About Metazome

Overview

Metazome is a joint project of the U.S. Department of Energy's Joint Genome Institute and the University of California to facilitate comparative genomic studies among metazoans. Clusters of orthologous and paralogous genes that represent the modern descendants of ancestral gene sets are constructed at key phylogenetic nodes. These clusters allow easy access to clade specific orthology and paralogy relationships as well as clade specific genes and gene expansions.

As of version 2.0.4, Metazome provides access to twenty four sequenced and annotated metazoan genomes, clustered at nine evolutionarily significant nodes. Where possible, each gene has been annotated with PFAM, KOG, KEGG, and PANTHER assignments, and publicly available annotations from RefSeq, UniProt, Ensembl, and JGI are hyperlinked and searchable.

Included organisms

Genes from the following organisms are clustered in release 2.0.4 of Metazome. Each organism name links to its genome record, which lists the assembly source, clade path, and related nodes.

Nodes

Clustering is used to group extant genes into sets representing the ancestral genes that existed just prior to various significant evolutionary events, called nodes. Extant genes have been clustered at nodes representing the following speciation events.

Clustering methodology

Clustering is performed hierarchically, from the crown nodes to the root. At each node, ingroup paralog clustering is followed by outgroup ortholog clustering. Ingroup and outgroup relationships are defined as follows. All descendant nodes, internal as well as crown, that connect through the same deepest branch to a given node are considered ingroup nodes with respect to that node. Descendant nodes that connect through the opposite deepest branch are considered outgroup nodes.

For example, human, mouse, rat, dog, opossum, chicken, frog, and the teleosts are all ingroup with respect to the chordate node. With respect to the vertebrate node, teleosts are an outgroup for tetrapods, and tetrapods are an outgroup for teleosts. Gene families are created at a given node by first creating paralog clusters among the ingroup members, with ingroup genes with greater similarity to each other than to their most similar outgroup gene being placed in the paralogous cluster.

Fourfold degenerate transversion rates (4DTV, one measure of the divergence time between genes based on the number of neutral substitutions) are used to preclude clustering of paralogs with low degrees of similarity that are drawn together simply by the lack of a high scoring hit to an outgroup gene. After paralog clustering along both branches, clusters are merged across branches to capture orthologous relationships.

This merging uses a combination of Mutual Best Hit (MBH, based on blastp sequence similarity) and synteny. Synteny is the hypothesis that disjoint genomic regions that contain a fair number of genes with high quality hits to each other likely share a common origin in a speciation, whole genome duplication, or segmental duplication event, though only the former is directly relevant in orthology identification. This process is repeated as the clustering moves from the crown nodes, which are individual organisms, to the root.

By construction, for any given node and gene family, the members of that family remain together in any larger gene family defined at a more ancient node closer to the root. The clustering is rigorously hierarchical. Every gene from an organism present at a particular node is in one and only one cluster at that node, so the clusters are hard rather than fuzzy.

Some clusters may contain only one extant gene. These singleton clusters can come from fast evolution leading to so much sequence divergence that sequence similarity based clustering is confounded, from gene loss, or from gene calling errors.

Clustering statistics

Release 2.0.4 reports the following gene family and singleton counts by node. The largest cluster size and defline are shown for each node.

Metazome team

Data sources

Metazome integrates public annotations and sequence resources. The links below identify the sources referenced in this release record and the public resources used by the comparative framework.