Lemoine2007

CREATED: 201004072013 LINK: url:~/Modules/Literature/Lemoine2007.pdf TITLE: Assessing the evolutionary rate of positional orthologous genes in prokaryotes using synteny data

Proposed two strategies to extract from a set of homologs, a collection of valid orthologs shared by at least two genomes.

First method is Reciprocal Smallest Distance (RSD) using PAM distances separating pairs of homologs.

Second method groups homologs in families, compute gene trees, distinguishing bona fide orthologs and paralogs created after the last speciation event.

Use orthologs generated by either method or their intersection to find orthologs that are adjacent for each pair of genomes (Positional Orthologous Genes).

BLAST searches often return as the highest scoring hit a protein that is not the nearest phylogenetic neigbour. Hence actual orthologs will be missed by RBH/BBH approaches. RSD is based on estimates of evolutionary distace rather than BLAST scores.

Show that POGs are subject to more evolutionary constraints than orthologs outside synteny groups, whatever the taxonomic distance separating the compared organisms.