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Dear colleagues,
If you have not visited ANISEED recently, you may want to take a few minutes to have a look at the latest much improved release (www.aniseed.cnrs.fr). This major upgrade includes several new functionally annotated ascidian genomes interlinked via orthology relationships. The resulting system, which we refer to internally as ANISEED v5, has replaced the previous v4. Aniseed v4 will be accessible next month as an archived system at www.aniseed.cnrs.fr/v4.
You will find below a short description of the data available for each new species in ANISEED v5.
General changes:
During the annotation process of the new genomes we have tried to follow the recently published guidelines for the nomenclature of tunicate genetic elements (Stolfi, Sasakura, Chalopin, Satou et al., Genesis 2015). In particular, each gene has received a unique gene ID that is independent of both genome assembly and specific gene models. We hope that this new ID will facilitate tracking successive gene model versions.
Direct links between the gene cards of ascidian orthologous genes (in the " Ortholog Prediction" tab at the bottom the gene card) facilitate comparative work.
Ciona intestinalis type A:
Functional annotation of Ciona genes has been upgraded, in part based on better orthology relationships with mouse, chicken, human, amphioxus and urchin genomes. The gene names found in ANISEED v4, which several of you rightfuly criticized, have been suppressed.
Most Ciona intestinalis genes currently have no names. New names, based on a more accurate phylogenetic work and following the tunicate nomenclature guidelines, will be assigned this fall. In the meanwhile, you can search genes of interest using the HUGO symbols of their most similar human genes.
Links to alternative gene models (JGI v1, Kyotograil, ENSEMBL), are currently not proposed. These links will come back in fall.
We have added to the genome browser tracks showing whole embryo RNA-seq data for egg, 64-cell, early gastrula, late gastrula, late neurula, mid tailbud and hatching larva stages.
The anatomical ontology has been refined and several bugs in the fates of cells/tissues corrected. This ontology can now be downloaded from the BioPortal (http://bioportal.bioontology.org/), in addition to the Aniseed download section.
Ciona intestinalis type B:
You will find in a dedicated genome browser a preliminary assembly of Ciona intestinalis type B genome. The quality of this assembly is not sufficient to build gene models, but the assembly is searchable via the central Blast page of the system (http://www.aniseed.cnrs.fr/aniseed/default/blast_search).
A track in the type A browser shows the local sequence conservation between type A and type B genomes.
Phallusia mammillata, Halocynthia roretzi
The two genomes are functionally annotated with the same strategy as Ciona intestinalis.
The public genome browser shows tracks for gene models, sequence conservation with P. fumigata and H. aurantium respectively, ESTs, and RNA-seq data at the same stages as C. intestinalis.
Species-specific anatomical ontologies were designed and can be downloaded from the BioPortal.
These genomes are publicly released ahead of publication. If you wish to carry out large-scale analyses, please contact Hiroki Nishida, Hitoyoshi Yasuo or Patrick Lemaire
Phallusia fumigata, Halocynthia aurantium
The two genomes are available in the public section of the genome browser and are accessible via the ANISEED Blast page.
Gene models for Halocynthia aurantium will be annotated in fall
Because of several assembly issues, Phallusia fumigata will not be annotated with gene models in the short term but the sequence is sufficiently accurate to identify orthologous regulatory elements in P. mammillata and P. fumigata.
These genomes are publicly released ahead of publication. If you wish to carry out large-scale analyses, please contact Hitoshi Sawada <[log in to unmask]> or Patrick Lemaire <[log in to unmask]>
Anatomical ontologies were designed and are downloadable from the BioPortal
Molgula oculata, Molgula occulta, Molgula occidentalis
The three genomes can be accessed via the genome browser and are accessible via the central Blast page.
The Molgula oculata genome is fully functionally annotated
Anatomical ontologies are available and are downloadable from the BioPortal
Botryllus schlosseri
We functionally annotated a subset of 46 thousand gene models corresponding to all published models that are either multiexonic or monoexonic and longer than 1kb.
The BODA anatomical ontology for asexual development is supported.
Biocuration: help us improve the system!
Please use the feedback button on the left side of each page to report bugs and request features
You can submit your own data in any of the supported species through our intuitive curation site. You can obtain an annotator login and password upon request at [log in to unmask]
This can be used to organize and backup unpublished expression and cis-regulatory sequence data, which will remain private if you wish.
This can also be used to enter published articles, thereby giving them a higher visibility in the community. We are in particular looking for annotators for the rich Halocynthia roretzi literature.
Regular annotators will be rewarded by authorship in the next update paper of ANISEED.