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Arthropod Genomics Research (AGR) Working Group

AGR Logo

The AGR working group focuses on outreach within USDA-ARS aimed at enhancing the genomic analyse knowledge and skill sets of members and collaborators. This is delivered through monthly teleconferences and webinars by internal and external scientists focused on genome assembly, gene and protein expression, population genomics, and reverse genetic (RNAi and CRISPR) approaches. The AGR was initiated following two organizational meetings in 2014 (AGR Workshop I) and 2016 (AGR Workshop II), at which participants communicated needs and devised solutions for challenging analytical pipelines. The AGR facilitates internal and external collaborations by merging those with complementary knowledge, skills, and capabilities within a given research area. Collaborations among AGR members have also resulted in two published papers reviewing ARS arthropod genomics research1 and developing RNAi and CRISPR technologies2. Work within the AGR includes the Ag100Pest Initiative, which aims to provide reference quality genome sequence assemblies for arthropod pests of U.S. agricultural commodities.

The AGR is open to anyone within ARS, and those interested in joining can contact Brad Coates.

  1. Coates BS, Poelchau M, Childers C, Evans JD, Handler A, Guerrero F, Skoda S, Hopper K, Wintermantel WM, Ling KS, Hunter WB, Oppert B, Perez de Leon AA, Hackett K, Shoemaker D. 2015. Arthropod genomics research in the United States Department of Agriculture-Agricultural Research Service: Current impacts and future prospects. Trends in Entomology 11:1-27. (opens pdf in this browser window)

  2. Gundersen-Rindal D, Adrianos S, Allen M, Becnel JJ, Chen YP, Choi MY, Estep A, Evans JD, Garczynski S, Geib SM, Ghosh SKB, Handler AM, Hasegawa DK, Heerman M, Jull J, Hunter W, Kaur N, Li J, Li W, Ling KS, Nayduch D, Oppert B, Perera OP, Perkin L, Sanscrainte N, Sim S, Sparks M, Temeyer K, Vander Meer R, Wintermantel WM, James R, Hackett K, Coates BS. 2017. Arthropod genomics research in the United States Department of Agriculture-Agricultural Research Service: Applications of RNA interference and gene editing in pest control. Trends in Entomology 13: 109-137. (opens pdf in this browser window)

Workshops

July 2016: Arthropod Genomics Research Workshop 2

07/26/2016 - 07/28/2016 · Beltsville, MD · lead: Brad Coates

Thirty three members of the Arthropod Genomics Research (AGR) community representing all five Areas of the Agricultural Research Service (ARS) convened a workshop charged with building collaborative research communities and improving communication channels in the Agency. Participants assessed how the current knowledge, skills and abilities of the AGR scientists impact the effectiveness of genomic data analyses, and affect the capacity of the Agency to address arthropod-specific challenge areas; 1) Controlling Vectored Diseases, 2) Managing Herbivorous Insects, and 3) Implementing Biocontrol, as well as meet the Grand Challenge of reducing agricultural inputs and environmental impact by 25% while increasing output by 25% by 2025. Participants were charged with forming long-term scientific teams that will support the exchange of scientific knowledge and expertise. The workshop was structured to evaluate gaps in knowledge and communication that currently exist, and to subsequently propose solutions that would increase the capacity of ARS to pursue genomics-based scientific inquiry. This task is aligned with the ARS Big Data Vision aimed to develop a well-trained scientific and technical staff and enhance knowledge, skills and abilities within the ARS workforce.

Workshop Agenda (opens pdf in this browser window)

Participant List (opens pdf in this browser window)

Breakout Session I Exercise: Gap Analysis (opens pdf in this browser window)

Breakout Session II Exercise: Devising solutions within and among Grand Challenge Areas (opens pdf in this browser window)

Workshop Summary Document (opens pdf in this browser window)


Related Publications

Gundersen-Rindal D, Adrianos S, Allen M, Becnel JJ, Chen YP, Choi MY, Estep A, Evans JD, Garczynski S, Geib SM, Ghosh SKB, Handler AM, Hasegawa DK, Heerman M, Jull J, Hunter W, Kaur N, Li J, Li W, Ling KS, Nayduch D, Oppert B, Perera OP, Perkin L, Sanscrainte N, Sim S, Sparks M, Temeyer K, Vander Meer R, Wintermantel WM, James R, Hackett K, Coates BS. 2017. Arthropod genomics research in the United States Department of Agriculture-Agricultural Research Service: Applications of RNA interference and gene editing in pest control. Trends in Entomology 13: 109-137. (opens pdf in this browser window)

Poelchau M, Coates BS, Childers CP, Perez de Leon AA, Evans JD, Hackett K, Shoemaker D. 2016. Agricultural applications of insect ecological genomics. Current Opinions in Insect Science 13:61-69.

Coates BS, Poelchau M, Childers C, Evans JD, Handler A, Guerrero F, Skoda S, Hopper K, Wintermantel WM, Ling KS, Hunter WB, Oppert B, Perez de Leon AA, Hackett K, Shoemaker D. 2015. Arthropod genomics research in the United States Department of Agriculture-Agricultural Research Service: Current impacts and future prospects. Trends in Entomology 11:1-27. (opens pdf in this browser window)



September 2014: Arthropod Genomics Research Workshop 1

09/17/2014 - 09/19/2014 · Beltsville, MD · lead: Brad Coates

Workshop Goals/Deliverables:

  • Build tighter linkages and communication among ARS scientists involved in arthropod genomics research (AGR).
  • Forge new collaborations within ARS by explicitly highlighting current and planned AGR within ARS.
  • Define critical research gaps or strengths of AGR within ARS.
  • Provide a clearer picture of current strengths and weaknesses within ARS relative to cyberinfrastructure, data storage, and analytical resources needed to accomplish ARS-wide goals with respect to AGR.
  • Develop a better understanding of available bioinformatics resources (infrastructure and personnel) within ARS.
  • Train participating ARS scientists in publicly available analysis tools (iPlant) that will facilitate research on high-throughput genomic data.
  • Provide guidance and input for future bioinformatics training of ARS scientists.
  • Define role for NAL in AGR in coordinating data standardization and database integration.
  • Build roadmap to accomplish ARS-wide goals with respect to AGR.
  • Plan movement towards integrative, multidisciplinary, and translational genomics.

Workshop Agenda (opens pdf in this browser window)

Participant List (opens pdf in this browser window)

Breakout Session Questions (opens pdf in this browser window)

AGR Impact on Agriculture Statement (opens pdf in this browser window)