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 |
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| Authors: | Meganathan P R Pagan Heidi J T McCulloch Eve S Stevens Richard D Ray David A |
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| Affiliation: | a Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USAb Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USAc Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA |
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| 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. |
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| 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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