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The southern elephant seal Mirounga leonina is the largest member of the phocid seals and is a highly sexually dimorphic predator at circumpolar regions. In this study, we generated the first high-quality de novo assembly of the blood transcriptome of M. leonina using the Illumina MiSeq platform. A total of 40.5 million raw reads were obtained and assembled using the Oases assembly platform, resulting in 46,445 contigs with an N50 value of 634 bp. We performed functional gene annotations through pathway analyses of the Gene Ontology (GO), Eukaryotic Orthologous Groups (KOG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Ortholog comparison revealed that a high proportion of the M. leonina blood transcriptome had significant sequence homology within pinnipeds. M. leonine, a deep and long-diving seal, is routinely exposed to progressive hypoxia during dives. KEGG analyses detected an intact hypoxia-inducible factor-1 (HIF-1) signaling pathway, which is a key metabolism pathway in the adaptive homeostatic responses to hypoxia. In the blood transcriptome, many essential genes involved in innate immunity were detected, which suggests that the blood serves as a host defense modulator against exogenous infections in M. leonina. This genomic resource will be useful for understanding adaptive metabolism upon repeated breath-hold dives and determining the health status of southern elephant seals without the need to sacrifice them in experiments.

Temperature is an important abiotic factor that directly influences the physiology of marine fish. The Antarctic bullhead notothen Notothenia coriiceps inhabits water with temperatures ranging from — 1.9 to 2°C at circumpolar regions. Thus, N. coriiceps is useful as a model animal for understanding the effects of temperature stress. To assess the transcriptional response of skin tissue to temperature changes, Antarctic bullhead notothen were exposed to two temperature stresses, 4°C and — 2°C, following acclimatization at 2°C. Twenty-four hours after the temperature change, skin transcriptomes were sequenced using the Illumina Hiseq 2000 platform and analyzed using a series of bioinformatics tools. Functional gene annotations through pathway analyses of the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes databases revealed commonly or distinctively modulated transcriptional changes in skin. Both temperature stressors significantly upregulated the actin cytoskeleton regulation pathway and the skin’s water barrier function, while the stressors downregulated the metabolism involved in muscle contraction, choline receptor regulation, collagen regulation, and immunity. Cold stress caused significant downregulation of the mRNA expression of genes involved in vasopressin-regulated water reabsorption. Neither the heat- nor cold-stressed skin transcriptomes exhibited significant heat shock protein expression. Our results suggest that, as a first barrier for fish, the skin has complex metabolisms with high transcriptional sensitivity against environmental temperature stress. These results will be useful for understanding the skin-specific molecular mechanisms that Antarctic fish use to adapt to temperature fluctuations.

Background The common long-arm octopus (Octopus minor) is found in mudflats of subtidal zones and faces numerous environmental challenges. The ability to adapt its morphology and behavioral repertoire to diverse environmental conditions makes the species a promising model for understanding genomic adaptation and evolution in cephalopods. Findings The final genome assembly of O. minor is 5.09 Gb, with a contig N50 size of 197 kb and longest size of 3.027 Mb, from a total of 419 Gb raw reads generated using the Pacific Biosciences RS II platform. We identified 30,010 genes; 44.43% of the genome is composed of repeat elements. The genome-wide phylogenetic tree indicated the divergence time between O. minor and Octopus bimaculoides was estimated to be 43 million years ago based on single-copy orthologous genes. In total, 178 gene families are expanded in O. minor in the 14 bilaterian species. Conclusions We found that the O. minor genome was larger than that of closely related O. bimaculoides, and this difference could be explained by enlarged introns and recently diversified transposable elements. The high-quality O. minor genome assembly provides a valuable resource for understanding octopus genome evolution and the molecular basis of adaptations to mudflats.

The purplish Washington clam (Saxidomus purpuratus) in the family Veneridae is distributed widely along the intertidal zones of northeast Asia and is increasingly being utilized as a commercially important food resource. Bivalves maintain homeostasis by regulating their food intake and digestion, innate immunity, and biotransformation in a mollusk-specific organ, the digestive gland. To understand digestive gland-specific pathways, we generated a high-quality de novo assembly of the digestive gland transcriptome of this clam using the Illumina Miseq platform. A total of 9.9 million raw reads were obtained and assembled using the Oases assembly platform, resulting in 27,358 contigs with an N50 of 433 bp. Functional gene annotations were performed using Gene Ontology, Eukaryotic Orthologous Groups, and Kyoto Encyclopedia of Genes and Genomes pathway analyses. In the transcriptome, many crucial genes involved in innate immunity and digestion metabolism were detected. A number of enzymes associated with drug metabolism were annotated, as much as that identified from the whole transcriptome of the Pacific oyster Crassostrea gigas. We provide valuable sequence information of S. purpuratus to predict functional understandings of the bivalve-specific digestive gland. This resource will be valuable for researchers comparing gene compositions and their expression levels in the digestive glands of bivalves.

Bathynellacea (Crustacea, Syncarida, Parabathynellidae) are subterranean aquatic crustaceans that typically inhabit freshwater interstitial spaces (e.g., groundwater) and are occasionally found in caves and even hot springs. In this study, we sequenced the whole transcriptome of Allobathynella bangokensis using RNA-seq. De novo sequence assembly produced 74,866 contigs including 28,934 BLAST hits. Overall, the gene sequences were most similar to those of the waterflea Daphnia pulex. In the A. bangokensis transcriptome, no opsin or related sequences were identified, and no contig aligned to the crustacean visual opsins and non-visual opsins (i.e. arthropsins, peropsins, and melaopsins), suggesting potential regressive adaptation to the dark environment. However, A. bangokensis expressed conserved gene family sets, such as heat shock proteins and those related to key innate immunity pathways and antioxidant defense systems, at the transcriptional level, suggesting that this species has evolved adaptations involving molecular mechanisms of homeostasis. The transcriptomic information of A. bangokensis will be useful for investigating molecular adaptations and response mechanisms to subterranean environmental conditions.

The chinstrap (Pygoscelis antarcticus) and gentoo (P. papua) penguins are distributed throughout Antarctica and the sub-Antarctic islands. In this study, high-quality de novo assemblies of blood transcriptomes from these penguins were generated using the Illumina MiSeq platform. A total of 22.2 and 21.8 raw reads were obtained from chinstrap and gentoo penguins, respectively. These reads were assembled using the Oases assembly platform and resulted in 26,036 and 21,854 contigs with N50 values of 929 and 933 base pairs, respectively. Functional gene annotations through pathway analyses of the Gene Ontology, EuKaryotic Orthologous Groups, and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases were performed for each blood transcriptome, resulting in a similar compositional order between the two transcriptomes. Ortholog comparisons with previously published transcriptomes from the Adélie (P. adeliae) and emperor (Aptenodytes forsteri) penguins revealed that a high proportion of the four penguins’ transcriptomes had significant sequence homology. Because blood and tissues of penguins have been used to monitor pollution in Antarctica, immune parameters in blood could be important indicators for understanding the health status of penguins and other Antarctic animals. In the blood transcriptomes, KEGG analyses detected many essential genes involved in the major innate immunity pathways, which are key metabolic pathways for maintaining homeostasis against exogenous infections or toxins. Blood transcriptome studies such as this may be useful for checking the immune and health status of penguins without sacrifice.

Background: HP0892 of H. pylori shares high structural similarity with other toxin-antitoxin (TA) system toxins. Results: RNase activity and cell toxicity of HP0892 is inhibited by HP0893 via strong protein-protein interaction. Conclusion: HP0892-HP0893 pair is a TA system with a protein-protein interaction mode similar to other TA pairs. Significance: It is highly probable that HP0892-HP0893 TA pair is involved in H. pylori virulence., Bacterial chromosomal toxin-antitoxin (TA) systems have been proposed not only to play an important role in the stress response, but also to be associated with antibiotic resistance. Here, we identified the chromosomal HP0892-HP0893 TA proteins in the gastric pathogen, Helicobacter pylori, and structurally characterized their protein-protein interaction. Previously, HP0892 protein was suggested to be a putative TA toxin based on its structural similarity to other RelE family TA toxins. In this study, we demonstrated that HP0892 binds to HP0893 strongly with a stoichiometry of 1:1, and HP0892-HP0893 interaction occurs mainly between the N-terminal secondary structure elements of HP0892 and the C-terminal region of HP0893. HP0892 cleaved mRNA in vitro, preferentially at the 5′ end of A or G, and the RNase activity of HP0892 was inhibited by HP0893. In addition, heterologous expression of HP0892 in Escherichia coli cells led to cell growth arrest, and the cell toxicity of HP0892 was neutralized by co-expression with HP0893. From these results and a structural comparison with other TA toxins, it is concluded that HP0892 is a toxin with intrinsic RNase activity and HP0893 is an antitoxin against HP0892 from a TA system of H. pylori. It has been known that hp0893 gene and another TA antitoxin gene, hp0895, of H. pylori, are both genomic open reading frames that correspond to genes that are potentially expressed in response to interactions with the human gastric mucosa. Therefore, it is highly probable that TA systems of H. pylori are involved in virulence of H. pylori.

Fish are a representative population of lower vertebrates that serve as an essential link to early vertebrate evolution, and this has fueled academic interest in studying ancient vertebrate immune defense mechanisms in teleosts. Notothenia coriiceps, a typical Antarctic notothenioid teleost, has evolved to adapt to the cold and thermally stable Antarctic sea. In this study, we examined adaptive signaling pathways and immune responses to bacterial and viral pathogenic exposure in N. coriiceps. Using RNA sequencing, we investigated transcriptional differences in the liver tissues of N. coriiceps challenged with two pathogen-mimicking agonists, a bacterial ligand (heat-killed Escherichia coli, HKEB) and a viral ligand (polyinosinic:polycytidylic acid, Poly I:C). We found that 567 unique genes were up-regulated two-fold in the HKEB-exposed group, whereas 392 unique genes, including 124 immune-relevant genes, were up-regulated two-fold in the Poly I:C-exposed group. A KEGG pathway analysis of the 124 immune-relevant genes revealed that they exhibited major features of antigen processing and presentation bacterial ligand exposure, but they were down-regulated after viral ligand exposure. A quantitative real time RT-PCR analysis revealed that TNFα and TNF2, major inducers of apoptosis, were highly up-regulated after exposure to the viral ligand but not the bacterial ligand. The results suggest that the bacterial and viral ligands up-regulate inducers of different immune mechanisms in N. coriiceps liver tissue. N. coriiceps has an immune response defense strategy that uses antigen presentation against bacterial infection, but it may use a different defense, such as TNF-mediated apoptosis, against viral infection. The specific immune responses of N. coriiceps may be adaptations to the Antarctic environment and pathogens. These results will help define the characteristics of Antarctic fish and increase our understanding of their immune response mechanisms.

The complete mitochondrial genome of the Antarctic dragonfish, Parachaenichthys charcoti (Vaillant, 1906), is described, representing the first complete mitochondrial genome sequence of the family Bathydraconidae. The mitochondrial genome is 18,202 base pairs in length and encodes 13 protein-coding genes, 23 tRNAs, 2 rRNAs and 2 control regions. The overall base composition is A: 25.8%, T: 25.3%, G: 17.9% and C: 31.0%, with an A:T content of 51.1%. The complete mitochondrial genome sequence will be useful for phylogenetic, evolutionary and functional studies of Antarctic Notothenioids.

A Gram-negative, rod-shaped, red-pink in color, and UV radiation-resistant bacterium Hymenobacter sp. strain PAMC26554 was isolated from Usnea sp., an Antarctic lichen, and belongs to the class of Cytophagia and the phylum of Bacteroidetes. The complete genome of Hymenobacter sp. PAMC26554 consists of one chromosome (5,244,843bp) with two plasmids (199,990bp and 6421bp). The genomic sequence indicates that Hymenobacter sp. strain PAMC26554 possesses several genes involved in the nucleotide excision repair pathway that protects damaged DNA. This complete genome information will help us to understand its adaptation and novel survival strategy in the Antarctic extreme cold environment.

Ionizing radiation-resistant Hymenobacter sp. strain PAMC26628 was isolated from Stereocaulon sp., an Arctic lichen. Complete genome sequencing of Hymenobacter sp. PAMC26628 revealed one chromosome (5,277,381 bp), one plasmid (89,596 bp), and several genes involved in nucleotide excision repair, a DNA damage removal pathway. An analysis of the Hymenobacter sp. PAMC26628 genome will help us understand its evolution and provide novel insight into the adaptations that allow this organism to survive in the extreme cold of the Arctic.

The complete sequence of the mitochondrial genome of Notothenia coriiceps was obtained by genome assembly. The complete sequence was determined to be 18,347 base pairs in length and to contain 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 2 control regions. Of the thirteen protein-coding genes, two genes (cox1 and atp6) had GTG start codons, and six genes (nad2, cox2, cox3, nad3, nad4, and cytb) had incomplete stop codons that require the post-transcriptional addition of A bases. The base composition of the mitogenome was 26.3% A, 27.6% T, 17.5% G, and 28.5% C.

Notothenia coriiceps, a typical Antarctic notothenioid teleost, has evolved to adapt to the extreme Antarctic marine environment. We previously reported an extensive analysis of the Antarctic notothenioid transcriptome. In this study, we focused on a key component of the innate immune system, the Toll-like receptors (TLRs). We cloned the full-length sequence of 12 TLRs of N. coriiceps. The N. coriiceps transcriptome for TLR homologue (ncTLR) genes encode a typical TLR structure, with multiple extracellular leucine-rich regions and an intracellular Toll/IL-1 receptor (TIR) domain. Using phylogenetic analysis, we established that all of the cloned ncTLR genes could be classified into the same orthologous clade with other teleost TLRs. ncTLRs were widely expressed in various organs, with the highest expression levels observed in immune-related tissues, such as the skin, spleen, and kidney. A subset of the ncTLR genes was expressed at higher levels in fish exposed to pathogen-mimicking agonists, heat-killed Escherichia coli, and polyinosinic-polycytidylic acid (poly(I:C)). However, the mechanism involved in the upregulation of TLR expression following pathogen exposure in fish is currently unknown. Further research is required to elucidate these mechanisms and to thereby increase our understanding of vertebrate immune system evolution.

The complete mitogenome of the Antarctic soft-shelled clam, Laternula elliptica was determined to be 14,622 bp in length, and to contain 13 protein coding genes (PCGs), 22 tRNA genes, and large (rrnL) and small (rrnS) rRNA genes. Its total A + T content is 55.09%. The L. elliptica mitogenome is the smallest one among those of bivalvia, due to the existence of relatively small intergenic non-coding sequences. All genes are transcribed from the light-strand as a template like bivalve taxa except Unionoidea.

For the past 10 to 13 million years, Antarctic notothenioid fish have undergone extraordinary periods of evolution and have adapted to a cold and highly oxygenated Antarctic marine environment. While these species are considered an attractive model with which to study physiology and evolutionary adaptation, they are poorly characterized at the molecular level, and sequence information is lacking. The transcriptomes of the Antarctic fishes Notothenia coriiceps, Chaenocephalus aceratus, and Pleuragramma antarcticum were obtained by 454 FLX Titanium sequencing of a normalized cDNA library. More than 1,900,000 reads were assembled in a total of 71,539 contigs. Overall, 40% of the contigs were annotated based on similarity to known protein or nucleotide sequences, and more than 50% of the predicted transcripts were validated as full-length or putative full-length cDNAs. These three Antarctic fishes shared 663 genes expressed in the brain and 1,557 genes expressed in the liver. In addition, these cold-adapted fish expressed more Ub-conjugated proteins compared to temperate fish; Ub-conjugated proteins are involved in maintaining proteins in their native state in the cold and thermally stable Antarctic environments. Our transcriptome analysis of Antarctic notothenioid fish provides an archive for future studies in molecular mechanisms of fundamental genetic questions, and can be used in evolution studies comparing other fish.

Calcineurin is a heterodimeric serine/threonine protein phosphatase, important for many cellular processes such as T-cell regulation, cardiac hypertrophy and kidney development. We previously reported the characterization of Caenorhabditis elegans calcineurin mutants as providing a simple but excellent genetic model system for studying in vivo functions of calcineurin. Calcineurin loss-of-function mutants, cnb-1(lf), and gain-of-function mutants, tax-6(gf), show certain opposite phenotypes as well as some similar phenotypes. In order to explain the phenotypic similarity observed in both loss-of-function and gain-of-function mutants, we examined the proteins that followed similar trends in both mutants relative to wild-type worms by using 2-DE. Interestingly, VHA-13, HSP-6 and phosphoenolpyruvate carboxykinase are down-regulated in both mutants. A total of 96 differentially regulated proteins were identified by MALDI-TOF/MS. Among these, 42 proteins are up-regulated and 54 proteins are down-regulated in calcineurin mutants. Furthermore, knock-down of about 30% of the genes, which are down-regulated in calcineurin mutants, showed some of the phenotypes of calcineurin-null mutants. This analysis suggests the functional relevance of these proteins to calcineurin activity in C. elegans.