Gene Losses

Overview

Gene content shows considerable variation among eukaryotic genomes and the recent availability of many complete-genome sequences allowed us to consistently quantify gene losses in 5 insect and 5 vertebrate species.

Goals

- quantification of gene losses and mapping them to the species tree - identification of functionally linked lost genes and, possibly, identification of lost or rearranged pathways - measuring the constraints of the gene repertoire evolution

Methods

Groups of orthologous groups of the complete proteomes of 5 insect and 5 vertebrate species were automatically identified using a variant of a strategy used previously (on the basis of all-against-all protein Smith-Waterman comparisons, followed by merging of reciprocally best matching triangles between each set of three species and addition of inparalogs, genes that are more similar within the genome than to any other protein in the other genomes). Mapping of the losses to the tree was done assuming parsimony by minimizing the total number of losses over the phylogenetic tree.

Results

We identified known gene losses that confirmed our approach as well as hundreds of new gene losses in each lineage. Insects lost 2-3x more ancient genes than vertebrates. Interestingly, the number of losses per branch correlates with evolutionary rate and divergence time. We are studying some selected coordinated losses in more detail.
Quantification of orthologous gene losses in insects and vertebrates.Quantification of orthologous gene losses in insects and vertebrates.

Quantification of ortholog losses in insects and vertebrates

Wyder S, Kriventseva EV, Schroder R, Kadowaki T and Zdobnov EM
Genome Biol. 2007 Nov 16;8(11):R242
PMID: 18021399