Annual Scientific Report 2015

Non-vertebrate Genomics
High-throughput sequencing is transforming both understanding and
application of the biology of many organisms. Our team integrates, analyses
and disseminates these data for scientists working in domains as diverse as
agriculture, pathogen-mediated disease and the study of model organisms.
We run services for bacterial, protist, fungal, plant
and invertebrate metazoan genomes, mostly using
the power of the Ensembl software suite, and usually
in partnership with interested communities. In such
collaborations we contribute to the development
of many resources, including VectorBase (Giraldo-
Calderon et al., 2015) for invertebrate vectors of human
disease, WormBase (Howe et al. 2016) for nematode
biology, PomBase (McDowall et al., 2015) for fission
yeast Schizosaccharomyces pombe, and PhytoPath
(Pedro et al. 2016) for plant pathogens. In the plant
domain, we collaborate closely with Gramene in the US
and with a range of European groups in the transPLANT
and ELIXIR-EXCELERATE projects.
By collaborating with EMBL-EBI and re-using our
established toolset, small communities with little
informatics infrastructure can perform and interpret
highly complex and data-generative experiments—
the type of work once the sole domain of large,
internationally co-ordinated sequencing projects. We
also work on large, complex genomes like hexaploid
bread wheat, establishing informatics frameworks for
the analysis of species for which genomic data is only
now gaining traction as technologies improve.
Our major activities include genome annotation,
broad-range comparative genomics and the
visualisation and interpretation of genomic variation,
which is studied increasingly in species throughout
the taxonomy.
Major achievements
In 2015 we issued six public releases of Ensembl
Genomes. Ensembl Bacteria now includes almost 30
000 genomes from over 5000 distinct species; while
the number of fungal and protist genomes included
have increased approximately 10-fold and 5-fold,
respectively, in one year. It is likely that we will deploy
a similar, automated approach to that currently taken
for incorporating microorganism genomes for those of
multicellular species in 2016.
With each release we have updated cross-references
and comparative genomics, introduced improved
assemblies and annotations, and sourced additional
data sets, mapping them onto the relevant genomes and
incorporating them into the resource.
We contributed to the regular data releases of and
PomBase, VectorBase, WormBase and PhytoPath. As
part of VectorBase, we contributed to the publications
of the genome of Anopheles stephensi, the primary
mosquito vector of malaria in urban India.
In WormBase, we made substantial progress towards
the implementation of a new database framework
that should allow for improved performance and more
rapid updates to the public site. In both WormBase and
PhytoPath, we released new data-mining solutions.
In each project there are specific challenges, but by
re-using infrastructural components in different
contexts we have gained efficiencies of scale.
Community curation is a good way of capturing
high-value data from the experts. We are also now
running community curation portals for 30 insect vector
species using the Web Apollo framework, allowing
scientists to modify gene models directly for subsequent
incorporation into VectorBase and Ensembl.
In PomBase, we collect functional annotations using
the Canto tool. In 2015 we extended our use of Web
Apollo to plant pathogens for the first time, working
with the community to improve the annotation of the
necrotrophic fungus Botrytis cinerea, and prepared to
deploy Canto for these phytopathogenic species.
In December, we released a new “pre-site” offering
access to a new genomic assembly for bread wheat.
Bread wheat has a large, complex genome and we have
been working as part of a BBSRC-funded project to
develop and disseminate a new assembly through a
collaboration with The Genome Analysis Centre, The
John Innes Centre, and Rothamsted Research. The new
assembly is the most complete, contiguous assembly
yet released for this species and we will be working to
annotate it fully over the course of 2016.
In the context of the transPLANT project, we continued
to work with the plant science community to develop
standards for phenotypic data, and set out our findings
with a publication (Krajewski et al., 2015).
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2015 EMBL-EBI Annual Scientific Report