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

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.     

Evolutionary relatedness of mackerels of the genus Scomber based on complete mitochondrial genomes: Strong support to the recognition of Atlantic Scomber colias and Pacific Scomber japonicus as distinct species

Mackerels of the genus Scomber are commercially important species, but their taxonomic status is still controversial. Although previous phylogenetic data support the recognition of Atlantic Scomber colias and Pacific Scomber japonicus as separate species, it is only based on the analysis of partial mitochondrial and nuclear DNA sequences. In an attempt to shed light on this relevant issue, we have determined the complete mitochondrial DNA sequence of S. colias, S. japonicus, and Scomber australasicus. The total length of the mitogenomes was 16,568 bp for S. colias and 16,570 bp for both S. japonicus and S. australasicus. All mitogenomes had a gene content (13 protein-coding, 2 rRNAs, and 22 tRNAs) and organization similar to that observed in Scomber scombrus and most other vertebrates. The major noncoding region (control region) ranged between 865 and 866 bp in length and showed the typical conserved blocks. Phylogenetic analyses revealed a monophyletic origin of Scomber species with regard to other scombrid fish. The major finding of this study is that S. colias and S. japonicus were significantly grouped in distinct lineages within Scomber cluster, which phylogenetically constitutes evidence that they may be considered as separate species. Additionally, molecular data here presented provide a useful tool for evolutionary as well as population genetic studies.     

The relation between hairpin formation by mitochondrial WANCY tRNAs and the occurrence of the light strand replication origin in Lepidosauria

Mitochondrial light strand DNA replication is initiated at light strand replication origins (OLs), short stem-loop hairpins formed by the heavy strand DNA. OL-like secondary structures are also formed by heavy strand DNA templating for the five tRNAs adjacent to OLs, the WANCY tRNA cluster. We tested whether natural OL absence associates with greater capacities for formation of OL-like structures by WANCY tRNA genes. Using lepidosaurian taxa (Sphenodon, lizards and amphisbaenids), we compared WANCY tRNA capacities to form OL-like structures between 248 taxa possessing an OL with 131 taxa without OL (from different families). On average, WANCY tRNA genes form more OL-like structures in the absence of a regular OL than in its presence. Formation of OL-like structures by WANCY tRNAs follows hierarchical patterns that may reduce competition between the tRNA's translational function and its secondary OL function: the rarer the tRNA's cognate amino acid, the greater the capacity to form OL-like structures. High OL-forming capacities for neighboring tRNAs are avoided. Because OL absence usually occurs in taxa with reduced genomes, increased formation of OL-like structures by WANCY tRNAs might result from selection for greater metabolic efficiency. Further analyses suggest that OL loss is one of the latest steps in genome reduction, and promotes the increase in formation of OL-like structures by WANCY tRNA genes in Lepidosauria.