Distribution of nuclear mitochondrial DNA in cattle nuclear genome.

The nuclear mitochondrial pseudogenes (numts), originated from mtDNA insertions into the nuclear genome, have been detected to exist in many species. However, the distribution of numts in cattle nuclear genome yet has not been fully reported. By referring to the whole cattle mtDNA sequence and to the recently released cattle nuclear genome by Human Genome Sequencing Center (HGSC), 303 numts were identified by BLAST with 55 numts unmapped to cattle nuclear genome. Further analysis found that the size of the numts ranges from 37 to 1932 bp, and the homologous identity between numts and their corresponding mtDNA fragments varies from 73 to 98%. Furthermore, the identified cattle numts cover nearly all the mitochondrial genes including mtDNA control region, distributing over all the chromosomes with the exception of the chromosome 23 and Y chromosome (in the latter the sequence data are not available). In the discovered numts, 29 relatively complete mitochondrial genes, which were distributed in 72 numts, were detected. Undoubtedly, this research would provide some valuable information for successive research related to mitochondrial genes and the evolution of cattle.

[1]  Laura C. Greaves,et al.  Mitochondrial DNA mutations in human disease , 2006, IUBMB life.

[2]  S. O’Brien,et al.  Evolutionary analysis of a large mtDNA translocation (numt) into the nuclear genome of the Panthera genus species. , 2006, Gene.

[3]  J. Schmitz,et al.  Forty Million Years of Independent Evolution: A Mitochondrial Gene and Its Corresponding Nuclear Pseudogene in Primates , 2005, Journal of Molecular Evolution.

[4]  E. Willerslev,et al.  Review Paper. Ancient DNA , 2005, Proceedings of the Royal Society B: Biological Sciences.

[5]  Fredj Tekaia,et al.  Continued Colonization of the Human Genome by Mitochondrial DNA , 2004, PLoS biology.

[6]  A. Baker,et al.  Low number of mitochondrial pseudogenes in the chicken (Gallus gallus) nuclear genome: implications for molecular inference of population history and phylogenetics , 2004, BMC Evolutionary Biology.

[7]  Dario Leister,et al.  NUMTs in sequenced eukaryotic genomes. , 2004, Molecular biology and evolution.

[8]  S. Pääbo,et al.  Unreliable mtDNA data due to nuclear insertions: a cautionary tale from analysis of humans and other great apes , 2004, Molecular ecology.

[9]  Michael Zuker,et al.  Mfold web server for nucleic acid folding and hybridization prediction , 2003, Nucleic Acids Res..

[10]  M. Woischnik,et al.  Pattern of organization of human mitochondrial pseudogenes in the nuclear genome. , 2002, Genome research.

[11]  P. Arctander,et al.  The Human Genome Project reveals a continuous transfer of large mitochondrial fragments to the nucleus. , 2001, Molecular biology and evolution.

[12]  W. Martin,et al.  How do mitochondrial genes get into the nucleus? , 2001, Trends in genetics : TIG.

[13]  D. Hartl,et al.  Mitochondrial pseudogenes: evolution's misplaced witnesses. , 2001, Trends in ecology & evolution.

[14]  S. Pääbo,et al.  Nuclear insertion sequences of mitochondrial DNA predominate in hair but not in blood of elephants , 1999, Molecular ecology.

[15]  S. Dimauro,et al.  Apparent mtDNA heteroplasmy in Alzheimer's disease patients and in normals due to PCR amplification of nucleus-embedded mtDNA pseudogenes. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[16]  D. Murdock,et al.  Ancient mtDNA sequences in the human nuclear genome: a potential source of errors in identifying pathogenic mutations. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[17]  N Howell,et al.  Mutations in mitochondrial cytochrome c oxidase genes segregate with late-onset Alzheimer disease. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[18]  C. Stewart,et al.  Insertions and duplications of mtDNA in the nuclear genomes of Old World monkeys and hominoids , 1995, Nature.

[19]  Jose V. Lopez,et al.  Numt, a recent transfer and tandem amplification of mitochondrial DNA to the nuclear genome of the domestic cat , 1994, Journal of Molecular Evolution.

[20]  K. Kidd,et al.  Eliminating mitochondrial DNA competition for nuclear DNA primers. , 1993, PCR methods and applications.

[21]  S. Vries,et al.  Mitochondrial cytochrome b: evolution and structure of the protein. , 1993, Biochimica et biophysica acta.

[22]  F. Riley,et al.  HYBRIDIZATION BETWEEN THE NUCLEAR AND KINETOPLAST DNA'S OF Leishmania enriettii AND BETWEEN NUCLEAR AND MITOCHONDRIAL DNA'S OF MOUSE LIVER. , 1967, Proceedings of the National Academy of Sciences of the United States of America.

[23]  M. Attimonelli,et al.  Structural elements highly preserved during the evolution of the D-loop-containing region in vertebrate mitochondrial DNA , 2005, Journal of Molecular Evolution.