Monthly Archives: October 2019

Building Bridges from Genomes to Phenomes: A 2020 SICB Symposium

The members of the AG2P RCN are leading a new Symposium for the January 2020 Annual Meeting of the Society for Integrative and Comparative Biology (SICB). This society-wide Symposium is entitled: “Building Bridges from Genomes to Phenomes: Molecules, Methods and Models”.  At its core, the 2020 symposium- with associated complementary oral and poster paper sessions, lunch planning session and policy workshop- will delve into recent progress linking phenotype plasticity to changes at the level of the genome, epigenome, proteome, and metabolome, while exploring the boundaries between variation and speciation. Presentations, discussions and syntheses will focus on new approaches, models and methodological challenges in melding different types of datasets (genomic, transcriptomic, epigenetic, proteomic, metabolomic) to address questions about linkages between the genome and phenome in non-model organisms. Invited Speakers, their research topics and additional information on the Symposium are located below. We seek input from the larger community regarding what they see as important topics to be covered in the workshops and its final policy paper. Feedback will be used to begin compiling a list of promising questions, research directions, major hurdles and vision statements from a wide community of investigators.

Invited Speakers, Topics, Schedule for the Symposium and Related Activities to Broaden Participation

The invited symposium program consists of 11 presentations by investigators all focused on elucidating the genome to phenome framework, using a variety of non-model organisms and distinctive approaches to address the same central questions. Their names, position title, affiliations, and presentation titles are listed below. For each research group, the speaker is designated by an asterisk (*), and the study organisms are indicated in parentheses. Each speaker will have 25 min to present her/his current research. The last 5 min will be reserved for questions and conversations between the speakers and attendees moderated by the symposium organizers.

7:45 am. Karen Burnett*], Research Professor, Grice Marine Laboratory, College of Charleston. Overview of the symposium.

8:00am. Alex Mauro*, PhD Candidate, and Cameron Ghalambor, Professor, Department of Biology, Colorado State University.

Title: Transcriptomic basis of salinity tolerance in two euryhaline fish with different realized niches. (fish)

8:30am. Frank Lyko*, Professor, Division of Epigenetics, German Cancer Research Center, Heidelberg, Germany.

Title: Epigenetic adaptation in a clonal invasive crayfish. (crustaceans)

9:00am. Jonathan Li*, Graduate Student, and Dietmar Kueltz, Professor, Dept. of Animal Sciences, University of California at Davis.

Title: Quantitation and comprehension of context-dependent changes of dynamic proteomes. (fish)

9:30am. Justin Havird*, Assistant Professor, Dept. of Integrative Biology, University of Texas at Austin.

Title: The roles of mitonuclear epistasis and mitochondrial physiology in environmental plasticity. (crustaceans, plants, insects)

10:00am. Coffee Break

10:30am. Sharbrough, J*, Department of Biology, Colorado State University, Montooth, K, Neiman, M, Department of Biology, University of Iowa.

Title: Phenotypic variation in mitochondrial function across New Zealand snail populations

11:00am. Scott Santos*, Professor, Dept. of Biology, Auburn University, and Justin Havird, Assistant Professor, Dept. of Integrative Biology, University of Texas at Austin

Title: Intrinsic ability or extrinsic source for chromatosome and carotenoid variability in an endemic Hawaiian crustacean “cryptic species complex” (crustaceans)

11;30am. Kathryn Milligan-Myhre* Assistant Professor, University of Alaska Anchorage.

Title: Using an evolutionary model organism to reveal host genetic influence on host-microbe interactions (stickleback fish)

Noon. Lunch

1:30pm. Rob Schaefer*, Postdoctoral Fellow, Equine Genetics and Genomics Laboratory, College of Veterinary Medicine, University of Minnesota

Title: Integrating genome-wide association studies with context specific co-expression networks in corn and horses. (horses and corn)

2:00pm. Kurt A. Gust*, Team Leader, Environmental Genomics and Systems Biology, U.S. Army.

Title: ‘Omics in non-model species: Closing the loop among genes, molecular systems, and phenotypes to predict adverse outcomes to environmental stress. (birds, fish, corals, reptiles)

2:30pm. Dan Hahn*, Professor, Dept. of Entomology and Nematology, University of Florida

Title: Combining ‘omics approaches to pick apart the genetic and physiological architecture of diversification by seasonal dormancy timing. (insects)

3:00pm. Melissa Pespeni*, Assistant Professor, University of Vermont

Title: Linking genome to phenome in marine invertebrates to validate the mechanisms of resilience to global change conditions. (corals)

Related Activities for Broadening Symposium Participation

We will use a combination of activities, including an introductory planning lunch, complementary oral and poster sessions, Twitter feed, and policy white paper workshop to inform and promote participation in the symposium across a wide range of investigators, representing a diversity of disciplines, career stage, gender and underrepresented groups. The organizers will work with all of the participants to share and synthesize their visions of Genome to Phenome community successes, best methods, leading edges of research and the needs of the community to support further advancement in the field.

Complementary sessions. Both oral and poster complementary sessions will be scheduled during the meeting with exact dates and times to be determined by the SICB Program Officers. Complementary session participants will be selected by the organizers from among abstracts submitted to SICB to illustrate the breadth of questions, models and analytical approaches that are currently being used to link ‘omic datasets toward the overall goal of predicting phenotypes. As funds permit, the organizers will select at least 6 student/postdoc participants in the complementary session to receive travel and subsistence support from the AG2P RCN and a pending NSF proposal, with a particular aim to maximize participation by women and underrepresented groups.

Planning session and lunch. A luncheon to introduce the symposium participants to each other and to the AG2P RCN, as well as to familiarize the research groups with the aims of the symposium, will be held early in the meeting, preferably on the first full day (Jan. 4, 2020). Box lunches will be available for purchase. The lunch will be scheduled from noon to 1:30 pm. Symposium participants from the invited and complementary sessions will be in attendance and provide a brief introduction to their research topics, focusing on how their research experiences relate to those of other participants. The organizers and other members of the AG2P RCN will then lead a discussion on outlining the framework for a G2P community white paper. Informational materials with the RCN contact information and web site will be given at the luncheon. We will work with SICB to develop a Twitter feed during the meeting to augment the gathering and synthesis of comments. The symposium participants will receive a daily update on this input.

Policy workshop and white paper. The major purpose of the symposium is to evaluate recent progress in linking phenotype plasticity to changes at the level of the genome, epigenome, and proteome, while exploring the boundaries between variation and speciation. The organizers of the Building Bridges Symposium will work with SICB to advertise, invite and encourage attendance at the policy workshop by participants in the invited and complementary sessions, their collaborators and colleagues with research interests in phenotype variation across all of the SICB divisions, The policy workshop will be held on one of the last two days of the meeting (January 7 or 8) and discussions will be led by the symposium organizers. Workshop attendees will be asked to evaluate newly developed approaches and models presented or discussed in the Building Bridges sessions in the context of the grand challenge of linking genome to phenome. They will work to identify the leading edges as well as the key barriers to this research with respect, for example, to melding different types of datasets and working across levels of biological organization to inform our understanding of how phenotype variation arises. The workshop will be formatted to foster discussion, concept integration, and audience participation, by first gathering input to a structured series of questions in smaller discussion groups (6-8 participants/group), with each reporting back their findings to the larger workshop, followed by synthesis of common and unique outcomes (a format which was successful in prior AG2P RCN workshops). This synthesis will form the basis for the symposium policy white paper, which will be published in Integrative and Comparative Biology as part of the symposium volume. Participants who have substantial and creative input into the workshop discussions will be considered for authorship of the white paper. An off-site dinner will accompany the workshop as the meeting schedule permits.

Working Group Recruitment Strategies

The technologies (RNAseq, bioinformatics, etc.) that investigators in both vertebrate and invertebrate systems are exploiting have extensive overlap. Overall, we believe the AG2P network will leverage the technical and biological expertise of both groups, hastening discoveries linking genomes to phenotypes. To accomplish this task, we seek to establish working groups that would be responsible for recommending standard procedures for both experimental and bioinformatic methodologies that fall within their purview. In broad terms, participants for the working groups are requested:

Trait working group: the objective of this group would be to think broadly about the relationships between invertebrates and vertebrates, identifying the evolutionary commonalities and differences that constitute trait determination bridging these disparate animal groups. This group would propose methodologies at the genomic, transcriptomic and bioinformatic level to help reveal the evolutionary origins of unique and shared traits.

Functional annotation group: this group will make recommendations regarding RNAseq, chromatin, histone and DNA methylation mapping, along with genome confirmation HiCstudies.

Bioinformatics working group: This group will work closely with iPlant to develop standard data analysis pipelines along with appropriate database schema and user-friendly Web interfaces. This group will be an important interface between the other working groups and iPlant. This would mean that the AG2P network would have an embedded resource in the iPlant milieu that could meet the needs of any participant.

Phenotype Ontology working group: The objective of this group would be to work with thecurrent Phenotype Ontology RCN to develop terms appropriate to the AG2P efforts and to promote usage of the ontology by members of the AG2P RCN and other members of the scientific community.

Communication, Recruitment and Outreach working group: This group would be responsible for integrating efforts needed for communication within the group (web resources, wikis) and with the larger community (web resources, blogs, social media). These resources, along with RCN sponsored workshops and meetings, will be used as recruitment tools to engage other scientific communities (for example, communities studying insects or fish). This group will also be engaged in developing web based instructional modules suitable for classroom teaching.

Meetings, Workshop and Symposia working group: This group will propose meetings and
workshop themes and identify participants from the AG2P network to lead workshops. The group will also liaise with professional societies to help members of the IVG2P network present at appropriate venues such as Plant and Animal Genome or the Society for Integrative and Comparative Biology meetings (see post on upcoming meeting and workshop). This RCN will have a particular focus on engaging and supporting undergraduate and graduate student involvement in all phases of its work, including participation in working groups, meetings and workshops.

Live De novo Transcriptomics Pipeline Webinar

Blake Joyce of CyVerse will be hosting a live webinar this Friday, March 24th, 2017 at 1 PM EDT, noon CDT, 11 AM MDT, 10 AM PDT to demonstrate the “De novo transcriptomics analysis” pipeline.  If you’d like to see it live, you can register here:

Attending the live webinar means you can ask Blake questions at any step. If you can’t make the live demo, you can always watch the recorded webinar and then email Blake questions later on.

Welcome to the Animal Genome to Phenome Research Coordination Network Website

Welcome to the Animal Genome to Phenome Research Co-ordination Network Website

Understanding the relationship between an organism’s DNA (the genome) and the set of phenotypic characteristics that result from genomic expression (the phenome) is a central challenge in biology. High throughput sequencing and phenotypic data from multiple species provides an opportunity for comparative analysis of genome to phenome data. The objective of the Animal Genome to Phenome Network (AG2PN) Research Collaboration Network (RCN) is to promote comparative analysis of vertebrate and invertebrate animals to enrich our understanding of the relationship between genomes and phenomes. The AG2PN will bring together groups using diverse experimental approaches to understand how the genome ultimately manifests the phenome. The AG2PN will provide tools necessary for scientists to exploit comparative genomics approaches to understand genome to phenome relationships. In addition, the activities of the AG2PN will provide training for undergraduates, graduate students and post-doctoral fellows in the science of comparative biology and genome to phenome relationships. Participation of researchers from universities and colleges serving historically underrepresented groups will be particularly encouraged. The AG2PN will also generate educational modules to further enhance student training in G2P concepts. All of the resources developed by the AG2PN will be freely available to the scientific community, communicated at scientific meetings, and published in peer-reviewed journals.

A major objective of the AG2PN will be to encourage researchers to leave their silos and develop collaborative teams that will exploit comparative approaches to enhance our understanding of genome to phenome relationships. The AG2P RCN goals include: Establishing an international AG2PN with scientists studying a diverse range of animals; AG2PN activities that will directly foster the development of comparative studies by promoting standardization of experimental approaches, data and metadata collection and bioinformatic analyses; promoting new collaborations and proposals among scientists from different specialties through international meetings, web sites, publications and social media; and promoting understanding of comparative genomic studies through the development of training modules using diverse educational modalities. Ultimately, this RCN will improve our understanding of the relationships between selective pressures, genomic changes and phenotypic outcomes. The standards developed by this RCN will find applicability far beyond the science directly affected by the AG2P network. These standards will facilitate laboratory work and data comparability across a broad range of species and studies.