De novo assembly of the complete mitochondrial genome of Mycetophylax simplex Emery, 1888 through organelle targeting revels no substantial expansion of gene spacers, but rather some slightly shorter genes.

Mitochondria play a key role in cell biology and have their own genome, residing in a highly oxidative environment that induces faster changes than the nuclear genome. Because of this, mitochondrial markers have been exploited to reconstruct phylogenetic and phylogeographic relationships in studies of adaptation and molecular evolution. In this study, we determined the complete mitogenome of the fungus-farming ant Mycetophylax simplex (Hymenoptera, Formicidae) and conducted a comparative analysis among 29 myrmicine ant mitogenomes. Mycetophylax simplex is an endemic ant that inhabits sand dunes along the southern Atlantic coast. Specifically, the species occur in the ecosystem known as "restinga", within the Atlantic Forest biome. Due to habitat degradation, land use and decline of restinga habitats, the species is considered locally extinct in extremely urban beaches and is listed as vulnerable on the Brazilian Red List (ICMBio). We employed a mitochondrion-targeting approach to obtain the complete mitogenome through high-throughput DNA sequencing technology. This method allowed us to determine the mitogenome with high performance, coverage and low cost. The circular mitogenome has a length of 16,367 base pairs enclosing 37 genes (13 protein-coding genes, 22 tRNAs and 2 rRNAs) along with one control region (CR). All the protein-coding genes begin with a typical ATN codon and end with the canonical stop codons. All tRNAs formed the fully paired acceptor stems and fold into the typical cloverleaf-shaped secondary structures. The gene order is consistent with the shared Myrmicinae structure, and the A + T content of the majority strand is 81.51%. Long intergenic spacers were not found but some gene are slightly shorter. The phylogenetic relationships based on concatenated nucleotide and amino acid sequences of the 13 protein-coding genes, using Maximum Likelihood and Bayesian Inference methods, indicated that mitogenome sequences were useful in resolving higher-level relationship within Formicidae.

The complete mitochondrial genome of Sporophila nigricollis (Aves, Passeriformes).

BACKGROUND: Sporophila nigricollis, popularly known as Yellow-bellied Seedeater, is a commonly trafficked bird in Brazil. This study describes the complete mitogenome of the species and its phylogenetic position. METHODS AND RESULTS: DNA sample was sequenced on MiSeq (Illumina®) sequencer. Reads were assembled to reference using Geneious. A total of 11,740 paired sequence reads were used to produce the complete mitochondrial DNA sequence with average coverage of 176x. The mitogenome was found to be circular in shape and consisted of 16,777 base pairs. The mitochondrial genome was annotated with MITOS and verified with ExPASy. Its structure contains two ribosomal RNA (rRNA) genes, 22 transporter RNA (tRNA) genes, 13 protein-coding genes (PCGs) and one control region. Twelve of the 13 PCGs have ATG as start codon. Seven of the 13 PCGs contain a TAA stop codon. Most of the tRNA genes and PCGs are encoded on the heavy strand. Phylogenetic analyses were conducted with MEGA using the maximum likelihood method. Sporophila nigricollis grouped together with other Thraupidae species. CONCLUSION: This study presents the first complete mitogenome of Sporophila nigricollis and can be useful for research on evolution, ecology and conservation of this species.

The complete mitochondrial genome of Abramites hypselonotus (Günther, 1868) (Ostariophysi: Characiformes: Anostomidae): an aquarium headstander.

Abramites hypselonotus, commonly known as marbled headstander, is an important freshwater aquarium fish from Brazil, found in the Orinoco, Amazon, Paraguay and lower Parana River basins. This genus has only two species and only this species occurs in Brazil. The complete mitochondrial genome of Abramites hypselonotus is 16,685 bp in length and it includes 13 protein-coding genes (PCGs), 2 rRNAs, 22 tRNAs genes and a control region with 1,028 bp. It has two PCGs with GTG start codon and the others with ATG start codon. Four of the 13 PCGs appear TAA stop codon, three incomplete TA_ stop codon, four incomplete T_ _ stop codon, one contain AGG stop codon and one TAG stop codon. Phylogenetic analysis showed that Abramites hypselonotus formed a sister group of Leporinus affinis (AP011994.1), thus maintaining the Family Anostomidae as a clade.

Novel components of Tityus serrulatus venom: A transcriptomic approach.

Several research groups have studied the components produced by the venom gland of the scorpion Tityus serrulatus, which has one of the most lethal venoms in the world. Various methodologies have been employed to clarify the complex mechanisms of action of these components, especially neurotoxins and enzymes. Transcriptomes and proteomes have provided important information for pharmacological, biochemical, and immunological research. Next-generation sequencing (NGS) has allowed the description of new transcripts and completion of partial sequence descriptions for peptides, especially those with low expression levels. In the present work, after NGS sequencing, we searched for new putative venom components. We present a total of nine new transcripts with neurotoxic potential (Ts33-41) and describe the sequences of one hyaluronidase (TsHyal_4); three enzymes involved in amidation (peptidyl-glycine alpha-amidating monooxygenase A, peptidyl-alpha-hydroxyglycine alpha-amidating lyase, and peptidylglycine alpha-hydroxylating monooxygenase), which increases the lethal potential of neurotoxins; and also the enzyme Ts_Chitinase1, which may be involved in the venom's digestive action. In addition, we determined the level of transcription of five groups: toxins, metalloproteases, hyaluronidases, chitinases and amidation enzymes, including new components found in this study. Toxins are the predominant group with an expression level of 91.945%, followed by metalloproteases with only 7.790% and other groups representing 0.265%.

Genetic evaluation of migratory fish: Implications for conservation and stocking programs.

Fish stocking programs have been implemented to mitigate the blockage of original riverbeds by the construction of hydropower dams, which affects the natural migration of fish populations. However, this method raises concerns regarding the genetic rescue of the original populations of migratory fish species. We investigated the spatial distribution of genetic properties, such as genetic diversity, population structure, and gene flow (migration), of the Neotropical migratory fish Prochilodus costatus in the Três Marias dam in the São Francisco River basin, Brazil, and examined the possible effects of fish stocking programs on P. costatus populations in this region. In total, 1,017 specimens were sampled from 12 natural sites and a fish stocking program, and genotyped for high-throughput sequencing at 8 microsatellite loci. The populations presented low genetic variability, with evidence of inbreeding and the presence of only four genetic pools; three pools were observed throughout the study region, and the fourth was exclusive to one area in the Paraopeba River. Additionally, we identified high unidirectional gene flow between regions, and a preferred migratory route between the Pará River and the upper portion of the São Francisco River. The fish stocking program succeeded in transposing the genetic pools from downstream to upstream of the Três Marias dam, but, regrettably, promoted genetic homogenization in the upper São Francisco River basin. Moreover, the data show the fragility of this species at the genetic level. This monitoring strategy could be a model for the development of conservation and management measures for migratory fish populations that are consumed by humans.