News highlights

News from the transPLANT project and partners. See also the transPLANT newsletter.

Ensembl Plants, Release 15

We have added a set of homoeologous SNPs between wheat A, B and D genomes using wheat contigs aligned to Brachypodium distachyon as a reference framework, a structural variation dataset for

Training workshop in plant pathogenic genomics

Registration now closed!

A hands-on training workshop in plant pathogenic genomics, focused on the new resource PhytoPath and including coverage of Ensembl Fungi, Ensembl Protists and PHI-base will be held at the EBI in September, aimed at PhD students and post-doctoral researchers who are working on fungal and oomycete-induced disease in plants. Find out more details and register.

Genome-wide patterns of genetic variation in Arabidopsis published

Published today in Nature Genetics, Magnus Nordborg and colleagues have produced a high-resolution description of the global pattern of genetic variation in Arabidopsis.

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Relevant publications

Biological Process Annotation of Proteins across the Plant Kingdom

Accurate annotation of protein function is key to understanding life at the molecular level, but automated annotation of functions is challenging.

Genome interplay in the grain transcriptome of hexaploid bread wheat.

Allohexaploid bread wheat (Triticum aestivum L.) provides approximately 20% of calories consumed by humans. Lack of genome sequence for the three homeologous and highly similar bread wheat genomes (A, B, and D) has impeded expression analysis of the grain transcriptome.

A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome.

An ordered draft sequence of the 17-gigabase hexaploid bread wheat (Triticum aestivum) genome has been produced by sequencing isolated chromosome arms. We have annotated 124,201 gene loci distributed nearly evenly across the homeologous chromosomes and subgenomes.

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The transPLANT integrated search

Get results from ten different plant genomics databases in a single click.
Try a sample search...

The transPLANT variation archive

variation archive

Store, accession and update plant variation data. Now accepting submissions.

transPLANT training resources

Training resources

A collection of training resources from transPLANT related events. Browse the materials.

The transPLANT resource registry

Search for genomic resources for plant species of agricultural and scientific importance. Try a sample search...

transPLANT

is a European-Union funded e-infrstructure to support computational analysis of genomic data from crop and model plants. The project funds coordination and research activities; and provides free access to tools, training and data standards.

You can use this site to:

For more information contact us or join to the mailing list.

Training

transPLANT is running a series of training courses across Europe. The next one will be held at EMBL-EBI, Hinton, UK, 1st-3rd July, 2015. When registration is opened, details will be posted here.

  • You can access material from the previous transPLANT training courses here.
  • We are developing a series of videos, guiding users through some of the most interesting and complex data sets available for plants. View the first video, focused on resources for the barley genome, here.

Standards

The development and adoption of data standards is vital to the interoperability of data. transPLANT is currently pursuing the development of standards for plant phenotyping data, in collaboration with other interested groups. Visit our Phenotype standardisation portal to see the latest proposals and get involved.