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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
Authors:Meganathan P R  Pagan Heidi J T  McCulloch Eve S  Stevens Richard D  Ray David A
Institution:
  • a Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA
  • b Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
  • c Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
  • Abstract:Order Chiroptera is a unique group of mammals whose members have attained self-powered flight as their main mode of locomotion. Much speculation persists regarding bat evolution; however, lack of sufficient molecular data hampers evolutionary and conservation studies. Of ~ 1200 species, complete mitochondrial genome sequences are available for only eleven. Additional sequences should be generated if we are to resolve many questions concerning these fascinating mammals. Herein, we describe the complete mitochondrial genomes of three bats: Corynorhinus rafinesquii, Lasiurus borealis and Artibeus lituratus. We also compare the currently available mitochondrial genomes and analyze codon usage in Chiroptera. C. rafinesquii, L. borealis and A. lituratus mitochondrial genomes are 16438 bp, 17048 bp and 16709 bp, respectively. Genome organization and gene arrangements are similar to other bats. Phylogenetic analyses using complete mitochondrial genome sequences support previously established phylogenetic relationships and suggest utility in future studies focusing on the evolutionary aspects of these species. Comprehensive analyses of available bat mitochondrial genomes reveal distinct nucleotide patterns and synonymous codon preferences corresponding to different chiropteran families. These patterns suggest that mutational and selection forces are acting to different extents within Chiroptera and shape their mitochondrial genomes.
    Keywords:mtDNA  mitochondrial DNA  mt-genome  mitochondrial genome  tRNA  transfer RNA  rRNA  ribosomal RNA  H-strand  heavy strand of mitochondrial genome  L-strand  light strand of mitochondrial genome  OriL  origin of replication of L-strand  bp  base pair  kb  kilobase  PCR  polymerase chain reaction  BLAST  Basic Local Alignment Search Tool  MP  maximum parsimony  ML  maximum likelihood  MCMC  Markov Chain Monte Carlo  ATPase 6 and ATPase 8  genes encoding ATP synthase F0 subunits 6 and 8  ND1-6 and ND4L  genes encoding NADH dehydrogenase subunits 1-6 and 4   L  COI-III  genes encoding cytochrome c oxidase subunits I-III  cyt b  gene encoding cytochrome b  WANCY  cluster of tRNA genes corresponding to amino acids tryptophan  alanine  asparagines  cysteine  and tyrosine  AA  amino acid(s)  ka  non-synonymous substitutions  ks  synonymous substitutions  DHU  dihydrouridine  D-loop  displacement loop  TAS  termination associated sequences  ENC  effective number of codons  RSCU  relative synonymous codon usage  Nc  effective codon usage statistics  Nc*  expected Nc
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