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

doi:10.4137/EBO.S9886

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 journal › Review article › peer-review

7 Scopus citations

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 language	English (US)
Journal	Evolutionary Bioinformatics
Volume	8
DOIs	https://doi.org/10.4137/EBO.S9886
State	Published - Jan 1 2012

All Science Journal Classification (ASJC) codes

Ecology, Evolution, Behavior and Systematics
Genetics
Computer Science Applications

Access to Document

10.4137/EBO.S9886

Cite this

@article{d3d4e3a914cc4b04b8ba42e39ce1ecfe,

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

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/.",

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

note = "Publisher Copyright: {\textcopyright} 2012 SAGE Publications.",

year = "2012",

month = jan,

day = "1",

doi = "10.4137/EBO.S9886",

language = "English (US)",

volume = "8",

journal = "Evolutionary Bioinformatics",

issn = "1176-9343",

publisher = "Libertas Academica Ltd.",

}

TY - JOUR

T1 - PhyloMarker–-A Tool for Mining Phylogenetic Markers through Genome Comparison

T2 - Application of the Mouse Lemur (Genus Microcebus) Phylogeny

AU - Lei, Runhua

AU - Rowley, Thaine W.

AU - Zhu, Lifeng

AU - Bailey, Carolyn A.

AU - Engberg, Shannon E.

AU - Wood, Mindy L.

AU - Christman, Mary C.

AU - Perry, George H.

AU - Louis, Edward E.

AU - Lu, Guoqing

PY - 2012/1/1

Y1 - 2012/1/1

N2 - 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/.

AB - 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/.

UR - http://www.scopus.com/inward/record.url?scp=84894281344&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84894281344&partnerID=8YFLogxK

U2 - 10.4137/EBO.S9886

DO - 10.4137/EBO.S9886

M3 - Review article

AN - SCOPUS:84894281344

SN - 1176-9343

VL - 8

JO - Evolutionary Bioinformatics

JF - Evolutionary Bioinformatics

ER -

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

Abstract

All Science Journal Classification (ASJC) codes

Access to Document

Other files and links

Fingerprint

Cite this