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Abstract 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.

Understanding feeding ecology is essential for ecosystem-based management. As dietary data can show differences depending on the spatiotemporal and ontogenetic aspects of the sample, the results should be derived based on various size classes and samples over a wide spatiotemporal range. Morphological analysis of the stomach contents of Dissostichus mawsoni, a piscivore, collected at depths of 603–2,113 m in subarea 88.3 during the Antarctic summer fishing seasons from 2016 to 2020 was used to assess the dietary composition according to the research block, fishing season, depth, and size. Here, we used 1,639 D. mawsoni specimens with a total length range of 44.5–189.0 cm. The dietary composition of D. mawsoni did not show significant differences by fishing season but differed with research block, depth, and size. Macrouridae dominated research blocks 88.3_1 and 88.3_3; Nototheniidae dominated research blocks 88.3_2 and 88.3_6; and Channichthyidae dominated research blocks 88.3_4 and 88.3_5. The proportion of Nototheniidae decreased as depth increased, whereas the consumption of Channichthyidae increased gradually with depth in research blocks 88.3_3 and 88.3_4. The proportion of Channichthyidae decreased as body size increased, whereas the consumption of Macrouridae increased gradually with body size in both blocks 88.3_3 and 88.3_4. During the study period, the dietary composition of D. mawsoni in both blocks 88.3_3 and 88.3_4 did not show significant temporal differences, suggesting that these data could be used as a baseline for identifying future environmental changes in the region. This study provides information on the relationships between various species and benthic fish fauna, which are essential for ecosystem-based management.

The taxonomy and geographical distributions of Osteobrama species have historically posed challenges to ichthyologists, leading to uncertainties regarding their native ranges. While traditional taxonomy has proven valuable in classification, the utility of an integrated approach is restricted for this particular group due to limitations in combining information from biogeography, morphology, and genetic data. This study addresses the taxonomic puzzle arising from the recent identification of Osteobrama tikarpadaensis in the Mahanadi and Godavari Rivers, casting doubt on the actual distribution and systematics of both O. tikarpadaensis and Osteobrama vigorsii. The research reveals distinctions among specimens resembling O. vigorsii from the Krishna and Godavari riverine systems. Notably, specimens identified as O. vigorsii from the Indian Museum exhibit two pairs of barbels, while those from the Godavari River in this study are identified as O. tikarpadaensis. Inter-species genetic divergence and maximum likelihood phylogeny provide clear delineation between O. vigorsii and O. tikarpadaensis. The study suggests that O. vigorsii may be limited to the Krishna River system in southern India, while O. tikarpadaensis could potentially extend from the Mahanadi River in central India to the Godavari River in southern India. Proposed revision to morphological features for both species, accompanied by revised taxonomic keys, aim to facilitate accurate differentiation among Osteobrama congeners. The data generated by this research provide a resource for future systematic investigations into cyprinids in India and surrounding regions. Further, the genetic diversity information obtained from various riverine systems for Osteobrama species will be instrumental in guiding aquaculture practices and formulating effective conservation action plans.

The collective understanding of global-scale evolutionary trends in barracuda mitogenomes is presently limited. This ongoing research delves into the maternal evolutionary path of Sphyraena species, with a specific focus on the complete mitogenome of Sphyraena sphyraena, sourced from the Atlantic Ocean through advanced next-generation sequencing. This mitogenome spans 16,841 base pairs and encompasses 37 genes, including 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and an AT-rich control region. Notably, the mitogenome of S. sphyraena exhibits a preference for AT-base pairs, constituting 55.06% of the composition, a trait consistent with a similar bias found in related species. Most protein-coding genes initiate with an ATG codon, with the exception of Cytochrome c oxidase I (COI), which begins with a GTG codon. Additionally, six PCGs terminate with a TAA codon, COI with AGA, while six others exhibit incomplete termination codons. In the S. sphyraena mitogenome, the majority of transfer RNAs exhibit typical cloverleaf secondary structures, except for tRNA-serine, which lacks a DHU stem. Comparative analysis of conserved blocks within the D-loop regions of six Sphyraenidae species reveals that the CSB-I block extends to 22 base pairs, surpassing other blocks and containing highly variable sites. Both maximum-likelihood and Bayesian phylogenetic analyses, using concatenated 13 mitochondrial PCGs, distinctly separate all Sphyraenidae species. The European Barracuda, S. sphyraena, demonstrates a sister relationship with the ‘Sphyraena barracuda’ group, including S. barracuda and S. jello. In conclusion, this study advances our understanding of the evolutionary relationship and genetic diversity within barracudas. Furthermore, it recommends comprehensive exploration of mitogenomes and broader genomic data for all existing Sphyraenidae fishes, providing invaluable insights into their systematics, genetic characterization, and maternal evolutionary history within marine environments.

The diet of the Antarctic toothfish (Dissostichus mawsoni) was analyzed using metabarcoding to determine whether spatiotemporal factors are related to its feeding ecology. A diet metabarcoding analysis was conducted for five years from 2016 to 2020 using 1,777 samples collected from two distantly located subareas, 88.3 and 58.4.1. Metabarcoding results revealed 105 prey haplotypes (29 families, 45 genera) in the stomach contents of D. mawsoni, which can serve as valuable genetic information for the accurate identification of piscine species inhabiting the Southern Ocean. Most of the stomach contents of D. mawsoni consisted of fish taxa, comprising 99.61% of read count, which is consistent with other studies indicating that D. mawsoni is piscivorous. The prey compositions were highly different between the two subareas (88.3 and 58.4.1) regardless of the year, indicating that the diet of D. mawsoni strongly reflects the fish assemblages in geographically different habitats. These results strongly suggest that the stomach contents are good ecological indicators for monitoring any changes in the marine ecosystem caused by either the fishery of D. mawsoni, the most voracious piscine predator in its habitat, or environmental changes. In addition, quantitative polymerase chain reaction results of the two most abundant Macrourus prey species of Antarctic toothfish, M. caml and M. whitsoni, showed that the distribution of these two species may be related to the dynamics of gyres, which flow along the Antarctic continent.

The Antarctic toothfish, Dissostichus mawsoni, serves as a valuable fishery resource around the Antarctic Continent since 1997, managed by the Commission for the Conservation of Antarctic Marine Living Resources (CCAMLR). Although delineating genetic or stock structure of populations is crucial for improving fishery management of this species, its number of genetic populations and genetic diversity levels remain ambiguous. In the present study, we assessed the population genetic and phylogeographic structure of the Antarctic toothfish across 20 geographic localities spanning from Subareas 88 (88.1, 88.2, and 88.3) to Subareas 58 (58.4 and 58.5) by using mitochondrial DNA (mtDNA) cytochrome oxidase I (COI) and 16S rRNA (16S) sequences and seven nuclear microsatellite loci. MtDNA revealed a low level of polymorphism (h = 0.571, π = 0.0006) with 40 haplotypes in 392 individuals, connected only by 1–5 mutational steps, which is indicative of shallow evolutionary history. Microsatellites showed a range of allelic richness (AR) from 6.328 (88.3 RB3) to 7.274 (88.3 RB6) within populations. Overall genetic diversity was generally higher in Subareas 58 than in Subareas 88, suggesting that effective population size (NE) is larger in Subareas 58. The results of population analyses using microsatellites suggest that the sampled populations are likely to comprise a well-admixed single gene pool (i.e., one genetic stock), perhaps due to high contemporary gene flow occurring during the prolonged larval phase of this fish. However, given weak, but significant microsatellite differentiation found in six population-pairs, the possibility of existence of multiple genetic populations could not be completely excluded. The mtDNA AMOVA suggests a genetic break between the Subareas 88 and 58 groups (FCT = 0.011, P = 0.004). Moreover, mtDNA genetic distances (FST) between populations were proportionally greater as geographic distances increase. The patterns of isolation by distance (IBD) shown only in mtDNA, but not in microsatellites might suggest that population differentiation or divergence processes underwent faster in mtDNA than microsatellites, due to its NE being only one-quarter of nuclear DNA. Temporal stability in the genetic structure of D. mawsoni is also indicated by the results of no genetic differentiation between juveniles and adults. The findings of this study will help to design effective stock management strategies for this valuable fishery resource. We suggest that a long-term genetic monitoring is needed to understand the population structure and dynamics of toothfish in response to ongoing climate changes.

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.

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.