Complete mitochondrial genome sequence of
            <i>Piaractus mesopotamicus</i>
            (Holmberg, 1887)

Pimentel, Juliana da Silva Martins; Carmo, Anderson Oliveira do; Maciel, Danielle de Cássia Lima; Siqueira, Flávia de Faria; Kalapothakis, Evanguedes

doi:10.3109/19401736.2014.971297

Cited by 7 publications

(5 citation statements)

References 6 publications

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“…Only five out of 13 PCGs (ND1, ND2, ATPase8, ND4L and ND5) contained a TAA stop codon; four (COII, ND3, ND4 and Cytb) displayed incomplete termination codon (T-); three genes (ATPase6, COIII and ND6) displayed the incomplete TA-stop codon. Only COI presented AGG as stop codon, similar to others Characiformes (Siqueira et al 2014;Brandão-Dias et al 2016;Pimentel et al 2016); considered a vertebrate evolution (Osawa et al 1989). …”

supporting

confidence: 69%

“…The mitochondrial genome of L. elongatus was 16,784 bp (GenBank KU980144) solved with 205.16 folds of coverage. The GC content of the total sequence was 43%, with individual base content being: 29.9% A, 15.7% G, 27.1% T and 27.3% C. The mtDNA genome contains 2 rRNA and 22 tRNA genes, 13 protein-coding genes (PCGs) and a control region (D-loop) with 1115 bp, being consistent with mitochondrial genome structure of the fishes Carmo et al 2016;Chagas et al 2016;N uñez-Rodriguez et al 2016;Pimentel et al 2016;Resende et al 2016;Siqueira et al 2014). Only gene COI started with GTG codon, differing from all other PCGs that display the usual start codon ATG.…”

supporting

confidence: 66%

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Leporinus elongatus(Characiformes, Anostomidae): complete mtDNA sequence of an economically important fish from the Paraná and La Plata river basins

Bedore

Resende

Carmo

et al. 2017

Mitochondrial DNA Part B

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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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supporting

confidence: 69%

supporting

confidence: 66%

Leporinus elongatus(Characiformes, Anostomidae): complete mtDNA sequence of an economically important fish from the Paraná and La Plata river basins

Bedore

Resende

Carmo

et al. 2017

Mitochondrial DNA Part B

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“…Read representation was evaluated by mapping the cleaned reads back to generated assembly with BOWTIE2 v.2.3.4.3 (Langmead and Salzberg, 2012). A. hydrophila genome (Yang et al, 2016), zebrafish ribosomal RNA (rRNA) sequences and pacu mitochondrial genome (da Pimentel et al, 2014) were then downloaded from the NCBI (National Center for Biotechnology Information) database and mapped against the assembly using BOWTIE2 v.2.3.4.3 (Langmead and Salzberg, 2012) to remove any contamination. Redundancy was reduced using CD-HIT-EST v.4.6.8 software by clustering sequences at 95% identity (Li and Godzik, 2006).…”

Section: Data Processing and Analysismentioning

confidence: 99%

Transcriptome Profiling of Pacu (Piaractus mesopotamicus) Challenged With Pathogenic Aeromonas hydrophila: Inference on Immune Gene Response

et al. 2020

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Pacu (Piaractus mesopotamicus) is a Neotropical fish of major importance for South American aquaculture. Septicemia caused by Aeromonas hydrophila bacteria is currently considered a substantial threat for pacu aquaculture that have provoked infectious disease outbreaks with high economic losses. The understanding of molecular aspects on progress of A. hydrophila infection and pacu immune response is scarce, which have limited the development of genomic selection for resistance to this infection. The present study aimed to generate information on transcriptome of pacu in face of A. hydrophila infection, and compare the transcriptomic responses between two groups of time-series belonging to a disease resistance challenge, peak mortality (HM) and mortality plateau (PM) groups of individuals. Nine RNA sequencing (RNA-Seq) libraries were prepared from liver tissue of challenged individuals, generating ∼160 million 150 bp pair-end reads. After quality trimming/cleanup, these reads were assembled de novo generating 211,259 contigs. When the expression of genes from individuals of HM group were compared to individuals from control group, a total of 4,413 differentially expressed transcripts were found (2,000 upregulated and 2,413 downregulated candidate genes). Additionally, 433 transcripts were differentially expressed when individuals from MP group were compared with those in the control group (155 upregulated and 278 downregulated candidate genes). The resulting differentially expressed transcripts were clustered into the following functional categories: cytokines and signaling, epithelial protection, antigen processing and presentation, apoptosis, phagocytosis, complement system cascades and pattern recognition receptors. The proposed results revealing relevant differential gene expression on HM and PM groups which will contribute to a better understanding of the molecular defense mechanisms during A. hydrophila infection.

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“…Studies of vertebrate species have shown a mutation rate that exceeds, by multiple times, nuclear DNA mutation rates that may be due to a lack of repair mechanisms during replication [116]. The complete mtDNA sequences have been sequenced to facilitate analyses of molecular markers in many economically important Neotropical fish species, such as S.brasiliensis [117], P. mesopotamicus [118] and L. elongatus [119].The DNA of cytoplasmic organelles has a non-Mendelian inheritance, and the mtDNA must be considered a single locus in genetic investigations [94]. Inheritance occurs via the mitochondria of the oocyte from which an animal develops [120].…”

mentioning

confidence: 99%

Genetic Applications in the Conservation of Neotropical Freshwater Fish

Mastrochirico-Filho¹,

Freitas²,

Ariede³

et al. 2018

Biological Resources of Water

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Neotropical fish correspond to approximately 30% of all fish species worldwide. The diversity of fish species found in Neotropical basins reflects variations in life-history strategies and exhibition of particular morphological, physiological and ecological attributes. These attributes are mainly related to different forms of feeding, life maintenance and reproduction. Today, fish populations are being threatened by anthropogenic actions that are having a visible impact on the natural state of continental aquatic ecosystems. The main causes are overfishing, non-native species introduction, reservoir-dam systems, mining, pollution and deforestation. The biology and population dynamics of the species are still unclear due to lack of research. Genetic tools can be useful resources for the conservation of Neotropical fish species in several ways. Molecular genetic markers are considered powerful tools to identify cryptic and hybrid fish and also allow the evaluation of the genetic variability and structure of populations of Neotropical ichthyofauna. Several analyses of molecular markers have been performed on Neotropical fish, including allozyme analysis, restriction fragment length polymorphisms in regions of DNA (RFLP), randomly amplified polymorphic DNA (AFLP), randomly amplified polymorphic DNA (RAPD), microsatellites, single nucleotide polymorphisms (SNPs) and mitochondrial DNA (mtDNA) markers. In order to analyse a high number of markers, next generation sequencing has allowed researchers to generate a large amount of genomic information that can be applied to the conservation of Neotropical fish.Keywords: molecular markers, genetic conservation, Neotropical ichthyofauna, overfishing, dam © 2018 The Author(s). Licensee IntechOpen. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Rivers of the Neotropical regionThe distribution of freshwater fish around the world was mediated by historical climatic and geological events at different time points. Today, each global region has distinct patterns of distribution due to physical barriers obstructing species dispersion, representing different tolerances to environmental variables [1]. The tropics of the American continent are well known for their high biodiversity. This is due to habitat heterogeneity and a complex geological history. The Neotropical region is a biogeographic region that comprises Central America (including the southern part of Mexico and the peninsula of Baja California), the south of Florida, the Caribbean and South America. The origin and evolution of the Neotropical region arose through a process of synergism between its fauna that experienced local rainfall variations and gradual climate change resulting in a mosaic of habitats controlled by river migrations, sea-level fluctuations, local dryness and local uplifts [2,3].Regional geo...

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Complete mitochondrial genome sequence of Piaractus mesopotamicus (Holmberg, 1887)

Cited by 7 publications

References 6 publications

Leporinus elongatus(Characiformes, Anostomidae): complete mtDNA sequence of an economically important fish from the Paraná and La Plata river basins

Leporinus elongatus(Characiformes, Anostomidae): complete mtDNA sequence of an economically important fish from the Paraná and La Plata river basins

Transcriptome Profiling of Pacu (Piaractus mesopotamicus) Challenged With Pathogenic Aeromonas hydrophila: Inference on Immune Gene Response

Genetic Applications in the Conservation of Neotropical Freshwater Fish

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