The Arabidopsis community has always been very open, so today researchers and funding bodies can look back on more than 20 years of strong international collaboration and data sharing. The efforts of the Arabidopsis community have always been guided by decadal plans, which alongside led to the establishment of many Arabidopsis community projects and resources:
- The Arabidopsis genome research project (1990-2001) led to the completion of the Arabidopsis genome. During this decade two out of three stock and resource centers ABRC (Arabidopsis Biological Resource Center, US) and NASC (Nottingham Arabidopsis Stock Center, UK) were founded.
- The Multinational Coordinated Arabidopsis thaliana Functional Genomics Project (2002-2011) led to the functional annotation of most of the Arabidopsis thaliana genes. Alongside, The Arabidopsis Information Resource (TAIR) was founded in 2001 to meet the needs of the growing Arabidopsis research community.
- From Bench to Bountiful Harvests (2012-2021) aims to obtain in-depth knowledge of how the genome is translated into a continuum of processes, from the single molecule to cells and tissues, the whole plant, plant populations, and fields of plants, to be able to build a predictive model of an Arabidopsis plant. In order to provide a flexible platform to enable open sharing of the vast amount of data generated by today’s omics approaches, the International Arabidopsis Informatics Consortium (IAIC) founded the Arabidopsis Information Portal in 2013 (Araport).
The directors of Arabidopsis community projects and resources have been contributing to the MASC reports for several years, by presenting their respective goals, progress and news. Since 2014, general plant projects and resources have also been included, reflecting the growing connections between researchers focussing on different plant species.
Resource and Stock Centers
Arabidopsis Biological Resource Center (ABRC) Open or Close
Recent Open Tools and Resources for Arabidopsis Researchers
ABRC provides seed, clones, vectors, host strains,In 2018 ABRC distributed close to 100,000 samples to 2,245 individuals located in 50 countries. Close to 50% of these samples were seed lines of insertion mutants. We also sent over 8,000 seed lines to NASC, either as bulk seed for distribution by NASC, or as individual aliquots for NASC users where we were not able to provide bulk seed. In return, ABRC received bulk seed for over 6000 stocks from NASC. The seed collection is now composed of more than 535,000 stocks.
The non-seed collection includes individual clones, and libraries from Arabidopsis thaliana and several other members of the Brassicaceae numbering almost 450,000 stocks as well as vectors, host strains, antibodies, cell lines and education resources. Most of the A. thaliana seed stocks donated in 2018 were T-DNA insertion mutant lines. These include lines from the GABI- Kat collection donated by B. Weisshaar through NASC and lines derived from the SALK institute T-DNA insertion population that have been characterized to some extent and were donated by R. Last. We also received a number of well characterized mutant and transgenic lines as well as seed stocks of other members of the Brassicaceae including accessions of Boechera stricta from T. Mitchell-Olds.
Distribution of seed pools expressing amiRNAs designed to target functionally redundant genes for forward genetic screening began this year. These were developed and donated by J. Schroeder and F. Hauser and were amplified at ABRC prior to release. Vectors added to the collection include CRISPR/Cas9 vectors from D. Weigel. ABRC has performed quality control testing of 6,684 lines in 2018 including germination testing and verifying stock identity.
Planned future activities of your project or resource.
ABRC will continue to solicit donations of Arabidopsis seed resources and to expand the stock collection to other resources and species. In particular, we are emphasizing a new focus on “legacy collections” – donations of collections of seed stocks from retiring researchers or from those switching away from Arabidopsis as their main research organism. We have recently taken possession of such collections from Rob Last and David Meinke and are in the process of curating and amplifying their donations.
Distribution is expected to continue at the current levels, as is quality control testing. ABRC and NASC continue to collaborate sharing seed stock resources and related data. In 2019 ABRC expects to release a new web site and database to replace the ordering system currently hosted by TAIR. The new site will allow access to stock data, ordering, payment and donation information as well as general information about Arabidopsis and ABRC. All stock information will continue to be available in the TAIR web site through ongoing collaboration between ABRC and TAIR. After the release of the new web site and database we plan to develop an application programming interface (API) to allow TAIR, NASC and others easy access to stock data.
Conferences, Workshops and Training events
ABRC organized a booth at ICAR 2018 in conjunction with NASC, and participated in a data resources booth at Plant Biology 2018. Jelena Brkljacic presented plans for our new website and database in a workshop at PAG XXVII. ABRC outreach and education ran booths at two local events, the Science Education Council of Ohio’s annual conference and the Center of Science and Industry Teacher Resource Fair. ABRC also organized a Teacher workshop at Ohio State to familiarize local teachers with our Arabidopsis based teaching resources. In 2019 ABRC and NASC will organize a booth together at ICAR in Wuhan, China and will again participate in the data resources booth at Plant Biology in San Jose, California.
The ABRC published an education paper, Price, C.G., Knee, E.M., Miller, J.A., Shin, D., Mann, J.W., Crist, D.K., Grotewold, E., and Brkljacic, J. (2018) Following Phenotypes: An Exploration of Mendelian Genetics using Arabidopsis plants. American Biology Teacher, 80(4):291-300.
We are very grateful to Dr. Jelena Brkljacic for her many years of dedicated service as ABRC Associate Director and welcome Dr. Emma Knee as our new Associate Director.
Nottingham Arabidopsis Stock Center (uNASC) Open or Close
Sean May, Director
Marcos Castellanos-Uribe, Operations Manager.
In 2018 we sent over 120,000 tubes of seed worldwide to 49 countries (even more nations than last year). This year’s top five receiving countries (in descending order), are the UK, Germany, China, Japan and France. The biggest donor of stocks by far is Germany (for yet another year) and we are now receiving large numbers of the final stocks from the GABI-KAT project - with many, many thanks to Bernd Weisshaar for such unstinting service to the community over the years.
If we (NASC and ABRC) can help you or promote your research to the community by distributing seed on your behalf then please do contact us - don’t wait for us to come to you.
See you in Wuhan!
RIKEN BioResource Center (BRC) Open or Close
Masatomo Kobayashi (RIKEN coordinator)
Recent activities and newly developed tools and resources of your project or resource.
We have developed the Exp-Plant Catalog that provides the information of our Arabidopsis resources including natural accessions, individual mutants and transgenic lines, transposon-tagged lines, full-length cDNA clones, ORF clones of transcription factor genes, and genomic DNA clones to the community. In addition, a list of cultured cell lines such as Arabidopsis T87 cells and Tobacco BY-2 cells are also available from the Catalog.
Exp-Plant catalog: https://plant.rtc.riken.jp/resource/index.html
Project HP: https://epd.brc.riken.jp/en/
Planned future activities
We are going to add some new resources such as Arabidopsis Transcription Factor – Glucocorticoid Receptor mutant seeds and insertional mutants of Arabidopsis Nuclear-Encoded Chloroplast Proteins to the Exp-Plant Catalog.
Conferences, Workshops and Training events
The 11th Asian Network of Research Resource Centers (ANRRC) International Meeting will be held in Philippines in this autumn.
The RIKEN BRC is a member of National BioResource Project (NBRP) funded by the Japanese government. Not only Arabidopsis but also rice, wheat, barley, lotus/glycine, tomato, morning glory, chrysanthemum and algae resources are preserved and provided through the project.
Project HP: http://nbrp.jp/index.jsp
Arabidopsis Informatics and Data Sharing Resources
International Arabidopsis Informatics Consortium (IAIC) Open or Close
By Blake C. Meyers (Interim Director) and Joanna D. Friesner (Assistant), http://www.arabidopsisinformatics.org/.
The IAIC was initiated by Arabidopsis community members in 2009 and formally established in 2011 via a US National Science Foundation RCN award (Award #1062348) to PI Blake Meyers (Danforth Center). The RCN award is set to conclude this year (2016); however, mechanisms for sustaining IAIC are currently being explored. Key community coordination overlap exists between the IAIC steering committee and the steering committee of a recent NSF award to Siobhan Brady (PI) and Joanna Friesner (co-PI) entitled ‘RCN Arabidopsis Research and Training for the 21st century (ART-21)’; NSF Award #1518280 (http://www.nsf.gov/awardsearch/showAward?AWD_ID=1518280). The ART-21 steering committee consists of the 8 member North American Arabidopsis Steering Committee (NAASC), key IAIC liaisons (Blake Meyers and Nick Provart), and Terri Long (USA), Jim Murray (UK), and Ute Kraemer (Germany).
The purpose of establishing the IAIC was to facilitate a coordinated global Arabidopsis informatics efforts to maintain the continuity of key Arabidopsis resources while simultaneously expanding their breadth and depth. Key aims were to include in the IAIC new technologies, resources, and participants on a global scale and advance plant biology while creating novel opportunities for research and education, and strengthening international collaborations. Arabidopsis community members, led largely by elected NAASC members, have participated in all stages of Consortium development and activities. In addition, a Scientific Advisory Board was elected by the Multinational Arabidopsis Steering Committee (MASC) and community participation was solicited in ten workshops including several organized specifically to enable IAIC design and development, and others at public conferences such as the annual International Conference on Arabidopsis Research (ICAR) and the Plant and Animal Genomes (PAG) meetings.
Two key project goals that have been achieved were (1) to facilitate a collaborative effort to establish and fund a new web-based “Arabidopsis Information Portal” for the global plant biology community (now entitled ‘Araport’, see NSF Award #1262414: ABI Development: The Arabidopsis Information Portal, http://www.nsf.gov/awardsearch/showAward?AWD_ID=1262414) and (2) to develop a public platform via an IAIC web page to coordinate activities and serve as a community resource (http://www.arabidopsisinformatics.org/).
Joint sponsorship of a community workshop (with Araport) at the 2016 Plant and Animal Genomes (PAG) meeting in San Diego, California this past January. On behalf of the IAIC and NAASC, Joanna Friesner gave a presentation entitled “Community Collaborations: Advancing Arabidopsis Research and Training (ART-21) and the International Arabidopsis Informatics Consortium (IAIC)”. The publicly-available presentation can be downloaded and viewed at: http://bit.ly/1QfMh4V.
Additional presentations on Araport were given by Araport staff including “A Tour of the Arabidopsis Information Portal (Agnes P Chan, J. Craig Venter Institute) and Module Development for Araport (Jason R. Miller, J. Craig Venter Institute).
(1) NAASC recently received a 5 year NSF award for a collaborative project entitled ‘Arabidopsis Research and Training for the 21st Century (ART-21)’, mentioned above. This coordinated program has these three core objectives: (1) identify emerging technologies where using Arabidopsis as a model organism will provide fundamental discoveries and enable translational research in crop species; (2) enhance interdisciplinary training of scientists for academia and extra-academic careers; and (3) increase the diversity of Arabidopsis research scientists. The IAIC project has overlapping steering committee members with ART-21 and intends to partner with NAASC to expand its outreach to community members to enable analysis of future training needs and emerging bioinformatic and computational skills.
The proposed collaboration includes several activities:
(a) May 2016: A NAASC and IAIC co-organized Focus Group on “Computational training of biologists for academia and industry in the 21st Century” led by Blake Meyers, Nick Provart, Siobhan Brady and Joanna Friesner. The Focus Group will include 35 participants discussing these over-arching questions (1) What are the bioinformatics and computational skills needed by plant scientists of the 21st century to deal with more complex datasets (predictive, quantitative and theory-driven)? (2) What are the bottlenecks to providing students with the needed skills? (3) What do employers (of various types) need/want from employees; what are marketable skills in this area? Key topics include: (i) Training and Education: Skills needed for positions: Industry Positions; Faculty Positions; Undergraduate, Graduate and Postdoc Education (ii) Collaborations:Working with a biologist: a quantitative expert’s perspective; Working with a quantitative expert: a biologist’s perspective; Retraining: Yourself; From a funding perspective (iii) Training Arabidopsis Biologists for High-Throughput Phenotyping; and (iv) Translating from Arabidopsis to Crop Species, and Vice versa. A workshop white paper, led by IAIC members Blake Meyers and Nick Provart, will be produced and include recommendations and analysis.
(b) Another future IAIC goal is to incorporate the outcomes from the activity described above into a hands-on workshop prior to ICAR 2017, envisioned to span 4-5 days and encompass both wet-lab and computational and bioinformatic analysis and techniques. ICAR 2017 will be organized by NAASC in St. Louis, USA, June 19-23, 2017.
Conferences and Workshops
- Plant and Animal Genomes (PAG) meetings: IAIC presentation: January 2016: San Diego. Presentation available at: http://bit.ly/1QfMh4V
- International Conference on Arabidopsis Research (ICAR): July 2015 (Paris)
The Arabidopsis Information Portal (Araport) Open or Close
By Chris Town (Principal Investigator), www.araport.org.
The Araport team extended its fully functional web portal by adding many data types to its ThaleMine data mining tool and many tracks to its JBrowse browser. The team delivered web site infrastructure that, even in its prototype stage, allows community participants to develop and deploy their own web services and data integration applications.
We have also completed the most up-to-date and complete re-annotation of the Col-0 genome to produce Araport11 that consists of 37,523 genes (27,688 protein-coding, 5,051 non-coding, 952 pseudogenic, and 3901 transposable element-related loci) and 58,149 transcripts. The annotation contains 738 new protein-coding loci and a further 508 novel transcribed loci. In addition, we retired 388 genes that encoded short (hypothetical) proteins for which there was no database or RNA-seq support. Araport11 is available on the Araport project site (http://www.araport.org) and will also be released in GenBank by the time this report is published.
JBrowse and ThaleMine continue to be central features of the portal’s user interface
JBrowse now hosts over 100 data tracks, including the latest gene models from Araport11 and their supporting evidence, as well as many community sourced tracks including 1001 genomes SNP data. Methods to allow community members to post and share their data through JBrowse using either GitHub or the CyVerse data store are in active development.
ThaleMine is a data warehouse which hosts and integrates a large collection of Arabidopsis genomics data including gene expression, orthologs, pathways, interactions, publications and others. We have continued to add new content and functionalities to ThaleMine. These include GeneRIFs, together with a portal to NCBI’s submission page that will allow community members to submit their own comments on gene function, and phenotype and stock data with links to ordering from ABRC and eNASC. The most recent addition is an RNA-seq-based expression module that allows users to view expression levels of their favorite genes across the 113 RNA-seq data sets used in the Araport11 re-annotation process.
Science Apps, Web Services and Modules
Despite its technical success and demonstrated ability to assimilate and integrate a wide range of data types, the site sees many fewer visitors than expected. Furthermore, although the attendees at the 2011 Design Workshop were enthusiastic about their vision of a federated data model with many community-contributed modules, their enthusiasm has so far not translated into the level of participation envisaged in the white paper. This is of concern to all of us, including our funders - the US National Science Foundation and the UK Biotechnology and Biological Sciences Research Council. As we develop a proposal for continued funding of the project, we will be pro-actively recruiting major data generators to the project to facilitate assimilation of their data into Araport and demonstrate the value of integration of multiple data types within the portal.
Conferences and Workshops
Project PIs attended the 25th ICAR in Paris in July 2015. In addition to a talk in a Plenary Session, there was a well-attended Araport workshop with contributions both from project PIs and from community contributors. We attended the ASPB meeting in Minneapolis, July 2015, presented a talk in the “Bioinformatics Resources for Plant Biology Research“ and also staffed a booth in the Exhibitor area together with colleagues from other resources. Project staff presented posters and/or talks at the Mid-Atlantic ASPB meeting (April, 2015), University of Maryland Mini-symposium (May 2015), the Mid-Atlantic Plant Molecular Biology Society Meeting (August 2015). Two team members spent one and a half days at Purdue University in November 2015 giving talks, a hands-on workshop and having one-on-one discussions with various faculty members. We organized the IAIC/Araport workshop at PAG, San Diego in January 2016 that included presentations from project personnel and community members.
Araport gave a talk at the ASPB mid-Atlantic Regional Meeting at Swarthmore in April 2016 and has been invited to give talks at ICAR 2016 in Korea in July and at the “GARNet2016: Innovation in the Plant Sciences” meeting in Wales in September 2016. We also plan a presence at the ASPB meeting in Austin in July 2016.
The Arabidopsis Information Resource (TAIR) Open or Close
Leonore Reiser (TAIR curator)
Recent activities and newly developed tools and resources of your project or resource.
The primary activity of TAIR is functional annotation of the Arabidopsis genome, with an emphasis on literature curation, to produce a ‘gold-standard’ reference genome dataset. From March 2018-Feb 2019, TAIR added 4431 experimental Gene Ontology (GO) and Plant Ontology (PO) annotations generated by TAIR curators, TAIR community, UniProt and Gene Ontology Consortium (GOC) to the database. A total of 558 articles were used to annotate to 1696 distinct loci. We added 3783 articles of which 2302 were linked to 3921 genes. We curated 849 new gene symbols, 164 alleles, 304 phenotypes and added/updated 5867 gene summaries. We processed 610 annotations provided by 89 community members spanning 99 papers. TAIR database is updated weekly and the most up to date annotations are accessible via TAIR’s website and tools (www.arabidopsis.org). TAIR also continues to provide quarterly public releases of year-old datasets(https://www.arabidopsis.org/download/index-auto.jsp?dir=/download_files/Public_Data_Releases).
In the past year we have made many changes to the back end of TAIR that have significantly reduced downtime, as well as performance improvements to speed page loading. Other changes to enhance the data and user experience include (1) integration of the Bio Analytic Resource (BAR) ePlant expression viewer into TAIR locus pages, and (2) the complete integration of Araport 11 genome annotation into all of our tools (e.g. SeqViewer/GBrowse/Bulk downloads).
New tools and Resources
Phoenix Bioinformatics, which maintains TAIR, has developed a new tool for inferring gene function called Phylogenes (www.phylogenes.org), in collaboration with the PANTHER project at the University of Southern California (USC). Phylogenes displays phylogenetic trees of gene families along with related data to facilitate inference of function for unknown genes. The first release contains 29 plant species across a wide taxonomic range, along with 10 non-plant, well-annotated reference genomes.
To complement our social media outreach on Twitter (@tair_news) and Facebook (https://www.facebook.com/tairnews/), we have also started a TAIR blog (https://conf.arabidopsis.org/blog/) to share interesting news and insights from a curator’s perspective.
Planned future activities of your project or resource.
In the coming year we plant to continue our literature based functional annotation of the Arabidopsis genome, to produce weekly updates to the TAIR database and quarterly public releases of bulk data sets. We plan additional improvements to TAIR’s underlying software and interfaces to improve usability. Additional enhancements/tools we hope to add in the coming year include JBrowse and an improved community curation tool.
Conferences, Workshops and Training events
TAIR staff presented at ICAR2018 (Making Published Data FAIR) and ICAR2019 (Arabidopsis Bioinformatics Resources), ASPB 2018 (Plant Bioinformatics Resources), and will co-organize the workshop for ASPB 2019. TAIR/Phoenix Staff led workshops at PAG2019 on (1) Data Resource Sustainability, (2) Arabidopsis Bioinformatics Resources, and ran an annotation training workshop (3) Functional Annotation Hands-On Most Ever Fun Session.
In addition to workshops and trainings we co-authored two papers both of which broadly deal with topics of best practices around data management/data sharing/FAIR data.
1.Reiser L, Harper L, Freeling M, Han B, Luan S. FAIR: A Call to Make Published Data More Findable, Accessible, Interoperable, and Reusable. Mol Plant. 2018 Sep 10;11(9):1105-1108. doi: 10.1016/j.molp.2018.07.005.
2.Harper L, Campbell J, Cannon EKS, Jung S, Poelchau M, Walls R, Andorf C,
Arnaud E, Berardini TZ, Birkett C, Cannon S, Carson J, Condon B, Cooper L, Dunn N, Elsik CG, Farmer A, Ficklin SP, Grant D, Grau E, Herndon N, Hu ZL, Humann J,Jaiswal P, Jonquet C, Laporte MA, Larmande P, Lazo G, McCarthy F, Menda N, Mungall CJ, Munoz-Torres MC, Naithani S, Nelson R, Nesdill D, Park C, Reecy J,Reiser L, Sanderson LA, Sen TZ, Staton M, Subramaniam S, Tello-Ruiz MK, Unda V,Unni D, Wang L, Ware D, Wegrzyn J, Williams J, Woodhouse M, Yu J, Main D. AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture. Database (Oxford). 2018 Jan 1;2018. doi: 10.1093/database/bay088.
We gratefully acknowledge the support of the research community for their data contributions, suggestions for improvement and financial support.
Plant Projects and Resources with Strong Participation of the Arabidopsis Community
Bio-Analytic Resource for Plant Biology (BAR) Open or Close
By Nicholas Provart (Director), http://bar.utoronto.ca.
Open Tools and Resources for Arabidopsis Researchers
The Bio-Analytic Resource is a collection of user-friendly web-based tools for working with functional genomics and other data for hypothesis generation and confirmation. Most are designed with the plant (mainly Arabidopsis) researcher in mind. Data sets include:
* 150 million gene expression measurements (75 million from A.th.), plus “expressologs” (homologs showing similar patterns of expression in equivalent tissues) for many genes across 10 species. View expression patterns with our popular eFP Browser or newer ePlant tool.
* 70,944 predicted protein-protein interactions plus 62,626 experimentally-determined PPIs (rice interologs also available!) and ~2.8 million protein-DNA interactions, which can be explored with our new Arabidopsis Interactions Viewer 2 tool.
* 29,180 predicted protein tertiary structures and experimentally-determined structures for 402 Arabidopsis proteins.
* Millions of non-synonymous SNPs from the 1001 Arabidopsis Genomes project, delivered through the MASC Proteomics Subcommittee’s site at 1001proteomes.masc-proteomics.org.
* Documented subcellular localizations for 11.7k proteins, predicted localization for most of Arabidopsis proteome, from the SUBA database at the University of Western Australia.
Recent activities of your project or resource.
We worked with collaborators Yuling Jiao and colleagues to incorporate cell-type-specific meristem data from Tian et al. (2019) into our Arabidopsis eFP Browser and ePlant tools.
We released a new Arabidopsis Interactions Viewer 2, which accesses our updated database of 91,175 experimentally-document protein-protein interaction entries encompassing 62,626 unique pairs of proteins (through a collaboration with BioGRID, with some interactions being documented by multiple methods and/or groups; see Dong et al., 2019). We also predicted 9,065 protein-protein interactions by docking and validated a subset using Y2H. These have added to the existing 70k PPIs predicted using the interolog method in our database (docking results are also described in Dong et al., 2019).
For translational researchers, publications came out for a new Wheat eFP Browser (Ramírez-González, 2018), an RNA-seq-based maize developmental atlas for the Maize eFP Browser by Hoopes et al. (2018), a new early maize seed development Maize eFP Browser view by Yi et al. (2018), and a tomato root Tomato eFP Browser view by Toal et al. (2018). We also released 15 ePlants (for maize, poplar, tomato, Camelina sativa, soybean, potato, barley, Medicago truncatula, eucalyptus, rice, willow, sunflower, Cannabis sativa, wheat and sugarcane), leveraging the Arabidopsis ePlant framework.
Dong S, Lau V, Song R, Ierullo M, Esteban E, Wu Y, Sivieng T, Nahal H, Gaudinier A, Pasha A, Oughtred R, Dolinski K, Tyers M, Brady SM, Grene R, Usadel B, Provart NJ (2019). Proteome-wide, Structure-Based Prediction of Protein-Protein Interactions/New Molecular Interactions Viewer. Plant Physiol. 179:1893-1907. doi: 10.1104/pp.18.01216.
Hoopes GM, Hamilton JP, Wood JC, Esteban E, Pasha A, Vaillancourt B, Provart NJ, Buell CR (2019). An Updated Gene Atlas for Maize Reveals Organ-Specific and Stress-Induced Genes. Plant J. 97:1154-1167. doi: 10.1111/tpj.14184.
International Arabidopsis Informatics Consortium, Doherty C, Friesner J, Gregory B, Loraine A, Megraw M, Provart NJ, Slotkin RK, Town C, Assmann SM, Axtell M, Berardini T, Chen S, Gehan M, Huala E, Jaiswal P, Larson S, Li S, May S, Michael T, Pires C, Topp C, Walley J, Wurtele E (2019). Arabidopsis bioinformatics resources: The current state, challenges, and priorities for the future. Plant Direct 3: e00109. doi: 10.1002/pld3.109
Mott GA, Smakowska-Luzan E, Pasha A, Parys K, Howton TC, Neuhold J, Lehner A, Grünwald K, Stolt-Bergner P, Provart NJ, Mukhtar MS, Desveaux D, Guttman DS, Belkhadir Y (2019). Map of physical interactions between extracellular domains of Arabidopsis leucine-rich repeat receptor kinases. Sci. Data. 6:190025. doi: 10.1038/sdata.2019.25.
Ramírez-González RH, Borrill P, Lang D, Harrington SA, Brinton J, Venturini L, Davey M, Jacobs J, van Ex F, Pasha A, Khedikar Y, Robinson SJ, Cory AT, Florio T, Concia L, Juery C, Schoonbeek H, Steuernagel B, Xiang D, Ridout CJ, Chalhoub B, Mayer KFX, Benhamed M, Latrasse D, Bendahmane A, International Wheat Genome Sequencing Consortium, Wulff BBH, Appels R, Tiwari V, Datla R, Choulet F, Pozniak CJ, Provart NJ, Sharpe AG, Paux E, Spannagl M, Bräutigam A, Uauy C (2018). The transcriptional landscape of polyploid wheat. Science 361: 662. doi: 10.1126/science.aar6089.
Tian C, Wang Y, Yu H, He J, Wang J, Shi B, Du Q, Provart NJ, Meyerowitz EM, Jiao Y (2019). A gene expression map of shoot domains reveals regulatory mechanisms. Nature Commun. 10:141. doi: 10.1038/s41467-018-08083-z.
Toal TW, Ron M, Gibson D, Kajala K, Splitt B, Johnson LS, Miller ND, Slovak R, Gaudinier A, Patel R, de Lucas M, Provart NJ, Spalding EP, Busch W, Kliebenstein DJ, Brady SM (2018). Regulation of Root Angle and Gravitropism. Genes, Genomes and Genetics (G3) 8: 3841-3855. doi: 10.1534/g3.118.200540.
Yi F, Gu W, Chen J, Song N, Gao X, Zhang X, Zhou Y, Ma X, Song W, Zhao H, Esteban E, Pasha A, Provart NJ, Lai J (2019). High-temporal-resolution Transcriptome Landscape of Early Maize Seed Development. Plant Cell. doi: 10.1105/tpc.18.00961.
Planned future activities of your project or resource.
A custom eFP view in ePlant for researcher’s own RNA-seq data is in the works, along with an “Intelligent Agent” (kind of like Siri or Alexa, but for Arabidopsis information) as part of a new award from Genome Canada. Several new ePlants are also planned as part of this project, and an ecosystem viewer will also be developed.
Conferences, Workshops and Training events
The BAR participated in the 2018 American Society of Plant Biology (ASPB) Plant Biology conference in Montreal, as part of the Plant AgData Outreach booth and in the Plant Bioinformatics workshop (the BAR also co-organized with Jason Williams of CSHL a workshop on “Data Carpentry/RNA-Seq Analysis/Custom ePlant” held after the main conference); and Plant and Animal Genomes (PAG) XXVII at the start of 2019 in San Diego, California. It also gave a talk in the Gene Regulatory Networks workshop at ICAR 2018 in Turku, Finland.
The BAR principal investigator Nicholas Provart released “Plant Bioinformatics” on Cousera.org at https://www.coursera.org/learn/plant-bioinformatics/, covering 33 tools from genome browsers to transcriptomic data mining to promoter/network analyses and more! The course is free of charge, unless you want a certificate for a small fee. Some of the tools are from the BAR, but many from other labs/sites are covered too.
The BAR principal investigator Nicholas Provart was successful in receiving an award from Genome Canada to integrate ecosystem-level data into its collection of ePlants, build an “Intelligent Agent” for Plant Biology, and a custom eFP view as mentioned above
BrassiBase Open or Close
By Marcus A. Koch (director), http://brassibase.cos.uni-heidelberg.de/.
BrassiBase is continously developed into a comprehensive Brassicaceae-knowledge-database system. During 2015/2016 a first family-wide species check-list has been created. In total, more than 15,000 taxonomic entities (“names” of species, subspecies, etc., including synonyms) have been collected, checked and cross-referenced. We are now in the process to use this most actual and accurate species check-list as “backbone” for BrassiBase and link given information whenever possible to this information.
Furthermore, morphological descriptions of characters of any genus are now finalized and implemented into an interactive key to the genera. We hope that this will help to identify cultivated and/or collected material more easily, particularly if used in combination with the “Phylogenetic placement tool” implemented with BassiBase.
We intend to release the third version of BrassiBase during 2016 and we invite and encourage the Arabidopsis community to register with BrassiBase (it’s free) and help improving the system - by reporting and contributing with results and data and/or spotting problems and making suggestions for future releases.
Conferences and Workshops
BrassiBase workshop held in Heidelberg in October 2015.
CyVerse Open or Close
By Parker Antin (principal investigator), Eric Lyons (co-principal investigator), Nirav Merchant (co-principal investigator), Matthew Vaughn (co-principal investigator) and Doreen Ware (co-principal investigator), http://www.cyverse.org/.
CyVerse is one of eight projects funded by the National Science Foundation (NSF) Directorate for Biological Sciences. CyVerse is a dynamic virtual organization led by the University of Arizona to fulfill a broad mission to design, deploy, and expand a national cyberinfrastructure for life sciences research and train scientists in its use. CyVerse partner institutions each contribute an important component to the endeavor: Texas Advanced Computing Center, Cold Spring Harbor Laboratory, and the University of North Carolina at Wilmington.
Developing the Science of the Future
CyVerse fills a niche created by the computing epoch and a rapidly evolving world. Developing solutions to today’s grand scientific challenges means that we must understand how the organisms that contribute to our food, fuels, and ecosystem are shaped by interactions with their environment. CyVerse provides life scientists with powerful computational infrastructure to handle huge datasets and complex analyses, thus enabling data-driven discovery. CyVerse provides access to a comprehensive and cohesive suite of computational resources supporting data management, cloud computing, high-performance computing, high-throughput computing, identity management, and collaboration tools, all built from open source components. CyVerse resources are accessible using multiple methods, including web-accessible applications, command-line-based access and well-described Application Programming Interfaces (APIs) for ease of automation and performing scalable data analysis. The powerful extensible platforms provide data storage, bioinformatics tools, image analyses, cloud services, and more. Answering the need of an era of data science, CyVerse makes broadly applicable computational resources available across the life sciences.
Engaging the Data Science Community
CyVerse was launched in 2008 as the iPlant Collaborative, aiming to serve the plant science research community. From its inception, iPlant quickly grew into a mature organization providing powerful resources and offering scientific and technical support services to researchers nationally and internationally. Now rebranded to CyVerse, the project has expanded the mandate to provide CI support across the life sciences. CyVerse CI architecture and implementation is agnostic with regards to scientific domain and supports many different life science disciplines and their associated data types and analyses. CyVerse allows researchers to analyze their growing datasets more efficiently, with greater flexibility, and to address previously difficult or impossible questions. Together, CyVerse CI permits researchers to deposit and share new data, programmers to easily deploy new tools and analytical workflows, and researchers of all skill levels to easily use and reuse those data and tools. CyVerse has created a robust, widely used, and evolving CI that is profoundly impacting life sciences and bioinformatics. CyVerse also provides training, learning material, and best practice resources to help all researchers make the best use of their data, expand their computational skill set, and effectively manage their data and computation when working as distributed teams.
Creating Global Collaborations
CyVerse envisions a future where all biologists have access to, are able to use, and know how to extend CI to solve problems and advance scientific discovery in research and apply CI to education. Through partnerships and direct engagement, CyVerse has helped accelerate the pace of science for many labs and individual researchers by offering computational and data management solutions that meet the demands of modern scientific technologies. Going forward, CyVerse aims to promote computational thinking and empower researchers to new scientific discoveries by enabling global collaborations in data sharing, management, analysis, and visualization.
European Plant Phenotyping Network (EPPN) & EMPHASIS Open or Close
By Roland Pieruschka & Ulrich Schurr, http://www.plant-phenotyping-network.eu/.
The European Plant Phenotyping Network is an EU funded project successfully managed to integrate the European plant phenotyping community by creating structural and functional collaborations between the leading plant phenotyping institutions in Europe and integrating the plant phenotyping community across Europe. EPPN followed the vision that the network of leading phenotyping infrastructures form the nucleus that provides a structured and efficient development of a persistently competitive plant phenotyping community in Europe.
EPPN addressed a wide stakeholder community from academia and industry in different levels of interaction. Joint Research Activities developed, adapted and benchmarked novel sensors and established experimental as well as IT standards for application in plant phenotyping. The standards were made available for the wider plant phenotyping community on the EPPN website and by publications in scientific journals. Networking Activities provided a link between phenotyping experts, user communities, and technology developers within Europe and beyond. EPPN realized communication, networking, and education throughout the duration of the project at different levels: i) between existing and newly developing phenotyping platforms; ii) between phenotyping platforms and users from academia and industry; iii) between platforms, developers, and users; iv) with other leading international phenotyping centres. This effort represented the basis for novel scientific approaches in the utilisation of the existing facilities through Transnational Access. The access was based on demand driven, transparent access procedure, which included independent reviewers from outside of EPPN. High demand from users across Europe for access to plant phenotyping facilities resulted in 66 experiments mostly from young scientists and new users of phenotyping facilities.
EPPN became an important nucleus for the integration of the plant phenotyping community by the establishment of cooperation with the user community and a number of national and international projects and initiatives. Successful EPPN activities have led to the creation of the EMPHASIS project, which was initiated by EPPN core members and has been listed in the ESFRI roadmap. EMPHASIS will facilitate structured development and use of plant phenotyping infrastructure in Europe based on the foundation of EPPN. Additionally, EPPN members represent the group of the International Plant Phenotyping Network (IPPN) which has been initiated as an association and an important hub for networking activities to successfully continue the integration of the plant phenotyping community on a global scale.
Phenotypic analysis has become a major limiting factor in genetic and physiological analyses in plant sciences as well as plant breeding. Molecular plant biology and molecular-based breeding techniques have developed rapidly within the last decade. In contrast, the understanding of the link between genotype and phenotype has progressed more slowly. Faster progress is currently hampered by insufficient technical and conceptual capacity in the plant science community to analyse the interaction between phenotypes of existing genetic resources and the environment. Improvement in phenotyping is a key factor for success in modern breeding as well as for advancement in basic plant research. Multi-scale plant phenotyping to analyse genotype performance under diverse environmental conditions is at the centre of the EMPHASIS project, a new large-scale European project coordinated by researchers at Forschungszentrum Jülich, Germany. EMPHASIS is part of the new ESFRI roadmap, in which the member states of the ESFRI Forums (European Strategy Forum for Research Infrastructures, http://www.esfri.eu) coordinate pan-European research strategies.
The current roadmap was made public on March 10th in Amsterdam, within the framework of the Dutch EU presidency. The project EMPHASIS – European Multi-Environment Plant Phenomics and Simulation Infrastructure – aims to create an integrated, European network of unique infrastructures for plant phenotyping. This includes research infrastructures bridging four dimensions (1) deep and high throughput research infrastructure in controlled environments (2) intense field site installations such as FACE facilities, field labs, etc., (3) lean phenotyping approaches with field sites across European climate zones and diverse soil conditions and (4) modelling platforms. The installations will be connected with common data management and standards and establish the competence to link the phenotypic with the genotypic data. EMPHASIS links national plant phenotyping platforms, such as the German Plant Phenotyping Network (DPPN, http://www.dppn.de/dppn/EN) and the French Plant Phenomic Network PHENOME (FPPN, https://www.phenome-fppn.fr/phenome_eng/) as well as the platforms in Great Britain (http://www.ukppn.org.uk/) and Belgium. EMPHASIS will also establish links with institutions, and include other European countries. The project will cooperate with users from industry such as technology developers and breeders and other international research organisations. After a preparatory phase funded by the European Union, EMPHASIS will be implemented and fully operational in the next few years with the goal to enable access to the key plant phenotyping facilities in Europe. Forschungszentrum Jülich will coordinate EMPHASIS in close cooperation with partners in France.
Gramene: A comparative resource for plants Open or Close
By Marcela Karey Tello-Ruiz (Project Manager) and Doreen Ware (PI), http://www.gramene.org/.
The Gramene database (http://www.gramene.org) is an integrated resource for comparative genome and functional analysis in plants. The database provides agricultural researchers and plant breeders with valuable biological information on genomes and plant pathways of numerous crops and model species, thus enabling powerful comparisons across species.
The genomes component of the Gramene project is developed in collaboration with the Ensembl Genomes project (EMBL-EBI) in the Ensembl infrastructure. The main pathways component of the project is the Plant Reactome (http://plantreactome.gramene.org); it was built on the Reactome framework.
The Gramene project has had 7 data releases since January 2015. The current data release contains 39 reference genomes including Arabidopsis thaliana and A. lyrata, rice, maize, wheat, barley, soybean, Brassicas, poplar, medicago, tomato, potato, banana, cocoa, peach, grapevine, Amborella, spikemoss and algae. Evolutionary histories are provided in phylogenetic gene trees classifying orthologous and paralogous relationships as speciation and duplication events. Orthologous genes inform synteny maps that enable inter-species browsing across ancestral regions. In addition, genome browsers from multiple species can be viewed simultaneously, with links showing homologous gene and whole-genome alignment mappings (WGAs). Within the last year, we added WGAs for tomato (Solanum lycopersicum), potato (S. tuberosum), grape (Vitis vinifera), and cocoa (Theobroma cacao) to enrich our existing collection against Arabidopsis thaliana (dicot model crop) and Oryza sativa Japonica (monocot staple food crop). Since April of 2015, we are providing links to gene annotations from external sources like Araport and Expression ATLAS. SNP and structural diversity data, including individual genotypes, are available for 11 species including A. thaliana, and are displayed in the context of gene annotation, along with the consequence of variation (e.g. missense variant). The Arabidopsis variation database contains data from the screening of 1,179 strains using the Affymetrix 250k Arabidopsis SNP chip (Horton et al, 2012), and an updated data set produced through a BBSRC funded multi-institutional collaboration involving resequencing 18 Arabidopsis lines (Clark et al, 2007). It also contains 392 strains from the 1001 Genomes Project (80 strains from the Cao pilot study; 132 strains from a study by the Salk Institute; and 180 strains from a study by the Nordborg group at GMI). Phenotype data was also added from a GWAS study of 107 phenotypes in 95 inbred lines carried out by Atwell et al (2010). The 1001 Arabidopsis Genomes project released data freely in a pre-publication format from the Salk Institute, WTCHG, MPI, and GMI, under the Fort Lauderdale agreement. Visual displays can be downloaded as high-resolution, publication-ready, image files. Our Blast and BioMart interfaces enable complex queries of sequence, annotation, homology, and variation data. Also in the past year, a new search interface (http://search.gramene.org) was developed and built. It provides a simple interface for expressive comparative queries and tools to view large datasets. New detailed views for search results featuring gene trees, pathway, and expression data from Atlas (EMBL-EBI). In addition to ~240 curated rice pathways, the Plant Reactome incorporates orthology-based pathway projections to 58 plant species including both, Arabidopsis thaliana and A. lyrata.
Outreach, Conferences & Workshops
During the reporting period, Gramene staff attended 1 international and 7 domestic conferences with a total of 15 oral presentations and 9 posters. Project workshops with live demos were presented at the Plant & Animal Genome (PAG 2015 & 2016) & another one will be presented at the 2016 Maize Genetic Conference. At the PAG conferences, we also co-organized a community outreach booth with the participation of the following Arabidopsis bioinformatics resources: Araport, BAR & NASC. Published 7 peer-reviewed articles and 5 book chapters, and another 2 manuscripts are under review. Delivered 12 monthly webinars between February 2015 & February 2016, including one devoted to Arabidopsis resources on Gramene (July 14, 2015) that is available on the Gramene YouTube channel. We are in the process of generating video-tutorials from the 6 talks offered during the Gramene Project Workshop at the 2016 Plant and Animal Genome Conference. We continue to foster ~55 international collaborations. Between CSHL & OSU, we trained 7 post-doctorates, 3 graduate students, 2 undergraduate students (summer only), 1 high-school student & 1 visiting scholar at OSU (Oct 2014-Oct 2015).
Besides the above listed projects and resources, there are many other international and multinational initiatives with major contributions from Arabidopsis researchers, e.g. the 1001 genomes Project (http://www.1001genomes.org/), the Epigenomics of Plants International Consortium (EPIC; http://www.plant-epigenome.org/), the Plant and Microbial Metabolomics Resource (http://metnetdb.org/PMR/) and the International Plant Phenotyping Network (http://www.plant-phenotyping.org/).