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Although the widely cultured Litopenaeus vannamei is highly tolerant to varying salinity levels, the rapid fluctuation of abiotic and biotic factors due to climatic changes may become stressors to the shrimp's physiology, resulting in impaired immunity and increased disease susceptibility. This study aimed to investigate the combined effects of both factors towards L. vannamei at transcriptomic level. L. vannamei were cultured at three different salinity levels (5 ppt, 20 ppt and 30 ppt) for 60 days and were challenged with Vibrio harveyi. RNA-seq analysis was conducted on the hepatopancreas to assess the differential expressed genes (DEGs) in both control and V. harveyi infected groups. Our results revealed 5,725 DEGs was observed in shrimp reared at 5 ppt, 3,643 DEGs at 20 ppt and 1,560 DEGs at 30 ppt. Most DEGs were identified to be associated with osmoregulation and transport activities, immune and stress regulation, nutrient metabolism, growth, chitin binding, gonadal development, and metal ion binding and toxicity. We identified that shrimp cultured at intermediate salinity of 20 ppt exhibits the greatest immunity level after infection by V. harveyi, given that low salinity (5 ppt) may augment the free ion metal toxicity, resulting in higher disease susceptibility. Both V. harveyi and salinity stress function together or separately to activate a wide range of immune and stress regulatory genes, which could be potential candidate markers for future RNAi and knockdown research in developing efficient prophylactic management strategies for L. vannamei.

Abstract Dorid nudibranchs are a large group of mollusks with approximately 2,000 recorded species. Although agreement exists on the monophyletic nature of the dorid nudibranch group, the interfamily relationships of the suborder are subject to debate. Despite efforts to elucidate this issue using short molecular markers, the conclusiveness of the findings has been hindered by branching polytomy. Mitogenomes are known to be effective markers for use in phylogenetic investigations. In this study, eight mitogenomes of dorid nudibranchs were decoded and analyzed. Gene content and structure showed little change among species, reflecting the conserved mitogenomes of dorid nudibranchs. For most genes, the direction was typical for nudibranchs; nevertheless, tRNACys had an inverse direction in Cadlinidae species. Phylogenetic trees based on nucleotide and amino acid datasets revealed a relatively consistent pattern of interfamily relationships with little difference for positions of Phyllidiidae and Cadlinidae. Species of Cadlinidae were clustered together and did not form a clade with Chromododidae. Additionally, Goniodorididae was sister to Aegiridae, whereas Discodoridae was sister to Dorididae. This finding was supported by tree topology test based on mitogenome data. The results of the present study indicate that complete mitogenomes are promising markers for investigating interfamily relationships among dorid nudibranchs.

Due to the close relationship between pets and humans, pet owners are highly invested in proper diets for their pets. Even though pet food mislabeling is concerning, there are few studies on this topic. This study investigated pet food mislabeling in South Korea’s market based on DNA barcoding. In total, 10 pet food products were purchased, and 200 sequences of the partial Cytochrome c oxidase subunit 1 (COI) gene were generated from clones of the samples. The obtained sequences were compared to available public databases to identify species present in the ingredients. The data analyses showed that the labeled species were consistent with species detected by COI sequences in 6 of the products. However, the expected species were not detected in 4 products, revealing possible mislabeling in these samples. Our findings indicated that DNA barcoding might represent a promising tool to detect pet food mislabeling.

Of the four species in the genus Cadlina present in the northwestern Pacific region, C. japonica has been the only species recorded from South Korea. For the purpose of investigating Cadlina in Korean waters, specimens were collected from the Korean East Sea (Sea of Japan) by scuba diving. The radula and morphology of these specimens were examined by stereoscopic and scanning electron microscopy. Based on morphology, three species were identified in Korean waters, including the new species, Cadlina koreana sp. nov., C. umiushi (first record in South Korea), and C. japonica. Cadlina koreana sp. nov. somewhat resembles C. umiushi but differs in both its morphology as well as the structure of its radula. The background color of Cadlina koreana sp. nov. is translucent white, tubercles on the dorsum are opaque white and the yellow marginal band is absent. The radular formula of Cadlina koreana sp. nov. is 57 × 23.1.23 with a rectangular rachidian tooth. In addition, mitochondrial cytochrome c subunit 1 (COI), 16S ribosomal RNA (16S rRNA), and nuclear 28S ribosomal RNA (28S rRNA) gene sequences were generated and used for analysis of Automatic Barcode Gap Discovery (ABGD) and reconstruction of the phylogenetic tree. Morphological distinction and genetic analyses confirm that three Cadlina species are present in Korean waters of which Cadlina koreana is a new species.

Freshwater ecosystems contain a large diversity of microeukaryotes that play important roles in maintaining their structure. Microeukaryote communities vary in composition and abundance on the basis of temporal and environmental variables and may serve as useful bioindicators of environmental changes. In the present study, 18S rRNA metabarcoding was employed to investigate the seasonal diversity of microeukaryote communities during four seasons in the Han River, Korea. In total, 882 unique operational taxonomic units (OTUs) were detected, including various diatoms, metazoans (e.g., arthropods and rotifers), chlorophytes, and fungi. Although alpha diversity revealed insignificant differences based on seasons, beta diversity exhibited a prominent variation in the community composition as per seasons. The analysis revealed that the diversity of microeukaryotes was primarily driven by seasonal changes in the prevailing conditions of environmental water temperature and dissolved oxygen. Moreover, potential indicator OTUs belonging to diatoms and chlorophytes were associated with seasonal and environmental factors. This analysis was a preliminary study that established a continuous monitoring system using metabarcoding. This approach could be an effective tool to manage the Han River along with other freshwater ecosystems in Korea.

Donkey croaker, Pennahia anea (Bloch, 1793) is a commercially important croaker in the Indo-Pacific region. In this study, we sequenced and analyzed the mitogenome of P. anea. The nearly complete mitochondrial genome of P. anea is 15,694 bp in size. It contained 13 protein-coding genes (PCGs), 2 rRNA genes, and 22 tRNA genes. The sequence had the A-T content of 55.4% and GC content of 44.6%. All 13 PCGs used ATG codon for initiation, while TAA codon was the most common for termination. Phylogenetic analysis demonstrated that P. anea is located within the genus Pennahia. This study provides additional data for the understanding of the phylogeny of the family Sciaenidae.

Rabbitfish (Siganidae) are coral reef fish that are distributed across diverse habitats that include estuaries, mangroves, reefs, and even seaweed mats. Given their ecological diversity and natural widespread distributions across the Indo-Pacific region, we were interested to investigate the evolutionary history of this group and patterns of divergence that have contributed to their present-day distributions. In the present study, samples were collected from the South China Sea to study taxonomic and phylogenetic relationships, and divergence times. We investigated the taxonomic relationships among modern rabbitfish species, reconstructed their molecular phylogeny, and estimated divergence times among selected lineages based on a fragment of the mtDNA cytochrome oxidase I (COI) and sequences of the nuclear rhodopsin retrogene (RHO). Our results indicate that modern rabbitfish likely originated in the Indo-West Pacific during the late Eocene [37.4 million years ago (mya)], following which they diverged into three major clades during the Pliocene/Pleistocene. Subsequent diversification and origins of the majority of siganids may likely be associated with episodes of paleo-oceanographic events, including greenhouse and glaciation events (Eocene–Miocene) as well as major plate tectonic events (Pliocene–Pleistocene). Some modern siganid species may naturally hybridize with congeneric species where their geographical ranges overlap. A comprehensive taxonomic analysis revealed that the phylogeny of Siganidae (cladogenesis of Clades I, II, and III) is characterized by divergence in several external morphological characters and morphometric parameters. Our study demonstrates that morphological characteristics, geographical heterogeneity, and environmental change have contributed to siganids’ historical diversification.

Okenia is a speciose genus of the family Goniodorididae with more than 50 valid species. The phylogenetic relationships within the genus are little known. The mitogenome is a good marker to understand the phylogenetic relationships of relative species. This study was performed to sequence the mitogenome of O. hiroi. The mitogenome of O. hiroi was 14,583 bp in size and was composed of 37 genes, including 13 protein-coding genes, two ribosomal RNA genes, and 22 tRNA genes. The nucleotide composition was 30.5% A, 13.6% C, 16.5% G, and 39.4% T. The phylogenetic analysis showed that O. hiroi is sister to Notodoris gardineri (Aegiridae). This study recorded the first mitochondrial genome sequence of the family Goniodorididae.

Haloa japonica is a bubble snail species in the family Haminoeidae. In the present study, the complete mitochondrial genome of H. japonica was decoded and analyzed. With the size of 13,797 bp, the mitogenome of H. japonica is the shortest among all known mitogenomes of the order Cephalaspidea. Overall base-pair composition of the mitogenome was 69% A–T and 31% C–G. The phylogenetic tree showed a clade of H. japonica and other species in the family Haminoeidae.

Protaeolidiella atra is an aeolid nudibranch found in Korean and Japanese waters. This study presents the complete mitochondrial genome of P. atra from Korea. The mitogenome size of P. atra was 14,445 bp, including 27.3% A, 39.3% T, 14.8% C, and 18.6% G. Identical to other nudibranchs, there were 13 protein-coding genes, 2 rRNA genes, and 22 tRNA genes in the mitogenome of P. atra. The result of the phylogenetic analysis indicated that P. atra is closest to Sakuraeolis japonica.

Acute Hepatopancreatic Necrosis Disease (AHPND), a disease caused by Vibrio parahaemolyticus (VpAHPND), kills Penaeid shrimps worldwide, resulting in severe economic losses during aquaculture. To further understand how Penaeus monodon post-larvae (PL) respond towards infection of this pathogenic bacterium, the expression of several important immune and bacterial toxin genes in three stages of P. monodon PL (PL15, PL30 and PL45) upon VpAHPND challenge, were determined. A 20-hrs challenge test with 2.7 × 107 cfu ml−1 of VpAHPND resulted 81, 65 and 1.7% mortality respectively for PL30, PL15 and PL45, indicating that PL30 was most vulnerable to VpAHPND. The immune response of shrimp PL at this stage was robust, with Toll-like receptor (TLR), prophenoloxidase (proPO), lysozyme (lyso) and penaeidin (PEN) augmented approximately 10.7, 4.7, 6.5 and 3.2-fold, respectively. The expression initiated at one hour post-infection (h.p.i), peaked at 16 h.p.i and 20 h.p.i, and decreased at 18 h.p.i, indicating the crucial involvement of these immune related genes in the defence and recovery of the first-line defence mechanisms during VpAHPND infection. This work also revealed that toxR gene represents a good indicator gene for Vibrio detection whereas PIR A, for VpAHPND pathogenicity determination of P. monodon. Overall, these findings provided novel insights into the immune response and VpAHPND susceptibility of different P. monodon PL stages during infection, with outcomes potentially useful in enhancing the application of health therapy and biosecured aquaculture practices to minimize the damaging risk of AHPND towards sustainable production of P. monodon. Keywords: Penaeus monodon, AHPND, PIR a, Immunity genes, Bacterial toxin gene

Temperature is an abiotic factor that affects various biological and physiological processes in fish. Temperature stress is known to increase the production of reactive oxygen species (ROS) that subsequently cause oxidative stress. Fish is known to evolve a system of antioxidant enzymes to reduce ROS toxicology. Glutathione peroxidase (GPx) family consists of key enzymes that protect fish from oxidative stress. In this study, full-length GPx1 cDNA (GenBank accession no. KY984468) of Tor tambroides was cloned and characterized by rapid amplification of cDNA ends (RACE). The 899-base-pair (bp) GPx1 cDNA includes a 576-bp open reading frame encoding for 191 amino acids, plus 28 bp of 5′-untranslated region (UTR) and 295 bp of 3′-UTR. Homology analysis revealed that GPx1 of T tambroides (Tor-GPx1) shared high similarity with GPx1 sequences of other fish species. The phylogenetic construction based on the amino acid sequence showed that Tor-GPx1 formed a clade with GPx1 sequences of various fish species. Real-time polymerase chain reaction (PCR) was performed to assess the levels of GPx1 gene expression in the liver and muscle of T tambroides under thermal stress. The results indicated that GPx1 gene expression was down-regulated under decreased temperature. However, there was no significant difference between GPx1 gene expression in fish exposed to high temperature and control. Our study provides the first data regarding GPx gene expression in T tambroides under thermal stress.

Lingula anatina is a brachiopod widely distributed in the western Pacific region. Even though L. anatina has been targeted for a number of biological studies, there is still limited information on intraspecific genetic variations of L. anatina. In this study, L. anatina specimens were collected from Korea and Vietnam, and complete mitochondrial genome (mitogenome) sequences were analyzed and compared with previous records. The total mitogenomes of L. anatina were 24,875 bp and 25,305 bp in size for Korean and Vietnamese specimens, respectively. Those mitogenomes are extraordinarily longer than the typical mitogenome size for an animal but shorter than the previous record from Yanagawa (Japan) for this species. The gene orders and the sizes of the protein-coding genes are also different from those for the Japanese specimen. Furthermore, the nonsynonymous (Ka) and synonymous (Ks) substitution rates in protein-coding genes (PCGs) were calculated to test the idea of evolutionary rate differences in mitochondrial genomes. The analyses showed relatively low Ka and Ks for the complete mitogenomes from Buan (Korea), Doson (Vietnam) and Yanagawa (Japan). The Ka/Ks ratio was less than 1 in comparisons of three localities, indicating the existence of purifying selection in this species. The phylogenetic analyses showed that L. anatina diverged among localities in the western Pacific region.

Doriprismatica atromarginata is a common nudibranch in the tropical and sub-tropical Indo-Pacific region. In this study, the complete mitogenome of D. atromarginata from Vietnam was recorded for the first time. The circular mitogenome had a size of 14,421 bp and consisted of 37 genes (13 protein-coding genes, two ribosomal RNA genes, and 22 tRNA genes). Phylogenetic tree based on amino acid sequences of coding genes demonstrated that D. atromarginata has sister group relationship with the genus Chromodoris.

In the present study, the complete mitogenome of a dorid nudibranch Phyllidiella pustulosa was sequenced and analyzed. The complete mitochondrial genome of P. pustulosa was 14,717 bp in length, containing 13 protein coding genes, two ribosomal RNA genes, and 22 tRNA genes. Phylogenetic analysis according to protein coding genes revealed that P. pustulosa has a close relationship with Phyllidia ocellata. This is the first complete mitochondrial genome record for the genus Phyllidiella.

In the present study, a complete mitochondrial genome of the moon crab species, Matuta planipes was sequenced and analyzed. This is the second complete mitochondrial genome record for the species and the first record from South Korea. The genome structure and gene orientation are identical but the protein-coding gene sizes are slightly different in comparison with the previous record. Additionally, the phylogenetic relationship of M. planipes was investigated using protein-coding genes of the complete mitochondrial genome. The present study suggests that the closest species to M. planipes is Ashtoret lunaris and they belong to the family Matutidae. This study provides additional data for the family Matutidae phylogeny.

Hermissenda emurai is a species of sea slugs in the northwestern Pacific region. In this study, the complete mitochondrial genome of H. emurai (Mollusca: Facelinidae) collected from Korea was recorded. The assembled mitogenome of H. emurai was circular and 13,880 bp in length, including 27.1% A, 15.9% C, 20.5% G, and 36.5% T nucleotide distributions. The overall A–T composition was 63.6% while the G–C composition was 36.4%. Phylogenetic analysis according to 12 protein coding genes (atp8 gene excluded) showed that H. emurai clustered with Sakuraeolis japonica in the order Nudibranchia.

Due to the close relationship between pets and humans, pet owners are highly invested in proper diets for their pets. Even though pet food mislabeling is concerning, there are few studies on this topic. This study investigated pet food mislabeling in South Korea's market based on DNA barcoding. In total, 10 pet food products were purchased, and 200 sequences of the partial Cytochrome c oxidase subunit 1 (COI) gene were generated from clones of the samples. The obtained sequences were compared to available public databases to identify species present in the ingredients. The data analyses showed that the labeled species were consistent with species detected by COI sequences in 6 of the products. However, the expected species were not detected in 4 products, revealing possible mislabeling in these samples. Our findings indicated that DNA barcoding might represent a promising tool to detect pet food mislabeling. [ABSTRACT FROM AUTHOR]