PUBLICATION
Phylogenetic analysis of vertebrate lactate dehydrogenase (LDH) multigene families
- Authors
- Li, Y.J., Tsoi, S.C., Mannen, H., and Shoei-lung Li, S.
- ID
- ZDB-PUB-050225-1
- Date
- 2002
- Source
- Journal of molecular evolution 54(5): 614-624 (Journal)
- Registered Authors
- Keywords
- Gene duplication, Transversion, Sequence convergence, Molecular clock, Phylogeny, Vertebrate evolution
- MeSH Terms
-
- Animals
- Evolution, Molecular
- Fishes/genetics
- Gene Duplication
- Isoenzymes/genetics
- L-Lactate Dehydrogenase/genetics
- L-Lactate Dehydrogenase/physiology*
- Mammals/genetics
- Models, Genetic
- Multigene Family*
- Phylogeny*
- Terminology as Topic
- Vertebrates/genetics*
- Xenopus/genetics
- PubMed
- 11965434 Full text @ J. Mol. Evol.
Citation
Li, Y.J., Tsoi, S.C., Mannen, H., and Shoei-lung Li, S. (2002) Phylogenetic analysis of vertebrate lactate dehydrogenase (LDH) multigene families. Journal of molecular evolution. 54(5):614-624.
Abstract
In this paper we analyzed 49 lactate dehydrogenase (LDH) sequences, mostly from vertebrates. The amino acid sequence differences were found to be larger for a human-killifish pair than a human-lamprey pair. This indicates that some protein sequence convergence may occur and reduce the sequence differences in distantly related species. We also examined transitions and transversions separately for several species pairs and found that the transitions tend to be saturated in the distantly related species pair, while transversions are increasing. We conclude that transversions maintain a conservative rate through the evolutionary time. Kimura's two-parameter model for multiple-hit correction on transversions only was used to derive a distance measure and then construct a neighbor-joining (NJ) tree. Three findings were revealed from the NJ tree: (i) the branching order of the tree is consistent with the common branch pattern of major vertebrates; (ii) Ldh-A and Ldh-B genes were duplicated near the origin of vertebrates; and (iii) Ldh-C and Ldh-A in mammals were produced by an independent gene duplication in early mammalian history. Furthermore, a relative rate test showed that mammalian Ldh-C evolved more rapidly than mammalian Ldh-A. Under a two-rate model, this duplication event was calibrated to be approximately 247 million years ago (mya), dating back to the Triassic period. Other gene duplication events were also discovered in Xenopus, the first duplication occurring approximately 60-70 mya in both Ldh-A and Ldh-B, followed by another recent gene duplication event, approximately 20 mya, in Ldh-B.
Errata / Notes
Erratum in: J Mol Evol. 2003 Dec;57(6):745.These two authors (Yi-Ju Li and Stephen C.-M. Tsoi) contributed equally Current address (Stephen C.-M. Tsoi): Institute of Marine Bioscience, Halifax, Nova Scotia B3H 321, Canada Current address(Steven Shoei-lung Li): Laboratory of Animal Breeding and Genetics, Faculty of Agriculture, Kobe University, Kobe 657, Japan
At the request of the authors, the lists of authors and affiliations of this article have been amended and are shown correctly above.
Furthermore, the following statement should be added to the Materials and Methods section of the article: The ten unpublished LDH sequences cited in this paper were determined by S. C.-M. Tsoi and H. Mannen at S.S.-L. Lirsquos laboratory at NIEHS, NIH. These sequences were deposited to GenBank in 1999.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping