Transcriptome analysis of reproductive tract tissues of male river prawn Macrobrachium americanum.

BACKGROUND: The river prawn, Macrobrachium americanum (M. americanum), is one of the largest prawns of the genus in Latin America and is an amphidromous species distributed along the Pacific coast of America. This prawn has commercial value due to its size and taste, making it a good option for aquaculture production. Its culture has been attempted in ponds and concrete tanks, but no successful technique can still support commercial production. Understanding the mechanisms that regulate reproduction at the molecular level is very important. This knowledge can provide tools for manipulating transcripts, which could increase the number or size of animals in the culture. Our understanding of the mechanism that regulates the reproduction of M. americanum at the molecular level is limited. AIM: Perform and analyze the transcriptome assembly of the testes, vas deferens, and terminal ampulla of M. americanum. to provide new molecular information about its reproduction. METHODS AND RESULTS: The cDNA library was constructed and sequenced for each tissue to identify novel transcripts. A combined transcriptome with the three tissues was assembled using Trinity software. Unigenes were annotated using BLASTx and BLAST2GO. The transcriptome assembly generated 1,059,447 unigenes, of which 7222 genes had significant hits (e-value < 1 × 10-5) when compared against the Swiss-Prot database. Around 75 genes were related to sex determination, testis development, spermatogenesis, spermiogenesis, fertilization, maturation of testicular cells, neuropeptides, hormones, hormone receptors, and/or embryogenesis. CONCLUSIONS: These results provide new molecular information about M. americanum reproduction, representing a reference point for further genetic studies of this species.

Chromosome-Level Genome Assembly of the Blacktail Brush Lizard, Urosaurus nigricaudus, Reveals Dosage Compensation in an Endemic Lizard.

Urosaurus nigricaudus is a phrynosomatid lizard endemic to the Baja California Peninsula in Mexico. This work presents a chromosome-level genome assembly and annotation from a male individual. We used PacBio long reads and HiRise scaffolding to generate a high-quality genomic assembly of 1.87 Gb distributed in 327 scaffolds, with an N50 of 279 Mb and an L50 of 3. Approximately 98.4% of the genome is contained in 14 scaffolds, with 6 large scaffolds (334-127 Mb) representing macrochromosomes and 8 small scaffolds (63-22 Mb) representing microchromosomes. Using standard gene modeling and transcriptomic data, we predicted 17,902 protein-coding genes on the genome. The repeat content is characterized by a large proportion of long interspersed nuclear elements that are relatively old. Synteny analysis revealed some microchromosomes with high repeat content are more prone to rearrangements but that both macro- and microchromosomes are well conserved across reptiles. We identified scaffold 14 as the X chromosome. This microchromosome presents perfect dosage compensation where the single X of males has the same expression levels as two X chromosomes in females. Finally, we estimated the effective population size for U. nigricaudus was extremely low, which may reflect a reduction in polymorphism related to it becoming a peninsular endemic.

Identification of a novel polyomavirus in wild Sonoran Desert rodents of the family Heteromyidae.

Rodents are the largest and most diverse group of mammals. Covering a wide range of structural and functional adaptations, rodents successfully occupy virtually every terrestrial habitat, and they are often found in close association with humans, domestic animals, and wildlife. Although a significant amount of research has focused on rodents' prominence as known reservoirs of zoonotic viruses, there has been less emphasis on the viral ecology of rodents in general. Here, we utilized a viral metagenomics approach to investigate polyomaviruses in wild rodents from the Baja California peninsula, Mexico, using fecal samples. We identified a novel polyomavirus in fecal samples from two rodent species, a spiny pocket mouse (Chaetodipus spinatus) and a Dulzura kangaroo rat (Dipodomys simulans). These two polyomaviruses represent a new species in the genus Betapolyomavirus. Sequences of this polyomavirus cluster phylogenetically with those of other rodent polyomaviruses and two other non-rodent polyomaviruses (WU and KI) that have been identified in the human respiratory tract. Through our continued work on seven species of rodents, we endeavor to explore the viral diversity associated with wild rodents on the Baja California peninsula and expand on current knowledge of rodent viral ecology and evolution.

DNA barcoding reveals global and local influences on patterns of mislabeling and substitution in the trade of fish in Mexico.

Mislabeling of seafood is a global phenomenon that can misrepresent the status and level of consumption of wild fish stocks while concealing the use of many other wild species or those originating from aquaculture and sold as substitutes. We conducted a DNA barcoding study in three cities within Mexico (Mazatlan, Mexico City and Cancun) and sequenced the COI gene in 376 fish samples sold as 48 distinct commercial names at fish markets, grocery stores, and restaurants. Our goal was to identify the main species sold, their mislabeling rates and the species most used as substitutes. Overall, the study-wide mislabeling rate was 30.8% (95% CI 26.4-35.6). Half of the samples collected belonged to five species traded globally (yellowfin tuna, Atlantic salmon, mahi, swai, and tilapia), most of them with important aquaculture or ranching production levels. These species were commonly used as substitutes for other species and showed low mislabeling rates themselves (≤ 11%, except mahi mahi with 39% mislabeling). The other half of the samples revealed nearly 100 species targeted by small-scale fishers in Mexico and sold under 42 distinct commercial names. Popular local commercial names (dorado, marlin, mero, robalo, mojarra, huachinango, pargo, sierra) showed the highest mislabeling rates (36.3% to 94.4%) and served to sell many of the 53 species identified as substitutes in our study. We discuss the observed patterns in relation to landing and import data showing differences in availability of commercial species and the links to explain observed mislabeling rates and the use of a species as a substitute for other species. We also outline some of the implications of establishing a labeling and traceability standard as an alternative to improve transparency in the trade of seafood products in Mexico.

New microsatellite loci for estimating genetic diversity and structure in Octopus hubbsorum from Nayarit, México.

BACKGROUND: Octopus hubbsorum Berry, 1953 is the most important species for commercial fishing in the Mexican Pacific. However, there is a lack of information regarding population structure that could have important management implications. We tested 44 microsatellite loci in O. hubbsorum by cross-amplification from O. bimaculatus. METHODS AND RESULTS: Genetic diversity and structure was tested over 30 octopus sampled from Santa Cruz de Miramar (Nayarit, México). A total of 11 loci were successfully amplified. All loci were polymorphic with the number of effective alleles ranging from 2.13 to 23.14, while three loci significantly deviated from Hardy-Weinberg equilibrium. No significant LD was observed between pairs of loci (P ≥ 0.05). The application of the new markers in a O. hubbsorum population from Santa Cruz de Miramar Nayarit, México, did not showed Wahlund or isolate breaking effects due to the mixing of distinct populations. CONCLUSIONS: The loci were useful to estimate levels of pairwise relatedness and to discard the presence of recent demographic bottlenecks in the population. We consider that eight microsatellites are adequate from the 11 amplified loci.

Multiple drivers behind mislabeling of fish from artisanal fisheries in La Paz, Mexico.

Seafood mislabeling has the potential to mask changes in the supply of species due to overfishing, while also preventing consumers from making informed choices about the origin, quality and sustainability of their food. Thus, there is a need to understand mislabeling and analyze the potential causes behind it to propose solutions. We conducted a COI DNA barcoding study in La Paz, Baja California Sur, Mexico, with 74 samples from fish markets and 50 samples from restaurants. We identified 38 species sold under 19 commercial names, from which at least ∼80% came from local small-scale fisheries. Overall, 49 samples, representing 40% (95% CI [31.4-48.3]) were considered mislabeled in our samples. Based on analyses where species were assigned to three price categories, economic incentives were associated with approximately half of the mislabeling events observed, suggesting that other motivating factors might simultaneously be at play. Using a network approach to describe both mislabeling (when species are mislabeled as the focal species) and substitution (when the focal species is used as substitute for others), we calculated proxies for the net availability of each species in the market. We found that local fish landings were a significant predictor of the net availability of the 10 most important commercial species at retail, but this true availability was masked to the eyes of the final consumer by both mislabeling and substitution. We hypothesize that the level of supply of each species could help explain mislabeling and substitution rates, where species in low supply and high demand could show higher mislabeling rates and rarely be used as substitutes, while species in high supply and low demand could be used as substitutes for the preferred species. Other factors affecting mislabeling include national regulations that restrict the fishing or commercialization of certain species and local and global campaigns that discourage specific patterns of consumption. We discuss how these factors might influence mislabeling and propose some solutions related to communication and education efforts to this local and global challenge.

Drivers for genetic structure at different geographic scales for Pacific red snapper (Lutjanus peru) and yellow snapper (Lutjanus argentiventris) in the tropical eastern Pacific.

The tropical eastern Pacific (TEP) is a highly dynamic region and a model system to study how habitat discontinuities affect the distribution of shorefishes, particularly for species that display ontogenetic habitat shifts, including snappers (Lutjanidae). To evaluate the genetic structure of the Pacific red snapper (Lutjanus peru) and the yellow snapper (Lutjanus argentiventris) throughout their distribution range along the TEP, 13 and 11 microsatellite loci were analysed, respectively. The genetic diversity of L. peru (N = 446) and L. argentiventris (N = 170) was evaluated in 10 and 5 localities, respectively, showing slightly higher but non-significant values in the Gulf of California for both species. The genetic structure analysis identified the presence of significant genetic structure in both species, but the locations of the identified barriers for the gene flow differed between species. The principal driver for the genetic structure at large scales >2500 km was isolation by distance. At smaller scales (<250 km), the habitat discontinuity for juveniles and adults and the environmental differences throughout the distribution range represented potential barriers to gene flow between populations for both species.

Fisheries management tools to support coastal and marine spatial planning: A case study from the Northern Gulf of California, Mexico.

A management approach was developed that combined spatial and non-spatial tools to inform a Coastal and Marine Spatial Planning Process (CMSP) in the Puerto Peñasco-Puerto Lobos Coastal Corridor, Northern Gulf of California, Sonora, Mexico. Four fisheries management tools were applied with an emphasis on ecosystem level management for eleven small-scale fisheries. Two spatial management tools, using a spatial prioritization approach, were combined with a permit regularization process, a non-spatial quota prioritization, and a tradeoff analysis in a novel way: • Locally Managed Marine Areas were developed, these are spatial areas where individual community fishermen are assigned the rights to harvest and manage specific fisheries within defined geographic areas. • Fishery refuges that incorporate information on fisheries, ecological importance, and connectivity. • A non-spatial quota prioritization process using a framework for the integrated assessment of stocks, encompassing a vulnerability analysis, a sustainability analysis, and a management framework analysis. • A trade-off analysis of the combination of these different management tools, using an Atlantis ecosystem model for the northern Gulf of California, that tested the ecosystem effects of alternative scenarios to assess benefits in support of ecosystem-based management.

Intestinal Microbiota Analyses of Litopenaeus vannamei During a Case of Atypical Massive Mortality in Northwestern Mexico.

This study investigated the intestinal microbial community structure of Litopenaeus vannamei at six different stages during shrimp farming. Our goal was to elucidate the bacterial profile and the changes in the relative abundance of taxa during an atypical massive mortality event in Sonora, Mexico. High-throughput sequencing of the 16S rRNA gene and denaturing gradient gel electrophoresis showed that Vibrionaceae was persistent with high relative abundances in the intestine from cultivated shrimp during all the studied stages. The massive mortality observed at day 63 could be related to an overabundance of different Operational Taxonomic Units (OTUs) of Vibrio, Shewanella and Clostridium. Principal coordinate analysis (PCoA) showed variations in microbial structure at different culture times. These findings suggest that OTUs of different taxa contributed to the community switch from healthy to diseased individuals, questioning the hypothesis that single bacterial species is the cause of disease outbreaks. This study provided data to improve the understanding of disease outbreaks during shrimp farming.

Life histories predict genetic diversity and population structure within three species of octopus targeted by small-scale fisheries in Northwest Mexico.

The fishery for octopus in Northwest Mexico has increased to over 2,000 tons annually, but to date the specific composition of the catch has been ignored. With at least three main species targeted by artisanal fisheries in the region with distinct life histories, the lack of basic biological information about the distribution, metapopulation size and structure of each species could impede effective fisheries management to avoid overexploitation. We tested if different life histories of three species of octopus could help predict observed patterns of genetic diversity, population dynamics, structure and connectivity and how this information could be relevant to the sustainable management of the fishery. We sequenced two mitochondrial genes and genotyped seven nuclear microsatellite loci to identify the distribution of each species in 20 locations from the Gulf of California and the west coast of the Baja California peninsula. We tested five hypotheses derived from population genetic theory based on differences in the fecundity and dispersal potential for each species. We discovered that Octopus bimaculoides with low fecundity and direct development (without a planktonic phase) had lower average effective population size and genetic diversity, but higher levels of kinship, population structure, and richness of private alleles, than the other two species. These features indicated limited dispersal and high local recruitment. In contrast, O. bimaculatus and O. hubbsorum with higher fecundity and planktonic phase as paralarvae had higher effective population size and genetic diversity, and overall lower kinship and population structure than O. bimaculoides. These observations supported higher levels of gene flow over a larger geographical scale. O. bimaculatus with the longest planktonic paralarval duration and therefore larger dispersal potential had differences in the calculated parameters possibly associated with increased connectivity. We propose O. bimaculoides is more susceptible to over exploitation of small, isolated populations and could have longer recovery times than the other two species. This species may benefit from distinct fishery management within each local population. O. bimaculatus and O. hubbsorum may benefit from fishery management that takes into account metapopulation structure over larger geographic scales and the directionality and magnitude of larval dispersal driven by ocean currents and population connectivity among individuals of each locality. The distribution of each species and variations in their reproductive phenology is also important to consider when establishing marine reserves or seasonal fishing closures.

Characterization of 32 microsatellite loci for the Pacific red snapper, Lutjanus peru, through next generation sequencing.

We developed a set of hypervariable microsatellite markers for the Pacific red snapper (Lutjanus peru), an economically important marine fish for small-scale fisheries in the west coast of Mexico. We performed shotgun genome sequencing with the 454 XL titanium chemistry and used bioinformatic tools to search for perfect microsatellite loci. We selected 66 primer pairs that were synthesized and genotyped in an ABI PRISM 3730XL DNA sequencer in 32 individuals from the Gulf of California. We estimated levels of genetic diversity, deviations from linkage and Hardy-Weinberg equilibrium, estimated the frequency of null alleles and the probability of individual identity for the new markers. We reanalyzed 16 loci in 16 individuals to estimate genotyping error rates. Eighteen loci failed to amplify, 16 loci were discarded due to unspecific amplifications and 32 loci (14 tetranucleotide and 18 dinucleotide) were successfully scored. The average number of alleles per locus was 21 (±6.87, SD) and ranged from 8 to 34. The average observed and expected heterozygosities were 0.787 (±0.144 SD, range 0.250-0.935) and 0.909 (±0.122 SD, range 0.381-0.965), respectively. No significant linkage was detected. Eight loci showed deviations from Hardy-Weinberg equilibrium, and from these, four loci showed moderate null allele frequencies (0.104-0.220). The probability of individual identity for the new loci was 1.46-62. Genotyping error rates averaged 9.58%. The new markers will be useful to investigate patterns of larval dispersal, metapopulation dynamics, fine-scale genetic structure and diversity aimed to inform the implementation of spatially explicit fisheries management strategies in the Gulf of California.