+ Site Statistics
References:
54,258,434
Abstracts:
29,560,870
PMIDs:
28,072,757
+ Search Articles
+ PDF Full Text Service
How our service works
Request PDF Full Text
+ Follow Us
Follow on Facebook
Follow on Twitter
Follow on LinkedIn
+ Subscribe to Site Feeds
Most Shared
PDF Full Text
+ Translate
+ Recently Requested

Comprehensive analysis of the pseudogenes of glycolytic enzymes in vertebrates: the anomalously high number of GAPDH pseudogenes highlights a recent burst of retrotrans-positional activity



Comprehensive analysis of the pseudogenes of glycolytic enzymes in vertebrates: the anomalously high number of GAPDH pseudogenes highlights a recent burst of retrotrans-positional activity



Bmc Genomics 10(): 480-480



Pseudogenes provide a record of the molecular evolution of genes. As glycolysis is such a highly conserved and fundamental metabolic pathway, the pseudogenes of glycolytic enzymes comprise a standardized genomic measuring stick and an ideal platform for studying molecular evolution. One of the glycolytic enzymes, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), has already been noted to have one of the largest numbers of associated pseudogenes, among all proteins. We assembled the first comprehensive catalog of the processed and duplicated pseudogenes of glycolytic enzymes in many vertebrate model-organism genomes, including human, chimpanzee, mouse, rat, chicken, zebrafish, pufferfish, fruitfly, and worm (available at http://pseudogene.org/glycolysis/). We found that glycolytic pseudogenes are predominantly processed, i.e. retrotransposed from the mRNA of their parent genes. Although each glycolytic enzyme plays a unique role, GAPDH has by far the most pseudogenes, perhaps reflecting its large number of non-glycolytic functions or its possession of a particularly retrotranspositionally active sub-sequence. Furthermore, the number of GAPDH pseudogenes varies significantly among the genomes we studied: none in zebrafish, pufferfish, fruitfly, and worm, 1 in chicken, 50 in chimpanzee, 62 in human, 331 in mouse, and 364 in rat. Next, we developed a simple method of identifying conserved syntenic blocks (consistently applicable to the wide range of organisms in the study) by using orthologous genes as anchors delimiting a conserved block between a pair of genomes. This approach showed that few glycolytic pseudogenes are shared between primate and rodent lineages. Finally, by estimating pseudogene ages using Kimura's two-parameter model of nucleotide substitution, we found evidence for bursts of retrotranspositional activity approximately 42, 36, and 26 million years ago in the human, mouse, and rat lineages, respectively. Overall, we performed a consistent analysis of one group of pseudogenes across multiple genomes, finding evidence that most of them were created within the last 50 million years, subsequent to the divergence of rodent and primate lineages.

Please choose payment method:






(PDF emailed within 0-6 h: $19.90)

Accession: 052269910

Download citation: RISBibTeXText

PMID: 19835609

DOI: 10.1186/1471-2164-10-480


Related references

The genomes of higher vertebrates contain an unusually high number of glyceraldehyde 3 phosphate dehydrogenase ec 1.2.1.12 pseudogenes. Biology of the Cell 52(2): 84A, 1984

Pseudogenes as weaknesses of ACTB (Actb) and GAPDH (Gapdh) used as reference genes in reverse transcription and polymerase chain reactions. Plos One 7(8): E41659, 2013

Examination of four HLA class I pseudogenes. Common events in the evolution of HLA genes and pseudogenes. Journal of Immunology 149(6): 1947-1956, 1992

Concerted evolution in the GAPDH family of retrotransposed pseudogenes. Mammalian Genome 4(12): 695-703, 1993

GAPDH Pseudogenes and the Quantification of Feline Genomic DNA Equivalents. Molecular Biology International 2013: 587680, 2013

Analysis of nuclear receptor pseudogenes in vertebrates: how the silent tell their stories. Molecular Biology and Evolution 25(1): 131-143, 2007

Frequency matrix approach demonstrates high sequence quality in avian BARCODEs and highlights cryptic pseudogenes. Plos One 7(8): E43992-E43992, 2013

Unusual evolutionary conservation of 5S rRNA pseudogenes in Aspergillus nidulans: similarity of the DNA sequence associated with the pseudogenes with the mouse immunoglobulin switch region. Journal of Molecular Evolution 28(1-2): 125-130, 1988

Unusual evolutionary conservation of 5s ribosomal rna pseudogenes in aspergillus nidulans similarity of the dna sequence associated with the pseudogenes with the mouse immunoglobulin switch region. Journal of Molecular Evolution 28(1-2): 125-130, 1988, 1989

Utility of syntenic relationships of VDAC1 pseudogenes for not only an understanding of the phylogenetic divergence history of rodents, but also ascertaining possible pseudogene candidates as genuine pseudogenes. Genomics 104(2): 128-133, 2015

Phylogenetic analysis and identification of pseudogenes reveal a progressive loss of zona pellucida genes during evolution of vertebrates. Biology of Reproduction 78(5): 796-806, 2007

Occurrence of mitochondrial CO1 pseudogenes in Neocalanus plumchrus (Crustacea: Copepoda): Hybridization indicated by recombined nuclear mitochondrial pseudogenes. Plos One 12(2): E0172710, 2017

Comprehensive analysis of amino acid and nucleotide composition in eukaryotic genomes, comparing genes and pseudogenes. Nucleic Acids Research 30(11): 2515-2523, 2002

Comprehensive analysis of pseudogenes in prokaryotes: widespread gene decay and failure of putative horizontally transferred genes. Genome Biology 5(9): R64, 2004

The abundance of processed pseudogenes derived from glycolytic genes is correlated with their expression level. Genome 55(2): 147-151, 2012