Effect of organic selenium on performance and gill transcriptome of whiteleg shrimp Penaeus vannamei.

Background: Shrimp gill health is an indicator of their overall health and environmental stress, as gills are in direct contact with the external environment. Organic selenium (OS), known for its high bioavailability and antioxidant properties, potentially enhances shrimp growth, survival, and immune responses. This study investigated the physiological features through comprehensive gill gene expression profiling and growth parameters by incorporating OS into Penaeus vannamei diets.

Comparative genomics highlights the virulence and evolutionary trajectory of white spot syndrome virus.

White spot syndrome virus (WSSV) poses a significant threat to shrimp aquaculture, leading to substantial economic losses. This study aims to evaluate the virulence and evolution of recent WSSV outbreaks in Japan. Shrimp infected with WSSV were collected from Okinawa, Miyakojima and Miyazaki prefectures, yielding a total of seven isolates.

De Novo Assembly and Annotation of the Siganus fuscescens (Houttuyn, 1782) Genome: Marking a Pioneering Advance for the Siganidae Family.

This study presents the first draft genome of Siganus fuscescens, and thereby establishes the first whole-genome sequence for a species in the Siganidae family. Leveraging both long and short read sequencing technologies, i.e.

sp. nov., a rapidly growing species isolated from diseased koi carp, .

A rapidly growing nontuberculous mycobacterium was isolated from diseased koi carp in Niigata, Japan, which was identified as representing a novel species through whole genome sequence analysis. The bacterial isolates (NGTWS0302, NGTWS1803 and NGTWSNA01) were found to belong to the genus through phylogenetic analysis using whole genome sequences of mycobacteria species. The bacterial colony was smooth, moist and non-chromogenic on 1% Ogawa medium at 30 °C.

Metagenome-assembled genomes of three provide insights into isopod-mollicute symbiosis.

The digestive organs of terrestrial isopods harbour bacteria of the recently proposed mollicute family . The only complete genome available so far for is that of ' Hepatoplasma crinochetorum'. The scarcity of genome sequences has hampered our understanding of the symbiotic relationship between isopods and mollicutes.

Integrase-associated niche differentiation of endogenous large DNA viruses in crustaceans.

Crustacean genomes harbor sequences originating from a family of large DNA viruses called nimaviruses, but it is unclear why they are present. We show that endogenous nimaviruses selectively insert into repetitive sequences within the host genome, and this insertion specificity was correlated with different types of integrases, which are DNA recombination enzymes encoded by the nimaviruses themselves. This suggests that endogenous nimaviruses have colonized various genomic niches through the acquisition of integrases with different insertion specificities.

FicD genes in invertebrates: A tale of transposons, pathogenic and integrated viruses.

Many gene families are shared across the tree of life between distantly related species because of horizontal gene transfers (HGTs). However, the frequency of HGTs varies strongly between gene families and biotic realms suggesting differential selection pressures and functional bias. One gene family with a wide distribution are FIC-domain containing enzymes (FicDs).

Comparative genome analyses of three serotypes of Lactococcus bacteria isolated from diseased cultured striped jack (Pseudocaranx dentex).

Lactococcosis, caused by members of the genus Lactococcus, represents a devastating disease inducing mass mortalities and economic losses in many fish species worldwide. The present work aimed to compare the whole genome sequences of three different serotypes of Lactococcus garvieae isolated from diseased cultured striped jack (Pseudocaranx dentex) in Ehime prefecture, Japan. The three serotypes showed different virulence in the challenge test using Japanese amberjack (Seriola quinqueradiata).

Genomic characterization and identification of virulence-related genes in Vibrio nigripulchritudo isolated from white leg shrimp Penaeus vannamei.

Vibrio nigripulchritudo causes vibriosis in penaeid shrimps. Here, we used Illumina and Nanopore sequencing technologies to sequence the genomes of three of its strains (TUMSAT-V. nig1, TUMSAT-V.

Genome sequence of Chionoecetes opilio bacilliform virus, a nimavirus infecting the snow crab Chionoecetes opilio.

Nimaviridae (class Naldaviricetes) is a family of double-stranded DNA viruses infecting crustaceans, with the only officially recognized representative being white spot syndrome virus (WSSV). Chionoecetes opilio bacilliform virus (CoBV) was isolated as the causative agent of milky hemolymph disease in the snow crab Chionoecetes opilio, an economically important crustacean in the northwestern Pacific. Here, we present the complete genome sequence of CoBV and show that it is unambiguously a nimavirus.

Whole-genome analysis of red sea bream iridovirus spread in 2021 in Japan provided epidemiological and viral traits insight.

Red sea bream iridovirus (RSIV) is the pathogen that causes red sea bream iridoviral disease. It causes a huge loss to the Japanese aquaculture industry. In 2021, outbreaks of red sea bream iridovirus occurred in South Japan.

Comparative genome analyses of five strains provide insights into their virulence-related factors.

(family ) is an important bacterial pathogen that affects Japanese shrimp aquaculture. Only two whole-genome sequences of are publicly available, which has hampered our understanding of the pathogenesis of shrimp vibriosis caused by this bacterium. To gain insight into the genetic features, evolution and pathogenicity of we sequenced five strains (IFO 15640, IFO 15641, IFO 15642, TUMSAT-OK1 and TUMSAT-OK2) and performed comparative genomic analyses.

Genome and transcriptome assemblies of the kuruma shrimp, Marsupenaeus japonicus.

The kuruma shrimp Marsupenaeus japonicus (order Decapoda, family Penaeidae) is an economically important crustacean that occurs in shallow, warm seas across the Indo-Pacific. Here, using a combination of Illumina and Oxford Nanopore Technologies platforms, we produced a draft genome assembly of M. japonicus (1.

Phylogenetic position of the Atlantic Gnomefish, (Teleostei: Scombropidae), within the genus , inferred from the sequences of complete mitochondrial genome and cytochrome oxidase subunit I genes.

We determined the complete mitochondrial genome of the Atlantic Gnomefish, (Scombropidae). The total length of mitochondrial DNA (mtDNA) was 16,515 bp and included 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and one control region. The gene arrangement of was identical to those of three Japanese scombropid species and those of other teleosts.

Genome Sequence of Lymphocystis Disease Virus 2 LCDV-JP_Oita_2018, Isolated from a Diseased Japanese Flounder (Paralichthys olivaceus) in Japan.

Here, we present the genome sequence of lymphocystis disease virus 2 LCDV-JP_Oita_2018 (genus , family ), which was isolated from a diseased Japanese flounder (Paralichthys olivaceus) in Japan. The LCDV-JP_Oita_2018 genome was assembled into a circular contig of 186,627 bp, with 140 predicted protein-coding genes and a GC content of 27%.

Draft Genome Sequences of the Lipid-Degrading Bacteria sp. Strains F1 and F3, Isolated from Mesopelagic Seawater from the Sagami Trough, in Japan.

sp. strains F1 and F3 are lipid-degrading bacteria that were isolated from intermediate water from the Sagami Trough, in Japan. We present the draft genome sequences of these two strains, which have 4,983,334 bp and 4,967,310 bp, respectively.

Distribution of class IId bacteriocin-producing Virgibacillus salexigens in various environments.

We performed several experiments using three strains of Virgibacillus salexigens, namely, P2, NT N53, and C-20Mo (DSM 11483), which were isolated from completely different sources, in relation to bacteriocin production ability. Results of whole-genome sequencing analysis revealed that all strains have very similar sequences encoding class IId bacteriocin. Although a partial amino acid sequence of the purified bacteriocin produced by strain P2 isolated from fermented food was previously reported, whole-genome sequencing and the N-terminal sequencing results in this study showed that its complete amino acid sequence consisted of 48 residues, which corresponded to that of the hypothetical bacteriocin encoded by the gene in Virgibacillus massiliensis strain Vm-5 (DSM 28587) isolated from the human gut.

Genome Sequence of Vibrio nigripulchritudo Strain TUMSAT-TG-2018, Isolated from Diseased Pacific White Shrimp, .

The Gram-negative bacterium is an important shrimp pathogen. Here, we present the genome sequence of TUMSAT-TG-2018, which was isolated from a diseased Pacific white shrimp (). The assembly totaled 6.

Draft Genome Sequences of Vibrio atypicus Strains DSM 25292 and TUMSAT1.

is a Gram-negative bacterium associated with the digestive tract of penaeid shrimp. Here, we present the draft genome sequences of two strains, DSM 25292 and TUMSAT1. Both assemblies were approximately 4.

Crustacean Genome Exploration Reveals the Evolutionary Origin of White Spot Syndrome Virus.

White spot syndrome virus (WSSV) is a crustacean-infecting, double-stranded DNA virus and is the most serious viral pathogen in the global shrimp industry. WSSV is the sole recognized member of the family , and the lack of genomic data on other nimaviruses has obscured the evolutionary history of WSSV. Here, we investigated the evolutionary history of WSSV by characterizing WSSV relatives hidden in host genomic data.

The complete mitochondrial genome sequence of the sakura shrimp, (Crustacea, Decapoda, ).

Here, we present the complete mitochondrial genome of the sakura shrimp, (Crustacea, Decapoda, ). The circular genome is 16,087 base pairs in length and contains 13 protein-coding genes, 22 tRNA genes, and two rRNA genes. The nucleotide composition of the mitogenome is biased towards A + T (69.

Draft Genome Sequence of Vibrio penaeicida Strain TUMSAT-NU1, Isolated from Diseased Shrimp in Japan.

is a bacterial pathogen of cultured shrimp. The draft genome sequence of strain TUMSAT-NU1 consists of 100 scaffolds with a total of 6.41 Mbp.