FB2014_04, released July 21st, 2014
 
 

A Database of Drosophila Genes & Genomes

New and Improved Orthologies

The orthology calls in FlyBase are now grouped phylogenetically. The groups and the organisms they include are as follows:

Drosophila Species

  • Drosophila melanogaster
  • Drosophila simulans
  • Drosophila sechellia
  • Drosophila erecta
  • Drosophila yakuba
  • Drosophila ananassae
  • Drosophila pseudoobscura pseudoobscura
  • Drosophila persimilis
  • Drosophila willistoni
  • Drosophila virilis
  • Drosophila mojavensis
  • Drosophila grimshawi

non-Drosophila Dipterans

  • Aedes aegypti (Yellow fever mosquito)
  • Anopheles gambiae (Malaria mosquito)
  • Culex quinquefasciatus (Southern house mosquito)

non-Dipteran Insects

  • Apis mellifera (Western honey bee)
  • Nasonia vitripennis (Parasitic wasp)
  • Acromyrmex echinatior (Panamanian leafcutter ant)
  • Atta cephalotes (Leafcutter ant)
  • Harpegnathos saltator (Jerdons jumping ant)
  • Linepithema humile (Argentine ant)
  • Pogonomyrmex barbatus (Red harvester ant)
  • Solenopsis invicta (Red fire ant)
  • Acyrthosiphon pisum (Pea aphid)
  • Bombyx mori (Silkworm)
  • Pediculus humanus (Human body louse)
  • Tribolium castaneum (Red flour beetle)

non-Insect Arthropods

  • Daphnia pulex (Common water flea)
  • Ixodes scapularis (Black-legged tick)

non-Arthropod Metazoa

  • Caenorhabditis elegans (Nematode)
  • Strongylocentrotus purpuratus (Purple sea urchin)
  • Danio rerio (Zebrafish)
  • Xenopus tropicalis (African clawed Frog)
  • Mus musculus (House mouse)
  • Rattus norvegicus (Norway rat)
  • Homo sapiens (Human)

The orthology calls in FlyBase are D. melanogaster-centric, that is to say that we only report orthologies between D. melanogaster and other species.

Where will you see changes?

In gene reports, we have replaced the “Genome-wide drosophilid orthologs”, “Curated drosophild orthologs” and Linkout ortholog subsections with our new orthology presentation using a uniform set of calls solely from OrthoDB. At the top of this section is the “OrthoDB Ortholog Groups” subsection. This subsection contains links to OrthoDB for each of the groups mentioned above. Clicking on the link will take you to OrthoDB where you can see additional details of the genes contained in the group. Below this is the list of genes organized by each of the groups. The groups and species within them are listed in order of increasing phylogenetic distance relative to D. melanogaster. The columns include Organism, Common Name, OrthoDB Group, and Gene. The OrthoDB Group column may contain one or more OrthoDB group IDs. In the “Gene” column you will find the target gene that is indicated as being an ortholog of the current gene. This column provides the symbol and a link to an appropriate database when possible.

For non D. melanogaster FlyBase gene reports, the Orthologs sections will include links to the OrthoDB Ortholog groups (if any are identified) as well as a link to the orthologous D. melanogaster gene (where one has been identified).

a portion of the 'Orthologs' section of an example gene report
Figure 1 – A partial example of the gene report orthology section.

In our GFF files, we have removed our previous orthology lines and replaced them with lines that use a source (column 2) of 'OrthoDB' and a type (column 3) of 'orthologous_to'. In our previous versions, we used the same type but the sources included OrthoDB (version 4), FlyBase and InParanoid.

2L OrthoDB orthologous_to 9839 21376 . - . ID=FBgn0002121_d3011e29939;Name=l(2)gl;to_species=Ggal;to_name=Ggal\LLGL1;Dbxref=OrthoDB5_Metazoa:EOG5N33CC

Figure 2 – A single GFF line for an ortholog call.

In our Chado PostgreSQL database, the orthology calls are associated with D. melanogaster genes via the feature_relationship table using a relationship type of 'orthologous_to'. The gene symbols hang off of the gene ortholog features in the synonym table and the model organism database and OrthoDB group IDs are in the feature_dbxref table.

We hope you find this revised dataset to be useful and easy to use. If you have any questions, comments or ideas on this or anything relating to FlyBase please don't hesitate to contact us.

1. Waterhouse et al, Nucleic Acids Research, January 2011, PMID: 20972218 OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011.