PhyloMarker–-A Tool for Mining Phylogenetic Markers through Genome Comparison: Application of the Mouse Lemur (Genus Microcebus) Phylogeny

Runhua Lei, Thaine W. Rowley, Lifeng Zhu, Carolyn A. Bailey, Shannon E. Engberg, Mindy L. Wood, Mary C. Christman, George H. Perry, Edward E. Louis, Guoqing Lu

Research output: Contribution to journalReview article

5 Citations (Scopus)

Abstract

Molecular phylogeny is a fundamental tool to understanding the evolution of all life forms. One common issue faced by molecular phylogeny is the lack of sufficient molecular markers. Here, we present PhyloMarker, a phylogenomic tool designed to find nuclear gene markers for the inference of phylogeny through multiple genome comparison. Around 800 candidate markers were identified by PhyloMarker through comparison of partial genomes of Microcebus and Otolemur. In experimental tests of 20 randomly selected markers, nine markers were successfully amplified by PCR and directly sequenced in all 17 nominal Microcebus species. Phylogenetic analyses of the sequence data obtained for 17 taxa and nine markers confirmed the distinct lineage inferred from previous mtDNA data. PhyloMarker has also been used by other projects including the herons (Ardeidae, Aves) phylogeny and the Wood mice (Muridae, Mammalia) phylogeny. All source code and sample data are made available at http://bioinfo-srv1.awh.unomaha.edu/phylomarker/.

Original languageEnglish (US)
JournalEvolutionary Bioinformatics
Volume8
DOIs
StatePublished - Jan 1 2012

Fingerprint

Cheirogaleidae
Microcebus
Phylogeny
phylogeny
genome
Genes
Genome
phylogenetics
Ardeidae
Muridae
Apodemus
genetic markers
Mitochondrial DNA
Mammalia
Aves
Birds
Sequence Analysis
Mammals
Wood
comparison

Keywords

  • Microcebus phylogeny
  • genome comparison
  • phyloinformatics
  • single copy gene markers

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Computer Science Applications

Cite this

PhyloMarker–-A Tool for Mining Phylogenetic Markers through Genome Comparison : Application of the Mouse Lemur (Genus Microcebus) Phylogeny. / Lei, Runhua; Rowley, Thaine W.; Zhu, Lifeng; Bailey, Carolyn A.; Engberg, Shannon E.; Wood, Mindy L.; Christman, Mary C.; Perry, George H.; Louis, Edward E.; Lu, Guoqing.

In: Evolutionary Bioinformatics, Vol. 8, 01.01.2012.

Research output: Contribution to journalReview article

Lei, Runhua ; Rowley, Thaine W. ; Zhu, Lifeng ; Bailey, Carolyn A. ; Engberg, Shannon E. ; Wood, Mindy L. ; Christman, Mary C. ; Perry, George H. ; Louis, Edward E. ; Lu, Guoqing. / PhyloMarker–-A Tool for Mining Phylogenetic Markers through Genome Comparison : Application of the Mouse Lemur (Genus Microcebus) Phylogeny. In: Evolutionary Bioinformatics. 2012 ; Vol. 8.
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