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In this study, the complete mitochondrial genomes of the Mexican golden trout, Oncorhynchus chrysogaster, and Nelson's trout, O. mykiss nelsoni, were assembled and characterized. The mitogenomes were 16,655 bp and 16,661 bp long, respectively, and were composed of 13 protein-coding genes (PCGs), two ribosomal RNA genes, and 22 transfer RNA genes (all with typical 'cloverleaf' secondary structures). The length of the D-loop regions was among the longest found in Salmonids, and mitochondrial synteny in both species was identical to that reported in other Salmonids. Selective pressure analysis in the PCGs indicated that purifying selection, mainly among cox and nd genes families, likely generated the main differences between the two studied species. Nine tRNA genes showed slight differences relative to other O. mykiss subspecies, which were identical between the two study taxa. The origin of the light-strand replication has a loop that was especially large in O. mykiss nelsoni. Phylogenetic analysis indicated that O. chrysogaster and O. mykiss nelsoni are sister species, contrary to the expectation that O. chrysogaster would cluster with O. gilae. As previous studies have suggested, O. chrysogaster and O. mykiss nelsoni share common ancestry with North American trout species. [ABSTRACT FROM AUTHOR]

“Octopus” rubescens Berry, 1953 is an octopus of temperate waters of the western coast of North America. This paper presents the first record of “O.” rubescens from the tropical Mexican Pacific. Twelve octopuses were studied; 10 were collected in tide pools from five localities and two mature males were caught by fishermen in Oaxaca. We used morphometric characters and anatomical features of the digestive tract to identify the species. The five localities along the Mexican Pacific coast provide solid evidence that populations of this species have become established in tropical waters. [ABSTRACT FROM AUTHOR]

The totoaba, Totoaba macdonaldi , is an endangered fish of the Gulf of California with high economic and ecological potential. Therefore, our purpose was to characterize the Primordial Germ Cells (PGCs) of this Sciaenid with two objectives: (1) to provide the basis for PGCs cryopreservation to preserve the genetic resources and (2) to take the first step to know the gonadal genesis and sex differentiation of totoaba. Immunofluorescence analysis performed from 2-cell stage to 8-day after hatch (DAH) shows that Vasa protein is specific for PGCs. These cells were first observed in the peripheral and dorsal regions of the blastodisc at approximately the 50%-epiboly stage and migrated to both sides of embryo body during the development. Finally, at 7 DAH the PGCs of the hatching embryo reached the place where the gonad will be developed. Histology analysis of larvae showed a genital ridge with enclosed PGCs on the dorsal side of the peritoneum at 9 DAH, gonadal primordium growth was observed at 11 DAH as a result of the interaction between PGCs and somatic cells derived from the peritoneum. Results of qPCR showed that vasa expression was restricted to the embryonic and early larval development, highest values were observed in 2-cell and mid-blastula stage suggesting the maternal inheritance of vasa mRNA. These findings support the hypothesis of preformation in T. macdonaldi PGCs. The migration pattern of PGCs allow us to recommend the isolation and subsequent cryopreservation of these cells before 7 DAH when the embryonic and larval development is given at 21 °C. [ABSTRACT FROM AUTHOR]

The complete mitochondrial genome of the giant electric ray is 17,081 bp long (GenBank accession KM386678) and includes 2 ribosomal RNA, 22 transfer RNA, 13 protein-coding genes, an origin of replication, 2 non-coding regions. The mitochondrial gene arrangement is similar to that found in other batoids. The control region possessed a set of tandem repeats. Start codon ATG and stop codon TAA/T were found in most protein-coding genes. The base composition of the genome is 36.2% A, 29.9% T, 21.9% C, and 11.9% G. [ABSTRACT FROM PUBLISHER]

The complete mitochondrial genome of the banded guitarfish is 17,310 bp long and includes 2 ribosomal RNA, 22 transfer RNA, and 13 protein-coding genes, a replication origin and a control region (GenBank accession number KM370325). Gene arrangement is similar to that found in other batoids. An extra non-coding region was found between the genes coding for transfer RNA proline and threonine possessing a set of tandem repeat motifs pointing to its origin as a duplication remnant. Start codon ATG and stop codon TAA/T were found in most protein-coding genes. The base composition of the genome is 32.3% A, 30.2% T, 24.3% C and 13.1% G. [ABSTRACT FROM PUBLISHER]

The complete mitochondrial genome sequence of the Desert Pupfish,Cyprinodon macularius(Gene accession number KM985373) has a length of 16,940 bp, and the arrangement consisted of 13 protein-coding genes, 2 ribosomal RNA (rRNA) genes and 22 transfer RNA, which are similar to other known mitogenomes for the family Cyprinodontidae. [ABSTRACT FROM AUTHOR]

The complete mitochondrial genome of the sablefish,Anoplopoma fimbria(Genbank accession KP777542) is 16,507 bp in size and contains the typical 37 genes (13 protein-coding, 2 ribosomal RNA, and 22 transfer RNA) found in teleosts mitogenomes. The genome varies in 118 positions with respect to another mitogenome sablefish specimen. [ABSTRACT FROM AUTHOR]

The complete mitochondrial genome of the Pacific GeoduckPanopea generosa(Genbank accession KM580067) is 15,585 bp in size and contains the typical 37 genes (13 protein-coding, 2 ribosomal RNA and 22 transfer RNA) found in metazoan mitogenomes, including the rare ATPase subunit 8 gene (ATP8). All genes are coded in the same strand but the gene arrangement is novel among heterodont bivalves. The base composition was: A 25.0%, T 38.7%, C 11.2% and G 25.0%. The genome is structurally similar to that of its congener the Cortes GeoduckPanopea globosa. [ABSTRACT FROM PUBLISHER]

The lionfish,Pterois volitans, native from the Indo-Pacific, has been found in Atlantic and Caribbean waters and is considered as an invasive species. Here we sequence its mitogenome (Genbank accession number KJ739816), which has a total length of 16,500 bp, and the arrangement consist of 13 protein-coding genes, 2 ribosomal RNA (rRNA) genes and 22 transfer RNA similar to other Pteroinae subfamily (family Scorpaenidae). This mitogenome will be useful for phylogenetic and population genetic studies of this invasive species. [ABSTRACT FROM AUTHOR]

The mitogenome of the tenguayaca,Petenia splendida(GenBank accession number KJ914664) has a total length of 16,518 bp, and the arrangement consist of 15 protein-coding genes, 2 ribosomal RNA (rRNA) genes and 22 transfer RNA (tRNA) genes. Gene order was equal to the mitogenomes of other new world cichlids. [ABSTRACT FROM AUTHOR]

The mitogenome of the endemic coralPorites panamensis(Genbank accession number KJ546638) has a total length of 18,628 bp, and the arrangement consist of 13 protein-coding genes, 2 ribosomal RNA (rRNA) genes and 2 transfer RNA (tRNA) genes. Gene order was equal to other scleractinian coral mitogenomes. [ABSTRACT FROM AUTHOR]

The mitogenome of the tropical gar,Atractosteus tropicus,(GeneBank accession number KJ531198) has a total length of 16,280 bp, and the arrangement consist of 13 protein-coding genes, 2 ribosomal RNA (rRNA) genes and 22 transfer RNA similar to other Lepisosteidae family mitogenomes. [ABSTRACT FROM AUTHOR]

Bacteriophages are recognized as major mortality agents of microbes, among them intracellular marine rickettsiales-like bacteria. Recently, a phage hyperparasite of Candidatus Xenohaliotis californiensis (CXc) has been described. This bacterium is considered the causal agent of Withering Syndrome (WS) which is a chronic and potentially lethal disease of abalone species from California, USA and the peninsula of Baja California, Mexico. This hyperparasite which infects CXc could be used as a biocontrol agent for WS. Therefore, it is necessary to obtain genomic information to characterize this phage. In this study, the first complete genome sequence of a novel phage, Xenohaliotis phage (pCXc) was determined. The complete genome of pCXc from red abalone (Haliotis rufescens) is 35,728 bp, while the complete genome of pCXc from yellow abalone (Haliotis corrugata) is 35,736 bp. Both phage genomes consist of double-stranded DNA with a G + C content of 38.9%. In both genomes 33 open reading frames (ORFs) were predicted. Only 10 ORFs encode proteins that have identifiable functional homologues. These 10 ORFs were classified by function, including structural, DNA replication, DNA packaging, nucleotide transport and metabolism, life cycle regulation, recombination and repair, and additional functions. A PCR method for the specific detection of pCXc was developed. This information will help to understand a new group of phages that infect intracellular marine rickettsiales-like bacteria in mollusks. [ABSTRACT FROM AUTHOR]

[Display omitted] • The Rickettsiales-like organism from Crassostrea corteziensis is a commensal endosymbiont. • The prevalence and intensity of the Rickettsiales-like organism is low. • 16S rRNA amplicon sequencing shows the presence of intracellular parasite OTUs. Fastidious endosymbiotic Rickettsiales-like organisms (RLOs) have been observed in the digestive diverticula of the cultured pleasure oyster (Crassostrea corteziensis) from Nayarit, Mexico since 2007. In a few mollusk species, these bacteria have been associated with mortality events and production losses. The type of relationship between the RLOs and the pleasure oyster is largely unknown and further investigations are needed to determine if these bacteria warrant management concern in C. corteziensis. In this study, the morphological characteristics of the RLOs were studied by histology and SEM, and the taxonomic affiliations of the bacteria were evaluated by 16S rRNA amplicon sequencing. In addition, the prevalence and intensity of the RLOs was recorded from 2007 to 2017 by histology. The RLOs were observed inside circular basophilic cytoplasmic membrane bound vacuoles (MBVs) that had an average length and width of 15.70 ± 15.24 µm and 15.42 ± 14.95 µm respectively. Apart from cellular hypertrophy, no tissue alterations were observed in the areas adjacent to the RLOs. Individual bacteria within the MBVs were coccoid in shape with an average length of 0.65 ± 0.12 µm and an average width of 0.38 ± 0.09 µm. The bacterial microbiota of a selected number of samples (one sample without RLOs and two samples with RLOs) showed the presence of intracellular parasite OTUs corresponding to the families Rickettsiaceae and Anaplasmataceae, suggesting that the RLOs from the pleasure oyster is associated with the order Rickettsiales. A mean prevalence of 5 % was observed throughout the study period and the majority of the organisms (89 %) presented low intensity of Grade 1 (30–61 RLOs) of the MBVs. A higher prevalence of the RLOs was observed during warmer months. The lack of tissue alterations, the low prevalence and the low intensity of the MBVs suggest that the RLOs from C. corteziensis is a commensal endosymbiont that presents little risk for oyster production in Nayarit, México. However, regular monitoring is needed to detect if any variation in this relationship occurs, mainly in a scenario where extreme environmental fluctuations may occur. [ABSTRACT FROM AUTHOR]

Commercial abalone culture is carried out using flow-through systems with a high water volume exchange in Baja California, Mexico. The objective of this work was to compare the growth rate and survival of red abalone cultured in two systems. Flow through (daily water exchange rate of 800%) and recirculating systems consisted of a 250 L fibreglass tank and constant aeration, but biofiltration in the recirculating system was provided with a 28 L (1 ft) bubble-washed bead filter. Water variables were measured either daily (dissolved oxygen, temperature, pH and salinity) or three times a week (total ammonia nitrogen, nitrate-nitrogen, nitrite-nitrogen and alkalinity). Shell length was measured every 2 weeks for 18 weeks. Only the alkalinity and pH were significantly different due to the addition of sodium bicarbonate to the recirculating system. Abalone growth rate was 26.1 ± 15.96 μm day in the recirculating systems and 22.21 ± 18.69 μm day in the flow-through systems. The final survival was 78.74% in the recirculating systems and 71.82% in the flow-through systems. Significant differences in the final size and survival of the abalones were found between systems ( P<0.05). Therefore, recirculating aquaculture systems is a feasible alternative for juvenile red abalone culture. [ABSTRACT FROM AUTHOR]

The physical location of 18S-5.8S-28S rDNA, telomeric sequences with (TTAGGG)n DNA probe and (GATA)n microsatellites were performed by fluorescence in situ hybridization in chromosomes of red abalone Haliotis rufescens. The karyotype of red abalone showed a diploid number of 36 (8M+9SM+1ST). FISH performed with rDNA probe, showed the location of major ribosomal clusters in the terminal region of the large arms of two submetacentric pairs (chromosome 4 and 5). Localization of heteromorphisms of FISH-rDNA was found between chromosome homologues and sister chromatids in all metaphases analyzed. This indicates that rDNA clusters are variable within the red abalone genome. The variability in the NOR-bearing reported using silver staining in other gastropods and our result are discussed. In addition, the presence of microsatellite (TTAGGG)n and (GATA)n was demonstrated after FISH treatment by DNA probes. The telomeric sequence occurred at the ends of all mitotic chromosomes, while the (GATA)n repetitive was found on chromosomal interstitial zones as well as at the telomeres in abalone chromosomes. [ABSTRACT FROM AUTHOR]

The California halibut, Paralichthys californicus, is a highly priced flatfish because of its size and meat quality. This work presents the complete mitochondrial genome of P. californicus. Total DNA from muscle tissue was extracted and sequenced using the Illumina platform. Reads were cleaned, trimmed, assembled de novo, and annotated. The California halibut mitogenome is 16,858 bp in length (GenBank accession number: MT859134), containing 13 protein-coding genes, 22 tRNAs, 2 rRNAs, and the control region. P. californicus mitogenome was most similar to Paralichthys olivaceus than to other flatfish mitogenomes, in agreement with their geographic distribution. This information deepens the knowledge of the California halibut, which is not only ecologically important, but also a socioeconomically relevant resource for fishery and aquaculture in California, USA, and Baja California, Mexico. [ABSTRACT FROM AUTHOR]

The shortfin silversideChirostoma humboldtianum, is an endemic fish from the Mesa Central of Mexico, it is considered the “ancestral” species of the “peces blancos” and plays an important role as a potential species for aquaculture.Here we sequence its mitogenome (Genbank accession number KJ921739), which has a total length of 16,447 bp, and the arrangement consist of 13 protein-coding genes, 2 ribosomal RNA (rRNA) genes and 22 transfer RNA similar to other Atheriniformes. This mitogenome will be useful for phylogenetic, population and phylogeographic studies of this and other important atherinopsid species. [ABSTRACT FROM AUTHOR]

Unfortunately, the family name of the co-author Roberto Cruz-Flores was incorrectly published in the original publication and corrected here by this correction. The original article has been corrected. [ABSTRACT FROM AUTHOR]

Withering syndrome (WS) is a chronic wasting disease affecting abalone species attributed to the pathogen Candidatus Xenohaliotis californiensis ( C Xc). Wild populations of blue ( Haliotis fulgens ) and yellow ( H. corrugata ) abalone have experienced unusual mortality rates since 2009 off the peninsula of Baja California and WS has been hypothesized as a possible cause. Currently, little information is available about the genetic diversity of C Xc and particularly the possible existence of strains differing in pathogenicity. In a recent phylogenetic analysis, we characterized five coding genes from this rickettsial pathogen. Here, we analyze those genes and two additional intergenic non-coding regions following multi-locus sequence typing (MLST) and multi-spacer typing (MST) approaches to assess the genetic variability of C Xc and its relationship with blue, yellow and red ( H. rufescens ) abalone. Moreover, we used 16S rRNA pyrosequencing reads from gut microbiomes of blue and yellow abalone to complete the genetic characterization of this prokaryote. The presence of C Xc was investigated in more than 150 abalone of the three species; furthermore, a total of 385 DNA sequences and 7117 16S rRNA reads from Candidatus Xenohaliotis californiensis were used to evaluate its population genetic structure. Our findings suggest the absence of polymorphism in the DNA sequences of analyzed loci and the presence of a single lineage of C Xc infecting abalone from California (USA) and Baja California (Mexico). We posit that the absence of genetic variably in this marine rickettsia may be the result of evolutionary and ecological processes. [ABSTRACT FROM AUTHOR]

The red abalone,Haliotis rufescens(Swanson 1822), is an important species for commercial aquaculture in Mexico, with annual production levels around 68 t. Not surprisingly, there is great interest in increasing production and its cultivation success. In order to have a better understanding of the genes involved in the sexual differentiation, this study analyzed the early differential expression of eight sex-related genes (VCP 2.2,VERL,VTGI,DMRT1,FP,LYS,SARIP,TEKT A1) by RT-qPCR in abalones from 5 to 45 mm of shell length. Sex identification was evaluated usingVERLandLYSgenes expression levels. These genes differentiated females and males from 16 mm of shell length and above. All eight sex-specific genes showed expression in all organisms. However, their level was higher in the sex group to which they correspond. In contrast, differential expression levels occurred in individuals with a shell length of 26–35 mm and 36–45 mm. These results suggest that sex gene expression is not entirely sex specific, and sexual differentiation in red abalone occurs between 16 and 25 mm of shell length. More studies are needed to determine the function of these genes in the sex that they are not associated with. [ABSTRACT FROM PUBLISHER]

Candidatus Xenohaliotis californiensis ( C Xc) is a Rickettsiales-like prokaryote that is considered the causal agent of Withering Syndrome (WS), a chronic disease of abalone, from the west coast of North America and it is listed by the International Organization for Animal Health (OIE) as a reportable agent due to its pathogenicity. This bacterium in red abalone Haliotis rufescens , black abalone Haliotis cracherodii , and yellow abalone Haliotis corrugata from California, US and Baja California, Mexico has been found to be infected by a bacteriophage. To date, there is no information on the epizootiology of C Xc and its bacteriophage in natural populations of abalone; furthermore, it is unknown if the bacteriophage was also present in C Xc infecting blue abalone Haliotis fulgens . The objective of this study was to determine the distribution, prevalence and intensity of C Xc, as well as to determine the distribution and prevalence of the bacteriophage and to study interactions between host sex and hyperparasitism in blue abalone and yellow abalone. Tissue samples were obtained from seven localities where the commercial capture of wild abalone is carried out. Samplings were conducted throughout the 2012–2013 capture seasons and a total of 182 blue abalone and 170 yellow abalone were obtained. The prevalence and intensity of C Xc and the prevalence of the bacteriophage were determined by histology. The identity of C Xc was confirmed by PCR, product sequence analysis and in situ hybridization while the identity of the bacteriophage was corroborated by TEM. The prevalence of C Xc infected and uninfected by the bacteriophage was 80% in blue abalone and 62% in yellow abalone. Low infection intensities were found in 86% of blue abalone and 82% of yellow abalone. Infection intensity was significantly higher in undifferentiated yellow abalone. The bacteriophage in C Xc showed a prevalence of 22% and 31% in blue abalone and yellow abalone respectively. These results show that C Xc and its bacteriophage are widely distributed in the peninsula of Baja California and that they are well established in natural populations of blue abalone and yellow abalone. Additionally, this data constitutes the first record of a bacteriophage in blue abalone. [ABSTRACT FROM AUTHOR]

This study presents the characterization of a series of 10 microsatellite loci developed for the funnel-eared bat Natalus mexicanus. A total of 35 pairs of primers, in 32 exemplars of N. mexicanus collected at two localities in Mexico, were selected by pyrosequencing for testing via cross-amplification in other bat species ( Corynorhinus townsendii , Natalus major, Natalus tumidirostris, Nyctinomops laticaudatus and Tadarida brasiliensis ). All 10 loci of this species amplified positively with medium and high resolution of genetic variation (2–15 alleles per locus, mean H E 0.7217, mean H O 0.6074). We consider that these polymorphic loci will be useful in genetic studies of this species as well as that of other bat families. [ABSTRACT FROM AUTHOR]

The red abalone Haliotis rufescens is one of the most important species for aquaculture in Baja California, México, and despite this, few gene expression studies have been done in tissues such as gill, head and gonad. For this purpose, reverse transcription and quantitative real time PCR (RT-qPCR) is a powerful tool for gene expression evaluation. For a reliable analysis, however, it is necessary to select and validate housekeeping genes that allow proper transcription quantification. Stability of nine housekeeping genes ( ACTB , BGLU , TUBB , CY , GAPDH , HPRTI , RPL5 , SDHA and UBC ) was evaluated in different tissues of red abalone (gill, head and gonad/digestive gland). Four-fold serial dilutions of cDNA (from 25 ng μL − 1 to 0.39 ng μL − 1 ) were used to prepare the standard curve, and it showed gene efficiencies between 0.95 and 0.99, with R 2 = 0.99. geNorm and NormFinder analysis showed that RPL5 and CY were the most stable genes considering all tissues, whereas in gill HPRTI and BGLU were most stable. In gonad/digestive gland, RPL5 and TUBB were the most stable genes with geNorm, while SDHA and HPRTI were the best using NormFinder. Similarly, in head the best genes were RPL5 and UBC with geNorm, and GAPDH and CY with NormFinder. The technical variability analysis with RPL5 and abalone gonad/digestive gland tissue indicated a high repeatability with a variation coefficient within groups ≤ 0.56% and between groups ≤ 1.89%. These results will help us for further research in reproduction, thermoregulation and endocrinology in red abalone. [ABSTRACT FROM AUTHOR]

The mitogenome of the beaubrummel damselfish,Stegastes flavilatusGill, 1862 (Genebank accession number KP136922), has a total length of 16,816 bp. It encodes 13 protein-coding, two ribosomal RNAs (rRNAs), and 22 transfer RNA (tRNA) genes. Base composition is 28.6% A, 26.0% T, 29.8% C, and 15.7% G and 45.5% GC content. The gene arrangement was found to be the same of other pomacentrid mitogenomes. [ABSTRACT FROM AUTHOR]