense genes. This integrated approach to quantifying plant molecular changes in leaves of CLas-infected plants supports the development of diagnostic technology for presymptomatic or early disease detection as part of efforts to control the spread of HLB into uninfected citrus groves.
The functional anatomy of the male psyllid reproductive system was recently updated. This revision uses modern tools to elucidate the system with high resolution so that molecular researchers can have a reference to cross-correlate their findings.
Improved Diaphorina citri alimentary canal animation
This version reviews the first version of the alimentary canal and adds VolumeScope footage at a high level of resolution using modern imaging technology. The output contains 3D tomographic reconstruction of TEM ultrasections.
Our colleagues in UC Davis have created this video about citrus greening disease (Huanglongbing or HLB) and how Californians can band together to prevent the spread and the end of fresh citrus for us all. Please report HLB to California Department of Food and Agriculture at 1-800-491-1899.
Gene models in C. sinensis and C. clementina can now be curated in the Apollo annotation tool. Please request access using the contact form. You can find more information about resources on the C. sinensis and C. clementina genome pages.
Citrus genomes are now available in the VIGS tool to design virus induced gene silencing experiments on C. sinensis and C. clementina. More details about the tool are available in the publication. Please report any issues using the contact form.
Updated metabolic pathway databases for C. sinensis and C. clementina have been constructed with the latest version of BioCyc Pathway Tools and MetaCyc. This is a collaboration with the Main lab at WSU. The new PGDBs are C clementina Cyc v3, C sinensis Cyc v3 and C sinensis Cyc v4.
Asian citrus psyllid stylets and potato psyllid stylets are comparable in structure including the stylet end-caps of the adult and atria of the pharate adult. Apparent presence of epicuticle cells at the stylet base is not proven. Of interest, Liberibacter may possibly use the stylet replacement apparatus for transmission. Please see Arthropod Structure & Development. Volume 47, Issue 5, September 2018, Pages 542-551 for more details.
Diaphorina citri alimentary canal animation is online
Psyllids have a highly modified alimentary canal wherein the esophagus, anterior midgut, posterior midgut and hindgut are co-located and complexed into an apparently paraphyletic structure called the filter chamber. The animation is crafted to allow for broad scientific audiences to understand basic alimentary canal anatomy and functionality of the Asian citrus psyllid.
Economic impact of citrus industry in California
The total economic impact of the iconic citrus industry is $7.117 billion according to a new study commissioned by the Citrus Research Board (CRB). You can read the full report here.
Hunter et al. awarded patent for dsRNA treatment to reduce D. citri in citrus
dsRNA generated from D. citri trehalase gene is effective in reducing fitness and/or survival of D. citri. Thus genetically altered plants expressing the dsRNA and plants to which dsRNA solutions are applied increase D. citri mortality and reduce D. citri infestation. Read more
Diaphorina citri stylet biogenesis animation is online
The manufacture of new stylets (stylet biogenesis) is an extremely complex process that has been detailed in the potato psyllid. The animation shows examples of key features of the potato psyllid's process that are present in Diaphorina citri, indicating that both are comparable.
Missed the webinar for new Diaphorina citri v2.0 genome release?
The slides are available on slideshare. The v2.0 reference assembly and official Gene Set (v2.0) can be downloaded from the FTP site. You can browse the genome using jbrowse and explore the gene pages.
Webinar for new Diaphorina citri v2.0 genome and Official gene set v2.0 release
The improved v2.0 reference assembly has 1906 contigs and a contig N50 of 759Kb. We are also releasing a new Official Gene Set (v2.0) with 20,967 genes. We will be announcing more details in a webinar on March 5, 2018 (12-1pm EST, 9-10am PST, 5-6pm GMT). No login is required to join the webinar. Please click here to connect at the meeting time.
New updates posted on Diaphorina citri genome and annotation pages
We have added details about the interim genome v1.91 and the new WebApollo system that is hosted at Boyce Thompson Institute. Links to the BioCyc metabolic pathway databases have also been added to the genome pages.
Our paper describing the Diaci v1.1 genome, MCOT transcriptome and Official gene set v1.0 is now available online. Please see the supplementary data for details of manual curation.
The Official Gene Set (OGS v1.0) reported in our paper is now available for blast analysis. This includes the automatically predicted genes from the last version of annotation (XP,XM) as well as 530 manually curated gene models.
The interim genome v1.9 for Asian citrus psyllid assembled from Pacbio data is now available on Jbrowse. The genome build is also available at the Ag Data Commons site. Please cite this resource if you publish any analysis based on this dataset.
The Cilia, Shatters, Mueller, Slupsky and Hunter labs presented multiple talks and posters at the IRCHLB meeting in Orlando in March 2017. Please see the agenda for more details.
We have added more details of the curation process as well as a detailed workflow, tutorial and slides used for training annotators. The preprint focuses on specific gene families in developmental, physiological, RNAi regulatory, and immunity-related pathways.
We are releasing a interim Pacbio assembly (Diaci v1.9) for the ACP genome that is a major improvement over the current genome (Diaci v1.1).You can download the genome at our FTP site. Please note that this is an interim assembly so we will not be annotating it but you can blast DNA and protein sequences to it.
More than 20 undergraduate students contributed to the annotation of the Asian citrus psyllid genome. The preprint 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.
President Obama named 102 scientists and researchers as recipients of the Presidential Early Career Awards for Scientists and Engineers (PECASE), the highest honor bestowed by the United States Government on science and engineering professionals in the early stages of their independent research careers. More..
UF survey: Citrus greening in 90 percent of Florida's citrus acres
A paper recently released by Ariel Singerman, extension economist at the University of Florida's Citrus Research and Education Center in Lake Alfred, reported 90 percent of the state's 501,396 commercial citrus acres have at least some greening infection.
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BioCyc's for Drosophila melanogaster and Wolbachia endosymbiont of Drosophila melanogaster are now available on CitrusgreeningCyc.
USDA Announces $22 Million Available for Research to Combat Citrus Greening
The U.S. Department of Agriculture (USDA) today announced the availability of $22 million in grants to help citrus producers fight Huanglongbing (HLB), commonly known as citrus greening disease.
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USDA projects citrus output will continue slide
U.S. citrus production will steadily decline over the next ten years, according to new projections from the U.S. Department of Agriculture.
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DiaphorinaCyc 1.0 was created with NCBI Gnomon gene models and added to the site. The PGDB contains 12543 genes and 185 pathways with 1524 enzymatic reactions.
Citrus disease threat continues
Experts urge caution as homeowners harvest and gift fruit
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Letâs Lay Waste To Floridaâs Abandoned Citrus Groves
Twenty years ago, the Florida citrus industry covered more than 810,000 acres. Through a variety of reasons we all know, the industry is now at well less than 500,000. Unfortunately, that number is expected to shrink further in the near future.
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USDA awards $20 million for citrus greening research
The U.S. Department of Agriculture awarded $20.1 million in grants to university researchers for research and extension projects to help citrus producers fight Huanglongbing. More..
How Long Can Florida's Citrus Industry Survive?
In Florida, citrus is so important, oranges are on the state's license plate. But a disease, citrus greening, has taken a severe toll on Florida's signature crop. More..
Florida orange crop getting wiped out
Florida oranges are threatened with destruction if scientists and the government can't find a way to stop an Asian bug from spreading a tree-killing disease. More..
Citrus greening in Texas
Citrus greening is now threatening Texas backyards. More..
Can Florida citrus hang on until greening cure comes?
Florida orange output has fallen off the table, and if it goes down much further the emblematic orange may slide off the stateâs license plate. More..
GMOs might be the solution
Opinion piece on why GMOs might be the solution to invasive diseases like citrus greening. More..
Growing urgency to stop disease
Recent finds of infected citrus trees in San Gabriel Valley have growers and scientists increasingly worried. More..
New CLas field test under development
A new field test for Liberibacter has been developed using lateral flow technology. More information here.
The Big Squeeze
Huanglongbing quarantine announced in LA
Huanglongbing quarantine announced in San Gabriel-area of Los Angeles County.
$10M grant to save citrus from HLB
BTI and Cornell's CALS part of $10M grant to save citrus from citrusgreening disease.
Oranges bug 'hacks insect behaviour'
Infection of Diaphorina citri with Candidatus Liberibacter asiaticus (CLas) increases its propensity for dispersal. See paper.
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