https://repository.kopri.re.kr/handle/201206/5191 2026-04-16T00:06:56Z https://repository.kopri.re.kr/handle/201206/10832 Title: Antarctic blackfin icefish genome reveals adaptations to extreme environments Authors: Kim, Bo-Mi; Amores, Angel; Kang, Seunghyun; Ahn, Do Hwan; Kim, Jin-Hyoung; Kim, Il-Chan; Lee, Jun Hyuck; Lee, Sung Gu; Lee, Hyoungseok; Lee, Jong Eun; Kim, Han-Woo; Desvignes, Thomas; Batzel, Peter; Sydes, Jason; Titus, Tom; Wilson, Catherine A.; Catchen, Julian M.; Warren, Wesley C.; Schartl, Manfred; Detrich, H. William, III; John H. Postlethwait; Park, Hyun; Postlethwait, John H. Abstract: Icefishes (suborder Notothenioidei; family Channichthyidae) are the only vertebrates that lack functional haemoglobin genes and red blood cells. Here, we report a high-quality genome assembly and linkage map for the Antarctic blackfin icefish Chaenocephalus aceratus, highlighting evolved genomic features for its unique physiology. Phylogenomic analysis revealed that Antarctic fish of the teleost suborder Notothenioidei, including icefishes, diverged from the stickleback lineage about 77 million years ago and subsequently evolved cold-adapted phenotypes as the Southern Ocean cooled to sub-zero temperatures. Our results show that genes involved in protection from ice damage, including genes encoding antifreeze glycoprotein and zona pellucida proteins, are highly expanded in the icefish genome. Furthermore, genes that encode enzymes that help to control cellular redox state, including members of the sod3 and nqo1 gene families, are expanded, probably as evolutionary adaptations to the relatively high concentration of oxygen dissolved in cold Antarctic waters. In contrast, some crucial regulators of circadian homeostasis (cry and per genes) are absent from the icefish genome, suggesting compromised control of biological rhythms in the polar light environment. The availability of the icefish genome sequence will accelerate our understanding of adaptation to extreme Antarctic environments. 2019-03-01T00:00:00Z https://repository.kopri.re.kr/handle/201206/10898 Title: Transcriptome profiling suggests roles of innate immunity and digestion metabolism in purplish Washington clam Authors: Kim, Bo-Mi; Ahn, Do Hwan; Kim, Hyejin; Lee, Jung Sick; Rhee, Jae-Sung; Park, Hyun Abstract: 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 9.9million raw reads were obtained and assembled using the Oases assembly platform, resulting in 27,358 contigs with an N50 of 433bp. 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. 2019-02-01T00:00:00Z https://repository.kopri.re.kr/handle/201206/12524 Title: De novo genome assembly and annotation of Sanionia uncinata (Amblystegiaceae: Hypnales), a pleurocarpous moss dominant in Antarctica Authors: Lee, Chang Woo; Park, Ha Ju; Byun, Mi Young; Park, Mira; Lee, Jungeun; Reski, Ralf Abstract: Mosses in Antarctica grow mostly in coastal areas and are expected to have developed various unique physiological/molecular mechanisms to survive in extreme environments. Sanionia uncinata (Amblystegiaceae: Hypnales) is a dominant moss species in the maritime Antarctic and considered as a good target to investigate genes associated with abiotic stress tolerance of mosses. It has several distinct characteristics when compared to Physcomitrella patens, the first model moss species. First, S. uncinata is a pleurocarpous moss. Second, it belongs to the order Hypnales which contains the largest number of moss species. Third, it is an alpine species that lives in cold regions unlike P. patens mostly found in temperate regions. Here, we report the draft genome sequence of an Antarctic S. uncinata, obtained using third-generation PacBio sequencing technology. About 1 million reads were attained from four Sequel sequencing runs and merged together into a single dataset of 21 Gb. The de novo assembly produced 673 contigs with an N50 contig length of 2.18 Mb, and a total of 28,651 coding genes were inferred. Our dataset can be useful as a comparative genome for evolution and speciation studies for bryophytes, as well as for the analysis of molecular adaptation of plants to harsh environment. 2019-01-01T00:00:00Z https://repository.kopri.re.kr/handle/201206/10859 Title: De novo assembly and annotation of the blood transcriptome of the southern giant petrel Macronectes giganteus from the South Shetland Islands, Antarctica Authors: Kim, Bo-Mi; Ahn, Do Hwan; Kim, Jeong-Hoon; Jung, Jin-Woo; Rhee, Jae-Sung; Park, Hyun Abstract: The southern giant petrel is a large Procellariiform seabird of the southern oceans and has a circumpolar habitat. In this study, we generated the first high-quality de novo assembly of the blood transcriptome of the southern giant petrel (Macronectes giganteus) using the Illumina Miseq platform. A total of 28.7 million raw reads were obtained and assembled using the Oases assembly platform, resulting in 27,989 contigs with an N50 value of 1,044 bp. We performed functional gene annotations using Gene Ontology (GO), Eukaryotic Orthologous Groups (KOG), and Kyoto Encyclopedia of Genes and Genomes pathway analyses. As one of the top consumers in the southern oceans, M. giganteus feeds on carrion and carcasses, unlike most other Procellariiformes. However, geographical isolation is not an absolute defense against parasites or pathogens. We detected many genes that are critically involved in classic innate immunity. In terms of the GO terms analyzed, many genes were assigned to the subcategories of response to stimuli and immune system processes. These numbers were higher than those in the whole blood of lipopolysaccharide (LPS)-injected greenfinches and blood lymphocytes of the Chinese goose but lower than those found in the whole blood of the cinereous vulture. This genomic information will be useful for checking the immune status of southern giant petrels without sacrifice, as the species is vulnerable. 2018-12-01T00:00:00Z