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.

Chromosomal assembly of the Antarctic toothfish ( Dissostichus mawsoni) genome using third-generation DNA sequencing and Hi-C technology.

The Antarctic toothfish, Dissostichus mawsoni, belongs to the Nototheniidae family and is distributed in sub-zero temperatures below S60° latitude in the Southern Ocean. Therefore, it is an attractive model species to study the stenothermal cold-adapted character state. In this study, we successfully generated highly contiguous genome sequences of D. mawsoni, which contained 1 062 scaffolds with a N50 length of 36.98 Mb and longest scaffold length of 46.82 Mb. Repetitive elements accounted for 40.87% of the genome. We also inferred 32 914 protein-coding genes using in silico gene prediction and transcriptome sequencing and detected splicing variants using Isoform-Sequencing (Iso-Seq), which will be invaluable resource for further exploration of the adaptation mechanisms of Antarctic toothfish. This new high-quality reference genome of D. mawsoni provides a fundamental resource for a deeper understanding of cold adaptation and conservation of species.

Assessment of the Dynamics of Microbial Community Associated with Tetraselmis suecica Culture under Different LED Lights Using Next-Generation Sequencing.

Tetraselmis is a green algal genus, some of whose species are important in aquaculture as well as biotechnology. In algal culture, fluorescent lamps, traditional light source for culturing algae, are now being replaced by a cost-effective light-emitting diodes (LEDs). In this study, we investigated the effect of LED light of different wavelengths (white, red, yellow, and blue) on the growth of Tetraselmis suecica and its associated microbial community structures using the next-generation sequencing (NGS). The fastest growth rate of T. suecica was shown in the red light, whereas the slowest was in yellow. The highest OTUs (3426) were identified on day 0, whereas the lowest ones (308) were found on day 15 under red light. The top 100 OTUs associated with day 0 and day 5 cultures of T. suecica under the red and yellow LED were compared. Only 26 OTUs were commonly identified among four samples. The highest numbers of unique OTUs were identified at day 0, indicating the high degree of initial microbial diversity of the T. suecica inoculum. The red light-unique OTUs occupied 34.98%, whereas the yellow-specific OTUs accounted for only 2.2%. This result suggested a higher degree of interaction in T. suecica culture under the red light, where stronger photosynthesis occurs. Apparently, the microbial community associated with T. suecica related to the oxygen produced by algal photosynthesis. This result may expand our knowledge about the algaebacteria consortia, which would be useful for various biotechnological applications including wastewater treatment, bioremediation, and sustainable aquaculture.

Characterization of the complete mitochondrial genome of Chionobathyscus dewitti (Perciformes, Channichthyidae).

The complete mitochondrial genome sequence of the Icefish, Chionobathyscus dewitti was determined by the Next Generation Sequencing (NGS) analysis. The complete mitogenome was 17,452 bp in length, which encoded the canonical 13 protein-coding genes, 22 tRNAs, two rRNAs, and two non-coding regions. As shown in the other notothenids, translocation of ND6 and an additional non-coding region were identified, which is different from the typical vertebrate mitochondrial genomes. The C. dewitti was clustered distinctly from the those in the Chinodraco and Chaenocephalus, which supported the idea that this species should be classified in the different genus, Chionobathyscus in the family Channichthyidae.

Characterization of the complete mitochondrial genome of Melibe japonica (Eliot, 1913) collected from Korean water.

Melibe japonica is the rarely identified nudibranch species in Korean and Japanese waters. Total mitochondrial genome of M. japonica collected from the coastal water of Busan, Korea, was determined by the bioinformatic assembly of the contigs generated by Illumina Miseq platform. The circular complete mitochondrial genome of M. japonica was 13, 216 bp in length, which contains 13 proteins, 2 ribosomal RNAs, and 22 tRNAs. Mitochondrial gene order of M. japonica is considerably different from the mitochondrial genome of Melibe leonina in which 6 genes (ND1, COX2, CYTB, ND4L, ND5, and ND6) were differently located. Phylogenetic analysis with COI regions showed that M. japonica is most closely related to Melibe viridis. However, not all Melibe species formed a single clade based on the phylogenetic analysis by COI region and more mitochondrial genomes in this genus should be further studied to have a better knowledge of the evolutional relationship of the nudibranchs.