The complete mitochondrial genome of Trematomus hansoni Boulenger, 1902 (Perciformes, Nototheniidae).

The striped notothen Trematomus hansoni is an Antarctic fish species belonging to the family Nototheniidae (cod icefishes) that is distributed throughout the Southern Ocean. In this study, the complete mitochondrial genome of T. hansoni was sequenced using an Illumina MiSeq platform. The circular mitochondrial genome is 19,218 bp long and contains 13 protein-coding genes, 23 tRNA genes, two rRNA genes, and one control region. Notably, there are two trnG-UCC genes and the second gene, located between trnE-UUC and trnI-GAU, has no D-arm structure. The base composition is 56.18% of A + T and 43.82% of G + C. The phylogenetic analysis supports that T. hansoni is grouped into a single clade with T. bernacchii. This study will be a valuable resource for further research on the phylogeny and evolution of the genus Trematomus.

The complete mitochondrial genome of Gobionotothen gibberifrons (Perciformes, Nototheniidae).

The humped rockcod, Gobionotothen gibberifrons, is an Antarctic fish of the genus Gobionotothen in the family Nototheniidae and order Perciformes. To date, little biological information has been recorded about the genus Gobionotothen. Here, we report the first complete mitogenome of the genus Gobionotothen. The mitochondrial genome of G. gibberifrons is 18,631 bp in length, comprising 13 protein-coding genes, 24 tRNA genes (trnP-UGG and trnT-UGU were duplicated), 2 rRNA genes, and non-coding control regions. The base composition was 53.74% for A + T and 46.26% for G + C. This new mitochondrial genome of G. gibberifrons provides basic information for further phylogenetic analysis, suggesting the necessity to exploit a variety of newly discovered mitogenome sequences to infer inconclusive evolutionary relationships in Antarctic fishes.

Molecular evidence for multiple origins and high genetic differentiation of non-native winter crane fly, Trichocera maculipennis (Diptera: Trichoceridae), in the maritime Antarctic.

Native biodiversity and ecosystems of Antarctica safeguarded from biological invasion face recent threats from non-native species, accelerated by increasing human activities and climate changes. Over two decades ago, the winter crane fly, Trichocera maculipennis, was first detected on King George Island. It has now successfully colonized several research stations across King George Island. To understand the origin, genetic diversity, and population structure of this Holarctic species, we conducted mitochondrial DNA cytochrome c oxidase subunit I (COI) sequence analysis across both its native and invasive ranges. In parallel, we performed microsatellite loci analysis within the invasive ranges, utilizing 12 polymorphic microsatellite markers. Furthermore, we compared body sizes among adult males and females collected from three different locations of King George Island. Our COI sequence analysis exhibited two different lineages present on King George Island. Lineage I was linked to Arctic Svalbard and Polish cave populations and Lineage II was related to Canadian Terra Nova National Park populations, implying multiple origins. Microsatellite analysis further exhibited high levels of genetic diversity and significant levels of genetic differentiation among invasive populations. Body sizes of adult T. maculipennis were significantly different among invasive populations but were not attributed to genetics. This significant genetic diversity likely facilitated the rapid colonization and establishment of T. maculipennis on King George Island, contributing to their successful invasion. Molecular analysis results revealed a substantial amount of genetic variation within invasive populations, which can serve as management units for invasive species control. Furthermore, the genetic markers we developed in the study will be invaluable tools for tracking impending invasion events and the travel routes of new individuals. Taken together, these findings illustrate the highly invasive and adaptable characteristics of T. maculipennis. Therefore, immediate action is necessary to mitigate their ongoing invasion and facilitate their eradication.

Chromosome-level genome assembly and annotation of the Antarctica whitefin plunderfish Pogonophryne albipinna.

The Antarctic whitefin plunderfish Pogonophryne albipinna belongs to the family Artedidraconidae, a key component of Antarctic benthic ecosystems within the order Perciformes and the suborder Notothenioidei. While genome research on P. albipinna using short-read sequencing is available, high-quality genome assembly and annotation employing long-read sequencing have yet to be performed. This study presents a chromosome-scale genome assembly and annotation for P. albipinna, utilizing a combination of Illumina short-read, PacBio long-read, and Hi-C sequencing technologies. The resulting genome assembly spans approximately 1.07 Gb, with a longest scaffold measuring 59.39 Mb and an N50 length of 41.76 Mb. Of the 1,111 Hi-C scaffolds, 23 exceeded 10 Mb and were thus classified as chromosome-level. BUSCO completeness was assessed at 95.6%. The assembled genome comprises 50.68% repeat sequences, and a total of 31,128 protein-coding genes were predicted. This study will enhance our understanding of the genomic characteristics of cryonotothenioids and facilitate comparative analyses of their adaptation and evolution in extreme environments.

A chromosome-level reference genome of the Antarctic blackfin icefish Chaenocephalus aceratus.

The blackfin Icefish (Chaenocephalus aceratus) belongs to the family Channichthyidae and the suborder Notothenioidei which lives in the Antarctic. We corrected the mis-scaffolds in the previous linkage map results by Hi-C analysis to obtain improved results for chromosome-level genome assembly. The final assembly analysis resulted in a total of 3,135 scaffolds, a genome size of 1,065.72 Mb, and an N50 of 33.46 Mb. 820.24 Mb, representing 88.88% of the total genome, is anchored to 24 chromosomes. The final gene set of 38,024 genes, including AFGPs, was annotated using RNA evidence, proteins, and ab-initio predictions. The complete percentage of BUSCO analysis is 92.7%. In this study, we aim to contribute to the study of polar fishes by improving the genome sequences of the blackfin icefish with the AFGP genes belonging to the Notothenoidei.

Whole-Genome Survey and Microsatellite Marker Detection of Antarctic Crocodile Icefish, Chionobathyscus dewitti.

The crocodile icefish, Chionobathyscus dewitti, belonging to the family Channichthyidae, is an endemic species of the Southern Ocean. The study of its biological features and genetics is challenging as the fish inhabits the deep sea around Antarctic waters. The icefish, the sole cryopelagic species, shows unique physiological and genetic features, unlike other teleosts. It lacks hemoglobin and has evolved antifreeze proteins. Here, we report the genome sequencing data of crocodile icefish produced using the Illumina Novaseq 6000 platform. The estimated genome size was 0.88 Gb with a K-value of 19, and the unique sequence, heterozygosity, error, and duplication rates were 57.4%, 0.421%, 0.317%, and 0.738%, respectively. A genome assembly of 880.69 Mb, with an N50 scaffold length of 2401 bp, was conducted. We identified 2,252,265 microsatellite motifs from the genome assembly data, and dinucleotide repeats (1,920,127; 85.25%) had the highest rate. We selected 84 primer pairs from the genome survey assembly and randomly selected 30 primer pairs for validation. As a result, 15 primer pairs were validated as microsatellite markers.

Tissue Niche Miniature of Glioblastoma Patient Treated with Nano-Awakeners to Induce Suicide of Cancer Stem Cells.

Patient-specific cancer therapies can evolve by vitalizing the mother tissue-like cancer niche, cellular profile, genetic signature, and drug responsiveness. This evolution has enabled the elucidation of a key mechanism along with development of the mechanism-driven therapy. After surgical treatment, glioblastoma (GBM) patients require prompt therapy within 14 days in a patient-specific manner. Hence, this study approaches direct culture of GBM patient tissue (1 mm diameter) in a microchannel network chip. Cancer vasculature-mimetic perfusion can support the preservation of the mother tissue-like characteristic signatures and microenvironment. When temozolomide and radiation are administered within 1 day, the responsiveness of the tissue in the chip reflected the clinical outcomes, thereby overcoming the time-consuming process of cell and organoid culture. When the tissue chip culture is continued, the intact GBM signature gets lost, and the outward migration of stem cells from the tissue origin increases, indicating a leaving-home effect on the family dismantle. Nanovesicle production using GBM stem cells enables self-chasing of the cells that escape the temozolomide effect owing to quiescence. The anti-PTPRZ1 peptide display and temozolomide loading to nanovesicles awakes cancer stem cells from the quiescent stage to death. This study suggests a GBM clinic-driven avatar platform and mechanism-learned nanotherapy for translation.

Genomic Survey and Microsatellite Marker Investigation of Patagonian Moray Cod (Muraenolepis orangiensis).

The Muraenolepididae family of fishes, known as eel cods, inhabits continental slopes and shelves in the Southern Hemisphere. This family belongs to the Gadiformes order, which constitutes one of the most important commercial fish resources worldwide, but the classification of the fish species in this order is ambiguous because it is only based on the morphological and habitat characteristics of the fishes. Here, the genome of Patagonian moray cod was sequenced using the Illumina HiSeq platform, and screened for microsatellite motifs. The genome was predicted to be 748.97 Mb, with a heterozygosity rate of 0.768%, via K-mer analysis (K = 25). The genome assembly showed that the total size of scaffolds was 711.92 Mb and the N50 scaffold length was 1522 bp. Additionally, 4,447,517 microsatellite motifs were identified from the genome survey assembly, and the most abundant motif type was found to be AC/GT. In summary, these data may facilitate the identification of molecular markers in Patagonian moray cod, which would be a good basis for further whole-genome sequencing with long read sequencing technology and chromosome conformation capture technology, as well as population genetics.

Real-World Safety and Effectiveness of Denosumab in Patients with Osteoporosis: A Prospective, Observational Study in South Korea.

BACKGRUOUND: The efficacy and safety of denosumab have been established in a phase 3, randomized, placebo-controlled trial in Korean postmenopausal women with osteoporosis. This postmarketing surveillance study was aimed to investigate the safety and effectiveness of denosumab in Korean real-world clinical practice. METHODS: Patients with osteoporosis who had received denosumab per the Korean approved indications in the postmarketing setting between September 2014 and September 2019 were enrolled. The primary endpoint was the incidence of adverse events (AEs) and adverse drug reactions (ADRs). The secondary endpoint was the percent change from baseline in bone mineral density (BMD) of the lumbar spine, total hip, and femoral neck. RESULTS: Of the 3,221 patients enrolled, 3,185 were included in the safety analysis set; 2,973 (93.3%) were female, and the mean± standard deviation (SD) age was 68.9±9.9 years. The mean±SD study period was 350.0±71.4 days. AEs, fatal AEs, and ADRs occurred in 19.3%, 0.8%, and 1.6%, respectively. The most frequent AEs, occurring in >0.5% of patients, were dizziness (0.7%), arthralgia (0.7%), back pain (0.6%), and myalgia (0.6%). Hypocalcemia occurred in 0.3% of patients. There were no cases of osteonecrosis of the jaw and atypical femoral fracture. Mean±SD percent change from baseline in BMD of the lumbar spine, total hip, and femoral neck was 7.3%±23.6%, 3.6%±31.4%, and 3.2%±10.7%, respectively. CONCLUSION: The safety and effectiveness of denosumab in Korean patients with osteoporosis in this study were comparable with those in the Korean randomized controlled trial, with no new safety findings.

The complete mitochondrial genome of the Antarctic fairy shrimp Branchinectagaini Daday, 1910 (Branchiopoda, Anostraca, Branchinectidae).

The complete mitochondrial genome of Antarctic fairy shrimp Branchinectagaini Daday, 1910 was sequenced, assembled and annotated using next-generation sequencing technology. The mitogenome of B.gaini is circular at 15,536 bp in length, consisting of 13 protein-coding genes, 23 tRNAs, two rRNAs and two major non-coding regions. In particular, there are two tRNAGly genes and one non-coding region between these two tRNAGly genes. A phylogenetic tree was constructed using concatenated amino acid sequences of 13 protein-coding genes. It reveals that B.gaini is clustered with the Anostraca group within the Branchiopoda clade. This study helps us understand the evolution of Anostraca.

The complete mitochondrial genome of Cacopsyllaburckhardti (Hemiptera, Psylloidea, Psyllidae).

Cacopsyllaburckhardti Luo, Li, Ma & Cai, 2012 (Hemiptera, Psylloidea, Psyllidae) is a pear psyllid species, distributed in the East Asia. The complete mitogenome of C.burckhardti is obtained in this study for the first time. The mitogenome of C.burckhardti is circular form and 14,798 bp long, which consists of 13 protein-coding genes, 22 tRNAs and two rRNAs. The base composition is 38.80% for A, 34.89% for T, 9.99% for G and 16.33% for C, with the higher A + T contents (73.69%). The phylogenetic analysis, using 13 protein-coding genes, shows that C.burckhardti is clustered with other Cacopsylla species and nested in the Psyllidae clade within the superfamily Psylloidea.

The complete mitochondrial genome of the Arctic fairy shrimp Branchinectapaludosa (Müller, 1788) (Anostraca, Branchinectidae) from Sirius Passet, North Greenland.

Here we report the complete mitochondrial genome of the Arctic fairy shrimp, Branchinectapaludosa (Müller, 1788) (Anostraca, Branchinectidae), which was collected in the High Arctic of North Greenland. A complete 16,059 bp mitochondrion of B.paludosa was sequenced and assembled with the Illumina next generation sequencing platform. The B.paludosa mitogenome contains 13 PCGs, 22 tRNAs and 2 rRNA genes that are commonly observed in most metazoans and shows the conserved gene arrangement pattern of Anostraca. Our results of the phylogenomic analysis are consistent with the previous phylogenetic relationship, based on nuclear 18S ribosomal DNA. The B.paludosa mitogenome will be useful for understanding the geographical distribution and phylogenetic relationship of anostracans.

A First Genome Survey and Genomic SSR Marker Analysis of Trematomus loennbergii Regan, 1913.

Trematomus loennbergii Regan, 1913, is an evolutionarily important marine fish species distributed in the Antarctic Ocean. However, its genome has not been studied to date. In the present study, whole genome sequencing was performed using next-generation sequencing (NGS) technology to characterize its genome and develop genomic microsatellite markers. The 25-mer frequency distribution was estimated to be the best, and the genome size was predicted to be 815,042,992 bp. The heterozygosity, average rate of read duplication, and sequencing error rates were 0.536%, 0.724%, and 0.292%, respectively. These data were used to analyze microsatellite markers, and a total of 2,264,647 repeat motifs were identified. The most frequent repeat motif was di-nucleotide with 87.00% frequency, followed by tri-nucleotide (10.45%), tetra-nucleotide (1.94%), penta-nucleotide (0.34%), and hexa-nucleotide (0.27%). The AC repeat motif was the most abundant motif among di-nucleotides and among all repeat motifs. Among microsatellite markers, 181 markers were selected and PCR technology was used to validate several markers. A total of 15 markers produced only one band. In summary, these results provide a good basis for further studies, including evolutionary biology studies and population genetics of Antarctic fish species.

Sex-Biased Gene Expression and Isoform Profile of Brine Shrimp Artemia franciscana by Transcriptome Analysis.

The brine shrimp Artemia has a ZW sex determination system with ZW chromosomes in females and ZZ chromosomes in males. Artemia has been considered a promising model organism for ZW sex-determining systems, but the genes involved in sex determination and differentiation of Artemia have not yet been identified. Here, we conducted transcriptome sequencing of female and male A. franciscana using PacBio Iso-Seq and Illumina RNA-Seq techniques to identify candidate sex determination genes. Among the 42,566 transcripts obtained from Iso-Seq, 23,514 were analyzed. Of these, 2065 (8.8%) were female specific, 2513 (10.7%) were male specific, and 18,936 (80.5%) were co-expressed in females and males. Based on GO enrichment analysis and expression values, we found 10 female-biased and 29 male-biased expressed genes, including DMRT1 and Sad genes showing male-biased expression. Our results showed that DMRT1 has three isoforms with five exons, while Sad has seven isoforms with 2-11 exons. The Sad gene is involved in ecdysteroid signaling related to molting and metamorphosis in arthropods. Further studies on ecdysteroid biosynthetic genes are needed to improve our understanding of Artemia sex determination. This study will provide a valuable resource for sex determination and differentiation studies on Artemia and other crustaceans with ZW systems.

Genome of the Southern Giant Petrel Assembled Using Third-Generation DNA Sequencing and Linked Reads Reveals Evolutionary Traits of Southern Avian.

The southern giant petrel Macronectes giganteus, a large seabird of the southern oceans, is one of only two members of the genus Macronectes and is the largest species in the order Procellariiformes. Although these two families account for the vast majority of the avian fauna inhabiting the Antarctic and sub-Antarctic regions, studies on the status of some populations and the associated genetic data are currently extremely limited. In this study, we assembled the genome of M. giganteus by integrating Pacific Biosciences single-molecule real-time sequencing and the Chromium system developed by 10x Genomics. The final M. giganteus genome assembly was 1.248 Gb in size with a scaffold N50 length of 27.4 Mb and a longest scaffold length of 120.4 Mb. The M. giganteus genome contains 14,993 predicted protein-coding genes and has 11.06% repeat sequences. Estimated historical effective population size analysis indicated that the southern giant petrel underwent a severe reduction in effective population size during a period coinciding with the early Pleistocene. The availability of this newly sequenced genome will facilitate more effective genetic monitoring of threatened species. Furthermore, the genome will provide a valuable resource for gene functional studies and further comparative genomic studies on the life history and ecological traits of specific avian species.

Genome survey and microsatellite motif identification of Pogonophryne albipinna.

The genus Pogonophryne is a speciose group that includes 28 species inhabiting the coastal or deep waters of the Antarctic Southern Ocean. The genus has been divided into five species groups, among which the P. albipinna group is the most deep-living group and is characterized by a lack of spots on the top of the head. Here, we carried out genome survey sequencing of P. albipinna using the Illumina HiSeq platform to estimate the genomic characteristics and identify genome-wide microsatellite motifs. The genome size was predicted to be ∼883.8 Mb by K-mer analysis (K = 25), and the heterozygosity and repeat ratio were 0.289 and 39.03%, respectively. The genome sequences were assembled into 571624 contigs, covering a total length of ∼819.3 Mb with an N50 of 2867 bp. A total of 2217422 simple sequence repeat (SSR) motifs were identified from the assembly data, and the number of repeats decreased as the length and number of repeats increased. These data will provide a useful foundation for the development of new molecular markers for the P. albipinna group as well as for further whole-genome sequencing of P. albipinna.

The complete mitochondrial genome of Trematomus loennbergii (Perciformes, Nototheniidae).

The complete mitochondrial genome of Trematomus loennbergii was studied using NGS technology with PacBio platform. The mitochondrial genome size was 19,374bp and it had 13 protein-coding genes, 22 tRNAs and 2 rRNAs. There were 4 types of stop codons which were TAA, TAG, AGG and T(AA) but start codon type was only one (ATG). The contents of GC were 44.09% and AT contents were 55.91%. To conduct phylogenetic analysis, 12 species in 3 families were used. The result suggested that T. loennbergii was close to Pagothenia borchgrevinki in Nototheniidae. This study would provide a fundamental data for molecular evolution of T. loennbergii.

Whole genome survey and microsatellite motif identification of Artemia franciscana.

Artemia is an industrially important genus used in aquaculture as a nutritious diet for fish and as an aquatic model organism for toxicity tests. However, despite the significance of Artemia, genomic research remains incomplete and knowledge on its genomic characteristics is insufficient. In particular, Artemia franciscana of North America has been widely used in fisheries of other continents, resulting in invasion of native species. Therefore, studies on population genetics and molecular marker development as well as morphological analyses are required to investigate its population structure and to discriminate closely related species. Here, we used the Illumina Hi-Seq platform to estimate the genomic characteristics of A. franciscana through genome survey sequencing (GSS). Further, simple sequence repeat (SSR) loci were identified for microsatellite marker development. The predicted genome size was ∼867 Mb using K-mer (a sequence of k characters in a string) analysis (K = 17), and heterozygosity and duplication rates were 0.655 and 0.809%, respectively. A total of 421467 SSRs were identified from the genome survey assembly, most of which were dinucleotide motifs with a frequency of 77.22%. The present study will be a useful basis in genomic and genetic research for A. franciscana.

The complete mitochondrial genome of Eaton's skate, Bathyraja eatonii (Rajiformes, Arhynchobatidae).

The complete mitochondrial genome of Eaton's skate Bathyraja eatonii was studied using the long-read technology, PacBio Sequel System. The complete mitochondrial genome form of B. eatonii was 16,698 bp and it's comprised of 13 protein-coding genes, 22 tRNA and 2 rRNA. The base composition of B. eatonii is analyzed 31.94% for A, 33.94% for T, 13.49% for G, 20.64% for C, the result of GC content was 33.94%. Phylogenetic analysis showed that B. eatonii was closely related to Bathyraja meridionalis in Arhynchobatidae family, and this first mitochondrial genome of Antarctic skate would provide fundamental information to the evolutional relationship of Antarctic fishes.