Trans-national Infrastructure for Plant Genomic Science
Lead Research Organisation:
Earlham Institute
Department Name: UNLISTED
Abstract
Food and energy security are major challenges facing humanity in the coming decades. The falling costs of nucleotide sequencing are opening up significant opportunities for crop improvement through plant breeding and increased understanding of plant biology; in particular through interpreting the growing volume of plant genomics data in the context of phenotype. However, at present, there is no adequate infrastructure for plant genomic data. TransPLANT will develop a new infrastructure for this data, leveraging the experience of medical informatics while addressing the particular challenges and opportunities of plant genomics.
TGAC will lead the work package on the implementation of resource-intensive algorithms for plant genomics data. This will include the evaluation of current resource-intensive algorithms for plants genomics data; building a network of developers with expertise in algorithms for plant genomics; and the implementation of novel algorithmic solutions for concrete challenges in large plant genomes. One focus will be on the evaluation and development of strategies for plant genome sequencing and assembly. The aim being to develop guidelines for genome sequencing and assembly strategies taking into account the characteristics of the genome in question, including the presence of repeats, heterozygosity and polyploidy. Other tasks include the evaluation and development of data structures for algorithm optimisation; testing methods, tools and pipelines for gene and repeat annotation; and development of tools for the enablement of virtual plant breeding.
TGAC will lead the work package on the implementation of resource-intensive algorithms for plant genomics data. This will include the evaluation of current resource-intensive algorithms for plants genomics data; building a network of developers with expertise in algorithms for plant genomics; and the implementation of novel algorithmic solutions for concrete challenges in large plant genomes. One focus will be on the evaluation and development of strategies for plant genome sequencing and assembly. The aim being to develop guidelines for genome sequencing and assembly strategies taking into account the characteristics of the genome in question, including the presence of repeats, heterozygosity and polyploidy. Other tasks include the evaluation and development of data structures for algorithm optimisation; testing methods, tools and pipelines for gene and repeat annotation; and development of tools for the enablement of virtual plant breeding.
Publications
Thanki AS
(2018)
Aequatus: an open-source homology browser.
in GigaScience
Wilkinson PA
(2016)
CerealsDB 3.0: expansion of resources and data integration.
in BMC bioinformatics
Cocker JM
(2018)
Primula vulgaris (primrose) genome assembly, annotation and gene expression, with comparative genomics on the heterostyly supergene.
in Scientific reports
Spannagl M
(2016)
transPLANT Resources for Triticeae Genomic Data.
in The plant genome
Bolser DM
(2015)
Triticeae resources in Ensembl Plants.
in Plant & cell physiology
| Description | This research supported the development of a big data infrastructure for plant genomics in partnership with a large European consortium. The transPLANT project is an integrated infrastructure funded by the Framework 7 program of the European Union. It brought together 11 partners from seven countries with the aim of developing common standards, data, and technologies in the plant genomics area. A major focus of the work was variation data and the development of tools to organise, archive, and analyse them. Another major focus is the definition and use of common reference sequences so that annotation from different resources can be shared and com- pared. A third focus is the development of a distributed query infrastructure to provide a common point of entry to data held in multiple, dispersed resources. Data from barley, wheat, and other species have been exported to common data formats in accordance with established standards for data representation, exchanged between partners, and synchronized across the distributed transPLANT resources. |
| Exploitation Route | The plant genomics infrastructure provide the foundations for research and science development in plant science. The platform and data infrastructure are open and were developed using open source software. |
| Sectors | Agriculture, Food and Drink,Digital/Communication/Information Technologies (including Software),Environment |
| URL | http://www.transplantdb.eu |
| Description | With the expected emergence of additional genome sequence data from the Triticeae (wheat, barley), the framework for data integration, exchange, and aggregation established within the transPLANT project has addressed the challenges involved with even more distributed data repositories and heterogeneous data types. In this context, this project has supported the development of the International Wheat Information System (WheatIS) to support the wheat research community. The main objective is to provide a single-entry web-based system to access the available data resources and bioinformatics tools. The WheatIS project is an international project lead by an Expert Working Group of the Wheat Initiative. The Wheat Initiative is supported by the G20 Agricultural Ministers to coordinate world-wide research efforts in the fields of wheat genetics, genomics, physiology, breeding and agronomy. |
| First Year Of Impact | 2015 |
| Sector | Agriculture, Food and Drink,Digital/Communication/Information Technologies (including Software) |
| Impact Types | Economic,Policy & public services |
| Description | Potato Sentinel Site - FarmerZone |
| Organisation | Indian Institute of Technology Mandi |
| Country | India |
| Sector | Academic/University |
| PI Contribution | Founding member of the Potato Sentinel Site past of DBT's FarmerZone initiative. |
| Collaborator Contribution | Creation of the SentinelSite. NIAB is a founding member of the Potato Sentinel Site with a position of direct influence in the implementation of this project. |
| Impact | Membership of the Potato Sentinel Site. |
| Start Year | 2018 |
| Description | Proyecto Omicas / Omics project |
| Organisation | Pontifical Xavierian University |
| Country | Colombia |
| Sector | Academic/University |
| PI Contribution | Participation as an associated collaborator. The research program optimization Multiscale In-silico Agricultural Crops Sustainable (omics) is the winner of the second round of Colombia Science in focus Food which seeks, through seven projects, develop and implement strategies science and technology to improve agricultural varieties with the aim of contributing to food security and sustainable production worldwide . |
| Collaborator Contribution | Omic is made up of researchers, undergraduate and graduate students , and support staff from 16 institutions, including institutions are higher education (IES) accredited, national and international, IES national non - accredited, international research centers in agriculture and domestic enterprises in the industrial sector, with the Pontificia Universidad Javeriana Cali anchor entity . |
| Impact | This is a multidisciplinary project that involves collaborators working on genetics, genomics, bioinformatics, agriculture, phenotyping and social sciences. The Colombian government is also directly engaging with the collaborators. |
| Start Year | 2019 |
| Description | Invited Speaker - DBT's Smart Agriculture Conclave - New Delhi (India) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | The Department of Biotechnology (India) organised a conclave to discuss opportunities for the implementation of smart agriculture using modern digital approaches. The application of standards for phenotyping technologies was a key aspect of the meeting. |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.dbtindia.nic.in/dbts-smart-agriculture-conclave/# |
| Description | Invited Speaker at XI National Symposium of Biotechnology (RedBio) Argentina |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | I was invited to present at RedBio 2017 in Argentina. This was followed up with an opportunity to apply for BBSRC GCRF funding to establish a collaboration with the potato research group at INTA Argentina which has been successful. |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.redbioargentina.org.ar/simposio-2017-bahia-blanca/ |
| Description | Kick off event of the Omics Project - key note speaker |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Key note speaker at the Omicas project kick-off workshop in Cali (Colombia) |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.omicas.co/noticias/recomendaciones-y-agenda-del-taller-anual-omicas |
| Description | Myanmar - Green Fruits Dedicated Workshop |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Policymakers/politicians |
| Results and Impact | The Workshop, dedicated to Green Fruits in Green Horticulture, was organized in the context of (the ASEAN Institute for Green Economy, AIGE Component on Increasing and Improving Green and Blue Productivity and Sustainability The Dedicated Workshop was forward looking, taking into account fast emerging and converging regional and international trends on the imperative need for green and clean economy, articulated and adopted in an increasing number of national, regional and international for. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://geggmyanmar.org/green-fruits-dedicated-workshop-report/ |
| Description | Presentation at Monogram 2019 - rice and other grasses |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presentation to the Monogram event of the progress of the Vietnam rice project. Following this event we met with the Ensembl plant team to discuss how to integrate rice data in the genome browsers. |
| Year(s) Of Engagement Activity | 2019 |
| URL | http://www.monogram.ac.uk/MgNW2019.php |
| Description | Presentation in the 4th Plant Genomics Congress (May 2016) - London |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | I presented about the tools developed within TransPlant and about the Ash Tree genome project. |
| Year(s) Of Engagement Activity | 2016 |
| Description | Wheat Initiative - Expert Working Groups meeting (Saskatoon) |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | As part of the activities of the Wheat Information System I presented and contributed to the annual meeting of the Wheat Initiative in Saskatoon (Canada) on 27 July 2019. |
| Year(s) Of Engagement Activity | 2019 |
| URL | http://www.wheatinitiative.org |
| Description | Workshop on Plant Genomics Resources |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Postgraduate students |
| Results and Impact | A workshop on plant genomics resources organised in the Universidad Nacional del Comahue (San Antonio Oeste, Argentina) - 29 March 2016 |
| Year(s) Of Engagement Activity | 2016 |