The structure of the Australian and South American marsupial mitochondrial control region

The mitochondrial genome of the black-tailed dasyure (Murexia melanurus)

In this study, we report the mitochondrial genome of the black-tailed dasyure (Murexia melanurus) of New Guinea. The circular genome is 17,736 bp in length and has an AT content of 60.5%. Its gene content – 13 protein-coding genes (PCGs), 2 ribosomal (rRNA) genes, 21 transfer RNA (tRNA) genes, a tRNA pseudogene (tRNA^Lys), and a non-coding control region (CR) – and gene arrangement are consistent with previous marsupial mitogenome assemblies.

Complete mitochondrial genome of Black Soft-shell Turtle (Nilssonia nigricans) and comparative analysis with other Trionychidae

The characterization of mitochondrial genome has been evidenced as an efficient field of study for phylogenetic and evolutionary analysis in vertebrates including turtles. The aim of this study was to distinguish the structure and variability of the Trionychidae species mitogenomes through comparative analysis. The complete mitogenome (16796 bp) of an endangered freshwater turtle, Nilssonia nigricans was sequenced and annotated. The mitogenome encoded for 37 genes and a major non-coding control region (CR). The mitogenome was A + T biased (62.16%) and included six overlapping and 19 intergenic spacer regions. The Relative synonymous codon usage (RSCU) value was consistent among all the Trionychidae species; with the exception of significant reduction of Serine (TCG) frequency in N. nigricans, N. formosa, and R. swinhoei. In N. nigricans, most of the transfer RNAs (tRNAs) were folded into classic clover-leaf secondary structures with Watson-Crick base pairing except for trnS1 (GCT). The comparative analysis revealed that most of the tRNAs were structurally different, except for trnE (TTC), trnQ (TTG), and trnM (CAT). The structural features of tRNAs resulted ≥ 10 mismatched or wobble base pairings in 12 tRNAs, which reflects the nucleotide composition in both H- and L-strands. The mitogenome of N. nigricans also revealed two unique tandem repeats (ATTAT)8, and (TATTA)20 in the CR. Further, the conserved motif 5'-GACATA-3' and stable stem-loop structure was detected in the CRs of all Trionychidae species, which play an significant role in regulating transcription and replication in the mitochondrial genome. Further, the comparative analysis of Ka/Ks indicated negative selection in most of the protein coding genes (PCGs). The constructed Maximum Likelihood (ML) phylogeny using all PCGs showed clustering of N. nigricans with N. formosa. The resulting phylogeny illustrated the similar topology as described previously and consistent with the taxonomic classification. However, more sampling from different taxonomic groups of Testudines and studies on their mitogenomics are desirable for better understanding of the phylogenetic and evolutionary relationships.

Reducing the information gap on Loricarioidei (Siluriformes) mitochondrial genomics

Background

The genetic diversity of Neotropical fish fauna is underrepresented in public databases. This distortion is evident for the order Siluriformes, in which the suborders Siluroidei and Loricarioidei share equivalent proportion of species, although far less is known about the genetics of the latter clade, endemic to the Neotropical Region. Recently, this information gap was evident in a study about the structural diversity of fish mitochondrial genomes, and hampered a precise chronological resolution of Siluriformes. It has also prevented molecular ecology investigations about these catfishes, their interactions with the environment, responses to anthropogenic changes and potential uses.

Results

Using high-throughput sequencing, we provide the nearly complete mitochondrial genomes for 26 Loricariidae and one Callichthyidae species. Structural features were highly conserved. A notable exception was identified in the monophyletic clade comprising species of the Hemiancistrus, Hypostomini and Peckoltia-clades, a ~60 nucleotide-long deletion encompassing the seven nucleotides at the 3′ end of the Conserved Sequence Block (CSB) D of the control region. The expression of mitochondrial genes followed the usual punctuation pattern. Heteroplasmic sites were identified in most species. The retrieved phylogeny strongly corroborates the currently accepted tree, although bringing to debate the relationship between Schizolecis guntheri and Pareiorhaphis garbei, and highlighting the low genetic variability within the Peckoltia-clade, an eco-morphologically diverse and taxonomically problematic group.

Conclusions

Herein we have launched the use of high-throughput mitochondrial genomics in the studies of the Loricarioidei species. The new genomic resources reduce the information gap on the molecular diversity of Neotropical fish fauna, impacting the capacity to investigate a variety of aspects of the molecular ecology and evolution of these fishes. Additionally, the species showing the partial CSB-D are candidate models to study the replication and transcription of vertebrate mitochondrial genome.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3709-3) contains supplementary material, which is available to authorized users.

Structure and variation of the mitochondrial genome of fishes

Background

The mitochondrial (mt) genome has been used as an effective tool for phylogenetic and population genetic analyses in vertebrates. However, the structure and variability of the vertebrate mt genome are not well understood. A potential strategy for improving our understanding is to conduct a comprehensive comparative study of large mt genome data. The aim of this study was to characterize the structure and variability of the fish mt genome through comparative analysis of large datasets.

Results

An analysis of the secondary structure of proteins for 250 fish species (248 ray-finned and 2 cartilaginous fishes) illustrated that cytochrome c oxidase subunits (COI, COII, and COIII) and a cytochrome bc1 complex subunit (Cyt b) had substantial amino acid conservation. Among the four proteins, COI was the most conserved, as more than half of all amino acid sites were invariable among the 250 species. Our models identified 43 and 58 stems within 12S rRNA and 16S rRNA, respectively, with larger numbers than proposed previously for vertebrates. The models also identified 149 and 319 invariable sites in 12S rRNA and 16S rRNA, respectively, in all fishes. In particular, the present result verified that a region corresponding to the peptidyl transferase center in prokaryotic 23S rRNA, which is homologous to mt 16S rRNA, is also conserved in fish mt 16S rRNA. Concerning the gene order, we found 35 variations (in 32 families) that deviated from the common gene order in vertebrates. These gene rearrangements were mostly observed in the area spanning the ND5 gene to the control region as well as two tRNA gene cluster regions (IQM and WANCY regions). Although many of such gene rearrangements were unique to a specific taxon, some were shared polyphyletically between distantly related species.

Conclusions

Through a large-scale comparative analysis of 250 fish species mt genomes, we elucidated various structural aspects of the fish mt genome and the encoded genes. The present results will be important for understanding functions of the mt genome and developing programs for nucleotide sequence analysis. This study demonstrated the significance of extensive comparisons for understanding the structure of the mt genome.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-3054-y) contains supplementary material, which is available to authorized users.

Heteroplasmy and ancient translocation of mitochondrial DNA to the nucleus in the Chinese Horseshoe Bat (Rhinolophus sinicus) complex

The utility and reliability of mitochondrial DNA sequences in phylogenetic and phylogeographic studies may be compromised by widespread and undetected nuclear mitochondrial copies (numts) as well as heteroplasmy within individuals. Both numts and heteroplasmy are likely to be common across diverse taxa yet few studies have characterised their frequencies and variation at the intra-specific level. Here we report the presence of both numts and heteroplasmy in the mitochondrial control region of the Chinese horseshoe bat Rhinolophus sinicus. In total we generated 123 sequences from 18 bats, which contained two different numt clades (i.e. Numt-1 and Numt-2) and one mtDNA clade. The sequence divergence between Numt-1 and Numt-2 was 16.8% and each numt type was found in all four R. sinicus taxa, suggesting either two ancient translocations of mitochondrial DNA into the nucleus from the same source taxon, or a single translocation from different source taxa that occurred before the split of R. sinicus into different lineages. Within the mtDNA clade, phylogenetic relationships among the four taxa of R. sinicus were similar to those seen in previous results. Based on PCR comparisons, heteroplasmy was inferred between almost all individuals of R. sinicus with respect to sequence variation. Consistent with introgression of mtDNA between Central sinicus and septentrionalis, individuals from these two taxa exhibited similar signatures of repeated sequences in the control region. Our study highlights the importance of testing for the presence of numts and heteroplasmy when applying mtDNA markers to phylogenetic studies.

Molecular characteristics and evolution of the mitochondrial control region in three genera (Hipposideridae: Hipposideros Aselliscus and Coelops) of leaf-nosed bats

The mitochondrial control region (CR) was sequenced for three genera of Hipposideridae to give a detailed overview of its features. The CR of leaf-nosed bats (1288-1560 bp) was divided into three domains like that of other mammals. In addition to the common conserved blocks (ETAS1, ETAS2, F-B boxes, CSB1, CSB2, and CSB3) found in all species, a CSB1-like element was also detected in the conserved sequence blocks (CSB). Repeated motifs were examined in the ETAS of Aselliscus stoliczkanus (26 bp) and Hipposideros bicolor (80 bp) and were present in the CSB of all individuals (6, 8, 16, and 20 bp). Phylogenetic reconstructions using the CR sequences indicated that the phylogenetic relationships among Hipposideros species were consistent with the results of other molecular and phenetic analyses. Aselliscus and Coelops had a closer relationship. But the central domain could not be used for phylogenetic analyses at family and genus levels due to its high conservation.

Highly conserved d-loop sequences in woolly mouse opossums Marmosa (Micoureus)

This study reports the occurrence of highly conserved d-loop sequences in the mitochondrial genome of the woolly mouse opossum genus Marmosa subgenus Micoureus (Mammalia, Didelphimorphia, Didelphidae). Sixty-six sequences of Marmosa (Micoureus) demerarae, Marmosa (Micoureus) constantiae, and Marmosa (Micoureus) paraguayanus were amplified using universal d-loop primers and virtually no genetic differences were detected within and among species. These sequences matched the control region of the mitochondrial marsupial genome. Analyses of qualitative aspects of these sequences revealed that their structural composition is very similar to the d-loop region of other didelphid species. However, the total lack of variability has not been reported from other closely related species. The data analyzed here support the occurrence of highly conserved d-loop sequences, and we found no support for the hypothesis that these sequences are d-loop-like nuclear pseudogenes. Furthermore, the control and flanking regions obtained with different primers corroborate the lack of variability of the d-loop sequences in the mitochondrial genome of Marmosa (Micoureus).