Annual Scientific Report 2015

Vertebrate Annotation
The Vertebrate Annotation team aims to create comprehensive, up-to-date gene
annotation and comparative genomics resources that further our understanding
of biology, evolution and the mechanisms of disease. The data from these resources
are distributed by the Ensembl project, and provide a foundation for clinical and
research communities.
While the reference genome assembly is an increasingly
important tool for research, most scientists working in
this area need to link genomic sequence to biological
function. This is made possible by gene annotations,
which identify the location, structure and expression of
genes. Valuable insights can be gained by comparing the
annotated sequences of individuals of the same species,
or across a wide range of species.
Our team produces reference gene annotation that is
used by clinical, agricultural and research communities
as well as by other data services at EMBL-EBI. Our
gene annotation service provides high-quality gene
sets for human, mouse and almost 100 other vertebrate
species, including key model organisms and farmed
animals. These are the primary annotations used in the
initial genomic analyses of many international genome
projects. In collaboration with GENCODE, we produce
the gold-standard gene annotation for human and
mouse.
For every genome assembly in Ensembl, we also produce
comparative genomics resources that link diverse
species at the DNA and gene level. These data are used
for investigating gene function and evolution, adaptive
traits and conservation biology.
We are responsible for TreeFam, which clusters
similar gene sequences into homologous families and
indicates gene history events such as duplication and
speciation. Our comparative annotations include gene
families, gene orthologues, whole genome multi-species
alignments and conserved genomic regions across
many species.
We develop alignment and annotation methods
that integrate diverse data from the public archives.
We collaborate closely with other service teams at
EMBl-EBI including the ENA, UniProt, and Expression
Atlas to annotate new assemblies and to update
annotation on existing assemblies as new data
become available.
Major achievements
We are proud to maintain the reference human and
mouse gene sets through our GENCODE collaboration.
In 2015, we improved and updated these gene resources
by annotating assembly updates provided by the
Genome Reference Consortium (GRC), incorporating
new manual annotation, identifying gene alleles across
the various haplotypes, and contributing to the CCDS
project.
We released major updates to the rat and zebrafish
resources. We made new assemblies available for both
species, and produced genome-wide annotation for
them using our evidence-based methods to identify
protein-coding genes, noncoding RNA genes, and
pseudogenes. We produced tissue- and sample-specific
transcript sets from RNA-seq data in the public
archives. We updated the multi-species whole-genome
alignments, gene trees and orthologues in Ensembl to
include these new assemblies.
We extended our gene-annotation methods to include
annotation on lincRNA genes. We applied this method
to human, mouse, rat and sheep and will be producing
lincRNA annotation for more species in 2016.
TreeFam produces phylogenetic trees and orthology
predictions for all Ensembl eukaryotes. The number
of publicly available genomes is increasingly rapidly,
providing an opportunity for new insights via
comparative genomics. To achieve scalability, we
designed a novel workflow that will classify protein
sequences from thousands of genomes into gene
families in a quick and robust manner. This workflow is
now partially in production and uses our new library of
Hidden Markov Model (HMM) profiles.
Our comprehensive genome annotations are the
foundation for myriad downstream analysis tools
and research, including the Ensembl Variation Effect
Predictor (VEP). Access to consistent gene annotation
for a wide range of vertebrates is important for
evolutionary studies. Members of our team collaborated
with others in studying gene families in the vervet
(African green monkey) lineage, using freely available
data from ten of our annotation projects.
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2015 EMBL-EBI Annual Scientific Report