The novel circular RNA CircMef2c is positively associated with muscle growth in Nile tilapia.

Muscle growth in teleosts is a complex biological process orchestrated by numerous protein-coding genes and non-coding RNAs. A few recent studies suggest that circRNAs are involved in teleost myogenesis, but the molecular networks involved remain poorly understood. In this study, an integrative omics approach was used to determine myogenic circRNAs in Nile tilapia by quantifying and comparing the expression profile of mRNAs, miRNAs, and circRNAs in fast muscle from full-sib fish with distinct growth rates. There were 1947 mRNAs, 9 miRNAs, and 4 circRNAs differentially expressed between fast- and slow-growing individuals. These miRNAs can regulate myogenic genes and have binding sites for the novel circRNA circMef2c. Our data indicate that circMef2c may interact with three miRNAs and 65 differentially expressed mRNAs to form multiple competing endogenous RNA networks that regulate growth, thus providing novel insights into the role of circRNAs in the regulation of muscle growth in teleosts.

CircPrime: a web-based platform for design of specific circular RNA primers.

BACKGROUND: Circular RNAs (circRNAs) are covalently closed-loop RNAs with critical regulatory roles in cells. Tens of thousands of circRNAs have been unveiled due to the recent advances in high throughput RNA sequencing technologies and bioinformatic tools development. At the same time, polymerase chain reaction (PCR) cross-validation for circRNAs predicted by bioinformatic tools remains an essential part of any circRNA study before publication. RESULTS: Here, we present the CircPrime web-based platform, providing a user-friendly solution for DNA primer design and thermocycling conditions for circRNA identification with routine PCR methods. CONCLUSIONS: User-friendly CircPrime web platform ( http://circprime.elgene.net/ ) works with outputs of the most popular bioinformatic predictors of circRNAs to design specific circular RNA primers. CircPrime works with circRNA coordinates and any reference genome from the National Center for Biotechnology Information database).

Sea of opportunities: marine genomics in an era of global environmental change.

Overexploitation of natural resources and pollution of seas, acidification of the ocean, and rising temperatures all contribute to the destruction of marine habitats and, in 2015, the protection of the ocean became one of the UN Sustainable Development Goals (SDG 14: Life Below Water). This collection aims to highlight the molecular genetic changes currently happening in marine organisms.

Ancient DNA: the past for the future.

The last decade has seen advancements in sequencing technologies and laboratory preparation protocols for ancient DNA (aDNA) that have rapidly been applied in multiple research areas thus enabling large-scale scientific research. Future research could also refine our understanding of the evolution of humans, non-human animals, plants, invertebrate specimens, and microorganisms.

Caucasian treasure: Genomics sheds light on the evolution of half-extinct Sevan trout, Salmo ischchan, species flock.

Five ecologically and phenotypically divergent ecomorphs of the genus Salmo are known from a landlocked alpine lake in the Caucasus, Lake Sevan. It is an example of sympatric diversification within a species-rich lineage with predominate mode of speciation being allopatric. The diversification of Sevan trouts was accompanied by spawning resource partitioning. Four lacustrine ecomorphs with different temporal-spatial spawning strategies and divergent morphology and coloration evolved along with a fifth ecomorph, brook trout, inhabiting the tributaries. Unfortunately, the Sevan trout diversity was almost destroyed by human activity, with two ecomorphs becoming extinct in the 1980s. We performed reconstruction of the evolutionary history of Sevan trouts based on high-throughput sequencing of both contemporary and historical DNA (∼ 50 y.o.) of all Sevan trout ecomorphs. Our study of complete mitogenomes along with genome-wide SNP data revealed the monophyly of four lacustrine ecomorphs and local brook trout, all derived from the anadromous form Caspian salmon, S. caspius. The species tree suggests a scenario of stepwise evolution from riverine to lacustrine spawning. Three genomic clusters were revealed, of which two refer to the riverine and lacustrine spawners within the flock of Sevan trouts (with FST value = 0.069). A few SNP outliers under selection were discovered that could be responsible for assortative mating based on visual recognition. The Holocene climatic oscillations and the desiccation of tributaries could have played an important role in the origin of lacustrine spawning. The relationships between lacustrine ecomorphs were not yet fully resolved. This radiation warrants further investigation.

The first mitochondrial 5-methylcytosine map in a non-model teleost (Oreochromis niloticus) reveals extensive strand-specific and non-CpG methylation.

DNA methylation is one of the main epigenetic mechanisms that regulate gene expression in a manner that depends on the genomic context and varies considerably across taxa. This DNA modification was first found in nuclear genomes of eukaryote several decades ago and it has also been described in mitochondrial DNA. It has recently been shown that mitochondrial DNA is extensively methylated in mammals and other vertebrates. Our current knowledge of mitochondrial DNA methylation in fish is very limited, especially in non-model teleosts. In this study, using whole-genome bisulfite sequencing, we determined methylation patterns within non-CpG (CH) and CpG (CG) contexts in the mitochondrial genome of Nile tilapia, a non-model teleost of high economic importance. Our results demonstrate the presence of mitochondrial DNA methylation in this species predominantly within a non-CpG context, similarly to mammals. We found a strand-specific distribution of methylation, in which highly methylated cytosines were located on the minus strand. The D-loop region had the highest mean methylation level among all mitochondrial loci. Our data provide new insights into the potential role of epigenetic mechanisms in regulating metabolic flexibility of mitochondria in fish, with implications in various biological processes, such as growth and development.

Epigenetic mapping of the somatotropic axis in Nile tilapia reveals differential DNA hydroxymethylation marks associated with growth.

In vertebrates, the somatotropic axis comprising the pituitary gland, liver and muscle plays a major role in myogenesis. Its output in terms of muscle growth is highly affected by nutritional and environmental cues, and thus likely epigenetically regulated. Hydroxymethylation is emerging as a DNA modification that modulates gene expression but a holistic characterization of the hydroxymethylome of the somatotropic axis has not been investigated to date. Using reduced representation 5-hydroxymethylcytosine profiling we demonstrate tissue-specific localization of 5-hydroxymethylcytosines at single nucleotide resolution. Their abundance within gene bodies and promoters of several growth-related genes supports their pertinent role in gene regulation. We propose that cytosine hydroxymethylation may contribute to the phenotypic plasticity of growth through epigenetic regulation of the somatotropic axis.

Function of Circular RNAs in Fish and Their Potential Application as Biomarkers.

Circular RNAs (circRNAs) are an emerging class of regulatory RNAs with a covalently closed-loop structure formed during pre-mRNA splicing. Recent advances in high-throughput RNA sequencing and circRNA-specific computational tools have driven the development of novel approaches to their identification and functional characterization. CircRNAs are stable, developmentally regulated, and show tissue- and cell-type-specific expression across different taxonomic groups. They play a crucial role in regulating various biological processes at post-transcriptional and translational levels. However, the involvement of circRNAs in fish immunity has only recently been recognized. There is also broad evidence in mammals that the timely expression of circRNAs in muscle plays an essential role in growth regulation but our understanding of their expression and function in teleosts is still very limited. Here, we discuss the available knowledge about circRNAs and their role in growth and immunity in vertebrates from a comparative perspective, with emphasis on cultured teleost fish. We expect that the interest in teleost circRNAs will increase substantially soon, and we propose that they may be used as biomarkers for selective breeding of farmed fish, thus contributing to the sustainability of the aquaculture sector.

Molecular phylogeny of the extinct Steller's sea cow and other Sirenia species based on their complete mitochondrial genomes.

The Steller's sea cow - Hydrodamalis gigas (Dugongidae: Sirenia) - is an extinct herbivorous marine mammal which inhabited the North Pacific Ocean during the Pleistocene and Holocene. H. gigas was the largest member of the Sirenia order and disappeared in the middle of the 18th century. Here, we present the complete sequence of the mitochondrial genome of this extinct animal. The Steller's sea cow mitochondrial DNA (mtDNA) is 16,872 base pairs (bp) in length and contains a set of mitochondrial genes typical for mammals. Phylogenetic analysis based on complete mitochondrial genomes of the sirenian species allows accurate assessment of the degree of their mitogenomic diversification during millions of years of evolution.

Genome-Wide DNA Methylation Profiling Reveals Epigenetic Adaptation of Stickleback to Marine and Freshwater Conditions.

The three-spined stickleback (Gasterosteus aculeatus) represents a convenient model to study microevolution-adaptation to a freshwater environment. Although genetic adaptations to freshwater environments are well-studied, epigenetic adaptations have attracted little attention. In this work, we investigated the role of DNA methylation in the adaptation of the marine stickleback population to freshwater conditions. DNA methylation profiling was performed in marine and freshwater populations of sticklebacks, as well as in marine sticklebacks placed into a freshwater environment and freshwater sticklebacks placed into seawater. We showed that the DNA methylation profile after placing a marine stickleback into fresh water partially converged to that of a freshwater stickleback. For six genes including ATP4A ion pump and NELL1, believed to be involved in skeletal ossification, we demonstrated similar changes in DNA methylation in both evolutionary and short-term adaptation. This suggested that an immediate epigenetic response to freshwater conditions can be maintained in freshwater population. Interestingly, we observed enhanced epigenetic plasticity in freshwater sticklebacks that may serve as a compensatory regulatory mechanism for the lack of genetic variation in the freshwater population. For the first time, we demonstrated that genes encoding ion channels KCND3, CACNA1FB, and ATP4A were differentially methylated between the marine and the freshwater populations. Other genes encoding ion channels were previously reported to be under selection in freshwater populations. Nevertheless, the genes that harbor genetic and epigenetic changes were not the same, suggesting that epigenetic adaptation is a complementary mechanism to selection of genetic variants favorable for freshwater environment.

Tracking the origins of Yakutian horses and the genetic basis for their fast adaptation to subarctic environments.

Yakutia, Sakha Republic, in the Siberian Far East, represents one of the coldest places on Earth, with winter record temperatures dropping below -70 °C. Nevertheless, Yakutian horses survive all year round in the open air due to striking phenotypic adaptations, including compact body conformations, extremely hairy winter coats, and acute seasonal differences in metabolic activities. The evolutionary origins of Yakutian horses and the genetic basis of their adaptations remain, however, contentious. Here, we present the complete genomes of nine present-day Yakutian horses and two ancient specimens dating from the early 19th century and ∼5,200 y ago. By comparing these genomes with the genomes of two Late Pleistocene, 27 domesticated, and three wild Przewalski's horses, we find that contemporary Yakutian horses do not descend from the native horses that populated the region until the mid-Holocene, but were most likely introduced following the migration of the Yakut people a few centuries ago. Thus, they represent one of the fastest cases of adaptation to the extreme temperatures of the Arctic. We find cis-regulatory mutations to have contributed more than nonsynonymous changes to their adaptation, likely due to the comparatively limited standing variation within gene bodies at the time the population was founded. Genes involved in hair development, body size, and metabolic and hormone signaling pathways represent an essential part of the Yakutian horse adaptive genetic toolkit. Finally, we find evidence for convergent evolution with native human populations and woolly mammoths, suggesting that only a few evolutionary strategies are compatible with survival in extremely cold environments.

Koban culture genome-wide and archeological data open the bridge between Bronze and Iron Ages in the North Caucasus.

The North Caucasus played a key role during the ancient colonization of Eurasia and the formation of its cultural and genetic ancestry. Previous archeogenetic studies described a relative genetic and cultural continuity of ancient Caucasus societies, since the Eneolithic period. The Koban culture, which formed in the Late Bronze Age on the North Caucasian highlands, is considered as a cultural "bridge" between the ancient and modern autochthonous peoples of the Caucasus. Here, we discuss the place of this archeological culture and its representatives in the genetic orbit of Caucasian cultures using genome-wide SNP data from five individuals of the Koban culture and one individual of the early Alanic culture as well as previously published genomic data of ancient and modern North Caucasus individuals. Ancient DNA analysis shows that an ancient individual from Klin-Yar III, who was previously described as male, was in fact a female. Additional studies on well-preserved ancient human specimens are necessary to determine the level of local mobility and kinship between individuals in ancient societies of North Caucasus. Further studies with a larger sample size will allow us gain a deeper understanding of this topic.

Ancient DNA of the Don-Hares Assumes the Existence of Two Distinct Mitochondrial Clades in Northeast Asia.

Paleoclimatic changes during the Pleistocene-Holocene transition is suggested as a main factor that led to species extinction, including the woolly mammoth (Mammuthus primigenius), Steller's sea cow (Hydrodamalis gigas) and the Don-hare (Lepus tanaiticus). These species inhabited the territory of Eurasia during the Holocene, but eventually went extinct. The Don-hare is an extinct species of the genus Lepus (Leporidae, Lagomorpha), which lived in the Late Pleistocene-Early Holocene in Eastern Europe and Northern Asia. For a long time, the Don-hare was considered a separate species, but at the same time, its species status was disputed, taking into account both morphological data and mitochondrial DNA. In this study, mitochondrial genomes of five Don-hares, whose remains were found on the territory of Northeastern Eurasia were reconstructed. Firstly, we confirm the phylogenetic proximity of the "young" specimens of Don-hare and mountain or white hare, and secondly, that samples older than 39 Kya form a completely distinct mitochondrial clade.

Intergeneric hybridization of two stickleback species leads to introgression of membrane-associated genes and invasive TE expansion.

Interspecific hybridization has occurred relatively frequently during the evolution of vertebrates. This process usually abolishes reproductive isolation between the parental species. Moreover, it results in the exchange of genetic material and can lead to hybridogenic speciation. Hybridization between species has predominately been observed at the interspecific level, whereas intergeneric hybridization is rarer. Here, using whole-genome sequencing analysis, we describe clear and reliable signals of intergeneric introgression between the three-spined stickleback (Gasterosteus aculeatus) and its distant mostly freshwater relative the nine-spined stickleback (Pungitius pungitius) that inhabit northwestern Russia. Through comparative analysis, we demonstrate that such introgression phenomena apparently take place in the moderate-salinity White Sea basin, although it is not detected in Japanese sea stickleback populations. Bioinformatical analysis of the sites influenced by introgression showed that they are located near transposable elements, whereas those in protein-coding sequences are mostly found in membrane-associated and alternative splicing-related genes.

Genomic Signatures of Freshwater Adaptation in Pacific Herring (Clupea pallasii).

Pacific herring (Clupea pallasii) is an essential target of commercial fishing in the North Pacific Ocean. Previous studies have suggested the existence of marine and lake ecological forms of this species within its range. The lake ecological form of herring has a shortened life cycle, spending the winter and spawning in brackish waters near the shoreline without long migrations for feeding; it also has a relatively smaller body size than the marine form. Genetic-based studies have shown that brackish water Pacific herring not only can be distinguished as a separate lake ecological form but possibly has its genetic legacy. Here, as part of an ongoing study, using ddRAD-sequencing data for marine and lake ecological forms from a total of 54 individuals and methods of comparative bioinformatics, we describe genomic signatures of freshwater adaptivity in Pacific herring. In total, 253 genes containing discriminating SNPs were found, and part of those genes was organized into genome clusters, also known as "genomic islands of divergence". Moreover, the Tajima's D test showed that these loci are under directional selection in the lake populations of the Pacific herring. Yet, most discriminating loci between the lake and marine ecological forms of Pacific herring do not intersect (by gene name) with those in other known marine fish species with known freshwater/brackish populations. However, some are associated with the same physiological trait-osmoregulation.

Non-GCB Diffuse Large B-Cell Lymphoma With an Atypical Disease Course: A Case Report and Clinical Exome Analysis.

Diffuse large B-cell lymphoma (DLBCL) is the most common lymphoid tumor among other non-Hodgkin lymphomas (30-40% of all cases). This type of lymphoma is characterized by significant differences in treatment response and the heterogeneity of clinical traits. Approximately 60% of patients are cured using standard chemotherapy (CT), while in 10-15% of cases, the tumor is characterized by an extremely aggressive course and resistance to even the most high-dose programs with autologous stem cell transplantation (auto-SCT). The activated B-cell (ABC) subtype of DLBCL is characterized by poor prognosis. Here, we describe a clinical case of diffuse ABC-DLBCL with an atypical disease course. Complete remission was achieved after four courses of CT, followed by autologous hematopoietic stem cell transplantation (auto-HSCT). However, early relapse occurred 2 months after the completion of treatment. According to the results of cytogenetic studies, significant chromosome breakdowns were observed. Exome sequencing allowed for the detection of several novel mutations that affect components of the NOTCH2 and NF-κB signaling pathways, a number of epigenetic regulators (KMT2D, CREBBP, EP300, ARID1A, MEF2B), as well as members of the immunoglobulin superfamily (CD58 and CD70). Whether these mutations were the result of therapy or were originally present in the lymphoid tumor remains unclear. Nevertheless, the introduction of genomic technologies into clinical practice is important for making a diagnosis and developing a DLBCL treatment regimen with the use of targeted drugs.

Ancient DNA Reveals Maternal Philopatry of the Northeast Eurasian Brown Bear (Ursus arctos) Population during the Holocene.

Significant palaeoecological and paleoclimatic changes that took place during Late Pleistocene-Early Holocene transition are considered important factors that led to megafauna extinctions. Unlike many other species, the brown bear (Ursus arctos) has survived this geological time. Despite the fact that several mitochondrial DNA clades of brown bears became extinct at the end of the Pleistocene, this species is still widely distributed in Northeast Eurasia. Here, using the ancient DNA analysis of a brown bear individual that inhabited Northeast Asia in the Middle Holocene (3460 ± 40 years BP) and comparative phylogenetic analysis, we show a significant mitochondrial DNA similarity of the studied specimen with modern brown bears inhabiting Yakutia and Chukotka. In this study, we clearly demonstrate the maternal philopatry of the Northeastern Eurasian U. arctos population during the several thousand years of the Holocene.

Plasma proteome responses in zebrafish following λ-carrageenan-Induced inflammation are mediated by PMN leukocytes and correlate highly with their human counterparts.

Regulation of inflammation is a critical process for maintaining physiological homeostasis. The λ-carrageenan (λ-CGN) is a mucopolysaccharide extracted from the cell wall of red algae (Chondrus crispus) capable of inducing acute intestinal inflammation, which is translated into the production of acute phase reactants secreted into the blood circulation. However, the associated mechanisms in vertebrates are not well understood. Here, we investigated the crucial factors behind the inflammatory milieu of λ-CGN-mediated inflammation administered at 0, 1.75, and 3.5% (v/w) by i.p. injection into the peritoneal cavity of adult zebrafish (ZF) (Danio rerio). We found that polymorphonuclear leukocytes (neutrophils) and lymphocytes infiltrating the ZF peritoneal cavity had short-term persistence. Nevertheless, they generate a strong pattern of inflammation that affects systemically and is enough to produce edema in the cavity. Consistent with these findings, cell infiltration, which causes notable tissue changes, resulted in the overexpression of several acute inflammatory markers at the protein level. Using reversed-phase high-performance liquid chromatography followed by a hybrid linear ion-trap mass spectrometry shotgun proteomic approach, we identified 2938 plasma proteins among the animals injected with PBS and 3.5% λ-CGN. First, the bioinformatic analysis revealed the composition of the plasma proteome. Interestingly, 72 commonly expressed proteins were recorded among the treated and control groups, but, surprisingly, 2830 novel proteins were differentially expressed exclusively in the λ-CGN-induced group. Furthermore, from the commonly expressed proteins, compared to the control group 62 proteins got a significant (p < 0.05) upregulation in the λ-CGN-treated group, while the remaining ten proteins were downregulated. Next, we obtained the major protein-protein interaction networks between hub protein clusters in the blood plasma of the λ-CGN induced group. Moreover, to understand the molecular underpinnings of these effects based on the unveiled protein sets, we performed a bioinformatic structural similarity analysis and generated overlapping 3D reconstructions between ZF and humans during acute inflammation. Biological pathway analysis pointed to the activation and abundance of diverse classical immune and acute phase reactants, several catalytic enzymes, and varied proteins supporting the immune response. Together, this information can be used for testing and finding novel pharmacological targets to treat human intestinal inflammatory diseases.

Genetic structure of marine and lake forms of Pacific herring Clupea pallasii.

The Pacific herring (Clupea pallasii) is one of the most important species in the commercial fisheries distributed in the North Pacific Ocean and the northeastern European seas. This teleost has marine and lake ecological forms a long its distribution in the Holarctic. However, the level of genetic differentiation between these two forms is not well known. In the present study, we used ddRAD-sequencing to genotype 54 specimens from twelve wild Pacific herring populations from the Kara Sea and the Russian part of the northwestern Pacific Ocean for unveiling the genetic structure of Pacific herring. We found that the Kara Sea population is significantly distinct from Pacific Ocean populations. It was demonstrated that lake populations of Pacific herring differ from one another as well as from marine specimens. Our results show that fresh and brackish water Pacific herring, which inhabit lakes, can be distinguished as a separate lake ecological form. Moreover, we demonstrate that each observed lake Pacific herring population has its own and unique genetic legacy.

Breeding Strategy Shapes the Composition of Bacterial Communities in Female Nile Tilapia Reared in a Recirculating Aquaculture System.

In industrial animal production, breeding strategies are essential to produce offspring of better quality and vitality. It is also known that host microbiome has a bearing on its health. Here, we report for the first time the influence of crossbreeding strategy, inbreeding or outbreeding, on the buccal and intestinal bacterial communities in female Nile tilapia (Oreochromis niloticus). Crossbreeding was performed within a family and between different fish families to obtain the inbred and outbred study groups, respectively. The genetic relationship and structure analysis revealed significant genetic differentiation between the inbred and outbred groups. We also employed a 16S rRNA gene sequencing technique to understand the significant differences between the diversities of the bacterial communities of the inbred and outbred groups. The core microbiota composition in the mouth and the intestine was not affected by the crossbreeding strategy but their abundance varied between the two groups. Furthermore, opportunistic bacteria were abundant in the buccal cavity and intestine of the outbred group, whereas beneficial bacteria were abundant in the intestine of the inbred group. The present study indicates that crossbreeding can influence the abundance of beneficial bacteria, core microbiome and the inter-individual variation in the microbiome.