EvolMarkers: A database for mining exon and intron markers for evolution, ecology and conservation studies

Chenhong Li, Jean Jack M. Riethoven, Gavin J.P. Naylor

Research output: Contribution to journalArticle

12 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
Pages (from-to)967-971
Number of pages5
JournalMolecular Ecology Resources
Volume12
Issue number5
DOIs
StatePublished - Sep 1 2012

Fingerprint

Ecology
Introns
exons
introns
Exons
Genome
Databases
ecology
genome
Annelida
Placozoa
Echinodermata
Cnidaria
Chordata
Costs and Cost Analysis
Nematoda
divergence
Anolis
Lizards
Arthropods

Keywords

  • Coding sequence
  • Comparative genomics
  • Exon-primed-intron-crossing
  • Nuclear markers
  • Phylogenetics
  • Single-copy gene

ASJC Scopus subject areas

  • Biotechnology
  • Ecology, Evolution, Behavior and Systematics
  • Genetics

Cite this

EvolMarkers : A database for mining exon and intron markers for evolution, ecology and conservation studies. / Li, Chenhong; Riethoven, Jean Jack M.; Naylor, Gavin J.P.

In: Molecular Ecology Resources, Vol. 12, No. 5, 01.09.2012, p. 967-971.

Research output: Contribution to journalArticle

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