An official website of the United States government.
News Archive
Dear i5k Workspace@NAL community – Welcome to our first installment of our quarterly newsletter, with updates on the i5k Workspace@NAL and the i5k initiative.
Highlights:
- Six new or updated genomes ready for community annotation
- Major pipeline upgrade for better pathway predictions
- Save the date: i5k Annual Meeting Feb 4, 2026
- New i5k volunteer opportunities available
New and updated datasets
Ag100Pest genomes
Two new genomes, Diabrotica undecimpunctata (icDiaUnde3) and Anticarsia gemmatalis (ilAntGemm2), are now open for manual annotation.
Neodiprion pinetum is now updated to assembly version iyNeoPine1.2 and is open for manual annotation.
New and updated dung beetle genomes
Three genomes described in PLoS Genetics are now available: An updated assembly for Onthophagus taurus (IU_Otau_3.0), and new assemblies for Digitonthophagus gazella (IU_Dgaz_1.0) and Onthophagus sagittarius (IU_Osag_1.0). They are open for manual annotation.
Software updates
- We have updated our functional annotation pipeline! In our latest version, we annotate pathways via PathAnnotator, which uses KofamScan, the KEGG API, OrthoFinder, Flybase and Reactome to annotate proteins with KEGG, Flybase and Reactome Drosophila melanogaster pathways. Previously, we had used the KOBAS software for KEGG pathway annotation, and did not filter Reactome pathway annotations by species. New proteomes will be annotated with this new pipeline version moving forward.
- You can now find the link to a species’ JBrowse browser in its organism page under the ‘Summary’ section, in addition to the Available Genome Browsers page. See an example here: https://i5k.nal.usda.gov/organism/836529
- We now indicate in organism and analysis pages whether an analysis is ‘current’ or ‘suppressed’. This should make it easier for you to see which assemblies and annotations are the most up-to-date (=current), and which analyses have been superseded by newer ones (=suppressed). See an example here: https://i5k.nal.usda.gov/organism/836529
Outreach
The i5k Workspace@NAL was at PAG33! We had a presence at the AgBioData booth, and gave two talks. Dr. Kim Vertacnik presented an analysis of EGAP-x and NCBI-RefSeq annotations for the Beenome100 Project, which the i5k Workspace@NAL will host. Dr. Monica Poelchau presented an analysis of community-curated gene structures to identify major gaps in insect genome annotation.
i5k initiative news
The i5k initiative has a new date for the 2025-2026 i5k Annual Meeting: February 4th, 2026! Anyone with an interest in arthropod genomics is encouraged to join this open meeting. More details here:https://i5k.github.io/2025_annual_meeting
The i5k initiative is also recruiting volunteers for multiple roles across our working groups! More details here: https://i5k.github.io/i5k-community-roles
Contact us
Questions or comments? Reach out to us at https://i5k.nal.usda.gov/contact or i5k.ars.usda.gov.
Our next i5k Workspace webinar will be September 19th, 2023 at 1 pm MDT.
The webinar will last one hour and will cover:
- A review of the i5k Workspace gene and transcript nomenclature guidelines;
- Tips on how to use the i5k Workspace BLAST tool as an entry point to Apollo;
- Q&A from webinar attendees.
Click this link to view the event in your time zone: https://www.timeanddate.com/worldclock/fixedtime.html?msg=i5k+Workspace…
Connection details:
https://www.zoomgov.com/j/16121063291?pwd=WmFZd0JHZkVtZHRPSEJneThqSkl3Z…
Meeting ID: 161 2106 3291
Passcode: 537388
---
One tap mobile
+16692545252,,16121063291#,,,,*537388# US (San Jose)
+16692161590,,16121063291#,,,,*537388# US (San Jose)
---
Dial by your location
• +1 669 254 5252 US (San Jose)
• +1 669 216 1590 US (San Jose)
• +1 415 449 4000 US (US Spanish Line)
• +1 646 828 7666 US (New York)
• +1 646 964 1167 US (US Spanish Line)
• +1 551 285 1373 US (New Jersey)
• 833 568 8864 US Toll-free
Meeting ID: 161 2106 3291
Passcode: 537388
Find your local number: https://www.zoomgov.com/u/ac08bb1mk8
Dear all,
We are excited to announce six new Ag100Pest and two new Beenome 100 species at the i5k Workspace@NAL:
- Ag100Pest: Diorhabda carinulata, Vespa mandarinia, Anthonomus grandis grandis, Pectinophora gossypiella, Anastrepha ludens, Anastrepha obliqua
- Beenome 100: Hylaeus volcanicus, Hylaeus anthracinus
New organism and dataset pages (https://i5k.nal.usda.gov/organisms); browsers with mapped RNA-Seq (https://i5k.nal.usda.gov/available-genome-browsers); file downloads, including functional annotations (https://i5k.nal.usda.gov/content/data-downloads); and BLAST databases (https://i5k.nal.usda.gov/webapp/blast) are available. Apollo registration for all organisms can be accessed at https://i5k.nal.usda.gov/web-apollo-registration.
Finally, please see the below request from VeuPathDB:
Dear colleagues – The VEuPathDB project (including VectorBase) is up for renewal, which is likely to depend on strong support from our user community. Joshua Benoit has drafted a letter on behalf of the VectorBase community, for which we are seeking endorsement by lab heads worldwide (if you are a PI, feel free to bring this note to the attention of your lab head). Responses will be most helpful if received by 1 Aug 2023 ... do it today!
Follow this link to view the support letter and add your name, if desired. Or copy and paste the following URL into your internet browser: https://upenn.co1.qualtrics.com/jfe/form/SV_9pj0CnJgCziX0EK?Q_DL=KXpM4w9PN12ASAv_9pj0CnJgCziX0EK_CGC_smCVFBhJWpnnQHz&Q_CHL=email
- You are welcome to forward this email to other appropriate investigators.
- Researchers who regularly use multiple VEuPathDB databases are welcome to add their name to additional letters, accessible here:https://sites.google.com/view/veupathdb
- Apologies if this email is not relevant to you. Click here to opt out of future emails.
Sincerely -- Omar Harb, Mary Ann McDowell and David Roos... on behalf of the entire VEuPathDB team
We are excited to announce three new Ag100Pest species at the i5k Workspace@NAL: Plodia interpunctella, Dermatocenter andersonii, and Bombus affinis. The i5k Workspace now hosts 100 species!
New organism and dataset pages (https://i5k.nal.usda.gov/organisms); browsers with mapped RNA-Seq (https://i5k.nal.usda.gov/available-genome-browsers); file downloads, including functional annotations (https://i5k.nal.usda.gov/content/data-downloads); and BLAST databases (https://i5k.nal.usda.gov/webapp/blast) are available. Apollo registration for all organisms can be accessed at https://i5k.nal.usda.gov/web-apollo-registration.
Finally, please see the below job announcement for a USDA-ARS postdoctoral research fellow in chromosomal evolution and diversity in pest fruit flies in Hilo, Hawaii.
The Tropical Pest Genetics and Molecular Biology Research Unit is seeking a highly motivated individual to use genomic tools to investigate sex chromosomes and large structural variation in Tephritidae to contribute to foundational and applied research that supports fruit fly pest management programs in the United States.
In this position, the incumbent will investigate genomic structure and characterization of sex chromosome structure and structural variants with applications to species and strain identification and insect diagnostics. The ideal candidate for this position will have a Ph.D. in biology, genetics, bioinformatics or a related field, with a strong background in genomics and molecular biology. Experience working on a command-line interface is required, experience working with insects, particularly tephritid fruit flies, is a plus. Candidates willing to relocate to Hilo, HI are preferred, but remote applicants who are a great fit will also be considered. Starting salary is $71,877 with health benefits and a negotiable relocation allowance. As a postdoctoral fellow at the USDA Agricultural Research Service (ARS), you have access to several high-performance computing clusters, training opportunities, and a large and active network of postdoctoral research fellows as your peers.
About us: The USDA Agricultural Research Service (ARS) represents the research arm of the USDA and has about 100 research centers across the United States. The Pacific Basin Agricultural Research Center is located on the east side of the Big Island (Hawaii Island), in the town of Hilo which has a population of about 50,000. Our in-house multimillion dollar genomics facility has a suite of state-of-the-art instrumentation, with the capacity for high-accuracy short-read sequencing, high-fidelity long-read sequencing, and ultra-long read sequencing, as well as supporting laboratory equipment such as automated liquid handling devices, automated nucleic acid isolation devices, and molecular diagnostics methods.
To apply, please send your CV, cover letter, and most recent peer-reviewed publication to sheina.sim@usda.gov.
There is a time change to our next i5k Workspace webinar on December 13th. Due to a new scheduling conflict, this webinar will be at 11 am MST. The webinar will last one hour and will cover:
- Background on the AgBase functional annotation pipeline used by the i5k Workspace;
- Several use cases that you are likely to come across when using functional annotations during the manual curation process. These range from finding the functional annotations for specific proteins in Jbrowse, to strategies for finding all proteins annotated to a pathway in our resources, and more. We will use examples from the pink bollworm, Pectinophora gossypiella, and the American grasshopper, Schistocerca americana.
Click this link to view the event in your time zone: https://www.timeanddate.com/worldclock/fixedtime.html?iso=20221213T11&p1=1947&ah=1
Best,
Monica and the i5k Workspace team
Connection details:
Join ZoomGov Meeting
https://www.zoomgov.com/j/1618648233?pwd=bm9zcGNuRGxkdkJQRmNaU0ltUlZNZz09
Meeting ID: 161 864 8233
Passcode: 050284
One tap mobile
+16692545252,,1618648233#,,,,*050284# US (San Jose)
+16692161590,,1618648233#,,,,*050284# US (San Jose)
Dial by your location
+1 669 254 5252 US (San Jose)
+1 669 216 1590 US (San Jose)
+1 646 828 7666 US (New York)
+1 551 285 1373 US
833 568 8864 US Toll-free
Find your local number: https://www.zoomgov.com/u/abjAobQ9h3