Triticeae Gene Nomenclature

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1 A Wheat Initiative workshop Triticeae Gene Nomenclature October 2016, Munich (Germany) Report 1

2 Background A number of high quality genome sequences have been completed in recent years for species of the Triticeae tribe. In early 2016 the International Wheat Genome Sequencing Consortium (IWGSC) announced the completion of a whole-genome reference sequence for the Chinese Spring reference cultivar of the large hexaploid genome. This follows the generation of high quality genome sequences for other related Triticeae species that have also recently been sequenced and made available including wheat progenitors, barley and the first durum wheat genome. This will soon be followed by the re-sequencing of a number of wheat varieties and other related species adding to the plethora of increasing genomic resources. Most of these genomes have been annotated using high-throughput automatic approaches based on evidence from RNA-sequencing experiments and ab-initio methods. In addition comparative analyses to associate orthologous genes have also been performed across the Triticeae species offering more supporting evidence for the annotation of genes. Annotated gene structures are available at genome browsers such as Ensembl Plants 1, URGI 2, GrainGenes 3 and Gramene 4. There is, however, limited information regarding gene symbols for wheat and other Triticeae species associated to the current annotations restricting the adoption and access of the data. Since 1968 the gene symbols of wheat have been curated and compiled by the Catalogue of Gene Symbols of Wheat (the Catalogue). As a recognised authority in the wheat community the Catalogue is a reference used by researchers and breeders to identify standard names and symbols for genes within wheat and related species as well as the multiple alleles described for each of the genes. The correct identification of gene structures in annotated genome references using a coherent and standard nomenclature across the Triticeae species will support the wider adoption of the recently generated genomics resources. The Triticeae Gene Nomenclature Workshop was organised with the sponsorship of the Wheat Initiative by the Wheat Information System and Improving Wheat Quality for Processing and Health Expert Working Groups. The meeting was held in Munich on October at the Helmholtz Centrum in Munich (Germany). The aim of the workshop was to set the foundations for the development of a gene nomenclature scheme to define and assign names and symbols for gene structures across the Triticeae species. Workshop Objectives and Agenda Overview The workshop congregated bioinformaticians, genomicists and wheat geneticists to discuss and set up the principles for providing gene symbols across the Triticeae genomes (see Appendix B for attendee list). The objectives of the workshop were Identify the current challenges in the development of the wheat gene catalogue and how this could support the provision of gene symbols and names across the Triticeae tribe. 1 plants.ensembl.org 2 urgi.versailles.inra.fr 3 wheat.pw.usda.gov/gg3/ 4 2

3 Propose guidelines, criteria and a scheme for the annotation of gene symbols across the Triticeae species. Identify gaps in the current datasets to inform and guide projects for Triticeae species in the generation of genomic resources. The agenda of the workshop covered three days of work. The first day was focused on presentations by the attendees about the history and current activities of the Catalogue of Gene Symbols of Wheat and the current annotation of the wheat and other Triticeae genomes. The second day was focused on the work required to define a gene scheme across the Triticeae tribe. The workshop attendees were divided in groups with the task to identify key areas of development and the proposition for a set of actions to deliver the objectives of the workshops. Finally the third day was focused on the agreement of actions and next steps (see Appendix A for a detailed agenda). Findings and Outcomes 1. Discrepancies in the definition of key concepts 1.1. The understanding of the definitions of key concepts such as gene, locus and variant alleles differs between geneticists and genomicists and bioinformaticians. The Catalogue adopts the more traditional definition of these concepts based on the morphological and physiological traits. Genomicists and bioinformaticians use definitions that are driven by a sequence-based characterisation of these concepts The discrepancies in the understanding these key concepts can lead to misinterpretations. There was an agreement to work towards avoiding confusions in future communications by recognising and addressing these discrepancies. 2. Identification of different categories of genes 2.1. Four categories of gene objects (in the broadest sense) were identified drawing both from the Catalogue entries and the gene structures annotated in the databases as it follows Category I. These are the genes for which the Catalogue provides sequences (either DNA or peptide) that could be used to unambiguously identify a gene structure in a sequence reference. Although this category represents only a handful of genes, these are the ones that are present in the current literature and the best characterised across the mapping populations and germplasm collections Category II. These are high-quality annotated gene structures, which are not yet recognised as entries in the Catalogue, but which can be associated to orthologous genes in other species. These gene structures are the largest collection and have emerged from the highthroughput annotation efforts Category III. These are genes in the Catalogue which at the moment can only be characterised by genetic mapping. These genes are mapped as Quantitative Trait Loci (QTL) but have neither been cloned nor sequenced. The characterisation of these genes might result in more than one gene structure that will require to be named accordingly. 3

4 2.5. Category IV. These are the annotated gene structures for which there is no reliable predicted orthologue. A correct identification of these objects that can be tracked over annotation releases is already maintained by the databases (e.g. Ensembl gene estable ids). 3. Gene nomenclature scheme for the Triticeae tribe 3.1. A gene nomenclature that can be adopted across the Triticeae tribe was proposed. The nomenclature will need to be discussed by the wider community including colleagues working on related species. We expect that the adoption of the unified nomenclature will improve the use of genetic and genomic resources justifying the effort of the deployment and development of a scheme The proposed scheme focused on gene symbols assigned to the hexaploid bread wheat that can then be associated to genes in other related species via orthologous relationship. Figure 1 below exemplifies the scheme for an example gene symbol GX. The identification of the three homeoelogous genes in the A, B and D sub-genomes is associated to corresponding orthologous genes in the A and D progenitors (T. urartu and Ae. tauschii). Orthologous genes are also identified in other Triticeae species such as barley (identified by the letter H). Figure 1 Proposed gene nomenclature for the Triticeae - example gene symbol GX 3.3. Events such as gene gain and loss, or the effect of translocations, will require addressing on a case-by-case basis as different scenarios will present different challenges. We will work with the Catalogue to resolve these cases to ensure the proposed solutions are consistent with other similar cases and are also aligned with the current use in the literature (example Waxy genes) The proposed gene nomenclature scheme will not represent allele information. With more genetic diversity resources being currently generated by the community there will be an 4

5 increasing demand for the representation of allele information in the genomics databases. This is an area for future development. 4. High-throughout Assignment of Gene Names 4.1. We propose to adopt a high-throughout method to assign putative gene symbols, descriptions and names to genes in Category II (see above). This information will be assigned based on sequence similarity and other criteria such as conservation of synteny using orthologous sequences from barley, brachypodium, rice and Arabidopsis genes The gene symbols will include the prefix similar_to and the suffix will indicate the source of the name, e.g. similar_to_gx_in _At (for an GX gene in Arabidopsis thaliana) These gene symbols will be temporary and will be replaced by Catalogue symbols as they are curated and adopted. 5. Gene Name Authority for the Triticeae 5.1. Establishing a gene nomenclature authority for the Triticeae tribe was identified as a priority. One of the current priorities of the research community is the generation of highquality gene annotations by closing existing known gaps in available gene collections. These efforts are complemented by the increasing availability of genetic resources such as the wheat TILLING populations, the access to genotype information for seed banks (e.g. Seeds of Discovery project at CIMMYT) and the generation of diversity data (e.g. Whealbi project and CerealsDB). The annotation will require a level of coordination across several organisations that should be supported by the development of the Catalogue as the recognised authority The successful implementation of a gene nomenclature authority will be required to be resourced accordingly. This will need support for the recruitment of manual curators and bioinformaticians to support the generation of data and the hosting of informatics tools Building bridges with researchers working on data generated for related species will be a priority. Priorities As a conclusion of the workshop discussions on a number of priority areas were identified with the purpose to deliver on the objectives. 1. Establishing of a gene nomenclature authority for the Triticeae 2. Development of the Catalogue 3. Dissemination of the work of the Catalogue and the outcomes of the workshop 4. Work will be focused as a priority on genes in Category I. 5. Engage with the communities working with other Triticeae species. 5

6 Appendix Triticeae Gene Nomenclature Workshop October 2016 Munich, Germany A. Workshop agenda Tuesday 11 October - Afternoon 12:00pm 1:00pm Welcome and Lunch 1:00pm - 1:30pm Workshop objectives Mario Caccamo 1:30pm 3:30pm 3:30pm 4:00pm Wheat gene catalogue history, current status, challenges and opportunities Coffee break Craig Morris John Rogers 4:00pm 5:30pm Triticeae genome annotation (barley, wheat) Manuel Spannagl 5:30pm - 6:00pm Day conclusions and wrap up Mario Caccamo Carlos Guzman Wednesday 12 October 9:00am 10:30am Databases and browsers for Triticeae genomes current annotation for Triticeae species, challenges and opportunities. Paul Kersey Thomas Letellier 10:30am - 11:00am 11:00am 12:30pm 12:30pm 2:00pm 2:00pm 3:30pm 3:30pm 4:00pm 4:00pm - 6:00pm Coffee break Gene symbols in the context of homoeology orthology paralogy / subfunctionalisation alleles Examples from quality genes. Lunch Defining a strategy Break out groups to work on the annotation of few selected genes Coffee break Defining principles and strategy for gene symbol annotation. Bruno Santos Tatsuya Ikeda All All 6

7 Thursday 13 October Morning 9:00am 10:30am Revision of objectives and next steps Mario Caccamo Carlos Guzman Manuel Spannagl 10:30am - 11:00am Coffee break 11:00pm 12:30pm Agreement on Actions All 12:30pm 1:00pm Lunch and departure B. Attendees list Tatsuya Ikeda Quality EWG NARO tmikeda@affrc.go.jp John Rogers Quality EWG CONICET rogers@faa.unicen.edu.ar Craig Morris Quality EWG USDA morrisc@wsu.edu Carlos Guzman Quality EWG CIMMYT c.guzman@cgiar.org Manuel Spannagl WheatIS EWG PGSB manuel.spannagl@helmholtz-muenchen.de Heidrun Gundlach WheatIS EWG PGSB h.gundlach@helmholtz-muenchen.de Sven Twardziok WheatIS EWG PGSB sven.twardziok@helmholtz-muenchen.de Thomas Lux WheatIS EWG PGSB thomas.lux@helmholtz-muenchen.de Paul Kersey WheatIS EWG EBI pkersey@ebi.ac.uk Thomas Lettelier WheatIS EWG INRA thomas.letellier@inra.fr Bruno Santos WheatIS EWG NIAB bruno.santos@niab.com Mario Caccamo WheatIS EWG NIAB mario.caccamo@niab.com C. Agreed Actions 1. Regular conference calls meetings The group will meet on regular basis (monthly if possibly) to assess progress on the priority areas. The preferred option will be using Skype. We have set up a drop box space that we will use to share information. 2. Task Groups We will organise a task group to tackle the genes in category 1. The first objective is to produce a list of canonical sequences that can be used by the browsers to assign names to gene structures. 3. Funding 7

We will explore funding opportunities to implement a longer-term strategy to improve the functionality of the Catalogue. We will seek advice from the Wheat Initiative to coordinate this effort. 4.

8 We will explore funding opportunities to implement a longer-term strategy to improve the functionality of the Catalogue. We will seek advice from the Wheat Initiative to coordinate this effort. 4. Outreach We will engage with other groups working in species related to wheat focused initially on the Triticeae tribe. Similarly we will engage with other groups working on the generation of genomics resources for wheat (e.g. Whealbi, IWGSC). 5. Conferences and Meetings a. PAG 2017 we will submit a poster and prepare a presentation for the IWGSC standard and tools workshop. b. Monogram (UK) we will approach the organisers to present in this meeting in April. c. Wheat Genetics Symposium we will submit an abstract. D. Photographs from the workshop Figure 2 - group picture 8

9 Triticeae Gene Nomenclature Workshop October 2016 Munich, Germany Figure 3 - group deliberations 9

Integrating and Leveraging Cereal and Grass Genome Resources. David Marshall Information and Computational Sciences Group

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