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  • Wheat 10+ Genomes Project Release

    Wheat 10+ Genomes Project Releases Reference Sequences of a Global Panel of Wheat Varieties

    The Wheat Initiative is excited to announce a major milestone for wheat research. On Oct 1, 2019, the international team of scientists from the Wheat 10+ Genomes Project (http://www.10wheatgenomes.com) announced the public release of reference quality sequences of 10 wheat varieties, as well as scaffolded assemblies for five additional cultivars. The Wheat 10+ Genomes Project is a global partnership that leverages collaborative expertise and funding with the aim to characterize the wheat ‘pan genome’, with an emphasis on applied breeding. The partnership has generated multiple high-quality wheat genome assemblies of varieties representing breeding programs from around the globe.

    “We are excited to release reference-quality assemblies of wheat cultivars representing major breeding programs globally,” said Curtis Pozniak, Professor and Wheat Breeder (University of Saskatchewan, Canada) and the project Leader. “The assemblies released today provide a glimpse into the extensive diversity available in adapted germplasm, and promise to accelerate the efficiency of our breeding programs. Our challenge now is to translate these technological advances into practical outcomes for the world’s wheat growers.”

    The Project is an Associate Program of the Wheat Initiative, and represents an international collaboration comprised of researchers from Canada, Germany, UK, Australia, USA, Japan, Israel, Saudi Arabia and Switzerland, and industry partner Syngenta. A full list of project members is available here: http://www.10wheatgenomes.com/members/. Peter Langridge, Scientific Coordinator for the Wheat Initiative said, “the Wheat Initiative provides a framework to establish strategic research and organisation priorities for wheat research at the international level in both developed and developing countries. The 10 Genomes Project is an excellent example of coordination across leading research groups around the globe. Essentially every group working in wheat gene discovery, gene analysis and deployment of molecular breeding technologies will use the resource.”

    Nils Stein from the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) and Göttingen University and project co-leader from Germany noted, “This project demonstrates the strength of the Wheat Initiative to facilitate a major international collaboration. As a result, we have achieved an outcome that was regarded as unachievable just a few years ago”.
    Funding to support the 10+ Genomes project was critical to its success, and a full list of funders can be found here: http://www.10wheatgenomes.com/funders/. Head of Cereals Germplasm Development for Syngenta, Sjaak van der Ploeg stated, “Syngenta is a proud supporter and member of the 10+ Wheat Genomes Project. By expanding the available reference-quality genomes 10-fold, the results from this project will naturally extend our understanding of this complex genome, across varieties that feed the world today. At the same time, it will enable further collaborations across genetics, breeding and wheat biology, at a scale not previously possible.

    The 10+ Wheat Genomes Project is community driven and supports the release of data to advance wheat science. As a public service, the preliminary chromosome-scale sequence assemblies are publicly available prior to scientific publication. The genome assemblies are freely available under the Toronto Agreement and can be found here: https://wheat.ipk-gatersleben.de. The scaffolded assemblies can be found at: https://opendata.earlham.ac.uk/wheat/under_license/toronto/Clavijo_2017-....
    Seeds of all cultivars included in the project can be obtained for research use through the Germplasm Resources Unit in the UK, available as Collection 35 (https://www.seedstor.ac.uk/search-browseaccessions.php?idCollection=35).

  • IWGSC RefSeq v2.0 now available

    The International Wheat Genome Sequencing Consortium (IWGSC) is pleased to announce that announce that version 2 of the reference sequence of bread wheat, IWGSC RefSeq v2.0, is now available at the IWGSC data repository hosted by URGI-INRA.

    Under the leadership of Mingcheng Luo and Jan Dvorak (UC Davis, CA, USA) and with funding from the US National Science Foundation, an improved version of the reference wheat genome has been completed and is being released in advance of publication to the scientific community under the terms of Toronto agreement which affords the data producers the right to publish the first whole genome analyses of the data.

    The genome assembly of Triticum aestivum cv. Chinese Spring (IWGSC RefSeq v1.0; IWGSC, 2018) was improved using whole genome optical maps and contigs assembled from whole-genome-shotgun (WGS) PacBio SMRT reads (Zimin et al. 2017). Optical maps were used to detect and resolve chimeric scaffolds, anchor unassigned scaffolds, correct ambiguities in positions and orientations of scaffolds, create super-scaffolds, and estimate gap sizes more accurately. PacBio contigs were used for gap closing. Pseudomolecules of the Chinese Spring 21 chromosomes were re-constructed to develop a new reference sequence, IWGSC RefSeq v2.0. All revisions involved approximately 10% sequence length of the IWGSC RefSeq v1.0.

    Importantly, please note that this version has yet to be annotated. The IWGSC annotation team will be performing targeted annotation and QC of IWGSC RefSeq v2.0. In addition, all manually curated genes submitted to the IWGSC by the end of August 2019 (see call for contributions) will be integrated into IWGSC RefSeq v2.0, annotation v2.0. The IWGSC aims to release the annotation v2.0 in January 2020.

    How to access the data
    Access does require registration. For specific access terms, see the IWGSC General Data Access agreement .
    Individuals who have not sign the IWGSC Data Access Agreement should FIRST register on the IWGSC website or login if you are already registered, and THEN sign the Agreement; URGI login details will be provided subsequently for access to the data.
    Individuals who have already signed the IWGSC Data Access Agreement can go directly to the URGI website to access the data using their URGI login details. If you forgot your URGI credentials, please send an email to urgi-support@inra.fr
    Link to download the data (note: URGI login necessary)
    https://urgi.versailles.inra.fr/download/iwgsc/IWGSC_RefSeq_Assemblies/v...

  • GrainGenes-T3 Shared Genome Browsers

    In a show of close collaboration between two USDA-ARS databases, GrainGenes and the Triticeae Toolbox (T3) decided to maintain shared genome browsers for bread wheat and barley reference genomes (released in July 2019). The Chinese Spring wheat and Morex barley genome browsers will be housed at GrainGenes and will be populated by both teams. Going forward, users will be able to reach these genome browsers from both databases and will be able to link out from browsers to other GrainGenes and T3 pages in a facilitated manner, enabling them to reach a wide range of information in both databases in a way that was not possible before.

    Check out the new genome browser landing page and follow the link to your favorite genome assembly: /GG3/genome_browser.

  • Durum Wheat (cv. Svevo) RefSeq Release 1.0 at GrainGenes

    In collaboration with the International Durum Wheat Genome Sequencing Consortium, GrainGenes is releasing the Durum Wheat (cv. Svevo) RefSeq Rel. 1.0 and its annotations.

    The manuscript for the Svevo genome reference is published in Nature Genetics (link). Please cite the manuscript for your publications.

    Reference sequence, official annotations, and marker alignments are provided by the International Durum Wheat Genome Sequencing Consortium, and they are available at the GrainGenes Svevo Genome Browser. The pseudomolecules can be sequence searched at the GrainGenes BLAST interface.

    The assembly can be found at the Svevo BioProject page at NCBI: https://www.ncbi.nlm.nih.gov/bioproject/518793.

    GFF and VCF files are available online at https://figshare.com/articles/Durum_Wheat_cv_Svevo_annotation/6984035/1.

    For more information and access to the Durum Wheat (cv. Svevo) RefSeq Rel. 1.0 assembly, please go to the Consortium's site at https://www.interomics.eu/durum-wheat-genome.

  • All IWGSC reference sequence resources now publicly available

    The International Wheat Genome Sequencing Consortium is pleased to announce that all data related to the reference sequence of bread wheat, IWGSC RefSeq v1.0, are available without restriction.

    You can reach the Science article for the assembly here.

    The following resources are now publicly available, without registration, at the IWGSC Data Repository hosted by URGI-INRA:

    IWGSC RefSeq assembly v1.0
    IWGSC RefSeq annotation v1.0 including structural annotation (genes, transposable elements, ncRNAs), functional annotation, varietal SNPs, RH maps, GBS maps, optical maps
    IWGSC RefSeq annotation v1.1 including genes and RNAseq mapping
    Physical maps for all chromosomes
    MTP BAC WGPTM sequence tags for all chromosomes, except 3B
    BLAST , JBrowse and InterMine tools are available in open access to query and browse all these data.
    We are also pleased to announce that IWGSC RefSeq v1.0 and IWGSC RefSeq annotation v1.0 have been incorporated into Ensembl Plants and will be available in their upcoming release.

    The IWGSC data have also been incorporated into GrainGenes, where varietal SNP tracks generated and aligned by the Akhunov and Dubcovsky labs are available.

    While scientists may freely publish using the IWGSC data, we do request that the source of the data be properly acknowledged.

  • A new mobile app for plant breeding and genetics : Verify

    Researchers at Kansas State University and Cornell University have developed and released an Android application called “Verify” that will help plant breeders by decreasing the amount of time and energy it takes to manage samples and seed stocks. Verify makes integrating and utilizing barcodes a simple process by combining an intuitive interface with a new barcode processing library. Verify imports a list of entries and utilizes the device camera or external hardware to scan a sample barcode and identify whether the scanned barcode is present in the imported list. For more information on Verify, see the attached release.

  • "The first near-complete assembly of the hexaploid bread wheat genome, Triticum aestivum" is published by the Salzberg Group

    Steven Salzberg's group at Johns Hopkins published "the first near-complete assembly of the hexaploid bread wheat genome, Triticum aestivum" in the journal Gigascience. The link to the paper at the journal site can be found at https://doi.org/10.1093/gigascience/gix097.

    "The PacBio and Illumina reads are available under the same BioProject. The TriticumD 1.0 contigs are available separately at": ftp://ftp.ccb.jhu.edu/pub/data/Triticum_aestivum/Wheat_D_genome/.

    The article is described in a news article in Nature.

    You can BLAST your sequences against the Salzberg Chinese Spring assembly at GrainGenes: /cgi-bin/seqserve/blast_wheat.cgi (choose NCBI WGA 3.1, 2017 from the drop-down menu)

  • Triticum aestivum Chinese Spring pseudomolecules now available for BLAST on the NSF-IOS-1238231 Project site

    The National Science Foundation-funded NSF-IOS-1238231 project has released unmasked pseudomolecules (v1.0) of T. aestivum Chinese Spring (CS). They are available for BLAST searches at the project website ( http://aegilops.wheat.ucdavis.edu/ATGSP/). The BLAST input portal is at the DATA page link at this URL. (The download function is still under construction.) Successful searches will return alignments including coordinates of the target sequences on the pseudomolecules. These pseudomolecules were constructed from PacBio contigs anchored on CS BioNano genome maps. While short contigs are still not anchored and these pseudomolecules have not yet been annotated, they provide long, uninterrupted CS sequences which can be an asset to the wheat community. (November 2017).

    Posted on 11/7/2017.

  • Aegilops tauschii reference genome sequence now available for BLAST on the NSF-IOS-1238231 Project site

    Aegilops tauschii is the wild species that contributed the D genome to bread wheat and this National Science Foundation-funded project has released the reference sequence of its genome. Masked and unmasked pseudomolecules of Ae. tauschii acc. AL8/78 and a database of complete transposable elements annotated in the Ae. tauschii genome are available for BLAST and JBrowse searches at the project website (http://aegilops.wheat.ucdavis.edu/ATGSP/). The BLAST input portal is at the DATA page link at this website. BLAST output gives query/target alignments indicating pseudomolecule and coordinates of the target sequence. The latter can be used to zoom in on the relevant portion of the JBrowse track of choice (high-confidence genes, low-confidence genes, transposable elements, etc.). (November 3, 2017)

    You can reach the article here.

    Posted on 11/3/2017.

  • IWGSC Reference Sequence v1.0 Annotation NOW available at URGI

    The International Wheat Genome Sequencing Consortium is pleased to announce that the first version of the reference sequence of the bread wheat variety Chinese Spring (IWGSC RefSeq v1.0) is now available with annotation of genes, non-coding RNAs and transposable elements at the IWGSC sequence repository hosted by URGI-INRA .

    The pre-publication data are being made available under the IWGSC general data access agreement which is consistent with the Toronto Agreement and that grants the IWGSC the right to publish the first global analyses of the data. This includes descriptions of whole chromosome or genome-level analyses of genes, gene families, repetitive elements, and comparisons with other organisms.

    The IWGSC RefSeq v1.0 annotation includes gene models generated by integrating predictions made by INRA-GDEC using Triannot and PGSB using their customised pipeline (previously MIPS pipeline). The integration was undertaken by the Earlham institute (EI), who have also added UTRs to the gene models where supporting data are available. Gene models have been assigned to high confidence (HC) or low confidence (LC) classes based on completeness, similarity to genes represented in protein and DNA databases and repeat content. The automated assignment of functional annotation to genes has been generated by PGSB based on AHRD parameters. In addition, annotated transposable elements (TEs) and non-coding RNAs are available. More information about the annotation data is provided in README files from the IWGSC repository hosted on the URGI Sequence Repository .

    How to access the data

    Access does require registration and agreeing to respect the right of the IWGSC to publish first. For specific access terms, see the IWGSC General Data Access agreement .

    • Individuals who have not signed the IWGSC Data Access Agreement should FIRST register on the IWGSC website and sign the Agreement; URGI login details will be provided subsequently for access to the data.
    • Individuals who have already signed the IWGSC Data Access Agreement can go directly to the URGI website to access the data using their URGI login details.

    Jan. 2017 notice:
    The International Wheat Genome Sequencing Consortium is pleased to announce that the first version of the reference sequence of the bread wheat variety Chinese Spring (IWGSC RefSeq v1.0) is now available at the IWGSC sequence repository hosted by URGI-INRA (https://wheat-urgi.versailles.inra.fr/Seq-Repository/Assemblies)

    The IWGSC RefSeq v1.0 is an integration of the IWGSC WGA v0.4 – made available in June 2016 – with IWGSC chromosome-based and other resources, including but not limited to:

    • Physical maps for all chromosomes;
    • Sequenced BACs for 8 chromosomes (1A, 1B, 3B, 3D, 6B, 7A, 7B, 7D) and partial MTP BAC sequences for 2 chromosome arms (4AL, 5BS);
    • MTP BAC WGPTM sequence tags for all chromosomes, except 3B;
    • BioNano optical maps (7A, 7B, 7DS);
    • Alignment to RH maps (D chromosomes); and
    • GBS map of the SynOp RIL population CsxRn genetic map (INRA).

    With the addition of the resources that have been developed by IWGSC members over the past few years, the quality of the assembly increased substantially. When compared with IWGSC WGA v0.4, the chromosomal scaffold/ superscaffold N50 increased from 7.0 Mb to 22.8 Mb.

    The data are available for BLAST searches and can be downloaded from the IWGSC repository hosted on the URGI Sequence Repository .
    How to access the data

    Earlier Notice:
    The IWGSC is pleased to announce that the Genome Assembly (IWGSC WGA) of bread wheat, *T. aestivum* cv Chinese Spring (ERGE 2135), based on Illumina short sequence reads assembled with NRGene's DeNovoMAGICTM software is now available at the IWGSC sequence repository hosted by URGI-INRA.

    A BLAST server has been set up to facilitate rapid access to single or small numbers of queries. The data can also be downloaded from the URGI IWGSC repository.

    The data are being made available before publication in accordance with the Toronto Agreement under which the IWGSC reserves the right to publish the first global analyses of the data. This includes descriptions of whole chromosome or genome-level analyses of genes, gene families, repetitive elements, and comparisons with other organisms.

    Access does require registration and agreeing to the IWGSC General Data Access terms.

    *Useful links:*

    • Web announcement details on the data available, how to access them and links to URGI BLAST
      and download
    • Press release: Wheat Sequencing Consortium Releases Key Resource to the Scientific Community

    Best regards

    The IWGSC team

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