Phylogenetic utility of two existing and four novel nuclear gene loci in reconstructing Tree of Life of ray-finned fishes: The order Cypriniformes (Ostariophysi) as a case study

After the completion of several entire genome projects and a remarkable increase in public genetic databases in the recent years the results of post-genomic analyses can facilitate a better understanding of the genomic evolution underlying the diversity of organisms and the complexity of gene functi...

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Bibliographic Details
Published in:Gene 2008-11, Vol.423 (2), p.125-134
Main Authors: Chen, Wei-Jen, Miya, Masaki, Saitoh, Kenji, Mayden, Richard L.
Format: Article
Language:English
Subjects:
Animals
Cell Nucleus - genetics
Codon - genetics
Cypriniformes
Cypriniformes - genetics
Databases, Genetic
Gene duplication
Genome - genetics
Mutation - genetics
Nuclear gene
Nucleotides - genetics
Ostariophysi
PCR primers
Phylogenomic approach
Phylogeny
Polymerase Chain Reaction
Polyploidy
Sequence Analysis, DNA
Teleostei
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Summary:After the completion of several entire genome projects and a remarkable increase in public genetic databases in the recent years the results of post-genomic analyses can facilitate a better understanding of the genomic evolution underlying the diversity of organisms and the complexity of gene function. This influx of genomic information and resources is also beneficial to the discipline of systematic biology. In this paper, we describe a set of 6 previous and 22 new PCR/sequencing primers for RAG1, Rhodopsin and four novel nuclear markers from IRBP, EGR1, EGR2B and EGR3 that we developed through an approach making use of public genetic/genomic data mining for one of the ongoing tree of life projects aimed at understanding the evolutionary relationships of the planet's largest clade of freshwater fishes — the Cypriniformes. The primers and laboratory protocols presented here were successfully tested in 33 species comprising all cypriniform family and subfamily groups. Phylogenetic performance of each gene, as well as their implications in the investigation of the evolution of cypriniform fishes were assessed and discussed.
ISSN:0378-1119
1879-0038
DOI:10.1016/j.gene.2008.07.016