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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:
http://www.cyverse.org/events/webinar-transcriptomics-non-model-organisms

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.

Plant and Animal Genome 2017 Travel Awards

Plant and Animal Genome 2017 Travel Awards for Students and Post-Doctoral Fellows.

Erin N. Burns (U.C. Davis):  Poster: Generation of an Equine Tissue Biobank for Functional Annotation.

Bonnie Cantrell (U. Vermont): Poster: Facilitation of the Bovine Epigenome in the Limbic System: An Atlas of the Bovine Brain.

Emma Fare (U. Delaware): Poster: Hepatic Gene Expression Analysis of Wooden Breast Disorders in Chickens.

Michelle Halstead (U.C. Davis): Poster: Open Chromatin in Bovine Pluripotent Cells and Embryos.

Colin Kern (U.C. Davis): Poster: The Open chromatin Landscape of the Chicken Genome.

Hannah S. Lyman (U.C. Davis) Poster: Identification of lactation-related cis-regulatory regions in the bovine genome.

Victor C. Mason (Swiss Institute of Equine Medicine): Poster: eQTLs, Horses, and FAANG.

Melissa S. Monson (Iowa State): Presentation: Characterizing Responses to Heat Stress and Immune Stimulation Using Transcriptomics in Chicken Immune Tissues.

Robert Schaefer (U. Minnesota): Poster: Unraveling gene function using gene co-expression networks in the domestic horse.

Ying Wang (U.C. Davis): Poster: Transcriptome Analysis of Host Response to Heat Stress in Two Genetically Distinct Chicken Inbred Lines.

Workshop for RNA-seq data annotation, SICB 2017

The Animal Genomes to Phemones (AG2P) Research Coordination Network (RCN) is conducting a workshop on metadata and best practices for annotating RNA-seq data which will be held at noon, 4 January at the annual meeting in New Orleans. Participants will have the opportunity to analyze sample datasets using the CyVerse platform. No prior experience with transcriptomic tools is required. Participants should bring a laptop computer.

RCN Sponsored FAANG Meetings at PAG 2017

The NSF funded Animal Genome To Phenome research coordination network is sponsoring three meetings on Friday, January 13, 2017  (3-6 PM).  Meetings will be held at the Town and Country Hotel in San Diego, CA.  This is just prior to the start of the annual Plant and Animal Genome Meeting. The objective is to help investigators coordinate proposals and identify collaborations for the upcoming NIFA RFA, which is expected to be announced in February 2017. Sessions include:

Poultry Research Coordination Meeting:  Royal Palm 1

Cattle Research Coordination Meeting:  Royal Palm 2

Swine Research Coordination Meeting:  Royal Palm 3

Meetings are open, but individuals interested in attending should contact session organizers so we can have an approximate head count.

Poultry: Carl Schmidt: schmidtc@udel.edu

Cattle: Stephanie MacKay Stephanie.McKay@uvm.edu or

Juan Medrano jfmedrano@ucdavis.edu

Swine: Christopher K. Tuggle: cktuggle@iastate.edu

Transcriptomics Workshop Policy Paper, SICB 2016

Results of Transcriptomics Workshop at SICB 2016 Portland, OR

Members of the Animal Genome to Phenome Research Coordination Network  discussed best practices for the de novo assembly, annotation, and expression analysis of RNA-seq data.  The AG2P RCN collated comments from participants at the meeting regarding the challenges encountered when using transcriptomics in their research. Input came from novices and experts ranging from graduate students to principal investigators. Discussion participants studied a great variety of organisms, and represented laboratories present in both the US and abroad (see above figure). A policy paper summarizing community needs, computational pipelines, current resources and future directions has recently been published in  Integrative and Comparative Biology.

Symposium Summary, SICB Annual Meeting, 2016

Symposium: Tapping the Power of Crustacean Transcriptomes to Address Grand Challenges in Comparative Biology

The NSF’s “Genomes to Phenomes (G2P)” initiative is identifying key questions, such as how genetic mechanisms produce more fit phenotypes (adaptive evolution) and how genotype affects non-linear or non-additive molecular changes to produce a different phenotype. There is an emerging consensus behind the need to understand the mechanisms that govern the genome to phenome continuum, which requires integration across all levels of biological organization. As the product of the genome, a transcriptome is a key driver of phenotype and thus serves as a vital link between genes and the environment. A relatively small number of decapod crustacean species have been intensively studied at the molecular level; their availability, experimental tractability, and economic relevance factor into the selection of a particular species as a model. Transcriptomics, using high-throughput next generation sequencing (NGS, coupled with RNA sequencing or RNA-seq) is revolutionizing crustacean biology. The eleven symposium presentations presented at this symposium illustrated how RNA-seq is being used to study stress response, molting and limb regeneration, immunity and disease, reproduction and development, neurobiology, and ecology and evolution. A summary of the symposium has been recently been published in Integrative and Comparative Biology.

FAANG Meeting 2015

Hi G2P RCN Members:

I had a wonderful time at the Functional Annotation of Animal Genomes workshop last week held at the National Academy of Sciences.  I am very grateful to the RCN for the opportunity to attend, and certainly learned a lot about the F.A.A.N.G. community goals as well as some of the challenges they are facing in their consortium (and had a blast with Carl and Fiona of course).  I’ll do my best to summarize some of the main highlights of the meeting, but because of unavoidable personal preferences, my ‘highlights’ might not be as impartial (or brief) as one would hope.
The three plenaries were very insightful, and evoked much discussion later on in the breakout session.  John Stamatoyannopoulos (UW) spoke about the regulatory genome, and how the human genome community is getting very close to a complete lexicon for the recognition transcription factors.  He ended the plenary by setting up by the next 5 years in the field, and spoke about the transition from discovery to detection in the clinical setting, and that by 2018 he predicts about 1/2 of the regulatory DNA will be mapped to the genes being regulated.  He also answered questions from the group regarding SNP location, and how important it will be to identify the SNPs in the regulatory regions, and not just protein coding.  He urged the F.A.A.N.G. community to gather as much data as possible, on as many different cell types and tissues, even if analysis is lagging behind, in order to have the depth needed to understand the regulatory genome across animals.
Christine Wells (Univ. of Glasgow) spoke about functional annotation of mammalian genomes (mainly highlighting Atlas projects).  She organized her talk with three overall bullets:
  1. EMERGENCE: gaining insight from omics data
  2. MODULARITY: finding networks and pathways and
  3. ROBUSTNESS: understanding network properties.
She made the main point that none of these can really be answered with just one species and urged the community to think about
  1. generating quality data (metadata standards)
  2. tools for visualizing (she spoke about how this is one of the biggest challenges but did not offer solutions — obviously this is still a hard problem in the community)
  3. collaboration with bioinformatics groups (and how that collaboration is organized) is imperative.
  4. She brought up the fact that the community needs a new ontology for RNA and that noncoding/coding is just not cutting it.
Paul Flicek (EMBL-EBI) spoke a lot about the bioinformatic challenges the community faces (infrastructure beyond hardware and software) and the role EBI has been playing in the 1000 genomes project.  He outlined four stages of how a project ‘might go’, which made me giggle quite a bit — because he’s dead on.
  1. It’s so easy, but wait, how much is it going to cost?
  2. Time generation: way more time than you thought will go into the nitty gritty (quality, assembly, downstream analysis)
  3. It works! (mostly) — some agreement within the members of a given community on the ‘right’ way to do it.
  4. “See, that wasn’t so hard.”
But unrealistic time goals are made for the next phase because the technology changes, and the cycle repeats itself.  He really drove home the point that in this field, you really need to make things (i.e. analysis pipelines) as good as possible, but to not wait until they are perfect.
Funding agencies gave short talks (NSF, Canadian Genome Enterprise, USDA-NIFA, BBSRC, and European Commission).  Below are some highlights that I think matter most to our group:
Rob Miller (NSF) spoke about the directorate-wide initiatives 1. Understanding the Rules of Life (URL) and 2. Genome to Phenome (G2P) and mentioned EDGE (enabling discovery through genomics tools) as a resource to make the link between the transcriptome and phoneme, but I was unclear regarding the use in non-model organisms at this time.  He of course mentioned the G2P RCN.  Following Christine Wells’ plenary, Carl started an evocative discussion about the level to which we as a community are educating those that might sit on the review panels.  Jeremy Taylor from the Univ. of Missouri also brought up conflicts with reviewing USDA grants because of his network of associations which led to  Steve Ellis speaking about the NSF’s experimental review process whereby each submitter is required to review 7 other proposals, and some of the scoring is based on the quality of the reviews given for other proposals.  Parag Chitnis (USDA-NIFA) gave some numbers about NIFA’s overall extramural funding budget ($1.5 billion) with the aquaculture programs seeing about 200 – 300K of that.  Gulp.
The breakout sessions were a little lopsided regarding productivity (i.e. community agreement).  The breakout session dealing with sample collection standards (and how many cell/tissue types are needed for the F.A.A.N.G. goals), assay protocols, and sample storage did not come to a crisp agreement, but it did appear that a general direction was achieved.  I attended the data analysis breakout session (as did Carl and Fiona) and the group seemed to make several agreements.  The analysis group decided it would agree to hard pipelines for analysis, with periodic data freezes planned when a new pipeline needed to be rolled out; previous data will be re-analyzed, and a new hard pipeline put in place.  There was some stimulating conversation regarding how there is little reward for being a part of the F.A.A.N.G. initiative, and writing a community paper on the pipeline was suggested.  Student/post-doc ‘swapping’ for short bits of time in order to gain better analysis experience was suggested (something I think our RCN could really do).  Laura Clarke (EMBL) also gave a talk earlier that day driving home the importance of metadata standards and sharing scripts via Github for the F.A.A.N.G. community.
Carl was a champion for the decapods at this meeting, and because of that at several points various folks used ‘decapods’ as their example of where the community needs to go to expand the idea of ‘animal’ genomes past livestock.  Although, I will say that I got several questions regarding what a decapod was, and whether they were insects (insert a chuckle here).  He gave some slides on the RCN and spoke about the proposed meeting for next summer.
Finally, Jim Reecy (Iowa State), Jiuzhou Song (U. of Maryland), and Laura Clark (EMBL) summarized ‘the way forward’ for F.A.A.N.G. and specifically spoke about needing clear experimental treatments to understand function (which I think is a clear advantage that the decapod community has, even if we don’t have genomes!).  And finally, they cautioned the community about using students to generate the F.A.A.N.G. data, and that this is a better role for technicians.  Students should be carving out other projects within the F.A.A.N.G. datasets, but should not be in the pipeline per se.
I think the F.A.A.N.G. community has a lot to offer our RCN in several areas including guidelines for metadata in order to move towards cross-species/lab comparisons  and possible data-sharing mechanisms.