De novo assembly and characterization of a highly degenerated ZW sex chromosome in the fish Megaleporinus macrocephalus.

Background: Megaleporinus macrocephalus (piauçu) is a Neotropical fish within Characoidei that presents a well-established heteromorphic ZZ/ZW sex determination system and thus constitutes a good model for studying W and Z chromosomes in fishes. We used PacBio reads and Hi-C to assemble a chromosome-level reference genome for M. macrocephalus.

Characterization of the myostatin gene in the neotropical species Piaractus mesopotamicus and the possibility of its use in genetic improvement programs.

Background: The myostatin gene has played an important role in the genetic improvement of the main species of economic importance; however, it has not yet been described for some Neotropical fish essential for aquaculture. This study aimed to characterize the myostatin gene of pacu, Piaractus mesopotamicus, and investigate the association of a microsatellite marker in this gene with the weight of fish.

Methods And Results: The myostatin gene sequence was obtained after following a RACE-PCR strategy based on a partial mRNA sequence available in the GenBank database and the alignment of myostatin sequences from other fish species.

Accuracy of genotype imputation of a low-density SNP array for the Amazon fish Colossoma macropomum.

In South America, Tambaqui (Colossoma macropomum) stands as the primary target for aquaculture, yet breeding programs for this Amazon native species are in their early stages. While high-density single nucleotide polymorphism (SNP) arrays are pivotal for aquaculture breeding, their costs can be prohibitive for non- or semi-industrial species. To overcome this, a cost-effective approach involves developing low-density SNP arrays followed by genotype imputation to higher densities.

A high-density linkage map and sex-determination loci in Pacific white shrimp (Litopenaeus vannamei).

Background: Expansion of genomic resources for the Pacific white shrimp (Litopenaeus vannamei), such as the construction of dense genetic linkage maps, is crucial for the application of genomic tools in order to improve economically relevant traits. Sexual dimorphism exists in Pacific white shrimp, and the mapping of the sex-determination region in this species may help in future reproductive applications. We have constructed male, female, and sex-averaged high-density genetic maps using a 50 K single-nucleotide polymorphism (SNP) array, followed by a genome-wide association study (GWAS) to identify genomic regions associated with sex in white shrimp.

Computer vision system using deep learning to predict rib and loin yield in the fish Colossoma macropomum.

Computer vision system (CVSs) are effective tools that enable large-scale phenotyping with a low-cost and non-invasive method, which avoids animal stress. Economically important traits, such as rib and loin yield, are difficult to measure; therefore, the use of CVS is crucial to accurately predict several measures to allow their inclusion in breeding goals by indirect predictors. Therefore, this study aimed (1) to validate CVS by a deep learning approach and to automatically predict morphometric measurements in tambaqui and (2) to estimate genetic parameters for growth traits and body yield.

The Satellite DNA Catalogues of Two Serrasalmidae (Teleostei, Characiformes): Conservation of General satDNA Features over 30 Million Years.

Satellite DNAs (satDNAs) are tandemly repeated sequences that are usually located on the heterochromatin, and the entire collection of satDNAs within a genome is called satellitome. Primarily, these sequences are not under selective pressure and evolve by concerted evolution, resulting in elevated rates of divergence between the satDNA profiles of reproductive isolated species/populations. Here, we characterized two additional satellitomes of Characiformes fish ( and ) that diverged approximately 30 million years ago, while still retaining conserved karyotype features.

Genome-wide association study of host resistance to the ectoparasite Ichthyophthirius multifiliis in the Amazon fish Colossoma macropomum.

Background: Tambaqui, Colossoma macropomum, is the most important native fish species farmed in South America, particularly in Brazil, where its production is limited in the southern and southeastern regions due to disease outbreaks caused by the parasite Ichthyophthirius multifiliis. Therefore, genome level analysis to understand the genetic architecture of the host resistance against I. multifiliis is fundamental to improve this trait in tambaqui.

Genomic selection signatures in farmed from tropical and subtropical regions in South America.

Tambaqui or cachama () is one of the most important neotropical freshwater fish used for aquaculture in South America, and its production is concentrated at low latitudes (close to the Equator, 0°), where the water temperature is warm. Therefore, understanding how selection shapes genetic variations and structure in farmed populations is of paramount importance in evolutionary biology. High-throughput sequencing to generate genome-wide data for fish species allows for elucidating the genomic basis of adaptation to local or farmed conditions and uncovering genes that control the phenotypes of interest.

Use of Molecular Genetic Methods to Reduce the Risk of Incorrect Identification of Fish Strains in Brazilian Aquaculture.

The identification of fish species using traditional methods is generally based only on morphological characteristics and these methods are currently under review. This kind of identification of hybrid fishes solely based on their morphologies may be unreliable, especially when the samples include juveniles and post-F1 lineage fishes. Therefore, in the present study, we used molecular markers to accurately identify the fish species of economic interest that are used as materials in the projects developed in research institutions.

Sex-Dependent Inheritance of B Chromosomes in (Teleostei, Characiformes) Revealed by Directed Crossings.

B chromosomes are additional dispensable elements to the standard chromosomal set of an organism. In most cases, their transmission differs from Mendelian patterns, leading to their accumulation or extinction. The present study aimed to describe, for the first time, the transmission pattern of B chromosome in a population of through directed crosses, as well as to analyze the populational dynamics of B chromosome.

Development of a multi-species SNP array for serrasalmid fish Colossoma macropomum and Piaractus mesopotamicus.

Scarce genomic resources have limited the development of breeding programs for serrasalmid fish Colossoma macropomum (tambaqui) and Piaractus mesopotamicus (pacu), the key native freshwater fish species produced in South America. The main objectives of this study were to design a dense SNP array for this fish group and to validate its performance on farmed populations from several locations in South America. Using multiple approaches based on different populations of tambaqui and pacu, a final list of 29,575 and 29,612 putative SNPs was selected, respectively, to print an Axiom AFFYMETRIX (THERMOFISHER) SerraSNP array.

ETosis in tambaqui Colossoma macropomum: A programmed cell death pathway and approach of leukocytes immune response.

Tambaqui Colossoma macropomum is the most cultivated native fish in South America and Aeromonas hydrophila is one of the main bacteria infecting tropical fish. Despite the economic importance of this round fish, to date, there has been a paucity of investigations into haematological changes in tambaqui. In this study, detailed blood analyses (0 h, 6 h, 24 h, 7 d and 14 d) following intraperitoneal challenge with A.

Haplotypes traceability and genetic variability of the breeding population of pacu (Piaractus mesopotamicus) revealed by mitochondrial DNA.

The main objective of this study was to estimate the genetic diversity levels and haplotype traceability in pacu Piaractus mesopotamicus from the breeding program located in Brazil by analyses of the mitochondrial DNA control region (mtDNA). Moreover, broodstocks from eight commercial fish farms were used for comparative evaluation, four from Brazil (Br1-Br4) and four from Argentina (Ar1-Ar4). The descriptive results revealed 47 polymorphic sites and 51 mutations, which evidenced 34 haplotypes.

Corrigenda: Cytogenetic markers as a tool for characterization of hybrids of Baird & Girard, 1854 and Eigenmann, 1907. Comparative Cytogenetics 14(2): 231-242. https://doi.org/10.3897/CompCytogen.v14i2.49513.

[This corrects the article DOI: 10.3897/CompCytogen.v14i2.

Patterns of the innate immune response in tambaqui Colossoma macropomum: Modulation of gene expression in haemorrhagic septicaemia caused by Aeromonas hydrophila.

The production of tambaqui Colossoma macropomum has recently reached a milestone, being considered the main native species produced in South American continental waters. Despite the importance of this fish, its immunity is not well understood. In this study we established some patterns of innate immunity for the species via two experiments.

Development of a SNP linkage map and genome-wide association study for resistance to Aeromonas hydrophila in pacu (Piaractus mesopotamicus).

Background: Pacu (Piaractus mesopotamicus) is one of the most important Neotropical aquaculture species from South America. Disease outbreaks caused by Aeromonas hydrophila infection have been considered significant contributors to the declining levels of pacu production. The current implementation of genomic selection for disease resistance has been adopted as a powerful strategy for improvement in fish species.

Motile Aeromonas septicemia in tambaqui Colossoma macropomum: Pathogenicity, lethality and new insights for control and disinfection in aquaculture.

Tambaqui Colossoma macropomum is the most produced native fish in South America. Besides the lack of knowledge regarding bacteria-stricken diseases, the unappropriated using of off-label therapies are common. In this study, Aeromonas hydrophila pathogenicity for tambaqui was first established by Koch's Postulate.

Comparative eye and liver differentially expressed genes reveal monochromatic vision and cancer resistance in the shortfin mako shark (Isurus oxyrinchus).

The shortfin mako, Isurus oxyrinchus is an oceanic pelagic shark found worldwide in tropical and subtropical waters. However, the understanding of its biology at molecular level is still incipient. We sequenced the messenger RNA isolated from eye and liver tissues.

Transcriptome Profiling of Pacu () Challenged With Pathogenic : Inference on Immune Gene Response.

Pacu () is a Neotropical fish of major importance for South American aquaculture. Septicemia caused by 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 infection and pacu immune response is scarce, which have limited the development of genomic selection for resistance to this infection.

Cytogenetic markers as a tool for characterization of hybrids of Baird & Girard, 1854 and Eigenmann, 1907.

Baird et Girard, 1854, is one of the largest genera in the family Characidae and comprises 177 valid species. This genus has been the focus of cytogenetic studies primarily owing to the presence of B chromosomes and high karyotypic diversity among different populations. The intense genetic variability in is one of the factors responsible for the occurrence of species complexes, which are groups (1) with certain difficulties in establishing common genetic pools or (2) belonging to different cryptic species.

Publisher Correction: High-throughput analysis unveils a highly shared satellite DNA library among three species of fish genus Astyanax.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Assessing Genetic Diversity for a Pre-Breeding Program in by SNPs and SSRs.

The pacu () is a Neotropical fish with remarkable productive performance for aquaculture. Knowledge of genetic resources in Neotropical fish is essential for their applications in breeding programs. The aim of this study was to characterize the genetic diversity of seven farmed populations of pacu which will constitute the basis for a broodstock foundation for coming breeding programs in Brazil.

Satellitome landscape analysis of Megaleporinus macrocephalus (Teleostei, Anostomidae) reveals intense accumulation of satellite sequences on the heteromorphic sex chromosome.

The accumulation of repetitive DNA sequences on the sex-limited W or Y chromosomes is a well-known process that is likely triggered by the suppression of recombination between the sex chromosomes, which leads to major differences in their sizes and genetic content. Here, we report an analysis conducted on the satellitome of Megaleporinus macrocephalus that focuses specifically on the satDNAs that have been shown to have higher abundances in females and are putatively located on the W chromosome in this species. We characterized 164 satellite families in M.