RESUMEN
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.
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Leporinus elongatus is an important commercial fish found in the La Plata and Paraná River basins. Next-generation sequencing was used to sequence the mitochondrial DNA (mtDNA) of L. elongatus. The mtDNA was assembled using the CLC Workbench software v. 9.0 and subsequently aligned to other 10 complete fish mitochondrial sequences to enable phylogenetic analysis using MEGA 7.0. The complete mtDNA molecule had 16,784 bp and its GC content was 43%. The mtDNA structure was similar to that of other vertebrates: two ribosomal RNA, 22 transfer RNA, 13 protein-coding genes, and a D-loop region containing 1115 bp. Phylogenetic analysis yielded a tree with high bootstrap value that was coherent with the current phylogeny proposed for Characiformes.
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The first complete mitochondrial genome (mtDNA) for the genus Bokermannohyla (Hylidae) is presented. The mtDNA contains 17,325 bp and is similar in size, gene content, and gene location to other hylid mitochondrial genomes described, with 2 rRNA, 22 tRNA, and 13 PCGs. The control region (D-loop) is shorter than in mtDNAs of hylids from Asia. A phylogenetic tree based on homologous genes did not corroborate the monophyly of Hylidae neither the recently proposed monophyly of Hyla and Dryophytes.
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Sporophila maximiliani, commonly known as Great-billed Seed-Finch or 'bicudo', is a trafficked bird in Brazil due to the species' beauty and singing, which is appreciated by breeders and collectors. Generally, the Environmental Military Police and IBAMA maintain enforcement actions, rescue work, and seizure of illegally traded of 'bicudo' specimens. The genomic DNA of one specimen was sequenced on MiSeq (Illumina) sequencer. The reads obtained were analyzed, trimmed, and de novo assembled using CLC Workbench® v9.0 (CLC Bio-Qiagen). The mitochondrial genome of S. maximiliani consisted of 16,765 base pairs, 2 ribosomal RNA, 22 transporter RNA, 13 protein-coding genes, and 1 control region. The molecular phylogeny demonstrated that the mitochondrial genome of S. maximiliani diverged from others related Passeriformes.
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Envenoming resulting from Loxosceles spider bites (loxoscelism) is a recognized public health problem in Brazil. However, the pathophysiology of loxoscelism caused by L. similis bites, which is widespread in Brazil, remains poorly understood. In the present work, the RNA sequencing (RNA-Seq - Next Generation sequencing - NGS) of the L. similis venom gland was performed to identify and analyze the sequences of the key component phospholipase D. The sequences were aligned based on their classical domains, and a phylogenetic tree was constructed. In the bioinformatics analysis, 23 complete sequences of phospholipase D proteins were found and classified as Loxtox proteins, as they contained the characteristic domains of phospholipase D: the active site, the Mg(2+)-binding domain, and the catalytic loop. Three phospholipase D sequences with non-canonical domains were also found in this work. They were analyzed separately and named PLDs from L. similis (PLD-Ls). This study is the first to characterize phospholipase D sequences from Loxosceles spiders by RNA-Seq. These results contribute new knowledge about the composition of L. similis venom, revealing novel tools that could be used for pharmacological, immunological, and biotechnological applications.
Asunto(s)
Araña Reclusa Parda , Proteínas de Insectos/metabolismo , Fosfolipasa D/metabolismo , Venenos de Araña/enzimología , Secuencia de Aminoácidos , Animales , Secuenciación de Nucleótidos de Alto Rendimiento , Proteínas de Insectos/genética , Fosfolipasa D/genética , Hidrolasas Diéster Fosfóricas/genética , Filogenia , Homología de Secuencia de Aminoácido , Venenos de Araña/genéticaRESUMEN
Mitochondrial complete genome (mtDNA) of Hoplias intermedius, commonly known as "traírão" is presented. DNA from a muscle tissue sample was sequenced by next-generation sequencing. To corroborate the results, phylogenetic analysis was performed with MEGA6 to compare the complete mitogenome of H. intermedius with genomes of other Characiformes species. The mtDNA molecule was circular and 16,629 bp in length. Gene content included 22 tRNA genes, 2 rRNA genes, 13 protein-coding genes and a D-loop noncoding region. All genes had ATG as the start codon. Six genes carried complete stop codons of AGG (COI), TGA (ND6) and TAA (ND1, ATPase 8, ND4L and ND5), while seven genes had incomplete stop codons. Phylogenetic relationships with other Ostariophysi species placed H. intermedius together with H. malabaricus as a monophyletic group belonging to the order Characiformes.
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Prochilodus spp. are important Brazilian freshwater migratory fishes with substantial economic and ecological importance. Prochilodus argenteus and Prochilodus costatus are morphologically similar and a molecular species delimitation is impaired due to high degree of sequence identity among the available genetic markers. Here, the complete mitochondrial genome of P. argenteus and P. costatus and their comparison to the mitogenome of P. lineatus are described. The three species displayed a similar mtDNA annotation. A phylogenetic analysis was performed with other Characiformes species. The genus Prochilodus was recovered as a monophyletic group, as well as the family Prochilodontidae, both with high bootstrap probability.
Asunto(s)
Characiformes/genética , ADN Mitocondrial/genética , Genoma Mitocondrial/genética , Animales , Characiformes/clasificación , Secuenciación de Nucleótidos de Alto Rendimiento , FilogeniaRESUMEN
This is the first complete mitochondrial genome of a Tityus species, although it is the most medically important genus in South America. Tityus serrulatus (Brazilian yellow scorpion) mtDNA revealed the same gene arrangement of three out of four other mitogenomes published by now for the same family (Centruroides limpidus, Mesobuthus gibbosus, M. martensii and Buthus occitanus). However, it presented many unique characteristics such as possession of Cox1 gene, different from all other protein-coding genes of scorpion mtDNA, starts with an atypical start codon (CTG). Moreover, no tRNA gene have complete typical secondary structure and the Tytius genome presented three non-coding regions longer than 100bp. Also, it contains the smallest scorpion 16S gene reported by now. Phylogenetic analysis using concatenated homologous genes confirmed Buthidae as a monophyletic clade and supports a monophyletic group including T. serrulatus and the other American species, C. limpidus.
Asunto(s)
Genoma Mitocondrial , Escorpiones/genética , Animales , Proteínas de Artrópodos/genética , ADN Mitocondrial/genética , Complejo IV de Transporte de Electrones/genética , Orden Génico , Secuenciación de Nucleótidos de Alto Rendimiento , Filogenia , ARN Ribosómico 16S/genética , Homología de Secuencia de Ácido Nucleico , Secuenciación Completa del GenomaRESUMEN
We report the complete mitochondrial genome of the fish Salminus brasiliensis, popularly known as dourado. It is a circular, 17,721 bp long DNA molecule, containing 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a non-coding Control Region of 2128 bp, a relatively large molecule when compared to other closely related fishes. All protein-coding genes are on the heavy strand, except for Nd6, and all have ATG as the start codon, except for Cox1 gene which has a GTG start codon. Seven protein-coding genes have incomplete stop codons (Nd2, Cox2, Atp6, Nd4, and Cytb have T- -, and Cox3 and Nd3 have TA-). TAG is the stop codon for Nd6 and AGG is the stop codon for Cox1.
Asunto(s)
Characiformes/genética , Genoma Mitocondrial , Animales , Codón Iniciador , Codón de Terminación , Bases de Datos Genéticas , Sistemas de Lectura Abierta/genética , ARN Ribosómico/química , ARN Ribosómico/genética , ARN de Transferencia/química , ARN de Transferencia/genéticaRESUMEN
Prochilodus lineatus (curimba) is an important Brazilian freshwater migratory fish with substantial economic importance in fishing. The complete mitochondrial genome of P. lineatus is 16,699 bp and contains 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes and one control region (D-loop). The mtDNA of P. lineatus is the first mitogenome of the Prochilodontidae family to be fully characterized. All of the PCGs in the mtDNA use the standard ATG start codon, with the exception of Cox1 that utilizes the GTG start codon. Six of the 13 PCGs contain TAA stop codons, two contain the incomplete stop codon TA- (Atp6 and Nd6), and five contain the incomplete stop codon T- - (Nd2, Cox2, Nd3, Nd4 and Cytb).