Thiago E. Parente

Thyroid hormone disruption and cognitive impairment in rats exposed to PBDE during postnatal development.

Polybrominated diphenyl ether flame-retardants (PBDEs) are thyroid-disrupting environmental chemicals. We investigated the effects of postnatal exposure to DE-71 (a mixture of tetra- and penta-brominated congeners), n-propylthiouracil (PTU) and thyroxine (T4) replacement on open-field (OF) and radial maze (RAM) tests. Wistar rats (5 males/5 females per litter, 32 litters) were treated orally (PND 5-22) with PTU (4mg/kg bw/d), DE-71 (30mg/kg bw/d), with and without co-administration of T4 (15μg/kg bw/d, sc). PTU depressed T4 serum levels and body weight gain and enlarged thyroid gland. Although decreasing T4 levels, DE-71 did not change thyroid and body weights. PTU-treated rats showed hyperactivity (PND 42 and 70), and working and reference memory learning deficits (RAM, PND 100). Although not altering motor activity and working memory, DE-71 caused a reference memory deficit (females only). T4 co-administration averted hypothyroxinemia and long-term cognitive deficits caused by PTU and DE-71.

The use of transcriptomic next-generation sequencing data to assemble mitochondrial genomes of Ancistrus spp. (Loricariidae).

Mitochondrial genes and genomes have long been applied in phylogenetics. Current protocols to sequence mitochondrial genomes rely almost exclusively on long range PCR or on the direct sequencing. While long range PCR includes unnecessary biases, the purification of mtDNA for direct sequencing is not straightforward. We used total RNA extracted from liver and Illumina HiSeq technology to sequence mitochondrial transcripts from three fish (Ancistrus spp.) and assemble their mitogenomes. Based on the mtDNA sequence of a close related species, we estimate to have sequenced 92%, 95% and 99% of the mitogenomes. Taken the sequences together, we sequenced all the 13 protein-coding genes, two ribosomal RNAs, 22 tRNAs and the D-loop known in vertebrate mitogenomes. The use of transcriptomic data allowed the observation of the punctuation pattern of mtRNA maturation, to analyze the transcriptional profile, and to detect heteroplasmic sites. The assembly of mtDNA from transcriptomic data is complementary to other approaches and overcomes some limitations of traditional strategies for sequencing mitogenomes. Moreover, this approach is faster than traditional methods and allows a clear identification of genes, in particular for tRNAs and rRNAs.

The complete mitochondrial genome of Corydoras nattereri (Callichthyidae: Corydoradinae)

The complete mitogenome of Corydoras nattereri , a species of mailed catfishes from southeastern Brazil, was reconstructed using next-generation sequencing techniques. The mitogenome was assembled using mitochondrial transcripts from the liver transcriptomes of three individuals, and produced a circular DNA sequence of 16,557 nucleotides encoding 22 tRNA genes, two rRNA genes, 13 protein-coding genes and two noncoding control regions (D-loop, OrigL). Phylogeographic analysis of closely related sequences of Cytochrome Oxydase C subunit I (COI) demonstrates high diversity among morphologically similar populations of C. nattereri . Corydoras nattereri is nested within a complex of populations currently assigned to C. paleatus and C. ehrhardti . Analysis of mitogenome structure demonstrated that an insertion of 21 nucleotides between the ATPase subunit-6 and COIII genes may represent a phylogenetically informative character associated with the evolution of the Corydoradinae.

The mitochondrial genome of Hypancistrus zebra (Isbrücker & Nijssen, 1991) (Siluriformes: Loricariidae), an endangered ornamental fish from the Brazilian Amazon

Hypancistrus zebra is an ornamental fish endemic to the Xingu river, Amazon basin, which is under the impact zone of the world’s fourth-largest hydroelectric dam. Illegal capture is another threat to this species. Despite its critical conservation status only two nucleotide sequences from this fish are publicly available on GenBank and on the BOLD System. Here, the nearly complete mitochondrial genome of H. zebra is described; totalizing 16,330 nucleotides, including the complete sequences of the two ribosomal RNA subunits, the 22 transfer RNAs and the 13 protein coding genes. The mitochondrial genome was assembled from transcriptome data, from seven organs, two individual fish, and to an average sequencing depth of 7245x. Seven nucleotide differences were found between the individual fish sequenced here-in, while four were detected among these individuals and the unique mitochondrial sequence publicly available. Additionally, 21 heteroplasmic sites were found among seven organs. This is the first quasi complete mitochondrial genome of a species belonging to the Peckoltia Clade, a Loricariidae phylogenetically problematic tribe. This genetic resource will be valuable in the efforts to elucidate the phylogenetic relationships among the Peckoltia Clade species, as well as it shall subsidize future practices aiming the conservation of this endangered species.

Reducing the information gap on Loricarioidei (Siluriformes) mitochondrial genomics

BackgroundThe 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.ResultsUsing 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.ConclusionsHerein 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.

Mitochondrial transcripts and associated heteroplasmies of Ancistrus spp. (Siluriformes: Loricariidae)

This data-set complements our paper entitled “The use of transcriptomic next-generation sequencing data to assembly mitochondrial genomes of Ancistrus spp. (Loricariidae)” [6]. Here, we present the nucleotide sequences of each transcript used for mitogenomes assembly, as well as tables presenting the location of each transcript in the mitogenomes; the frequency, location and codon position of the detected heteroplasmic sites; and the start/stop codons usage, UTR, CDS and poliA-tail length for each protein coding gene. Readers are referred to the paper cited above for data interpretation and discussion.