Comparative analysis of whole-transcriptome RNA expression of lung tissue of Chinese soft-shell turtle infected by Trionyx sinensis Hemorrhagic Syndrome Virus.

Trionyx sinensis Hemorrhagic Syndrome Virus (TSHSV), the first aquatic arterivirus identified in China, causes severe mortality to T. sinensis. In this study, we sought to determine the functions of T. sinensis mRNAs and non-coding RNAs (ncRNAs) that were differentially expressed (DE) over different periods of TSHSV infection of T. sinensis lung. We used RT-qPCR to validate the sequencing results of select RNAs, confirming their reliable and referable nature. Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were used to predict multiple biological functions and signaling pathways in various comparison groups (1-day versus mock, 3-day versus 1-day, and 5-day versus 3-day). Multiple types of differentially expressed RNA, including mRNA, lncRNA, circRNA, and miRNA, were associated with cardiac dysfunction, coagulation abnormalities, and arachidonic acid metabolism at day 1. Pre-inflammatory cytokines and inflammatory factors such as PLA2G4A, cPLA2, γ-GGT1, TNFRSF14, TCP11L2, PTER CYP2J2 and LTC4S, were noticeably regulated at the same time. On day 3, multiple GO terms and KEGG pathways were implicated, including those related to virus defense, apoptosis, pyroptosis, and inflammatory response. Notably, key genes such as RSAD2, TRIM39, STAT4, CASP1, CASP14, MYD88, CXCL3, CARD11, ZBP1, and ROBO4 exhibited significant regulation. The lncRNAs and circRNAs that targeted the genes involved in viral recognition (TLR5), apoptosis (CARD11), pyroptosis (ZBP1), inflammatory processes (NEK7, RASGRP4, and SELE) and angiogenesis (ROBO4) exhibited significant regulation. Significantly regulated miRNAs were primarily linked to genes involved in apoptosis (Let-7f-3p, miR-1260a, miR-455-3p), and inflammation (miR-146a, miR-125a, miR-17a, miR-301b, and miR-30a-3p). The findings could advance our understanding of the host immunological response to TSHSV and offer new ideas for developing effective strategies to prevent infection of T. sinensis.

Metabonomics and Transcriptomics Analyses Reveal the Development Process of the Auditory System in the Embryonic Development Period of the Small Yellow Croaker under Background Noise.

Underwater noise pollution has become a potential threat to aquatic animals in the natural environment. The main causes of such pollution are frequent human activities creating underwater environmental noise, including commercial shipping, offshore energy platforms, scientific exploration activities, etc. However, in aquaculture environments, underwater noise pollution has also become an unavoidable problem due to background noise created by aquaculture equipment. Some research has shown that certain fish show adaptability to noise over a period of time. This could be due to fish's special auditory organ, i.e., their "inner ear"; meanwhile, otoliths and sensory hair cells are the important components of the inner ear and are also essential for the function of the auditory system. Recently, research in respect of underwater noise pollution has mainly focused on adult fish, and there is a lack of the research on the effects of underwater noise pollution on the development process of the auditory system in the embryonic development period. Thus, in this study, we collected embryo-larval samples of the small yellow croaker (Larimichthys polyactis) in four important stages of otic vesicle development through artificial breeding. Then, we used metabonomics and transcriptomics analyses to reveal the development process of the auditory system in the embryonic development period under background noise (indoor and underwater environment sound). Finally, we identified 4026 differentially expressed genes (DEGs) and 672 differential metabolites (DMs), including 37 DEGs associated with the auditory system, and many differences mainly existed in the neurula stage (20 h of post-fertilization/20 HPF). We also inferred the regulatory mode and process of some important DEGs (Dnmt1, CPS1, and endothelin-1) in the early development of the auditory system. In conclusion, we suggest that the auditory system development of L. polyactis begins at least in the neurula stage or earlier; the other three stages (tail bud stage, caudal fin fold stage, and heart pulsation stage, 28-35 HPF) mark the rapid development period. We speculate that the effect of underwater noise pollution on the embryo-larval stage probably begins even earlier.

Integration of transcriptome and proteome analyses reveals the regulation mechanisms of Larimichthys polyactis liver exposed to heat stress.

Small yellow croaker (Larimichthys polyactis) is one of the most economically important marine fishery species. L. polyactis aquaculture has experienced stress response and the frequent occurrence of diseases, bringing huge losses to the aquaculture industry. Little is known about the regulation mechanism of heat stress response in L. polyactis. In this study, to provide an overview of the heat-tolerance mechanism of L. polyactis, the transcriptome and proteome of the liver of L. polyactis on the 6 h after high temperature (32 °C) treatment were analyzed using Illumina HiSeq 4000 platform and isobaric tag for relative and absolute quantitation (iTRAQ). A total of 3700 upregulated and 1628 downregulated genes (differentially expressed genes, DEGs) were identified after heat stress in L. polyactis. Also, 198 differentially expressed proteins (DEPs), including 117 upregulated and 81 downregulated proteins, were identified. Integrative analysis revealed that 72 genes were significantly differentially expressed at transcriptome and protein levels. Functional analysis showed that arginine biosynthesis, tyrosine metabolism, pentose phosphate pathway, starch and sucrose metabolism, and protein processing in the endoplasmic reticulum were the main pathways responding to heat stress. Among the pathways, protein processing in the endoplasmic reticulum was enriched by most DEGs/DEPs, which suggests that this pathway may play a more important role in the heat stress response. Further insights into the pathway revealed that transcripts and proteins, especially HSPs and PDIs, were differentially expressed in response to heat stress. These findings contribute to existing data describing the fish response to heat stress and provide information about protein levels, which are of great significance to a deeper understanding of the heat stress responding regulation mechanism in L. polyactis and other fish species.

Neuropeptide FF-related gene in fish (Larimichthys polyactis): identification, characterization, and potential anti-inflammatory function.

BACKGROUND: Neuropeptide FF (NPFF), an octapeptide of the RFamide-related peptides (FaRPs), is involved in regulatory function in various biological processes. The regulatory role of NPFF in the immune and inflammatory response was currently being revealed. METHODS: Neuropeptide FF-related gene (termed LpNPFF) and its two receptors, NPFF receptor 1 (LpNPFFR1) and NPFF receptor 2 (LpNPFFR2) were identified by PCR and Semi-quantitative RT-PCR assay. Effect of LpNPFF on the production of nitric oxide (NO) in macrophage RAW264.7 cell was divided into PBS group, lipopolysaccharide (LPS) group, LPS treated with LpNPFF group, and LPS treated with LpNPFF and receptor antagonist RF9 group. Then specimens were measured by color reaction at 570 nm absorbance value. RESULTS: Sequence analysis showed that LpNPFF cDNA consists of 835 nucleotides with a 5'- untranslated region (UTR) of 150 base pair (bp), an open reading frame (ORF) of 384 bp and a 3'-UTR of 300 bp (Accession No. MT012894). The ORF encodes 127 amino acid (aa) residues with a hydrophobic signal peptide at N-terminus and two presumptive peptides with -PQRFa structure, LpNPFF (1) and LpNPFF (2). LpNPFFR1 and LpNPFFR2 encode 427 and 444 aa residues respectively, which both have seven hydrophobic TMDs and identified as G protein coupled receptors (GPCRs). Results of tissue distribution showed that LpNPFF and receptors were highly expressed in the brain and gonad. Furtherly, in vitro assay found LpNPFF could inhibit NO production in RAW 264.7 macrophages under inflammatory stress with LPS, while its receptor antagonist RF9 caused the evoke of NO generation. CONCLUSIONS: These results contribute to the further study of neuropeptide evolution in marine organisms, and also provide a new research idea for exploring the related functions of NPFF gene.

The potential function of KIF17 in large yellow croaker (Larimichthys crocea) spermatid remodeling: molecular characterization and expression pattern during spermiogenesis.

KIF17, which belongs to the kinesin-2 protein family, plays an indispensable role in mammalian spermiogenesis. However, the role of KIF17 in fish spermatid remodeling during spermiogenesis remains poorly understood. Therefore, we aimed to study the role of KIF17 in spermatid remodeling during Larimichthys crocea (L. crocea) spermiogenesis. The kif17 cDNA sequence, 3247 bp in length, was cloned from L. crocea testis, which consisted of a 347-bp 5'-untranslated region (UTR), 413-bp 3' -UTR, and 2487-bp open reading frame. Bioinformatic analyses revealed that KIF17 obtained from L. crocea (Lc-KIF17) exhibited a high sequence identity compared with those from other teleosts and possessed the structural features of other kinesin-2 proteins. Based on structural similarity, we speculate that the role of Lc-KIF17 may be similar to that of KIF17 in other animals. Lc-kif17 mRNA was diffusely expressed in L. crocea tissues and was highly expressed in the testis, especially at stage IV testicular development. Immunofluorescence analysis revealed that Lc-KIF17 signals colocalized with ß-tubulin signals and migrated from the perinuclear cytoplasm to the side of the nucleus where the tail forms during spermiogenesis. These findings revealed that KIF17 may be involved in L. crocea spermiogenesis. In particular, KIF17 may participate in spermatid remodeling by interacting with perinuclear microtubules during L. crocea spermiogenesis. Collectively, this study contributes to an improved understanding of the mechanism underlying L. crocea spermiogenesis and provides a basis for further research on L. crocea reproduction and development.

Updating specific PCR primer for detection of Cryptocaryon irritans from reared Larimichthys polyactis.

Artificial breeding of small yellow croaker (Larimichthys polyactis) was recently achieved, providing a bright future for its commercial farming. In May 2019, a disease outbreak occurred among small yellow croakers in an aquaculture farm near Xiangshan Bay, charactering by white spots spotted on the surface of fish skin, gills and fins. The parasite was preliminarily identified as Cryptocaryon irritans based on morphological feature of the parasite and the symptoms on fish. However, the previously published specific primer pairs failed to confirm the existence of C. iriitans. Six nucleotides mismatches were discovered after mapping specific forward primer back to targeted gene. Therefore, an updated PCR specific primer was developed within the 9th highly variable region of 18S rRNA gene and conserved in all C. irritans sequences available in GenBank database. The specificity was verified in silico by Primer-BLAST against GenBank nucleotide. Laboratory cultured ciliates (Mesanophrys, Pseudokeronopsis and Uronema) as well as natural microbial community samples collected from sea water and river water was used as negative control to verify the specificity of the primer in situ. Besides, tank transfer method was used to evaluate the treatment of the parasite infection. By tank transfer method, 2.00 ± 0.61 out of 10 fish that already sever infected were successfully survived after 8 days treatment, meanwhile the control group died out at d 6. More loss to the treatment group during first five days was observed and may attribute to the combined effect from infection and stress the recent domesticated fish suffered during rotation. Therefore, tank transfer method was also effective to prevent small yellow croaker from further infection, however the loss of the small yellow croaker suffered from stress during rotation also needs to be carefully concerned. In conclusion, this study reported the first diagnose of C. irritans infection on small yellow croaker, provided updated specific primer to detect C. irritans infection on fish body and reported the effect of tank transfer on small yellow croaker treatment.

Growth and gonadal development retardations after long-term exposure to estradiol in little yellow croaker, Larimichthys polyactis.

Endocrine disrupting chemicals (EDCs) including 17ß-estradiol (E2) are widely distributed in the aquatic environment and are known to negatively affect the reproductive system of many animals, including fish. EDCs leading to feminization, altered sex ratio and reduced fecundity, it is possibly posing potential risks to the ecosystems. To investigate the potentially toxic effects of E2 exposure on little yellow croaker (Larimichthys polyactis, L. poliactis) who have a unique gonadal development pattern that males undergo a hermaphroditic stage. An experiment was set up where L. poliactis were maintained in tanks and exposed to E2 concentrations of 10 µg/L or no E2 exposure (the ethanol and control groups) from 30 to 90 days post-hatching (dph). After exposure, the E2 withdrawal and continual cultured to 150 and 365 dph. The morphological and histological analyses were used to compare the changes in the fish body and gonad under E2 exposure. The results showed that E2 exposure caused three major phenotypes at 30 and 60 days after treatment (dat), including ovary, ovotestis and gonadal development retardation compared with the control groups. The average ratio of these three phenotypes is 60.6%, 11.97% and 27.43%, respectively. The body length and weight of E2 exposure groups were repressed during the E2 exposure period, while it can recover after E2 withdrawal. However, the gonadal development (Gonadosomatic Index) of E2 exposure groups testis were retarded at 60 dat and doesn't recover until 365 dph. The sex determination/differentiation-related genes erα, erßI, erßII, fshß and cyp11b2 were significantly decreased in E2-exposure male fish. This research highlights the E2 leads to feminization, disrupts testis maturation and spermatogenesis, this effect persisted into the stage of sexual maturity. Collectively, our findings provide insights into the molecular mechanisms underlying E2 disturbance of a marine economic fish reproduction.

Transcriptome analysis of the Larimichthys polyactis under heat and cold stress.

The small yellow croaker (Larimichthys polyactis) is an economically important marine fish that is widely distributed in the East Sea, Yellow Sea and Bohai of China. However, the wild populations of L. polyactis are severely depleted, and there is currently a developing large-scale artificial propagation of this fish for aquaculture. However, the current variety of L. polyactis that is cultivated is not capable to coping with large fluctuations in temperature. Therefore, it is important to understand the molecular mechanisms that are activated in response to temperature stress in the L. polyactis. Here, we conducted transcriptomic analysis of the liver of L. polyactis under heat and cold stress. A total of 270,844,888, 265,727,006 and 259,666,218 clean reads were generated from high temperature group, low temperature group and control group, respectively, and comparing expression of genes in these transcriptomes, 10,878 unigenes that were differential expressed were identified. Seventeen of the differentially expressed unigenes were validated by qRT-PCR. Pathway enrichment analysis identified that the ER pathway, immune signaling pathway and metabolic response pathway were affected by temperature stress. The results of this study provide a comprehensive overview of temperature stress-induced transcriptional patterns in liver tissues of the L. polyactis. In addition, these results can guide future molecular studies of heat and cold stress response in this species for improving the stock used for aquaculture.

Expression and potential functions of KIF3A/3B to promote nuclear reshaping and tail formation during Larimichthys polyactis spermiogenesis.

KIF3A and KIF3B are homologous motor subunits of the Kinesin II protein family. KIF3A, KIF3B, and KAP3 form a heterotrimeric complex and play a significant role in spermatogenesis. Here, we first cloned full-length kif3a/3b cDNAs from Larimichthys polyactis. Lp-kif3a/3b are highly related to their homologs in other animals. The proteins are composed of three domains, an N-terminal head domain, a central stalk domain, and a C-terminus tail domain. Lp-kif3a/3b mRNAs were found to be ubiquitously expressed in the examined tissues, with high expression in the testis. Fluorescence in situ hybridization (FISH) was used to analyze the expression of Lp-kif3a/3b mRNAs during spermiogenesis. The results showed that Lp-kif3a/3b mRNAs had similar expression pattern and were continuously expressed during spermiogenesis. From middle spermatid to mature sperm, Lp-kif3a/3b mRNAs gradually localized to the side of the spermatid where the midpiece and tail form. In addition, we used immunofluorescence (IF) to observe that Lp-KIF3A protein co-localizes with tubulin during spermiogenesis. In early spermatid, Lp-KIF3A protein and microtubule signals were randomly distributed in the cytoplasm. In middle spermatid, however, the protein was detected primarily around the nucleus. In late spermatid, the protein migrated primarily to one side of the nucleus where the tail forms. In mature sperm, Lp-KIF3A and microtubules accumulated in the midpiece. Moreover, Lp-KIF3A co-localized with the mitochondria. In mature sperm, Lp-KIF3A and mitochondria were present in the midpiece. Therefore, Lp-KIF3A/KIF3B may be involved in spermiogenesis in L. polyactis, particularly during nuclear reshaping and tail formation.

Molecular characterization and expression analysis of large yellow croaker (Larimichthys crocea) interleukin-12A, 16 and 34 after poly I:C and Vibrio anguillarum challenge.

Interleukin-12, 16 and 34 are important pro-inflammatory cytokines, some of the most important components of the innate immunity system. Herein, we identified interleukin-12A (lcIL12A), 16 (lcIL16) and 34 (lcIL34) in large yellow croaker (Larimichthys crocea), and determined their expression profile in unchallenged and challenged tissues. The coding sequence (CDS) of lcIL12A comprised 600 bp long encoding a protein of 199 amino acids (aa), the CDS of lcIL16 was 2454 bp encoding a protein of 817 aa, and the CDS of lcIL34 was 657 bp encoding a protein of 267 aa. Phylogenetic analysis revealed similar results to homology comparison that lcIL12A was closest to IL12A of Dicentrarchus labrax (73%) and Serola dumerili (73%), while lcIL16 had the closest relation to Lates calcarofer (72.6%), and lcIL34 to Sparus aurata (88.9%). Multiple sequence alignment showed these interleukins were highly conserved with other vertebrate interleukins in their functional domains. Further, quantitative real time PCR (qPCR) analysis revealed that lcIL12A, lcIL16 and lcIL34 were constitutively expressed in all examined tissues, with significantly higher expression in spleen, liver and kidney. This was especially true for lcIL34 gene. Importantly, when challenged with polyinosinic:polycytidylic acid (poly I:C) and Vibrio anguillarum (V. anguillarum), the mRNA expressions of these interleukins were up-regulated in liver, spleen and kidney. Their top values got over 4 folds at least relative to their expression at time 0, and even lcIL12 reached 13.37 fold at 12-h point in spleen. These suggested their anti-viral and anti-bacterial roles and their involvement in the innate immune response of Larimichthys crocea. These results would have major implications in improving our understanding of the functions of interleukins to defend against pathogen infections in teleost species.

Molecular characterization and expression analysis of the large yellow croaker (Larimichthys crocea) chemokine receptors CXCR2, CXCR3, and CXCR4 after bacterial and poly I:C challenge.

The large yellow croaker (Larimichthys crocea) has a well-developed innate immune system. We studied a component of this system, chemokine receptor CXCR family. In this study, we report the full-length open reading frames, as well as the identification and characterization of the chemokine receptor genes CXCR2 (LycCXCR2), CXCR3 (LycCXCR3), and CXCR4 (LycCXCR4) of large yellow croaker. We report that LycCXCR3 and LycCXCR4 are evolving neutrally according to PAML analyses. Quantitative real-time PCR analysis revealed that CXCR transcripts were expressed in all examined tissues. The expression of chemokine receptors LycCXCR2, LycCXCR3, and LycCXCR4 was elevated in the kidney, spleen, and particularly the liver of the large yellow croaker after challenge with Vibrio anguillarum and polyinosinic:polycytidylic acid (poly I:C). These results suggest that LycCXCR2, LycCXCR3, and LycCXCR4 may be important immune-related genes, playing crucial roles in immune defence against bacterial infection.

Deep2Pep: A deep learning method in multi-label classification of bioactive peptide.

Functional peptides are easy to absorb and have low side effects, which has attracted increasing interest from pharmaceutical scientists. However, due to the limitations in the laboratory funding and human resources, it is difficult to screen the functional peptides from a large number of peptides with unknown functions. With the development of machine learning and Deep learning, the combination of computational methods and biological information provides an effective method for identifying peptide functions. To explore the value of multi-functional active peptides, a new deep learning method named Deep2Pep (Deep learning to Peptides) was constructed, which was based on sequence encoding, embedding, and language tokenizer. It can achieve predictions of peptides on antimicrobial, antihypertensive, antioxidant and antihyperglycemic by converting sequence information into digital vectors, combined BiLSTM, attention-residual algorithm, and BERT Encoder. The results showed that Deep2Pep had a Hamming Loss of 0.095, subset Accuracy of 0.737, and Macro F1-Score of 0.734. which outperformed other models. BiLSTM played a primary role in Deep2Pep, which BERT encoder was in an auxiliary position. Deep learning algorithms was used in this study to accurately predict the four active functions of peptides, and it was expected to provide effective references for predicting multi-functional peptides.

[Variation in Phosphorus Concentration and Flux at Zhutuo Section in the Yangtze River and Source Apportionment].

Phosphorus (P) is a pollutant of great concern in the Yangtze River Basin. The Xiangjiaba Reservoir and Xiluodu Reservoir on the lower reach of the Jinsha River began to operate in 2012 and 2013, respectively, which greatly changed the concentrations of suspended sediment and characteristics of P form and transport in the reservoirs and the downstream reach from Yibin to Jiangjin of the Yangtze River. The Zhutuo section is representative in the water quality of the Yibin-Jiangjin reach, which can not only reflect the comprehensive effects of the formation of the two reservoirs and changes in the aquatic environment in the Min-Tuo Rivers but also reflect the quality of water flowing into the Three Gorges Reservoir. The runoff, concentrations and fluxes of suspended sediments (SS), and P concentrations and fluxes at Zhutuo section were studied during 2002-2019, and the source of P was apportioned based on the principle of river base flow. The results showed that in the past 18 years, the concentrations and fluxes of total phosphorus (TP) and particulate phosphorus (PP) at Zhutuo section in the wet season were higher than those in the level and dry seasons; the rule of positive correlation between PP and SS concentrations remained unchanged. From 2002 to 2019, the concentrations and fluxes of TP, PP, and dissolved P (DP) generally increased first and then decreased, and the operation of the Xiangjiaba Reservoir was a time node for the trend turning. Compared with that in the period from 2002-2012, the SS concentration and flux decreased by 94% and 77%, TP and PP concentrations decreased by 46% and 70%, and TP and PP fluxes decreased by 58% and 74%, respectively, during 2014-2019. The decline mainly occurred in the wet season, followed by that in the level season. After the formation of the two reservoirs, the relationship between water and sediment and the form of P greatly changed, and the proportion of DP in TP increased significantly, whereas the proportion of PP was the opposite. The TP pool in overlying water in the dry and level seasons shifted from mainly particulate to mainly dissolved. The change in water and sediment conditions was the main driving force for the significant change in P concentration, flux, and form. Before the operation of the Xiangjiaba Reservoir, the Jinsha River was the maximum contributor to the whole and diffuse source part of the TP load at Zhutuo section among the contributing catchment sub-basins; however, the Minjiang River became the largest contributor after the operation. The average TP load at Zhutuo section from 2017-2019 was 3.575×104 t·a-1 (after deducting the natural background value), of which the contribution of diffuse sources and point sources accounted for 68% and 32%, respectively. The Minjiang River represented 49%, 43%, and 62% of the total TP load, diffuse source TP load, and point source TP load at Zhutuo section, respectively. Considering the load contribution and pollution intensity, the key area for P pollution control in the area upstream of the Three Gorges Reservoir was the Min-Tuo River Basin.

A chromosome-level genome assembly of East Asia endemic minnow Zacco platypus.

Zacco platypus is an endemic colorful freshwater minnow that is intensively distributed in East Asia. In this study, two adult female individuals collected from Haihe River basin were used for karyotypic study and genome sequencing, respectively. The karyotype formula of Z. platypus is 2N = 48 = 18 M + 24SM/ST + 6 T. We used PacBio long-read sequencing and Hi-C technology to assemble a chromosome-level genome of Z. platypus. As a result, an 814.87 Mb genome was assembled with the PacBio long reads. Subsequently, 98.64% assembled sequences were anchored into 24 chromosomes based on the Hi-C data. The chromosome-level assembly contained 54 scaffolds with a N50 length of 32.32 Mb. Repeat elements accounted for 52.35% in genome, and 24,779 protein-coding genes were predicted, with 92.11% were functionally annotated with the public databases. BUSCO analysis yielded a completeness score of 96.5%. This high-quality genome assembly provides valuable resources for future functional genomic research, comparative genomics, and evolutionary studies of genus Zacco.

Isolation and characterization of a novel temperate bacteriophage infecting Aeromonas hydrophila isolated from a Macrobrachium rosenbergii larvae pond.

Aeromonas hydrophila is an opportunistic pathogen that frequently leads to significant mortality in various commercially cultured aquatic species. Bacteriophages offer an alternative strategy for pathogens elimination. In this study, we isolated, identified, and characterized a novel temperate A. hydrophila phage, designated as P05B. The bacteriophage P05B is a myovirus based on its morphological features, and possesses the capability to lyse A. hydrophila strains isolated from shrimp. The optimal multiplicity of infection (MOI), adsorption rate, latent period, and burst size for phage P05B were determined to be 0.001, 91.7 %, 20 min, and 483 PFU/cell, respectively. Phage P05B displayed stability across a range of temperatures (28-50 °C) and pH values (4.0-10.0). Sequence analysis unveiled that the genome of phage P05B comprises 32,302 base pairs with an average G + C content of 59.4 %. A total of 40 open reading frames (ORF) were encoded within the phage P05B genome. The comparative genomic analyses clearly implied that P05B might represent a novel species of the genus Bielevirus under Peduoviridae family. A phylogenetic tree was reconstructed, demonstrating that P05B shares a close evolutionary relationship with other Aeromonas and Aeromonas phages. In conclusion, this study increased our knowledge about a new temperate phage of A. hydrophila with strong lytic ability.

The chromosome-level genome of Cherax quadricarinatus.

Red claw crayfish (Cherax quadricarinatus) is an aquatic crustacean with considerable potential for the commercial culture and an ideal model for studying the mechanism of sex determination. To provide better genomic resources, we assembled a chromosome-level genome with a size of 5.26 Gb and contig N50 of 144.33 kb. Nearly 90% of sequences were anchored to 100 chromosomes, which represents the high-quality crustacean genome with the largest number of chromosomes ever reported. The genome contained 78.69% repeat sequences and 20,460 protein-coding genes, of which 82.40% were functionally annotated. This chromosome-scale genome would be a valuable reference for assemblies of other complex genomes and studies of evolution in crustaceans.

[Water Quality Change Trend and Risk Analysis of Wuhan Hanjiang River Water Source].

Hanjiang River is closely related to the middle route of the South-to-North Water Diversion Project, the Water Diversion Project from the Hanjiang River to the Wei River, and the Water Diversion Project in Northern Hubei. The Wuhan Hanjiang River water source is one of the important drinking water sources in China; its water quality safety is significant to living and production for millions of residents in Wuhan. Based on data from 2004 to 2021, the water quality variation trend and risk of Wuhan Hanjiang River water source were studied. The results showed that a certain gap existed between the concentrations of some pollutants such as total phosphorus, permanganate index, ammonia nitrogen, and correspondent water quality target, especially for the total phosphorus. The growth of algae in the water source was marginally limited by the concentrations of nitrogen, phosphorus, and silicon. When other factors remained unchanged, diatoms tended to grow rapidly when the water temperature was appropriate (6-12℃). The quality of water upstream had a great impact on the water quality of the Hanjiang water source. There may have been pollutants entering into the reach during the West Lake Water Plant and Zongguan Water Plant. There were differences in the temporal and spatial variation trend of concentrations between permanganate index, total nitrogen, total phosphorus, and ammonia nitrogen. Significant changes in the ratio of nitrogen and phosphorus in the water body will affect the population structure and quantity of planktonic algae and ultimately affect the safety of water quality. The water body in the water source area was generally in the state of medium nutrition to mild eutrophication, and middle eutrophication may have occurred in a few periods. In recent years, the nutritional level of the water source has been on the decline. It is necessary to make an in-depth investigation on the source, quantity, and change trend of pollutants in water sources in order to eliminate potential risks.

Whole-genome assembly and annotation for the little yellow croaker (Larimichthys polyactis) provide insights into the evolution of hermaphroditism and gonochorism.

The evolutionary direction of gonochorism and hermaphroditism is an intriguing mystery to be solved. The special transient hermaphroditic stage makes the little yellow croaker (Larimichthys polyactis) an appealing model for studying hermaphrodite formation. However, the origin and evolutionary relationship between of L. polyactis and Larimichthys crocea, the most famous commercial fish species in East Asia, remain unclear. Here, we report the sequence of the L. polyactis genome, which we found is ~706 Mb long (contig N50 = 1.21 Mb and scaffold N50 = 4.52 Mb) and contains 25,233 protein-coding genes. Phylogenomic analysis suggested that L. polyactis diverged from the common ancestor, L. crocea, approximately 25.4 million years ago. Our high-quality genome assembly enabled comparative genomic analysis, which revealed several within-chromosome rearrangements and translocations, without major chromosome fission or fusion events between the two species. The dmrt1 gene was identified as the male-specific gene in L. polyactis. Transcriptome analysis showed that the expression of dmrt1 and its upstream regulatory gene (rnf183) were both sexually dimorphic. Rnf183, unlike its two paralogues rnf223 and rnf225, is only present in Larimichthys and Lates but not in other teleost species, suggesting that it originated from lineage-specific duplication or was lost in other teleosts. Phylogenetic analysis shows that the hermaphrodite stage in male L. polyactis may be explained by the sequence evolution of dmrt1. Decoding the L. polyactis genome not only provides insight into the genetic underpinnings of hermaphrodite evolution, but also provides valuable information for enhancing fish aquaculture.

Joint toxic effects of phoxim and lambda-cyhalothrin on the small yellow croaker (Larimichthys polyactis).

Although pesticides commonly exist as combinations in real-life situations of the aquatic ecosystem, the impact of the toxicity of their mixtures has remained largely unclear. In this study, we investigated the combined effects of two neurotoxic pesticides, including one organophosphate insecticide phoxim (PHO) and one pyrethroid insecticide lambda-cyhalothrin (LCY), on the embryos of the small yellow croaker (Larimichthys polyactis), and their potential pathways. LCY exhibited higher toxicity relative to PHO, with a 72-h LC50 value of 0.0074 mg a.i. L-1, while the corresponding value for PHO was 0.12 mg a.i. L-1. The mixture of PHO and LCY exerted a synergistic effect on the embryos of L. polyactis. The activities of antioxidant enzyme CAT and apoptotic enzyme caspase 3 were substantially changed in most single and combined exposure groups relative to the baseline value. Under both single and combined exposures, more significant changes were found in the mRNA expression of five genes, including the immunosuppression gene ngln2, the apoptosis gene P53, the endocrine system gene cyp19a1b, as well as neurodevelopment genes of ap and acp2, relative to the baseline value. Furthermore, the non-target metabolomic analysis demonstrated that hundreds of differential metabolites, including two bile acids (taurodeoxycholic acid and tauroursodeoxycholic acid), were significantly increased in the exposure groups. The bile acids were closely associated with the gut microbiota, and 16S rRNA sequencing results demonstrated dysfunction of the gut microbiota after exposure, especially in the combined exposure group. Our findings indicated that there might be a potential risk connected to the co-occurrence of these two pesticides in aquatic vertebrates. Consequently, future ecological risk assessments should incorporate synergistic mixtures because the current risk assessments do not consider them.

Mixture effects of imidacloprid and difenconazole on enzymatic activity and gene expression in small yellow croakers (Larimichthys polyactis).

Agrochemicals usually exist as mixtures in aqueous ecosystems and have harmful impacts on the natural environment. Nonetheless, the combined effects and underlying mechanisms of agrochemicals on aqueous organisms remain poorly understood. In the present study, the interactive effects of imidacloprid (IMI) and difenconazole (DIF) on the embryos of small yellow croakers (Larimichthys polyactis) were assessed using various toxicological assays, including acute toxicity, enzymatic activity, and gene expression changes. The results showed that DIF (72-h LC50 value of 0.20 mg L-1) had higher toxicity than IMI (72-h LC50 value of 12.5 mgL-1). Simultaneously, combinations of IMI and DIF exerted synergistic acute effects on the embryos of L. polyactis. In addition, the SOD, CAT, GST, and CarE activities were noticeably altered in most single and mixed exposures, relative to the untreated control. The expression of four genes (cyp19a1b, ngln2, klf2a, and socs3a) related to the immune system, endocrine system, and neurodevelopment was also surprisingly altered when the embryos of L. polyactis were subjected to individual and combined exposures relative to the untreated control. Changes in enzymatic activity and gene expression might provide early warning indices for the identification of agrochemical co-exposure. The results of this study provide valuable insights into the comprehensive toxicity of agrochemical mixtures to L. polyactis. Further studies on the long-term effects of agrochemical mixtures on marine fish should be conducted to formulate definitive conclusions concerning hazards.