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Colossoma macropomum, known as “tambaqui”, is the largest Characiformes fish in the Amazon River Basin and a leading species in Brazilian aquaculture and fisheries. Good quality meat and excellent adaptability to culture systems are some of its remarkable farming features. To support studies into the genetics and genomics of the tambaqui, we have produced the first high-quality genome for the species. We combined Illumina and PacBio sequencing technologies to generate a reference genome, assembled with 39× coverage of long reads and polished to a consensus quality value (QV) of 36 with 130× coverage of short reads. The genome was assembled into 1269 scaffolds (a total of 1,221,847,006 bases), with a scaffold N50 size of 40 Mb, where 93% of all assembled bases were placed in the largest 54 scaffolds corresponding to the diploid karyotype of the tambaqui. Furthermore, the NCBI Annotation Pipeline annotated genes, pseudogenes, and non-coding transcripts using the RefSeq database as evidence, guaranteeing a high-quality annotation. A Genome Data Viewer for the tambaqui was produced, which will benefit groups interested in exploring the unique genomic features of the species. The availability of a highly accurate genome assembly for tambaqui provides the foundation for the discovery of novel ecological and evolutionary insights, and is a helpful resource for aquaculture.

We describe key production-related traits of trahira (Hoplias malabaricus), an aquaculture candidate species, in a semi-intensive fish farming system. We quantified growth from hatch through grow-out at two stocking densities and evaluated fillet protein, lipids and fatty-acid content. We made 2430 observations of growth and morphometrics on 270 juvenile fish allocated to four fish ponds, two at 5 fish/m2 (90 animals) and two at 10 fish/m2 (180 animals) through 11 months. The fish reached an average length of 27.5 cm (±0.38) and 27.0 cm (±0.24), and weight of 263.0 g (±10.54) and 246.7 g (±6.89), respectively, at the low and high densities. There was no significant difference in weight (P > 0.05) between the densities for any of the parameters assessed, and hence the same growth curve applied to both densities (A = 292.9; B = 28.1; and K = 0.65). Standard length, however, differed significantly (P

Abstract The dusky grouper, Epinephelus marginatus, is a well-known and widespread marine fish assessed as endangered by the International Union for the Conservation of Nature. Analyzing the genetic diversity of this species is, therefore, of utmost importance and necessary for conservation purposes. Microsatellites are molecular tools with advantages that are ideal for population analyses. This study provides the first set of species-specific microsatellite loci for E. marginatus that can be applied when assessing both intra- and interpopulation genetic variation. Twenty microsatellite loci were isolated and characterized for the dusky grouper by genotyping 20 individuals obtained from the North Eastern Atlantic Ocean (n = 4) and from the South Western Atlantic Ocean (n = 16). The number of alleles per locus varied from 2 to 11, while the observed and expected heterozygosities ranged from 0.25 to 0.94 and 0.34 to 0.89, respectively. The polymorphic information content varied from moderately to highly informative. This suite of markers provides the first specific nuclear tools for E. marginatus and, thus, allows to assess with more specificity different populations’ structures.

ABSTRACT The capture of live bait for sport fishing is an important activity for fishing communities. The main species used for this purpose are members of the genus Gymnotus, which comprises numerous species of cryptic nature that are difficult to identify based on external morphology. The aims of this work were to identify through partial sequences of the COI gene Gymnotus species fished in the Jacaré-Guaçu River, SP, and to develop a molecular diagnostic approach using PCR-RFLP to identify these species. Partial COI sequences were compared to those of other species deposited in GenBank. The sequences were assessed in the NEBCutter program to determine restriction sites in the sequence and the enzymes to be tested. Phenetic analysis performed by Neighbor-Joining method showed that the specimens sampled belong to two species preliminary identified here as G. cf. sylvius and G. cf. cuia, with G. cf. sylvius accounting for 95.2% of the individuals sampled. The enzymes NlaIII and SacI generated fragments that allowed distinguishing the Gymnotus species using PCR-RFLP. This analysis can be used to accurately identify these species, which is fundamental for monitoring Gymnotus fishing and assessing the conservation of this genetic resource.

Aim: This study aimed to assess the spatial and seasonal variation of the water quality and physical habitat characteristics along the upper-middle stretch of the Paraitinga River, a tributary of Tietê River, considering the potential influence of different riparian conditions along the stretch studied.MethodsSixteen sites with different riparian vegetation, including native forest, secondary forest, pasture, and eucalyptus were sampled during the dry and rainy seasons of 2004/2005, before the damming of the Paraitinga Reservoir. Several physicochemical and habitat parameters were determined and data analyzed in relation to spatial distribution and potential influence of riparian conditions.ResultsWater quality parameters were in general within the limits established by CONAMA for Class 2 waters, except for turbidity and total phosphorus. There were seasonal and spatial differences in the limnological parameters along the stretch studied and apparently they were related to point specific influences associated with land use and canopy cover. Habitat characteristics were markedly different between the upper and middle river stretches, especially in relation to depth, width, substrate and canopy cover.ConclusionsAlthough a direct influence on the observed variables could not be attributed solely to the riparian vegetation, vegetation cover seemed to affect particular stream characteristics. Open pasture and eucalyptus sites were subject to point specific effects that caused phosphorus inputs and higher turbidity and temperature, and showed different morphological features, suggesting that land use at the sub-watershed scale was an important factor affecting stream conditions.

RT-PCR was used for amplifying Piaractus mesopotamicus growth hormone (GH) cDNA obtained from mRNA extracted from pituitary cells. The amplified fragment was cloned and the complete cDNA sequence was determined. The cloned cDNA encompassed a sequence of 543 nucleotides that encoded a polypeptide of 178 amino acids corresponding to mature P. mesopotamicus GH. Comparison with other GH sequences showed a gap of 10 amino acids localized in the N terminus of the putative polypeptide of P. mesopotamicus. This same gap was also observed in other members of the family. Neighbor-joining tree analysis with GH sequences from fishes belonging to different taxonomic groups placed the P. mesopotamicus GH within the Otophysi group. To our knowledge, this is the first GH sequence of a Neotropical characiform fish deposited in GenBank.

O objetivo desse trabalho foi avaliar a variabilidade genética de duas variedades de tilápia nilótica (Oreochromis niloticus), Chitralada e Red Stirling, e de suas progênies submetidas a programas de melhoramento genético, em sistemas intensivos de cultivo por meio de marcadores microssatélites. Foram utilizados 30 animais de cada variedade parental, 30 animais híbridos (CH), provenientes do cruzamento entre as variedades Chitralada e Red Stirling, e 30 animais (RR) provenientes do cruzamento entre os parentais da variedade Red Stirling. Utilizaram-se cinco microssatélites: UNH104, UNH108, UNH118, UNH222 e UNH231. Observaram-se baixos índices de endogamia, com valores de F IS negativo para as duas variedades e seus cruzamentos. Verificou-se diferença genética entre as duas variedades, obtida pelo cálculo do índice de fixação de alelos (F ST = 0,131 e R ST = 0,130). As variedades parentais Chitralada e Red Stirling apresentaram 24,4% de distância genética, o que se refletiu na presença de vigor híbrido com 23,5% de incremento em rendimento no plantel CH.The objective of this work was to evaluate the genetic variability of two Nile tilapia strains (Oreochromis niloticus), Chitralada and Red Stirling, as well as its offsprings submitted to genetic enhancement programs, in intensive systems farming by microsatellites markers. Thirty individuals of each parental strain, 30 crossbred (CH) individuals from Chitralada and Red Stirling strains, and 30 individuals from Red Stirling progeny (RR) were used. Five microsatellites loci were utilized: UNH104, UNH108, UNH118, UNH222 e UNH231. Low values of inbreeding were observed with a negative F IS in both strains and their crossings. Genetic differences between the two strains were detected through F ST = 0.131 and R ST = 0.130. The parental strains Chitralada and Red Stirling presented 24.4% of genetic distance, which produced 23.5% of hybrid vigor in the CH stock.

Random amplified polymorphic DNA (RAPD) markers were used to investigate the genetic relationship among nests of the carpenter ant, Camponotus rufipes, located in the same area. Five random oligodecamers were used to amplify DNA from 108 ant workers collected from six nests. A total of 47 RAPD markers were identified, which revealed low levels of genetic differentiation among nests (Fst = 0.00218) and a low average Shannon index (0.3727) among workers within nests. These results together suggest that the C. rufipes nest may be formed by a single, once-mated queen and that nests produced by queens that are genetically related tend to keep their nests in close proximity to one other.

Genetic variation of Salminus hilarii was assessed by screening microsatellite loci and mitochondrial D-loop DNA across four sampling in the upper rio Paraná basin of Brazil. Genetic diversity - measured as mean expected heterozygosity (0.904) and mean number of alleles across populations (13.7) - was reasonably high. Differentiation of microsatellite allele frequencies among populations was shown to be low but significant by AMOVA Φ ST (0.0192), and high by D EST (0.185). D-loop variation was high, with haplotypic diversity of 0.950 and nucleotide diversity of 0.011. Mitochondrial DNA-based estimates for population differentiation were high, with an overall Φ ST of 0.173. The results of tests of nuclear and mitochondrial variation yielded no unequivocal inference of historical demographic bottleneck or expansion. Genetic differentiation observed among S. hilarii populations in the rio Grande may be caused by a combination of historical differentiation and recent gene-flow disruption caused by the dams followed by reproduction of isolated spawning assemblages in mid-sized tributaries of the respective reservoirs. We present spatially more intensive sampling of S. hilarii populations across the rio Paraná basin in order to more effectively distinguish between historical and contemporary differentiation.

Piabanha (Brycon insignis) is a freshwater fish species from the drainages in Southeastern Brazil. During the 1950s, it was an important economic and food resource for local populations, but dramatic and continuous environmental degradation seriously jeopardized the B. insignis populations in the region. Microsatellite markers were used to assess the genetic structure of wild populations of B. insignis and compare the genetic variability and integrity of the wild populations with a captive population. Samples of DNA from 208 specimens from geographically isolated populations were analyzed. Population genetic structure was investigated using F ST, R ST estimates as well as AMOVA. All five loci used in this study were polymorphic with observed heterozygosity ranging from 0.77 (± 0.15) to 0.88 (± 0.07) in the wild population and 0.90 (± 0.09) in the captive population and the allelic richness average were 7.56 (± 0.27) and 5.80 (± 1.02), respectively. Overall genetic differences were significantly partitioned among populations (F ST = 0.072, p = 0.034). Evidence of a genetic bottleneck was found in some of the wild populations, but especially in the captive population. The results showed that genetic variability still can be found in B. insignis populations which are currently structured possibly due to anthropic actions. The implications of these findings for the management and conservation of B. insignis populations are discussed.

Abstract Snails of the genus Stramonita are commonly found in the rocky intertidal habitat of the western Atlantic Ocean coast. They belong to a monophyletic taxon that occurs along the tropical and warm-temperate Atlantic and eastern Pacific rocky shores. This genus comprises different valid species and members of the S. haemastoma complex. In the present study, samples of Stramonita were collected from three different regions of southeastern Brazil. Partial sequences of two mitochondrial genes, COI and 16S rRNA, were used to compare nucleotides sequences between Stramonita specimens. Levels of nucleotide divergence greater than 2% across the three sampled regions were used for differentiation at the species level. One of the identified species was S. brasiliensis, which has recently been described by molecular analysis; the other species may represent S. haemastoma, not yet described in the southeastern Brazilian coast.