Complete mitochondrial genome sequences of three bats species and whole genome mitochondrial analyses reveal patterns of codon bias and lend support to a basal split in Chiroptera

Gene

Volumn 492, Issue 1, 2012, Pages 121-129

  Meganathan, P R ^a,b   Pagan, Heidi J T ^a   McCulloch, Eve S ^c   Stevens, Richard D ^c   Ray, David A ^a,b  

^a MISSISSIPPI STATE UNIVERSITY   (United States)

^b MISSISSIPPI STATE UNIVERSITY   (United States)

^c LOUISIANA STATE UNIVERSITY   (United States)

Author keywords

Artibeus lituratus; Codon usage bias; Corynorhinus rafinesquii; Evolutionary forces; Lasiurus borealis; Mitochondrial genome

Indexed keywords

NUCLEOTIDE;

ANIMAL TISSUE; ARTIBEUS LITURATUS; ARTICLE; BAT; CODON; CORYNORHINUS RAFINESQUII; GENE SEQUENCE; GENETIC CONSERVATION; GENETIC ORGANIZATION; GENOME ANALYSIS; LASIRUS BOREALIS; LOCOMOTION; MAMMAL; MITOCHONDRIAL GENOME; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL;

ANIMALS; BASE COMPOSITION; BASE SEQUENCE; CHIROPTERA; CODON; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; GENES, RRNA; GENOME, MITOCHONDRIAL; MOLECULAR SEQUENCE DATA; PHYLOGENY; PROTEIN BIOSYNTHESIS; RNA, TRANSFER; RNA, UNTRANSLATED; SEQUENCE ANALYSIS, DNA;

ARTIBEUS LITURATUS; CHIROPTERA; LASIURUS BOREALIS; MAMMALIA; PLECOTUS RAFINESQUII;

EID: 84155180868     PISSN: 03781119     EISSN: 18790038     Source Type: Journal    
DOI: 10.1016/j.gene.2011.10.038     Document Type: Article

References (65)

1. Akey J.M., et al. Population history and natural selection shape patterns of genetic variation in 132 genes. PLoS Biol. 2004, 2:e286.
2. Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 1990, 215:403-410.
3. Annex B.H., Williams R.S. Mitochondrial DNA structure and expression in specialized subtypes of mammalian striated muscle. Mol. Cell. Biol. 1990, 10:5671-5678.
4. Aota S., Ikemura T. Diversity in G + C content at the third position of codons in vertebrate genes and its cause. Nucleic Acids Res. 1986, 14:6345-6355.
5. Avise J.C. Mitochondrial DNA polymorphism and a connection between genetics and demography of relevance to conservation. Conserv. Biol. 1995, 9:686-690.
6. Banerjee T., Gupta S.K., Ghosh T.C. Role of mutational bias and natural selection on genome-wide nucleotide bias in prokaryotic organisms. Biosystems 2005, 81:11-18.
7. Boore J.L. Animal mitochondrial genomes. Nucleic Acids Res. 1999, 27:1767-1780.
8. Boore J.L., Brown W.M. Big trees from little genomes: mitochondrial gene order as a phylogenetic tool. Curr. Opin. Genet. Dev. 1998, 8:668-674.
9. Brown W.M., George M., Wilson A.C. Rapid evolution of animal mitochondrial DNA. Proc. Natl. Acad. Sci. U. S. A. 1979, 76:1967-1971.
10. Felsenstein J. PHYLIP - Phylogeny Inference Package (Version 3.2). Cladistics 1989, 5:164-166.
11. Fernandez-Silva P., Enriquez J.A., Montoya J. Replication and transcription of mammalian mitochondrial DNA. Exp. Physiol. 2003, 88:41-56.
12. Garey J.R., Wolstenholme D.R. Platyhelminth mitochondrial DNA: evidence for early evolutionary origin of a tRNA(serAGN) that contains a dihydrouridine arm replacement loop, and of serine-specifying AGA and AGG codons. J. Mol. Evol. 1989, 28:374-387.
13. Gibson A., Gowri-Shankar V., Higgs P.G., Rattray M.A. Comprehensive analysis of mammalian mitochondrial genome base composition and improved phylogenetic methods. Mol. Biol. Evol. 2005, 22:251-264.
14. Gissi C., Iannelli F., Pesole G. Evolution of the mitochondrial genome of Metazoa as exemplified by comparison of congeneric species. Heredity 2008, 101:301-320.
15. Gouy M., Gautier C. Codon usage in bacteria: correlation with gene expressivity. Nucleic Acids Res. 1982, 10:7055-7074.
16. Grantham R., Gautier C., Gouy M. Codon frequencies in 119 individual genes confirm consistent choices of degenerate bases according to genome type. Nucleic Acids Res. 1980, 8:1893-1912.
17. Grantham R., Gautier C., Gouy M., Mercier R., Pave A. Codon catalog usage and the genome hypothesis. Nucleic Acids Res. 1980, 8:r49-r62.
18. Guindon S., Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 2003, 52:696-704.
19. Guindon S., Dufayard J.F., Lefort V., Anisimova M., Hordijk W., Gascuel O. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol. 2010, 59:307-321.
20. Hassanin A., Leger N., Deutsch J. Evidence for multiple reversals of asymmetric mutational constraints during the evolution of the mitochondrial genome of metazoa, and consequences for phylogenetic inferences. Syst. Biol. 2005, 54:277-298.
21. Helm M., Brule H., Friede D., Giege R., Putz D., Florentz C. Search for characteristic structural features of mammalian mitochondrial tRNAs. RNA 2000, 6:1356-1379.
22. Hendy M.D., Penny D. Branch and bound algorithms to determine minimal evolutionary trees. Math. Biosci. 1982, 59:277-290.
23. Huelsenbeck J.P., Ronquist F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 2001, 17:754-755.
24. Jia W., Higgs P.G. Codon usage in mitochondrial genomes: distinguishing context-dependent mutation from translational selection. Mol. Biol. Evol. 2008, 25:339-351.
25. Kawai K., et al. Intra- and interfamily relationships of Vespertilionidae inferred by various molecular markers including SINE insertion data. J. Mol. Evol. 2002, 55:284-301.
26. Kimura M. On the probability of fixation of mutant genes in a population. Genetics 1962, 47:713-719.
27. Kruger D., Gargas A. New measures of topological stability in phylogenetic trees - taking taxon composition into account. Bioinformation 2006, 1:327-330.
28. Lack J.B., Van Den Bussche R.A. Identifying the confounding factors in resolving phylogenetic relationships in Vespertilionidae. J. Mammal. 2010, 91:1435-1448.
29. Laslett D., Canback B. ARWEN: a program to detect tRNA genes in metazoan mitochondrial nucleotide sequences. Bioinformatics 2008, 24:172-175.
30. McCulloch E.S., Stevens R.D. Rapid development and screening of microsatellite loci for Artibeus lituratus and their utility for six related species within Phyllostomidae. Mol. Ecol. Resour. 2011, 11:903-913.
31. Muto A., Osawa S. The guanine and cytosine content of genomic DNA and bacterial evolution. Proc. Natl. Acad. Sci. U. S. A. 1987, 84:166-169.
32. Ojala D., Merkel C., Gelfand R., Attardi G. The tRNA genes punctuate the reading of genetic information in human mitochondrial DNA. Cell 1980, 22:393-403.
33. Ojala D., Montoya J., Attardi G. tRNA punctuation model of RNA processing in human mitochondria. Nature 1981, 290:470-474.
34. Palidwor G.A., Perkins T.J., Xia X. A general model of codon bias due to GC mutational bias. PLoS One 2010, 5:e13431.
35. Perna N.T., Kocher T.D. Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes. J. Mol. Evol. 1995, 41:353-358.
36. Piaggio A.J., Perkins S.L. Molecular phylogeny of North American long-eared bats (Vespertilionidae: Corynorhinus); inter- and intraspecific relationships inferred from mitochondrial and nuclear DNA sequences. Mol. Phylogenet. Evol. 2005, 37:762-775.
37. Posada D. jModelTest: phylogenetic model averaging. Mol. Biol. Evol. 2008, 25:1253-1256.
38. Pumo D.E., Finamore P.S., Franek W.R., Phillips C.J., Tarzami S., Balzarano D. Complete mitochondrial genome of a neotropical fruit bat, Artibeus jamaicensis, and a new hypothesis of the relationships of bats to other eutherian mammals. J. Mol. Evol. 1998, 47:709-717.
39. Reyes A., Gissi C., Pesole G., Saccone C. Asymmetrical directional mutation pressure in the mitochondrial genome of mammals. Mol. Biol. Evol. 1998, 15:957-966.
40. Semon M., Lobry J.R., Duret L. No evidence for tissue-specific adaptation of synonymous codon usage in humans. Mol. Biol. Evol. 2006, 23:523-529.
41. Shackelton L.A., Parrish C.R., Holmes E.C. Evolutionary basis of codon usage and nucleotide composition bias in vertebrate DNA viruses. J. Mol. Evol. 2006, 62:551-563.
42. Sharp P.M., Tuohy T.M., Mosurski K.R. Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes. Nucleic Acids Res. 1986, 14:5125-5143.
43. Sharp P.M., Stenico M., Peden J.F., Lloyd A.T. Codon usage: mutational bias, translational selection, or both?. Biochem. Soc. Trans. 1993, 21:835-841.
44. Shen Y.Y., Shi P., Sun Y.B., Zhang Y.P. Relaxation of selective constraints on avian mitochondrial DNA following the degeneration of flight ability. Genome Res. 2009, 19:1760-1765.
45. Stenico M., Lloyd A.T., Sharp P.M. Codon usage in Caenorhabditis elegans: delineation of translational selection and mutational biases. Nucleic Acids Res. 1994, 22:2437-2446.
46. Stoletzki N., Eyre-Walker A. Synonymous codon usage in Escherichia coli: selection for translational accuracy. Mol. Biol. Evol. 2007, 24:374-381.
47. Subramanian S. Nearly neutrality and the evolution of codon usage bias in eukaryotic genomes. Genetics 2008, 178:2429-2432.
48. Sueoka N. On the genetic basis of variation and heterogeneity of DNA base composition. Proc. Natl. Acad. Sci. U. S. A. 1962, 48:582-592.
49. *and Other Methods) 2002, Sinauer Associates, Sunderland, Massachusetts.
50. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S. MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Mol. Biol. Evol. 2011, 28:2731-2739.
51. Teeling E.C., Scally M., Kao D.J., Romagnoli M.L., Springer M.S., Stanhope M.J. Molecular evidence regarding the origin of echolocation and flight in bats. Nature 2000, 403:188-192.
52. Teeling E.C., Madsen O., Van den Bussche R.A., de Jong W.W., Stanhope M.J., Springer M.S. Microbat paraphyly and the convergent evolution of a key innovation in Old World rhinolophoid microbats. Proc. Natl. Acad. Sci. U. S. A. 2002, 99:1431-1436.
53. Teeling E.C., Springer M.S., Madsen O., Bates P., O'Brien S.J., Murphy W.J. A molecular phylogeny for bats illuminates biogeography and the fossil record. Science 2005, 307:580-584.
54. Teletchea F., Maudet C., Hanni C. Food and forensic molecular identification: update and challenges. Trends Biotechnol. 2005, 23:359-366.
55. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., Higgins D.G. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 1997, 25:4876-4882.
56. Tiffin P., Hahn M.W. Coding sequence divergence between two closely related plant species: Arabidopsis thaliana and Brassica rapa ssp. pekinensis. J. Mol. Evol. 2002, 54:746-753.
57. Van den Bussche R.A., Hoofer S.R. Phylogenetic relationships among recent chiropteran families and the importance of choosing appropriate out-group taxa. J. Mammal. 2004, 85:321-330.
58. Wade X.F., Kalisz S. The causes of natural selection. Evolution 1990, 44:1947-1955.
59. Wan X.F., Xu D., Kleinhofs A., Zhou J. Quantitative relationship between synonymous codon usage bias and GC composition across unicellular genomes. BMC Evol. Biol. 2004, 4:19.
60. Wang Z., et al. Domestication relaxed selective constraints on the yak mitochondrial genome. Mol. Biol. Evol. 2011, 28:1553-1556.
61. Wilkinson G.S., Mayer F., Kerth G., Petri B. Evolution of repeated sequence arrays in the D-loop region of bat mitochondrial DNA. Genetics 1997, 146:1035-1048.
62. Wright F. The 'effective number of codons' used in a gene. Gene 1990, 87:23-29.
63. Yang Z., Nielsen R. Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol. Biol. Evol. 2000, 17:32-43.
64. Zhang Z., Li J., Zhao X.Q., Wang J., Wong G.K., Yu J. KaKs_Calculator: calculating Ka and Ks through model selection and model averaging. Genomics Proteomics Bioinformatics 2006, 4:259-263.
65. Zhou M., Li X. Analysis of synonymous codon usage patterns in different plant mitochondrial genomes. Mol. Biol. Rep. 2009, 36:2039-2046.