Progress 04/01/23 to 03/31/24
Outputs
Target Audience:The target audience is honey bee genomics researchers. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?A Genetics PhD student received training and experience in bioinformatics analysis to identify cis regulatory variants. An undergraduate student in Animal Sciences received training and experience in honey bee DNA extraction. How have the results been disseminated to communities of interest?
Nothing Reported
What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
(N/A)
Publications
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Progress 04/01/18 to 03/31/24
Outputs
Target Audience:The target audience is honey bee genomics researchers. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?A Genetics PhD student received training and experience in bioinformatics analysis to identify cis regulatory variants. An undergraduate student in Animal Sciences received training and experience in honey bee DNA extraction. How have the results been disseminated to communities of interest?
Nothing Reported
What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
(N/A)
Publications
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Progress 04/01/22 to 03/31/23
Outputs
Target Audience: The target audience is honey bee genomic researchers. Changes/Problems:We requested a no cost extension to complete this project. This extension was approved. What opportunities for training and professional development has the project provided?A workshop presentation at the Plant and Animal Genome conference included demonstration videos of HymenopteraMine. How have the results been disseminated to communities of interest?An overview of Aim 1 of the project was presented in talks at Louisiana Beekeepers Association, American Honey Producers Association and American Beekeeping Federation annual conferences. A talk on honey bee genomic resources at the Hymenoptera Genome Database, including HymenopteraMine (Aim 2), was presented in the Honey Bee Genomics workshop at the Plant and Animal Genome conference. What do you plan to do during the next reporting period to accomplish the goals? Complete steps required for marker panel selection: GWAS analysis to identify VSH genetic associations, RNA-seq processing, eQTL analysis, and candidate marker identification. (Aim 1) Complete DNA extraction and genotyping of bees for marker validation. (Aim 1) Submit sequencing data to the NCBI SRA, and genomic variation data to the European Variation Archive. (Aim 1) Complete a new release of HymenopteraMine with genomic variation data. (Aim 2) Prepare and submit manuscript. (Aims 1 and 2)
Impacts
(N/A)
Publications
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Elsik CG, Walsh AT, Triant DA, Schnabel RD, Avalos A, Bilodeau L, Simone-Finstrom M. Honey Bee Genomic Resources at the Hymenoptera Genome Database. Oral Presentation. Plant and Animal Genome Conference. San Diego, CA, January 13-18, 2023.
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Progress 04/01/21 to 03/31/22
Outputs
Target Audience:The target audience for HymenopteraMine is honey bee genomic researchers. Changes/Problems:Aim 1. 1) Nucleic acid extraction and sequencing was delayed due to the inability to travel to receive in-person training in honey bee brain dissection due to Covid-19. We overcame the problem when the ARS team developed a training video that was then used at MU. 2) The RNA yield from antenna extractions was low, requiring pooling a larger number of antenna per RNA sample than that originally proposed. Aim 2. We did not complete the new variant dataset set for HymenopteraMine due to sequencing delays. What opportunities for training and professional development has the project provided?A training video for honey bee brain dissection was created by ARS investigators, and was used to train a team member at the University of Missouri. How have the results been disseminated to communities of interest?We submitted an abstract on the Hymenoptera Genome Database to the Plant and Animal Genome Conference, but the conference was canceled due to Covid-19. An overview of the GWAS project was presented to Utah Apiary Inspectors, the Louisiana Beekeepers Association and the Mississippi Beekeepers Association. What do you plan to do during the next reporting period to accomplish the goals?Aim 1. We will complete nucleic acid extractions, library preparation, sequencing and complete bioinformatics analyses of sequencing data to identify candidate SNP markers; complete phenotyping and sample collection for marker validation; and perform marker validation. Aim 2. We will complete the next release of HymenopteraMine with new A. mellifera variant data and updated data from external sources.
Impacts
(N/A)
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2022
Citation:
Walsh AT, Triant DA, Le Tourneau JJ, Shamimuzzaman M, Elsik CG. Hymenoptera Genome Database: new genomes and annotation datasets for improved GO enrichment and orthologue analyses. Nucleic Acids Res. 2022 Jan 7;50(D1):D1032-D1039. doi: 10.1093/nar/gkab1018.
- Type:
Journal Articles
Status:
Published
Year Published:
2021
Citation:
Fouks B, Brand P, Nguyen HN, Herman J, Camara F, Ence D, Hagen DE, Hoff KJ, Nachweide S, Romoth L, Walden KKO, Guigo R, Stanke M, Narzisi G, Yandell M, Robertson HM, Koeniger N, Chantawannakul P, Schatz MC, Worley KC, Robinson GE, Elsik CG, Rueppell O. The genomic basis of evolutionary differentiation among honey bees. Genome Res. 2021 May 4;31(7):120315. doi: 10.1101/gr.272310.120.
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Progress 04/01/20 to 03/31/21
Outputs
Target Audience:The target audience for HymenopteraMine is honey bee genomic researchers. Changes/Problems:Aim 1. We have delayed nucleic acid extraction and sequencing due to the inability to travel to receive in-person training in honey bee brain dissection due to Covid-19. What opportunities for training and professional development has the project provided?We presented a virtual HymenopteraMine tutorial, which was announced on the ArthropodNews listserv and included 35 participants. The tutorial is available on YouTube. New HymenopteraMine documentation and tutorial examples are available at http://hymenopteragenome.org. How have the results been disseminated to communities of interest?In addition to the virtual tutorial reported above, HymenopteraMine was presented as virtual posters at two virtual meetings. What do you plan to do during the next reporting period to accomplish the goals?Aim 1. We will perform nucleic acid extractions, library preparation, submit samples for sequencing and complete bioinformatics analyses of sequencing data. We will also perform phenotyping and collect samples for SNP validation. Aim 2. We will complete the next release of HymenopteraMine with new A. mellifera variant data and updated data from external sources.
Impacts
(N/A)
Publications
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2020
Citation:
Triant, DA. HymenopteraMine: Genomic Data Mining Tool for Hymenopteran Insects. Virtual Poster. Virtual Arthropod Genomics Symposium. July 21-22, 2020.
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2021
Citation:
Triant DA, Walsh AT, Elsik CG. HymenopteraMine: A genomic data mining system with 40 eusocial bee, ant and wasp species. Virtual Poster. Cold Spring Harbor Biology & Genomics of Social Insects Virtual Meeting. March 30-April 1, 2021.
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Progress 04/01/19 to 03/31/20
Outputs
Target Audience:The target audience for HymenopteraMine is honey bee genomic researchers. Changes/Problems:Aim 1. Due to mortality or insufficient bees observed manipulating a cell capping in some crosses, we were unable to collect 12 bees performing the behavior for four L X H and seven H X L crosses, with numbers ranging from 0 to 9 behavior-performing and 2 to 15 non-performing bees collected and frozen. These crosses will be repeated in the next project year. Aim 2. Our relatively new production server failed in January 2020, so we moved HymenopteraMine to another server to keep it publicly accessible. The server vendor agreed to replace the server, but replacement was delayed until May due to Covid-19. Due to resource limitations until the production server was replaced, we were unable to complete the HymenopteraMine release anticipated in this project year. We expect to complete the next release of HymenopteraMine in the first half of the next project year. What opportunities for training and professional development has the project provided?We presented a HymenopteraMine Webinar to the USDA-ARS Arthropod Genomics Research (AGR) working group. We also demonstrated HymenopteraMine to an advisory group, and received feedback for improvements in the next release. How have the results been disseminated to communities of interest?The GWAS project (Aim 1) was presented in a talk at the American Beekeeping Federation Conference.HymenopteraMine (Aim 2) was presented as posters at two conferences. What do you plan to do during the next reporting period to accomplish the goals?Aim 1. Due to mortality or insufficient bees observed manipulating a cell capping in some crosses (see Changes/Problems), we will redo the first and second rounds of some crosses, individually phenotype workers for +/- VSH-associated behaviors, and collect samples. We will perform nucleic acid extractions and library preparation and will submit samples for sequencing. Aim 2. We will complete the next release of HymenopteraMine with new gene expression data, new gene ontology annotation data and updated data from external sources.
Impacts
(N/A)
Publications
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2019
Citation:
Walsh, AT, Triant, DA, Shamimuzzaman, M, Le Tournea JJ, Elsik CG. HymenopteraMine: Exploring Diverse Genomic Datasets of over 40 Hymenopteran Species. Poster. Entomology Society of America. St Louis, MO, November 17-20, 2019.
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2020
Citation:
Elsik, CG, Walsh AT, Triant DA, Shamimuzzaman M, Le Tourneau JJ. Hymenopteramine: Genomic Data Mining Tool for Honey Bee and Other Hymenopteran Insects. Plant and Animal Genome Conference. Poster. San Diego, CA, January 11- 15, 2020.
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2020
Citation:
Simone-Finstrom, M. From Genetic Characterization to New Trait Selection: Baton Rouge Efforts in Bee Breeding. Invited presentation at the 2020 American Beekeeping Federation Conference, Schuamburg, IL. January 2020.
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Progress 04/01/18 to 03/31/19
Outputs
Target Audience:The target audience for HymenopteraMine is honey bee genomic researchers. Changes/Problems:In the proposal, we had misestimated the time needed for phenotyping colonies, overwinter survival rates, and to identify Pol-line, Hawaiian ("Hilo"), and Italian parents, so we postponed performing crosses until Spring 2019. We also indicated that we would process public whole genome sequencing (WGS) data from the NCBI SRA in the first year, for adding variants to HymenopteraMine. However, we decided to postpone work with the public WGS data until we have completed generation of the new WGS data from this project, so that we can combine analyses to provide more reliable variant calls. Since we postponed working with public WGS data, we started working with public RNA-seq data in the first reporting period (originally scheduled to start in the third reporting period). What opportunities for training and professional development has the project provided?We presented a 2-hour HymopteraMine workshop at the University of Illinois, Urbana-Champaign, just prior to the June 2018 Arthropod Genomics Symposium. Around 20 individuals (students, postdocs, faculty) attended. We also presented a 20-minute HymenopteraMine talk including demo videos, at the Cold SpringHarbor Biology and Genomics of Social Insect Meeting. How have the results been disseminated to communities of interest?In addition to the HymenopteraMine workshop and the presentation at Cold Spring Harbor, we presented two HymenopteraMine posters at the Arthropod Genomics Symposium. The new HymenopteraMine and JBrowse/Apollo tools for the Apis mellifera genome Amel_HAv3.1 is publicly available at http://hymenopteragenome.org. What do you plan to do during the next reporting period to accomplish the goals?Aim 1. We will perform the first and second rounds of crosses, individually phenotype workers for +/- VSH-associated behaviors, and collect samples for DNA and RNA sequencing. We will then perform DNA and RNA extractions, and submit samples for library preparation and sequencing. Aim 2. We will continue to process RNA-seq to compute gene expression levels, curate BioSample metadata, and create new RNA-seq JBrowse tracks. We will release a new version of HymenopteraMine with new gene expression data and updated external data sets.
Impacts
What was accomplished under these goals?
One way to improve honey bee health is by breeding for traits that confer resistance to stressors such as Varroa mite. The honey bee genome sequence, combined with new efficient technologies for genotyping, can be used to develop DNA markers for use in honey bee breeding. Our long-term goal is to translate genomic information to tools that can be used in sustaining honey bee health. This project will produce DNA markers for Varroa resistance traits, as well as a honey bee genomic database, that will be used in breeding programs to mitigate honey bee colony. Aim 1. Identify genomic regulatory variants associated with Varroa Sensitive Hygiene (VSH) and validate those variants in diverse populations. 1) Major activities completed / experiments conducted The investigators met at the Honey Bee Breeding, Genetics, and Physiology Research Lab in Baton Rouge in June 2018 to plan phenotyping, queen and drone selection, and colony rearing. In summer 2018, colony phenotyping was performed to get Pol-line, Hawaiian ("Hilo Bees") and Italian parents secured before winter for crosses to be performed in Spring 2019. 2) Data collected In order to test the sequencing of bee genomes we performed whole genome sequencing of 7 test samples producing a total of 106 Gb of sequence yielding about 470x coverage of each individual. These data have been made publically available at NCBI SRA under BioProject PRJNA522435 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA522435). 3) Summary statistics and discussion of results We have nothing to report for this reporting period. 4) Key outcomes or other accomplishments realized We have nothing to report for this reporting period. Aim 2. Develop data mining resources to accelerate genomics research in honey bee health, including research to develop genetic markers for resistance traits. 1) Major activities completed / experiments conducted We have released a new version of the data mining warehouse, HymenopteraMine V1.4, with the new Apis mellifera genome assembly (Amel_HAv3.1). All other publically available datasets have been updated to the latest releases. We also mapped the official gene set, OGSv3.2, to the new genome assembly, and created a new JBrowse browser with Apollo annotation for Amel_HAv3.1. These tools are available at http://hymenopteragenome.org. We began processing existing RNA-seq data from honey bee health related experiments to compute gene expression levels to be loaded into the next release of HymenopteraMine and to create RNA-seq JBrowse tracks for the Amel_HAv3.1 assembly. Specifically, we downloaded 250 single-end and 657 paired-end Illumina runs from the SRA, based on a minimum read length of 75bp. We combined fastq files for technical replicates, resulting a fastq file for each of 238 single-end and 532 paired-end experiments. We also downloaded and began parsing and curating the associated NCBI BioSamples to create a consistent set of metadata for HymenopteraMine. 2) Data collected We did not generate raw data for this objective. We computed a new dataset of cross references between the Apis mellifera OGSv3.2 gene set (Amel_4.5) and the new RefSeq gene set (Amel_HAv3.1). We gathered and formatted updated Apis mellifera datasets for HymenopteraMine from the following sources: NCBI, UniProt, InterPro, OrthoDB, KEGG, BioGRID. 3) Summary statistics and discussion of results HymenopteraMine v1.4 will allow researchers to map the gene set of the newest Apis mellifera genome back to the official gene set (OGSv3.2) of the previous assembly, which will help them transition their research to the new assembly and to compare their results with previous studies. 4) Key outcomes or other accomplishments realized The key outcome is the change in knowledge that results when researchers use HymenopteraMine.
Publications
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2018
Citation:
Shamimuzzaman M, Triant DA, Tayal A, Unni D, Elsik CG. How to Perform Meta-analysis using Hymenopteramine. Poster. Arthropod Genomics Symposium, Urbana, IL, June 7-9, 2018.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2018
Citation:
Triant DA, Shamimuzzaman M, Tayal A, Unni D, Elsik CG. Integrating diverse datasets using the data mining warehouse, HymenopteraMine. Poster. Arthropod Genomics Symposium, Urbana, IL, June 7-9, 2018.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2018
Citation:
Elsik, CG. HymenopteraMine Workshop. Two-hour tutorial. University of Illinois and Arthropod Genomics Symposium, Urbana, IL, June 7, 2018.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2018
Citation:
Elsik CG, Unni DR, Tayal A, Triant DA. HymenopteraMine: Data Mining Warehouse of the Hymenoptera GenomeDatabase. Oral presentation. Cold Spring Harbor meeting: Biology & Genomics of Social Insects. Cold Spring Harbor, NY. May 5-8 2018.
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