Popular genomes
Caenorhabditis elegans
WBcel235
Anopheles gambiae
AgamP4
Drosophila melanogaster
BDGP6
Trichoplax adhaerens
ASM15027v1
Nasonia vitripennis
GCA_000002325.2
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New and Updated Drosophilid Assemblies
Ensembl Metazoa now includes the latest assembly for Drosophila melanogaster, BDGP6. FlyBase has full details on what has changed, but two of the main changes are that the old U "pseudo-chromosome" has been removed in favour of multiple scaffolds, and the heterochromatin regions have been incorporated onto the chromosomal arms. FlyBase provide a tool for converting between assembly versions.
This seemed like an apposite time to update the data for the other drosophilid assemblies in Ensembl Metazoa. Drosophila pseudoobscura was overdue an assembly update, to v3.1; the changes were relatively minor. The assemblies for the other drosophilids have not changed recently, but the way we stored the data was not ideal: scaffolds are now split into contigs with meaningful accessions rather than arbitrarily-sized chunks; and the "scaffold_*" notation used by FlyBase is used for scaffold names, rather than INSDC accessions (which are retained as synonyms).
These assembly updates necessitated new whole genome alignments between D. melanogaster and other species. The number of alignments was increased slightly, by including all dipterans in Ensembl Metazoa, rather than just the drosophilids and a subset of mosquitos. And LastZ was used for all species, rather than using tBLAT for the more evolutionarily-distant species (further details on our pairwise alignment strategy). Even in the mosquito alignments, the coverage of the new LastZ alignments is better than the old tBLAT alignments.
What's New in Release 25
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- Updated genomes
- Drosophila melanogaster: assembly (BDGP6) and FlyBase gene set (6.02, FB2014_05)
- Drosophila pseudoobscura: assembly (v3.0) and FlyBase gene set (3.2, FB2014_04)
- D. ananassae, D. erecta, D. grimshawi, D. mojavensis, D. persimilis, D. sechellia, D. simulans, D. virilis, D. willistoni, D. yakuba: assemblies reloaded to include contigs and scaffold names; FlyBase gene sets (FB2014_03)
- Caenorhabditis elegans: WormBase gene set (WS245)
- Updated data
- Pairwise genomic alignments between D. melanogaster and all other dipterans
- Synteny between D. melanogaster and Anopheles gambiae
- Synteny coverage statistics (e.g. between C. elegans and C. briggsae)
- Peptide comparative genomics
- BioMart
Future Releases
Release 26 of Ensembl Genomes is scheduled for 17th March 2015. For more details, see the release intentions.
