Premium
EvolMarkers: a database for mining exon and intron markers for evolution, ecology and conservation studies
Author(s) -
LI CHENHONG,
RIETHOVEN JEANJACK M.,
NAYLOR GAVIN J. P.
Publication year - 2012
Publication title -
molecular ecology resources
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.96
H-Index - 136
eISSN - 1755-0998
pISSN - 1755-098X
DOI - 10.1111/j.1755-0998.2012.03167.x
Subject(s) - biology , genome , phylogenetic tree , evolutionary biology , phylogenetics , genomics , range (aeronautics) , intron , genetics , gene , materials science , composite material
Recent innovations in next‐generation sequencing have lowered the cost of genome projects. Nevertheless, sequencing entire genomes for all representatives in a study remains expensive and unnecessary for most studies in ecology, evolution and conservation. It is still more cost‐effective and efficient to target and sequence single‐copy nuclear gene markers for such studies. Many tools have been developed for identifying nuclear markers, but most of these have focused on particular taxonomic groups. We have built a searchable database, EvolMarkers, for developing single‐copy coding sequence (CDS) and exon‐primed‐intron‐crossing (EPIC) markers that is designed to work across a broad range of phylogenetic divergences. The database is made up of single‐copy CDS derived from BLAST searches of a variety of metazoan genomes. Users can search the database for different types of markers (CDS or EPIC) that are common to different sets of input species with different divergence characteristics. EvolMarkers can be applied to any taxonomic group for which genome data are available for two or more species. We included 82 genomes in the first version of EvolMarkers and have found the methods to be effective across Placozoa, Cnidaria, Arthropod, Nematoda, Annelida, Mollusca, Echinodermata, Hemichordata, Chordata and plants. We demonstrate the effectiveness of searching for CDS markers within annelids and show how to find potentially useful intronic markers within the lizard Anolis .