e.g. CPR34 or chitin*

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Lophotrochozoan gene trees and orthologs

Release 31 of Ensembl Metazoa includes two new species in the Lophotrochozoa, an octopus and a brachiopod, bringing the total number of species in this superphylum to six; not a huge number of species, but enough to start mining the comparative data to highlight interesting Lophotrochozoan gene families. Gene trees and homology information are available across all metazoa, and this data can be accessed with the compara API.

Gene tree (EMGT00730000092365) showing speciation nodes (blue) and duplication nodes (red) for Lophotrochozoan species.Gene trees in which Lophotrochozoan genes are over-represented might suggest the expansion of gene family, and an interesting avenue for further study. There are 5418 gene trees with 20 nodes and genes from at least 4 Lophotrochozoan species. Comparing the total number of leaf nodes per species with the Lophotrochozoan leaf nodes per species, one can find trees in which gene family expansion occurred early in evolutionary history (e.g. EMGT00730000092365), within subgroups (e.g. species with shells, EMGT00070000028926), or within a single species (e.g. Lingula anatina, EMGT00050000007999).

Groups of orthologs can be filtered to find gene families which are unique to Lophotrochozoa. There are 265 ortholog groups that contain genes from at least 4 Lophotrochozoan species and which have 80% coverage between ortholog pairs. A few genes have one-to-one orthologs in all of the other species (e.g. g28287), but most include paralogs (e.g. Ocbimv22002610m.g). Many trees lack genes from one or two species (e.g. Ocbimv22011026m.g), which could be due to incomplete annotation (and therefore useful for directing re-annotation efforts), or genuine gene loss.

What's New in Release 31

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Data in CRAM format can be uploaded as tracks in the genome browser.