Abstract
Mitochondrial cytochrome b pseudogene sequences (numts) in ten birds of the order Galliformes were studied for the pattern of nucleotide substitutions. Our results showed that nucleotide transitions were much more common than transversion in the numts. No transversions were detected in the numts of Chrysolophus pictus and Chrysolophus amherstiae. Moreover, there was no evidence that the nucleotide substitutions could have significant neighboring biases (P>0.05) in the Cyt b gene numts. The identified nucleotide deletions ranged from 0 base pair (bp) to 12 bp, while only a thymidine was inserted at the 323th site of the numt sequence of Numida meleagris. Unexpectedly, 2 bp deletions was more frequent than 3 bp deletions and 5 bp deletions, which indicated the changes of encoding amino acids. Both mitochondrial Cyt b gene and the corresponding numt were abundant in the base contents of adenine (A) and thymidine (T).
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References
He, D.Q., et al.: A homogenous nature of native Chinese duck matrilineal pool. BMC Evolutionary Biology 8, 298 (2008)
Lai, S.J., et al.: Mitochondrial DNA sequence diversity and origin of Chinese domestic yak. Anim. Genet. 38, 77–80 (2007)
Liu, Y.P., et al.: Multiple maternal origins of chickens: out of the Asian jungles. Mol. Phylogenet. Evol. 38, 12–19 (2006)
Yao, Y.G., et al.: Phylogeographic differentiation of mitochondrial DNA in Han Chinese. Am. J. Hum. Genet. 70, 635–651 (2002)
Thalmann, O., et al.: Unreliable mtDNA data due to nuclear insertions: a cautionary tale from analysis of humans and other great apes. Mol. Ecol. 13, 321–335 (2004)
Yao, Y.G., et al.: Pseudomitochondrial genome haunts disease studies. J. Med. Genet. 45, 769–772 (2008)
Zhang, Z., Carriero, N., Gerstein, M.: Comparative analysis of processed pseudogenes in the mouse and human genomes. Trends Genet. 20, 62–67 (2004)
Benesh, D.P., et al.: Reliability of mitochondrial DNA in an acanthocephalan: the problem of pseudogenes. Int. J. Parasitol. 36, 247–254 (2006)
Woischnik, M., Moraes, C.T.: Pattern of organization of human mitochondrial pseudogenes in the nuclear genome. Genome. Res. 12, 885–893 (2002)
Bensasson, D., et al.: Mitochondrial pseudogenes: evolution’s misplaced witnesses. Trends Ecol. Evol. 16, 314–321 (2001)
Blanchard, J.L., Lynch, M.: Organellar genes: why do they end up in the nucleus? Trends Genet. 16, 315–320 (2000)
Qu, H., Ma, F., Li, Q.: Comparative analysis of mitochondrial fragments transferred to the nucleus in vertebrate. J. Genet. Genomics 35, 485–490 (2008)
Pereira, S.L., Baker, A.J.: Low number of mitochondrial pseudogenes in the chicken (Gallus gallus) nuclear genome: implications for molecular inference of population history and phylogenetics. BMC Evol. Biol. 4, 17 (2004)
Hall, T.: BioEdit: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucleic Acids Symp. Ser. 41, 95–98 (1999)
Tamura, K., et al.: MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24, 1596–1599 (2007)
Zhang, Z., Gerstein, M.: Patterns of nucleotide substitution, insertion and deletion in the human genome inferred from pseudogenes. Nucleic Acids Res. 31, 5338–5348 (2003)
Gojobori, T., Li, W.H., Graur, D.: Patterns of nucleotide substitution in pseudogenes and functional genes. J. Mol. Evol. 18, 360–369 (1982)
Richly, E., Leister, D.: NUMTs in sequenced eukaryotic genomes. Mol. Biol. Evol. 21, 1081–1084 (2004)
Hughes, A.L., Friedman, R.: Genome size reduction in the chicken has involved massive loss of ancestral protein-coding genes. Mol. Biol. Evol. 25, 2681–2688 (2008)
Gregory, T.R.: A bird’s-eye view of the C-value enigma: genome size, cell size, and metabolic rate in the class aves. Evolution 56, 121–130 (2002)
Fitch, W.M.: Evidence suggesting a non-random character to nucleotide replacements in naturally occurring mutations. J. Mol. Biol. 26, 499–507 (1967)
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Sun, J., Feng, Z., Liu, Y. (2012). Nucleotide Substitution Pattern in Mitochondrial Cytochrome b Pseudogenes of Ten Species in Galliformes. In: Zhu, E., Sambath, S. (eds) Information Technology and Agricultural Engineering. Advances in Intelligent and Soft Computing, vol 134. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-27537-1_34
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DOI: https://doi.org/10.1007/978-3-642-27537-1_34
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