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The Antarctic icefish, a family (Channichthyidae) of teleosts within the perciform suborder Notothenioidei, are the only known vertebrates without oxygen-transporting haemoglobins and that are largely devoid of circulating erythrocytes. To elucidate the evo-devo mechanisms underpinning the suppressed erythropoiesis in the icefish, we conducted comparative studies on the transcriptomes and micro RNAomes of the primary haematopoietic tissues between an icefish ( Chionodraco hamatus) and two red-blooded notothenioids ( Trematomus bernacchii and Gymnodraco acuticeps). We identified substantial remodelling of the haematopoietic programs in the icefish through which erythropoiesis is selectively suppressed. Experimental verification showed that erythropoietic suppression in the icefish may be attributable to the upregulation of TGF-β signalling, which coincides with reductions in multiple transcription factors essential for erythropoiesis and the upregulation of hundreds of micro RNAs, the majority (> 80%) of which potentially target erythropoiesis regulating factors. Of the six micro RNAs selected for verification, three mi RNAs (miR-152, miR-1388 and miR-16b) demonstrated suppressive functions on GATA1 and ALAS2, which are two factors important for erythroid differentiation, resulting in reduced numbers of erythroids in microinjected zebra fish embryos. Codon substitution analyses of the genes of the TGF-β superfamily revealed signs of positive selection in TGF -β 1 and endoglin in the lineages leading to Antarctic notothenioids. Both genes are previously known to function in erythropoietic suppression. These findings implied a general trend of erythropoietic suppression in the cold-adapted notothenioid lineages through evolutionary modulation of the multi-functional TGF-β signalling pathway. This trend is more pronounced in the haemoglobin-less icefish, which may pre-emptively hinder the otherwise defective erythroids from production. [ABSTRACT FROM AUTHOR]

Bigeye tuna Thunnus obesus is considered an important fishery species around the world. There is no adequate genetic data available for the T. obesus population. Polymorphism of sequence variations in mitochondrial Cyt b genes were assessed to explore the level of genetic variability and differentiation among eight populations of T. obesus sampled from the central Pacific Ocean. Overall, a total of 44 mtDNA haplotypes and 26 variable sites were detected in the 686 bp segment of mtDNA Cyt b gene. Nucleotide diversity ranged from 0.17 to 0.27 % and the haplotype diversity ranged from 0.604 to 0.793. An analysis of molecular variance (AMOVA) test of bigeye tuna revealed that 99.38 % of the genetic variation occurred within populations. Both the maximum likelihood tree and the haplotype network indicated that two lineages of bigeye tuna coexisted in the central Pacific Ocean. Hierarchical AMOVA tests and pairwise analysis revealed no geographical isolation among haplotypes within the two lineages. High Nm values from this investigation indicated high rates of gene flow between the two sampling regions. Furthermore, tests of neutrality and mismatch distribution suggested that T. obesus might have experienced a population expansion, one that possibly occurred 110,000 years ago. Our study firstly unraveled the population genetic structure of the T. obesus in the central Pacific Ocean, and addressed the related fishery management issues including fishery stock identification, management, and conservation. [ABSTRACT FROM AUTHOR]

This study isolated and characterized 11 novel microsatellite markers for the commercially important swimming crab species, Portunus trituberculatus. Genetic diversity and population structure of two populations of P. trituberculatus in the East China Sea were assessed using these loci. The microsatellite markers produced 242 alleles, varying from 17 to 26 alleles per locus. In all the samples, the range of heterozygosity was 0.6324-0.9403 (observed) and 0.8998-0.9547 (expected). An F-statistic analysis revealed low genetic differentiation between the populations (mean F = 0.0197), with 98% of the variation resulting from the within-population component. In addition, cross-amplification was tested in two other portunid species, and we found that many loci yielded useful information. The high degree of polymorphism exhibited by the 11 microsatellites suggests that these markers will be useful for both aquaculture and studies of natural populations of the genus. [ABSTRACT FROM AUTHOR]

Abstract: The swimming crab, Portunus trituberculatus, is an important marine fishery and aquaculture species. Although P. trituberculatus is a euryhaline species, water salinity condition influenced its distribution and migration route. In order to understand molecular mechanism of osmoregulation and discover genes involved in salinity adaptation, expressed sequence tags (ESTs) from gills of this crab were characterized under salinity challenges. From 4433 high-quality sequences, 2426 unique genes including 238 contigs and 2188 singlets were obtained. Only one third of the unigenes are homologous with known proteins, others are found only in the swimming crab, suggesting a high percent of unknown genes in this species. Nearly 292 transcripts, which accounted for about 12% (292/2426) of total unique genes and about 14% (629/4433) of the total sequenced ESTs, were candidate genes responsive to salinity challenge based on current knowledge. Gene ontology annotation further grouped these genes into seven function categories including: reactive oxygen scavengers (5.4%), transporter protein (15.8%), stress protein (11.0%), signal transduction (13.7%), protein synthesis and destination (22.4%), transcription (13.7%), and metabolism/energy (17.5%) indicating salinity adaptation may be involved with a series of cellular processes. This study represents the first functional profiling of genes expressed in P. trituberculatus gill and provides so far the largest gene collection of this species. The pertinent sequence would greatly facilitate the elucidating molecular mechanisms underlying salinity adaptation in this species. [ABSTRACT FROM AUTHOR]

Abstract: Portunus trituberculatus is a commercially important fishery species. In this study, intraspecific variation was examined by using mitochondrial DNA 16S rRNA gene in 213 individual crabs sampled from six localities along the coast of the East China Sea. Twenty-two polymorphic sites defined 25 distinct haplotypes, revealing a moderately high haplotype diversity and relatively low sequence divergence among the six localities. An excess of within population unique haplotypes at most sample locations were detected, which might influence genetic structure of the swimming crab populations. Neither neighbor-joining tree nor minimum spanning network (MSN) based on the haplotype data indicated distinct patterns of phylogeographic structure among the 25 haplotypes. Analyses of molecular variance (AMOVA) and F ST statistics supported the hypothesis that population samples from the East China Sea were genetically nonhomogenous, indicating that gene flow might be restricted across those regions, despite the high potential of dispersal. In addition, tests of neutral evolution and analysis of mismatch distribution suggested that P. trituberculatus might have undergone a population expansion, possibly within the last 127,000 and 429,000 years. Our study unraveled the extant population genetic structure of the P. trituberculatus, and addressed the related fishery management issues including artificial breeding, fishery stock identification and conservation. [Copyright &y& Elsevier]

Glioma, which originates in the brain, is the most aggressive tumor of the central nervous system. It has been shown that microRNA (miRNA) controls the proliferation, migration and apoptosis of glioma cells. The objective of the present study was to measure microRNA-3148 (miR-3148) expression and investigate its impact on the pathogenetic mechanism of glioma. In the present study, reverse transcription-quantitative real-time PCR was employed to detect miR-3148 expression levels in glioma tissues and cell lines. Cell Counting Kit-8 assay, 5-ethynyl-2'-deoxyuridine assay, and Transwell migration assay were performed to assess the influence of miR-3148 on the malignant biological behavior of glioma cells. The biological functions of miR-3148 in glioma were examined via a xenograft tumor growth assay. Furthermore, the association between miR-3148 and DCUN1D1 was investigated via immunohistochemistry, dual-luciferase reporter assay and western blotting. It was observed that miR-3148 was expressed at low levels in glioma cells, and this represented a poor survival rate. In addition, an increased level of miR-3148 in cells and animal models inhibited glioma cell migration and proliferation. Moreover, miR-3148 decreased DCUN1D1 and curbed the nuclear factor κ enhancer binding protein (NF-κB) signaling pathway, thus decreasing the growth of glioma. Thus, miR-3148 is expressed within glioma tissues at low levels where it suppresses glioma by curbing the NF-κB pathway and lowering DCUN1D1. [ABSTRACT FROM AUTHOR]

Simultaneous multiclass classification of tumor types is essential for future clinical implementations of microarray-based cancer diagnosis. In this study, we have combined genetic algorithms (GAs) and all paired support vector machines (SVMs) for multiclass cancer identification. The predictive features have been selected through iterative SVMs/GAs, and recursive feature elimination post-processing steps, leading to a very compact cancer-related predictive gene set. Leave-one-out cross-validations yielded accuracies of 87.93% for the eight-class and 85.19% for the fourteen-class cancer classifications, outperforming the results derived from previously published methods. [Copyright &y& Elsevier]

Abyssal (3501–6500 m) and hadal (>6500 m) fauna evolve under harsh abiotic stresses, characterized by high hydrostatic pressure, darkness and food shortage, providing unique opportunities to investigate mechanisms underlying environmental adaptation. Genomes of several hadal species have recently been reported. However, the genetic adaptation of deep sea species across a broad spectrum of ocean depths has yet to be thoroughly investigated, due to the challenges imposed by collecting the deep sea species. To elucidate the correlation between genetic innovation and vertical distribution, we generated a chromosome‐level genome assembly of the macrourids Coryphaenoides yaquinae, which is widely distributed in the abyssal/hadal zone ranging from 3655 to 7259 m in depth. Genomic comparisons among shallow, abyssal and hadal‐living species identified idiosyncratic and convergent genetic alterations underlying the extraordinary adaptations of deep‐sea species including light perception, circadian regulation, hydrostatic pressure and hunger tolerance. The deep‐sea fishes (Coryphaenoides Sp. and Pseudoliparis swirei) venturing into various ocean depths independently have undergone convergent amino acid substitutions in multiple proteins such as rhodopsin 1, pancreatic and duodenal homeobox 1 and melanocortin 4 receptor which are known or verified in zebrafish to be related with vision adaptation and energy expenditure. Convergent evolution events were also identified in heat shock protein 90 beta family member 1 and valosin‐containing protein genes known to be related to hydrostatic pressure adaptation specifically in fishes found around the hadal range. The uncovering of the molecular convergence among the deep‐sea species shed new light on the common genetic innovations required for deep‐sea adaptation by the fishes. [ABSTRACT FROM AUTHOR]

Na+/K+-ATPase is an important ion-transporting enzyme involved in osmoregulation. The swimming crab (Portunus trituberculatus) is a commercially important edible crab species in China. At salinities lower than 10 ‰ or higher than 40 ‰ , its production is seriously impacted; however, the mechanisms of how the Na+/K+-ATPase of swimming crabs responds to salinity changes, is unclear. In the current study, the Na+/K+-ATPase α -subunit (NAKA) and β -subunit (NAKB) cDNA of P. trituberculatus was identified. Multiple alignment was performed and the expression of NAKA and NAKB in the 6th gills under different salinity conditions were detected using semi-quantitative RT-PCR. The results showed that NAKA and NAKB mRNA both increased significantly at day 1, but they were maintained at low levels when exposed to 40 ‰ salinity for a long time. The hematoxylin and eosin staining showed that ionocytes increased in size at 40 ‰ salinity, but decreased at 10 ‰ salinity. Immunocytochemical analysis revealed that NAKA signals increased with exposure to 40 ‰ salinity for one day, but the signals were not strong at 10 ‰ salinity. Comparison of the conserved NAKA domain of P. trituberculatus and the Chinese mitten crab (Eriocheir sinensis) showed that the polypeptide binding site (α -subunit/ β -subunit interface) was different, which may be one of the reasons that P. trituberculatus is not as tolerant of fresh water as E. sinensis. [ABSTRACT FROM AUTHOR]

Largemouth bass (Micropterus salmoides) is an important commercially cultured freshwater fish. High temperature is a common challenge encountered in the summer cultivation of largemouth bass. In this study, we conducted a genome-wide association study using general linear models and linear mixed models to identify significant single nucleotide polymorphisms (SNPs) and candidate genes associated with loss of equilibrium (LOE) and weight gain (WG) during high temperature challenge. We collected fin tissue from 353 individuals of largemouth bass exposed to high water temperature (37.5 °C) and performed whole-genome resequencing. Through association analysis, we successfully identified 10 SNPs and 38 candidate genes that were significantly associated with LOE, and four SNPs and 19 candidate genes that were significantly associated with WG. Using quantitative PCR and Western blot, we tested the expression of eight genes related to LOE in heat-sensitive and heat-tolerant individuals, and identified significant differences in the expression of the following five genes: Tmub2 , Ngfr , Hgf , Hdac6 , and Sypl. For WG, we assessed the expression of three candidate genes, among which Mrc2l displayed significant differences in expression between the high WG group and low WG group. We discuss the functions and potential biological processes of candidate genes for LOE and WG. Our results provide basic genetic information for breeding largemouth bass with high temperature tolerance. • Reported a genome-wide association study with heat tolerant in largemouth bass. • A chronic, step ramping paradigm was designed to conduct the heat challenge trail. • Significant SNPs and candidate genes related to heat tolerance traits were analyzed and discussed. [ABSTRACT FROM AUTHOR]

Background: Antarctica harbors the bulk of the species diversity of the dominant teleost fish suborder—Notothenioidei. However, the forces that shape their evolution are still under debate. Results: We sequenced the genome of an icefish, Chionodraco hamatus, and used population genomics and demographic modelling of sequenced genomes of 52 C. hamatus individuals collected mainly from two East Antarctic regions to investigate the factors driving speciation. Results revealed four icefish populations with clear reproduction separation were established 15 to 50 kya (kilo years ago) during the last glacial maxima (LGM). Selection sweeps in genes involving immune responses, cardiovascular development, and photoperception occurred differentially among the populations and were correlated with population-specific microbial communities and acquisition of distinct morphological features in the icefish taxa. Population and species-specific antifreeze glycoprotein gene expansion and glacial cycle-paced duplication/degeneration of the zona pellucida protein gene families indicated fluctuating thermal environments and periodic influence of glacial cycles on notothenioid divergence. Conclusions: We revealed a series of genomic evidence indicating differential adaptation of C. hamatus populations and notothenioid species divergence in the extreme and unique marine environment. We conclude that geographic separation and adaptation to heterogeneous pathogen, oxygen, and light conditions of local habitats, periodically shaped by the glacial cycles, were the key drivers propelling species diversity in Antarctica. [ABSTRACT FROM AUTHOR]

Nile tilapia (Oreochromis niloticus) is one of the most important food fishes in global aquaculture. The optimal rearing temperature for Nile tilapia is 27–30 °C; however, in some Asian breeding areas, such as south China, water temperatures in summer frequently exceed 35 °C for several days. Potential effects of long-term exposure to high temperatures on the survival and metabolism of tilapia are unclear. In this study, genetically improved farmed tilapia, age six weeks, were exposed to water temperatures of 28, 32, and 36 °C for 15 weeks. Mean survival rates and tolerance to hypoxia were significantly reduced, and respiratory rates were increased in fish reared at 36 °C, compared to the 28 and 32 °C treatments (p < 0.05). Partial temperature compensation for routine metabolic rates was observed after 15 weeks at 36 °C. Gill morphology changes in the 36 °C treatment included curling of the lamellae and hyperplasia of the filament end, which became more pronounced after acute hypoxia (0.2 mg/L O2). Transcriptomics demonstrated that expression of numerous genes related to aerobic metabolism was altered in the 36 °C treatment, including down-regulation of nine genes of the tricarboxylic acid cycle. In summary, high temperature affected tilapia gill morphology, reduced hypoxia tolerance, and inhibited aerobic metabolism, thus ultimately threatening tilapia viability and survival. [ABSTRACT FROM AUTHOR]

Thunnus albacares is an important fishery species throughout the world. Polymorphisms of sequence variations in mtDNA COI genes were assessed to explore the genetic differentiations among 11 populations of T. albacares sampled from the central Pacific Ocean. Sixty-one mtDNA haplotypes and 38 variable sites were detected. Analysis of mtDNA COI sequences revealed that tuna from the 11 localities were characterized by moderately high haplotype diversity ( h = 0.650 ± 0.040), while sequence divergence between haplotypes was relatively low ( π = 0.00364 ± 0.00044). Analyses of molecular variance and F analysis supported that significant genetic differentiations existed between some of the sampled populations. Tests of neutral evolution and mismatch distribution analysis suggested that T. albacares might have experienced a population expansion, which possibly occurred within the last 0.82 million years. Our study unraveled the genetic structure of the extant population of T. albacares and addressed the related fishery management issues including fishery stock identification and management. [ABSTRACT FROM AUTHOR]

Amphipods are the dominant scavenging metazoan species in the hadal trenches at water depths below 6,000 m. The gut microbiota have been considered to be contribution to the adaptation of deep-sea organisms; however, few comparative analyses of animal gut microbiota between different isolated hadal environments have been done so far. Here, we employed high-throughput 16S rRNA sequencing to compare the gut microbial taxonomic composition and functional potential diversity of three hadal amphipod species, Hirondellea gigas, Bathycallisoma schellenbergi, and Alicella gigantea, collected from the Mariana Trench, Marceau Trench, and New Britain Trench in the Pacific Ocean, respectively. Results showed that different community compositions were detected across all the amphipod specimens based on the analyses of alpha-diversity, hierarchical cluster tree, and PCoA (principal coordinate analysis). Moreover, almost no correlation was observed between genera overrepresented in different amphipods by microbe-microbe correlations analysis, which suggested that the colonization of symbionts were host-specific. At genus level, Psychromonas was dominant in H. gigas, and Candidatus Hepatoplasma was overall dominant in A. gigantea and B. schellenbergi. Comparison of the functional potential showed that, though three hadal amphipod species shared the same predominant functional pathways, the abundances of those most shared pathways showed distinct differences across all the specimens. These findings pointed to the enrichment of particular functional pathways in the gut microbiota of the different isolated trench amphipods. Moreover, in terms of species relative abundance, alpha-diversity and beta-diversity, there was high similarity of gut microbiota between the two A. gigantea populations, which dwelled in two different localities of the same hadal trench. Altogether, this study provides an initial investigation into the gut-microbial interactions and evolution at the hadal depths within amphipod. Each of these three amphipod species would be a model taxa for future studies investigating the influence habitat difference and geography on gut-microbial communities. [ABSTRACT FROM AUTHOR]

When fish live in the wild or are cultured artificially, they will inevitably suffer from hypoxia. At the same time, blood physiological indexes represent the physiological state of fish. In order to study the effect of long-term hypoxia acclimation on fish hematogenesis, we cultured zebrafish embryos into adulthood in a hypoxia incubator (1.5 ± 0.2 mg/L). Then we compared the hematological parameters of zebrafish cultured in normoxia and hypoxia conditions. Transcriptome sequencing analysis of the main hematopoietic tissue, the head kidney, was also compared between the two groups. Results showed that the number of erythrocytes increased significantly in the long-term hypoxia acclimated group, while the size of several cell types, such as red blood cells, eosinophils, basophils, small lymphocytes and thrombocytes, decreased significantly. The transcriptomic comparisons revealed that there were 6475 differentially expressed genes (DEGs) between the two groups. A Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that hematopoiesis and cell proliferation signaling were the most significantly enriched pathways in the head kidney of hypoxia acclimated zebrafish. In addition, many genes involved in the hematopoietic process showed significantly higher levels of expression in the hypoxia acclimated zebrafish, when compared to the normoxia zebrafish. When considered together, these data allowed us to conclude that long-term hypoxia can promote the hematopoiesis process and cell proliferation signaling in the zebrafish head kidney, which resulted in higher red blood cell production. Higher numbers of red blood cells allow for better adaptation to the hypoxic environment. In conclusion, this study provides a basis for the in-depth understanding of the effects of hypoxia on hematogenesis in fish species. [ABSTRACT FROM AUTHOR]

Cold-induced injuries significantly restrict the potential and efficacy of suivival and growth, necessitating a deeper understanding of cold response in ectothermic fish. Understanding the mechanisms by which fish respond to low-temperature stress has thus become a critical research focus in aquaculture. This study aims to investigate the effects of different temperature gradients (28 °C, 10 °C, and 2 °C) on global gene transcription in grass carp Ctenopharyngodon idellus. Additionally, the study examines cold-induced chromatin accessibility and transcriptional regulation through an integration of RNA sequencing (RNA-seq) and assay for transposase-accessible chromatin using sequencing (ATAC-seq) analyses. Transcriptome analysis revealed that mitochondrial damage and endoplasmic reticulum stress are major factors contributing to grass carp mortality under cold stress. The dataset also disclosed hepatocyte nuclear factor 1 beta (Hnf1b) and peroxisome proliferator-activated receptor alpha (PPARa) as key transcription factors for lipid and energy metabolism in grass carp under cold stress. Notably, Hnf1b and PPARa form a complex transcriptional regulatory network with other transcription factors, decreasd binding activity inactivates the expression of genes related to lipid and energy metabolism under cold stress. These results highlight the transcriptional regulation of lipid and energy metabolism in response to cold stress in grass carp. Overall, this study enhances our understanding of low-temperature response mechanisms in grass carp, providing valuable insights for further investigations. [Display omitted] • Grass carp (Ctenopharyngodon idellus) were exposed to cold stress. • Global transcriptional patterns and chromatin accessibility were analyzed under cold stress in grass carp. • Mitochondrial damage and endoplasmic reticulum stress are key characteristics of the cold response. • Transcriptional regulatory network (TRN) was characterized by integrated of RNA-seq and ATAC-seq analysis. • Decreased Hnf1b and PPARa binding inactivate lipid and energy metabolism gene transcription under cold stress. [ABSTRACT FROM AUTHOR]

Antarctic icefish is the only known vertebrate species that lacks oxygen-carrying hemoglobin and functional erythrocytes. To reveal the unique hematopoietic process of icefish, we used an integrated approach including tandem mass tag (TMT) labeling and liquid chromatography–tandem mass spectrometry (LC–MS/MS) to quantify the dynamic changes in the head kidney whole proteome of a white-blooded icefish, Chionodraco hamatus, compared to those in two other red-blooded Antarctic fish, Trematomus bernacchii and Notothenia coriiceps. Of the 4672 identified proteins, in the Antarctic icefish head kidney, 123 proteins were significantly upregulated and 95 proteins were downregulated. The functional grouping of differentially expressed proteins (DEPs) based on KEGG pathway analysis shows that white blood fish and red blood fish have significant differences in erythropoiesis, heme biogenesis, leucocyte and platelet cell development. The proteins involved in the hematopoietic process in icefish showed a clear trend of downregulation of erythroid lineage marker proteins (β-Spectrin, hemoglobin, CTCF and tfr1a) and upregulation of lymphoid and megakaryocytic lineage marker proteins, including CD9, ITGB2, and mTOR, which suggests a shift in hematopoiesis in the icefish head kidney due to the loss of erythrocytes. Moreover, western blotting analysis showed that a significantly down expression level of CTCF protein was detected in the icefish head kidney, which was in line with the proteomics data. The results of the present study not only provide basic datasets for the head kidney proteins of Antarctic fishes, but also provide important references for studies on immunity and hematopoiesis in various species. [ABSTRACT FROM AUTHOR]

Scales, as key structures of fish skin, play an important role in physiological function. The study of fish scale development mechanisms provides a basis for exploring the molecular-level developmental differences between scaled and non-scaled fishes. In this study, alizarin red staining was used to divide the different stages of zebrafish (Danio rerio) scale development. Four developmental stages, namely stage I (~17 dpf, scales have not started to grow), stage II (~33 dpf, the point at which scales start to grow), stage III (~41 dpf, the period in which the scales almost cover the whole body), and stage IV (~3 mpf, scales cover the whole body), were determined and used for subsequent transcriptome analysis. WGCNA (weighted correlation network analysis) and DEG (differentially expressed gene) analysis were used for screening the key genes. Based on the comparison between stage II and stage I, 54 hub-genes were identified by WGCNA analysis. Key genes including the Scpp family (Scpp7, Scpp6, Scpp5, and Scpp8), the Fgf family (Fgfr1b and Fgfr3), Tcf7, Wnt10b, Runx2b, and Il2rb were identified by DEG analysis, which indicated that these genes played important roles in the key nodes of scale development signal pathways. Combined with this analysis, the TGF-β, Wnt/β-catenin, and FGF signaling pathways were suggested to be the most important signal pathways for scales starting to grow. This study laid a foundation for exploring the scale development mechanism of other fishes. The scale development candidate genes identified in the current study will facilitate functional gene identifications in the future. [ABSTRACT FROM AUTHOR]

The white‐blooded Antarctic icefish is the only known vertebrate lacking oxygen‐transporting haemoglobins. Fish skin mucus, as the first line of defence against pathogens, can reflect fish welfare. In this study, we analysed the skin mucus proteome profiles of the two Antarctic fish species, the white‐blooded Antarctic icefish, Chionodraco hamatus, and the red‐blooded Antarctic fish, Notothenia coriiceps, unfolding the different proteins by liquid chromatography coupled with tandem mass spectrometry isobaric tags for relative and absolute quantitation (iTRAQ) technology. Of the 4444 totally identified proteins, 227 differentially expressed proteins (DEPs) were found in the comparison between C. hamatus and N. coriiceps, of which 121 were upregulated and 106 were downregulated in the icefish. In the Kyoto Encyclopedia of Genes and Genomes pathway annotation, we found two pathways "Legionellosis" and "Complement and coagulation cascades" were significantly enriched, among of which innate immune candidate proteins such as C3, CASP1, ASC, F3 and C9 were significantly upregulated, suggesting their important roles in C. hamatus immune system. Additionally, the DEP protein–protein interaction network analysis and "Response to stress" GO category provided candidate biomarkers for deep understanding of the distinct immune response of the two Antarctic fish underlying the cold adaptation. [ABSTRACT FROM AUTHOR]

Amphipods of the superfamily Lysianassoidea that inhabit the hadal zone (> 6000 m) have large bathymetric ranges and play a key role in deep ocean ecosystems. The endemism of these amphipod species makes them a good model for investigating potent natural selection and restricted dispersal in deep ocean trenches. Here, we describe genetic diversity and intraspecific population differentiation among three amphipod species from four Pacific trenches based on a mtDNA concatenated dataset (CO Ι and 16S rRNA genes) from 150 amphipod individuals. All amphipod populations had low genetic diversity, as indicated by haplotype and nucleotide diversity values. Population geographic relationship analysis of two Alicella gigantea populations revealed no genetic differentiation between these two localities (pairwise genetic differentiation coefficient = 0.00032, gene flow = 784.58), and the major variation (99.97%) was derived from variation within the populations. Historical demographic events were investigated using Tajima's D and Fu's F neutrality tests and analysis of mismatch distribution. Consistent results provided strong evidence to support the premise that demographic expansion occurred only for the Mariana population of Hirondellea gigas, possibly within the last 2.1–3.4 million years. These findings suggest that the formation of amphipod population structure might be the result of multiple factors including high hydrostatic pressure, food distribution, trench topographic forcing and potential ecological interactions. [ABSTRACT FROM AUTHOR]

In this work, we reported the complete mitochondrial genome sequence of theSchizothorax nukiangensis Tsaofor the first time. The complete mtDNA genome sequence ofS. nukiangensis Tsaowas 16 585 bp in length, which contains 22 transfer RNA genes, 2 rRNA genes, 13 protein-coding genes, an origin of light-strand replication (OL) and a control region (D-Loop). The overall base composition of the mitogenome was calculated to be 29.6% for A, 27.0% for C, 17.9% for G and 25.5% for T. The complete mitogenome of theS. nukiangensis Tsaocan provide an important data set for further studies on population history, molecular systematics, phylogeography and stock assessment. [ABSTRACT FROM AUTHOR]

In this study, the complete mitochondrial DNA (mtDNA) sequence ofSchizothorax yunnanensis paoshanensisis determined for the first time. The complete mtDNA genome sequence ofS. yunnanensis paoshanensisis 16,585 bp in length. It consists of 13 protein-coding genes, 22 transfer RNA genes, 2 rRNA genes and a putative control region (D-loop region). The gene order ofS. yunnanensis paoshanensismtDNA is identical to most of the vertebrate mtDNAs. The complete mitogenome sequence information ofS. yunnanensis paoshanensiscan provide useful data for further studies on molecular systematics, taxonomic status and conservation genetics. [ABSTRACT FROM AUTHOR]

The complete mitochondrial DNA sequence ofCarcharhinus longimanuswas determined and analyzed. The complete mtDNA genome sequence ofC. longimanuswas 16,706 bp in length. It contained 22 tRNA genes, 2 rRNA genes, 13 protein-coding genes and 2 non-conding regions: control region (D-loop) and origin of light-strand replication (OL). The complete mitogenome sequence information ofC. longimanuscan provide a useful data for further studies on molecular systematics, stock evaluation, taxonomic status and conservation genetics. [ABSTRACT FROM PUBLISHER]

Chionodraco hamatus is a teleost within the suborder Notothenioidei, the members of which are known to lack functional erythrocytes with modified hematopoiesis. Hematopoiesis is an essential process during the development of animals, where it is tightly regulated by many different transcription factors, signaling proteins, chromatin modifications, and microRNAs (miRNAs). The miRNAs are known to regulate the expression of their target genes at the post-transcriptional level. However, little is known about the miRNA-mediated regulation of hematopoiesis. In this study, we confirmed that miR-152 plays a crucial role in hematopoiesis during the development of C. hamatus . The overexpression of miR-152 reduced hematopoiesis according to the decreased expression of GATA1 and reduced o -dianisidine staining of hemoglobin. Mechanistically, reduced hematopoiesis was regulated by the miR-152-mediated down-regulated expression of GATA1. Bioinformatics analysis was used to predict the target gene of miR-152. Western blotting as well as dual luciferase and EGFP reporter assays were employed to investigate the expression of GATA1 mediated by miR-152. Finally, verification experiments in the zebrafish autologous model strongly supported the effect of miR-152 on hematopoiesis. In conclusion, we suggest that miR-152 is a novel molecular factor that regulates hematopoiesis during the development of C. hamatus by down-regulating the expression of GATA1. [ABSTRACT FROM AUTHOR]

The Schizothoracine fishes are widely distributed in the Qinghai-Tibetan Plateau (QTP) area and its peripheral regions, which provide a prime example of adaptation in highland aquatic environments. Recent progresses have revealed various genetic adaptations of these fishes by comparing to distantly related lowerland species, however, comparative studies on closely-related species of different altitudes are still lacking. In this study, we sequenced and annotated a primitive Schizothoracine fish Schizothorax nukiangensis Tsao and a highly specialized one Gymnocypris dobula . We performed evolutionary analyses to investigate the candidate genes and signaling pathways involved QTP highland adaptation in both Schizothoracine fishes. Analysis of the 11,007 one-copy orthologs to the primitive cyprinid species, Danio rerio , revealed that both G. dobula and S. nukiangensis showed elevated evolutionary rates. A large number of genes related to hypoxia, including genes involved metabolic processes and cardiovascular system development, exhibited signatures of positive selection in both Schizothoracine fishes, but very few positively selected genes were found overlapping among these Schizothoracines. Our results indicated divergent genetic adaptation to highland environment for aquatic species living in QTP. [ABSTRACT FROM AUTHOR]

Gymnocypris dobula is a commercially important fishery species and mostly distributed in the freshwater of Tibetan plateau. In this study, genetic diversity and intraspecific population differentiation were examined by using mitochondrial DNA D-loop sequences in 97 individuals sampled from three localities (Pali, Lasa and Yanghu) in the Tibetan plateau. Two hundred and fourteen polymorphic sites and 50 haplotypes were defined among the three localities. Genetic diversity analysis showed that the highest genetic diversity level was found in Pali population. Phylogenetic relationships analysis results indicated that closer phylogenetic relationships were found between the Yanghu and Lasa populations. Genetic population differentiation analysis indicated that the majority of variation (84.91%) was attributed to variations among populations and the largest differentiation was found between Pali and Lasa localities ( F st = 0.874, Nm = 0.036). Moreover, the historical demographic events were assessed by implementing the mismatch distribution analysis, Fajima's D test and Fu's Fs test. The results indicated that the Pali population had undergone a demographic expansion, possibly within the last 0.163 MYA (Million Years Ago). Our study firstly identified the population genetic structure of the G. dobula , which could be helpful for artificial breeding, fishery stock identification and resource conservation for this species. [ABSTRACT FROM AUTHOR]

A correction to the article "Genetic Population Structure of Thunnus albacares in the Central Pacific Ocean Based on mtDNA COI Gene Sequences" that was published in the 2015 issue is presented.

In this study, we determined the complete mitogenome sequence ofPseudocarcharias kamoharai. The complete mitogenome ofP. kamoharaiis 16,694 bp in length, which contains 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs and 2 non-coding regions: control region (D-loop) and origin of light-strand replication (OL). Overall, base composition of mitogenome is estimated to be 32.06% for A, 23.63% for C, 13.21% for G and 31.10% for T. The complete mtDNA sequence ofP. kamoharaiprovides a useful data for the studies on the molecular systematic phylogeography and population genetics. [ABSTRACT FROM PUBLISHER]

Portunus trituberculatus is a commercially important species widely spread in the East China Sea. Intraspecific variation of the mitochondrial DNA cytochrome oxidase subunit I (mtDNA COI) gene was investigated in 213 individuals from six localities (Changjiang Estuary, Shengsi Islands, Zhoushan Islands, Dongtou Islands, Dinghai Bay, and Quanzhou Bay) ranging from north (31°21′N) to south (24°55′N) coastal waters of the East China Sea. Overall, a total of 27 mtDNA haplotypes and 21 variable sites were detected in the 787 bp segment of COI gene. Analysis of mtDNA COI sequence data revealed that crabs from the six localities were characterized by moderately high haplotypic diversity ( h = 0.787 ± 0.026), while sequence divergence values between haplotypes were relatively low (π = 0.00241 ± 0.00098). Each population was characterized by a single most frequent haplotype, shared among all six localities, and a small number of rare ones, typically present in only one or two individuals and representative of a specific population. However, neither the neighbor-joining tree nor the minimum spanning network (MSN) based on the haplotype data exhibited geographical patterns of the six populations. Mismatch distribution analysis of P. trituberculatus individuals sampled from the six localities suggested that sudden population expansion might have occurred in CJ and SS population that might be consistent with over-exploitation of the swimming crab. Analysis of molecular variance (AMOVA) and F ST statistics showed that significant genetic differentiation existed among the SS, ZS, DT, DH, and QZ populations, suggesting that gene flow might be reduced, even between the geographically close sites, despite the high potential of dispersal. The possible causes of the observed genetic heterogeneity among the P. trituberculatus populations and the potential applications of the mtDNA COI marker in the artificial breeding and fisheries... [ABSTRACT FROM AUTHOR]

Background The Southern Ocean is the coldest ocean on Earth but a hot spot of evolution. The bottom-dwelling Eocene ancestor of Antarctic notothenioid fishes survived polar marine glaciation and underwent adaptive radiation, forming >120 species that fill all water column niches today. Genome-wide changes enabling physiological adaptations and the rapid expansion of the Antarctic notothenioids remain poorly understood. Results We sequenced and compared 2 notothenioid genomes—the cold-adapted and neutrally buoyant Antarctic toothfish Dissostichus mawsoni and the basal Patagonian robalo Eleginops maclovinus, representing the temperate ancestor. We detected >200 protein gene families that had expanded and thousands of genes that had evolved faster in the toothfish, with diverse cold-relevant functions including stress response, lipid metabolism, protein homeostasis, and freeze resistance. Besides antifreeze glycoprotein, an eggshell protein had functionally diversified to aid in cellular freezing resistance. Genomic and transcriptomic comparisons revealed proliferation of selcys–transfer RNA genes and broad transcriptional upregulation across anti-oxidative selenoproteins, signifying their prominent role in mitigating oxidative stress in the oxygen-rich Southern Ocean. We found expansion of transposable elements, temporally correlated to Antarctic notothenioid diversification. Additionally, the toothfish exhibited remarkable shifts in genetic programs towards enhanced fat cell differentiation and lipid storage, and promotion of chondrogenesis while inhibiting osteogenesis in bone development, collectively contributing to the achievement of neutral buoyancy and pelagicism. Conclusions Our study revealed a comprehensive landscape of evolutionary changes essential for Antarctic notothenioid cold adaptation and ecological expansion. The 2 genomes are valuable resources for further exploration of mechanisms underlying the spectacular notothenioid radiation in the coldest marine environment. [ABSTRACT FROM AUTHOR]