Abstract
We present the sequencing and comparative analysis of 17 mitochondrial genomes of Nearctic and Neotropical amphipods of the genus Hyalella, most from the Andean Altiplano. The mitogenomes obtained comprised the usual 37 gene-set of the metazoan mitochondrial genome showing a gene rearrangement (a reverse transposition and a reversal) between the North and South American Hyalella mitogenomes. Hyalella mitochondrial genomes show the typical AT-richness and strong nucleotide bias among codon sites and strands of pancrustaceans. Protein-coding sequences are biased towards AT-rich codons, with a preference for leucine and serine amino acids. Numerous base changes (539) were found in tRNA stems, with 103 classified as fully compensatory, 253 hemi-compensatory and the remaining base mismatches and indels. Most compensatory Watson–Crick switches were AU -> GC linked in the same haplotype, whereas most hemi-compensatory changes resulted in wobble GU and a few AC pairs. These results suggest a pairing fitness increase in tRNAs after crossing low fitness valleys. Branch-site level models detected positive selection for several amino acid positions in up to eight mitochondrial genes, with atp6 and nad5 as the genes displaying more sites under selection.
Highlights
In the last decade, the advances in next-generation sequencing–coupled with the improvements in the computer programs for the assembly of short DNA sequences and bioinformatics pipelines for gene annotation–have facilitated the inference of metazoan phylogenies based on mitochondrial protein-coding genes (PCGs)
Features such as gene rearrangements, the underlying nucleotide substitution patterns involved in DNA sequence composition and the conservation of rRNA and tRNA secondary structures have emerged [2,9,10,11]
The remaining ones lacked one or two two non-coding segments corresponding to the control regions, and for most of them, we non-coding segments corresponding to the control regions, and for most of them, we could not recover trnC, trnM and trnY genes since they are adjacent to repetitive control could not recover trnC, trnM and trnY genes since they are adjacent to repetitive control regions
Summary
The advances in next-generation sequencing–coupled with the improvements in the computer programs for the assembly of short DNA sequences and bioinformatics pipelines for gene annotation–have facilitated the inference of metazoan phylogenies based on mitochondrial protein-coding genes (PCGs). The extensive complete or nearly complete mitochondrial sequences obtained to date have shed light on mitogenome evolution Features such as gene rearrangements, the underlying nucleotide substitution patterns involved in DNA sequence composition and the conservation of rRNA and tRNA secondary structures have emerged [2,9,10,11].
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