The RUBY reporter for visual selection in soybean genome editing.

Current systems to screen for transgenic soybeans (Glycine max) involve laborious molecular assays or the expression of fluorescent markers that are difficult to see in soybean plants. Therefore, a visual system for early screening of transgenic plants would increase the efficiency of crop improvement by genome editing. The RUBY reporter system, which consists of three genes encoding betalain biosynthetic enzymes, leading to the accumulation of purple pigment in transgenic tissue, has been employed in some plants and dikaryon fungi. Here, we assessed the RUBY reporter for visual verification during soybean transformation. We show that RUBY can be expressed in soybean, allowing for visual confirmation of transgenic events without the need for specialized equipment. Plants with visible accumulation of purple pigment in any tissue were successfully transformed, confirming the accuracy of the RUBY system as a visual indicator. We also assessed the genetic stability of the transgene across generations, which can be performed very early, using the cotyledons of the progeny. Transgene-free seedlings have a distinct green color, facilitating the selection of genome-edited but transgene-free soybean seedlings for harvest. Using the RUBY system, we quickly identified a transgene-free Gmwaxy mutant in the T1 generation. This system thus provides an efficient and convenient tool for soybean genome editing.

Multivitamins co-intake can reduce the prevalence of kidney stones: a large-scale cross-sectional study.

BACKGROUND: This research aimed to explore the association between changes in the intake of common individual vitamins and combinations of vitamins and the prevalence of kidney calculi. METHODS: We used data from NHANES to investigate the association between nine common vitamins and kidney stone prevalence. Participants were clustered into several vitamin exposure patterns using an unsupervised K-means clustering method. We used logistic regression models and restrictive cubic spline curves to explore the influence of vitamins. RESULTS: The regression model exposed that compared to lower intake, high intake of vitamin B6 [Q4: OR (95% CI) = 0.76 (0.62, 0.93)], vitamin C [Q4: OR (95% CI) = 0.73 (0.59, 0.90)] and vitamin D [Q4: OR (95% CI) = 0.77 (0.64, 0.94)] individually exerted protective effects against the prevalence of kidney stones. Furthermore, the restrictive cubic spline analysis showed that the protective effect against the prevalence of kidney stones is enhanced as the take of vitamin B6 and vitamin D increased. Moreover, with the increase in vitamin C intake, its protective effect may turn into a risk factor. Regarding mixed exposure, Cluster 4 exhibited a significant protective effect against kidney stones compared with Cluster 1 [Model 3: OR (95% CI) = 0.79 (0.64, 0.98)]. CONCLUSIONS: Our research revealed that high levels of vitamin B6 and vitamin D intake were linked to a lower prevalence of kidney stone. With the gradual increase intake of vitamin C, the prevalence of kidney calculi decreased first and then increased. In addition, the co-exposure of nine vitamins is a protective factor for kidney stone disease.

Rubus suavissimus S. Lee Extract Alleviates Oxidative Stress and Inflammation in H2O2-Treated Retinal Pigment Epithelial Cells and in High-Fat Diet-Fed Mouse Retinas.

BACKGROUND: Age-related macular degeneration (AMD) is the most common cause of visual disorders in the aged population and is characterized by the formation of retinal pigment epithelium (RPE) deposits and dysfunction/death of the RPE and photoreceptors. It is supposed that both oxidative stress and inflammation play a critical role in the pathogenesis of AMD. The development of therapeutic strategies against oxidative stress and inflammation in AMD is urgently needed. Rubus suavissimus S. Lee (RS), a medicinal plant growing in the southwest region of China, has been used as an herbal tea and medicine for various diseases. METHODS: In this project, we evaluate the therapeutic potential of RS extract for AMD. We prepared RS extracts from dried leaves, which contained the main functional compounds. RESULTS: RS extract significantly increased cell viability, upregulated the expression of antioxidant genes, lowered the generation of malondialdehyde and reactive oxygen species, and suppressed inflammation in H2O2-treated human RPE cells. In the in vivo study, treatment with RS extract attenuated body weight gain, lowered cholesterol and triglyceride levels in the liver and serum, increased antioxidant capacity, and alleviated inflammation in the retina and RPE/choroid of mice fed a high-fat diet. CONCLUSIONS: Our findings suggest that RS extract offers therapeutic potential for treating AMD patients.

Macrophages promote anti-androgen resistance in prostate cancer bone disease.

Metastatic castration-resistant prostate cancer (PC) is the final stage of PC that acquires resistance to androgen deprivation therapies (ADT). Despite progresses in understanding of disease mechanisms, the specific contribution of the metastatic microenvironment to ADT resistance remains largely unknown. The current study identified that the macrophage is the major microenvironmental component of bone-metastatic PC in patients. Using a novel in vivo model, we demonstrated that macrophages were critical for enzalutamide resistance through induction of a wound-healing-like response of ECM-receptor gene expression. Mechanistically, macrophages drove resistance through cytokine activin A that induced fibronectin (FN1)-integrin alpha 5 (ITGA5)-tyrosine kinase Src (SRC) signaling cascade in PC cells. This novel mechanism was strongly supported by bioinformatics analysis of patient transcriptomics datasets. Furthermore, macrophage depletion or SRC inhibition using a novel specific inhibitor significantly inhibited resistant growth. Together, our findings elucidated a novel mechanism of macrophage-induced anti-androgen resistance of metastatic PC and a promising therapeutic approach to treat this deadly disease.

CircRNA-ST6GALNAC6 increases the sensitivity of bladder cancer cells to erastin-induced ferroptosis by regulating the HSPB1/P38 axis.

Previous studies have demonstrated that circST6GALNAC6 is a tumor suppressor in bladder cancer. However, the role of circST6GALNAC6 in ferroptosis remains unclear. In the current study, ferroptosis was induced in bladder cancer cells by erastin. Functional experiments showed that overexpression of circST6GALNAC6 promoted ferroptosis of bladder cancer cells in vitro and in vivo. Mechanistic studies revealed that circST6GALNAC6 bound to the N-terminus of small heat shock protein 1 (HSPB1) and thus blocked the erastin-induced phosphorylation of HSPB1 at the Ser-15 site, a phosphorylation site in the protective response to ferroptosis stress. In addition, protein kinase C inhibited circST6GALNAC6-induced ferroptosis by increasing the overall phosphorylation level of HSPB1, further demonstrating the role of phosphorylation activation of HSPB1 in resistance to ferroptosis. Finally, the involvement of the HSPB1/p38 MAPK pathway in the downstream signal transduction of circST6GALNAC6 in bladder cancer ferroptosis regulation was determined. The regulatory mechanism of ferroptosis sensitivity dependent on circST6GALNAC6 expression levels in bladder cancer was revealed as circRNA regulation of various protein functions. CircST6GALNAC6 inhibits HSPB1 and promotes cell ferroptosis by occupying the phosphorylation site (Ser-15) of HSBP1 and activating the P38 MAPK signaling pathway. Therefore, enhancing the expression of circST6GALNAC6 to promote ferroptosis or using circST6GALNAC6 as a biomarker of ferroptosis sensitivity is of considerable importance to the development and application of ferroptosis intervention methods in bladder cancer.

Inflammatory Myofibroblastic Tumor of the Urinary Bladder: An 11-Year Retrospective Study From a Single Center.

Purpose: To share our experience in the diagnosis and treatment of an inflammatory myofibroblastic tumor of the urinary bladder (IMTUB). Materials and Methods: A database searches in the pathology archives by using the term "inflammatory myofibroblastic tumor" and" bladder" in our hospital department of pathology from 2010 to 2021. Patient characteristics, clinical features, histopathological results, immunohistochemical staining results, and treatment outcomes were reviewed. Results: Fourteen cases of IMTUB were retrieved. The mean age was 44.7 ± 18.9 years (range 12-74). Nine (64.3%) of the patients presented with hematuria, followed by seven (50%) with odynuria, five (35.7%) with urgent urination, and one (7.1%) with dysuria. Ten (71.4%) of the patients were treated with partial cystectomy (PC), three (21.4%) with transurethral resection of bladder tumor (TURBT), and one (7.1%) with radical cystectomy (RC). Histopathologically, eight (57.1%) had a compact spindle cell pattern. Anaplastic lymphoma kinase (ALK) staining was positive in six (75%) of 8 cases. During a mean follow-up period of 43.9 ± 38 months (range 3-117), a patient had recurrence within half a month. Then, the patient was treated with further TURBT surgery and had no recurrence within 6 months. Thirteen of the patients had no local recurrence or distant metastasis. Conclusion: Inflammatory myofibroblastic tumor of the urinary bladder (IMTUB) is clinically rare and has a good prognosis. The disease is mainly treated with surgery to remove the tumor completely. It can easily be misdiagnosed as bladder urothelial carcinoma, leiomyosarcoma, or rhabdomyosarcoma, which may result in overtreatment and poor quality of life of patients.

Genome and gene evolution of seahorse species revealed by the chromosome-level genome of Hippocampus abdominalis.

Seahorses belong to the teleost family Syngnathidae that evolved a distinct body plan and unique male pregnancy compared to other teleosts. As a classic model for studying evolution of viviparity and sexual selection of teleosts, seahorse species still lack a publicly available high-quality reference genome. Here, we generated the genome assembly of the big-belly seahorse, Hippocampus abdominalis with long-read and Hi-C technologies. We managed to place over 99% of the total length of 444.7 Mb of assembled genome into 21 linkage groups with almost no gaps. We reconstructed a phylogenomic tree with the big-belly seahorse genome and other representative Syngnathidae and teleost species. We also reconstructed the historical population dynamics of four representative Syngnathidae species. We found the gene families that underwent expansion or contraction in the Syngnathidae ancestor were enriched for immune-related or ion transporter gene ontology terms. Many of these genes were also reported to show a dynamic expression pattern during the pregnancy stages of H. abdominalis. We also identified putative positively selected genes in the Syngnathidae ancestor or in H. abdominalis, whose mouse mutants are enriched for abnormal craniofacial and limb morphological phenotypes. Overall, our study provides an important genome resource for evolutionary and developmental studies of seahorse species, and candidate genes for future experimental works.

Performance Characteristics of 3-D Power Doppler Ultrasound (3-D-PD) with the Virtual Organ Computer-Aided Analysis (VOCAL) Technique in the Detection of Prostate Cancer.

The purpose of this study was to test the diagnostic performance of 3-D power Doppler ultrasound (3-D-PD) with the virtual organ computer-aided analysis (VOCAL) technique in the detection of prostate cancers (PCa). A total of 99 male patients referred for needle prostate biopsy owing to elevated serum prostate-specific antigen or abnormal direct rectal examination were prospectively included. The transrectal 3-D-PD-VOCAL quantitative vascularity parameters of vascularization index (VI), flow index and vascularization/flow index (VFI) were obtained before biopsy and compared with histopathologic results. We evaluated the predictive values for the detection of clinically significant PCa in the foci from different zones and the discrimination among various cancer grades. 3-D-PD-VOCAL discriminated malignant from benign foci, with cutoff values of 27.4% for VI, 38.2 for flow index and 8.6 for VFI. All parameters had higher areas under the curve in detecting lesions in the peripheral zone than in the transition zone (p < 0.05). VI and VFI had better diagnostic performance in detecting clinically significant PCa than flow index (p < 0.05). The area under the curve, sensitivity, specificity and accuracy in detecting clinically significant PCa were, for the VI and VFI respectively, 95% and 95%, 86% and 94%, 87% and 76%, and 87% and 85%. 3-D-PD-VOCAL initially demonstrated favorable performance in detecting PCa. Further, larger-sample studies based on prostatectomy specimens are needed to evaluate the exact usefulness of the technique.

Comparison of bipolar plasmakinetic resection of prostate versus photoselective vaporization of prostate by a three year retrospective observational study.

Comprehensive evaluation of photoselective vaporization of the prostate (PVP) versus plasmakinetic resection of the prostate (PKRP) in treating benign prostatic hyperplasia (BPH) is inadequate. This single-centre, retrospective observational study was designed to compare their efficacy, complications and sexual function. A total of 215 patients under PVP or PKRP were included in the study, propensity score matching (PSM) was performed to match the baseline characteristics of the two groups, and perioperative and three-year follow-up data were compared between them. Finally, 120 patients (60 for PVP and 60 for PKRP) were matched after PSM. Compared with the PKRP group, the intraoperative haemoglobin loss was lower (9.08 vs 13.75 g/L, P < 0.001) and the duration of catheterization and postoperative hospital stay were shorter (2.97 vs 4.10 day, P < 0.001; 3.95 vs 5.13 day, P < 0.001, respectively), but the operation time was longer (56.72 vs 49, 90 min, P < 0.001) in the PVP group. Urination measurements were improved for both groups after surgery, although no significant differences were found between them during follow-up. Sexual function after surgery was partly increased; however, frequent retrograde and discomfortable ejaculation occurred in both groups. In addition, dysuria incidence and retreatment were higher in the PVP group at 12 months. In conclusion, PVP is safe and effective in relieving BPH-related lower urinary tract symptoms with less perioperative blood loss and earlier recovery without inferior sexual function effects. However, the study is potentially affected by residual unmeasured confounding.

miR-214-5p targeted by LncRNA DANCR mediates TGF-ß signaling pathway to accelerate proliferation, migration and inhibit apoptosis of prostate cancer cells.

OBJECTIVE: This research was designed to probe into the regulatory mechanism of long non-coding RNA (LncRNA) differentiation antagonizing non-protein coding RNA (DANCR) in potential applications and molecular mechanisms of prostate carcinoma (PC). METHODS: The DANCR and miR-214-5p levels in PC tissues and cell lines were tested via real-time PCR, and those of transforming growth factor-ß (TGF-ß) signaling pathway related proteins were evaluated via Western Blot (WB). Cell proliferation, migration, apoptosis and the regulatory relationship between target genes were assessed via MTT method, scratch test, flow cytometry, dual-luciferase report, RNA co-immunoprecipitation and RNA pull-down test, respectively. RESULTS: DANCR was up-regulated in PC patients' serum and cell lines, while miR-214-5p was opposite, showing negative correlation. Besides, DANCR was significantly correlated with PSA, Gleason score and T stage in PC patients. The area under the curve (AUC) of DANCR and miR-214-5p for diagnosing PC was not less than 0.850, while the AUC for predicting poor prognosis was more than 0.800. Cox analysis results also revealed that the two might be prognostic indicators of PC patients. We found that DANCR high levels or miR-214-5p low levels were related to PC patients' poor prognosis. Up-regulating DANCR or down-regulating miR-214-5p could promote PC cells' malignant proliferation and migration, prevent apoptosis, and activate TGF-ß signaling pathway, while reverse treatment of DANCR or miR-214-5p can reverse the above results. DANCR regulates miR-214-5p in a targeted manner, and DANCR over-expression can reduce the cancer inhibitory effect of miR-214-5p on PC cells. CONCLUSION: DANCR-miR-214-5p-TGF-ß axis regulatory network plays a key regulatory part in PC progression. It may provide new strategies for the screening and treatment of patients.

circST6GALNAC6 suppresses bladder cancer metastasis by sponging miR-200a-3p to modulate the STMN1/EMT axis.

Bladder cancer (BCa) is an aggressive malignancy because of its distant metastasis and high recurrence rate. Circular RNAs (circRNAs) exert critical regulatory functions in cancer progression. However, the expression patterns and roles of circRNAs in BCa have not been well investigated. In this study, we first screened circRNA expression profiles using a circRNA microarray of paired BCa and normal tissues, and the expression of circST6GALNAC6 was confirmed by qRT-PCR and fluorescence in situ hybridization (FISH). MTT, colony formation and Transwell assays were performed to measure cell proliferation, migration and invasion. We investigated the regulatory effect of circST6GALNAC6 on miRNA and its target genes to explore the potential regulatory mechanisms of circST6GALNAC6 by chromatin immunoprecipitation (ChIP), RNA immunoprecipitation (RIP), MS2-tagged RNA affinity purification (MS2-TRAP), immunofluorescence (IF) and dual luciferase activity assays. A nude mouse xenograft model was used to examine the functions of circST6GALNAC6/STMN1 in tumour metastasis in vivo. We found that 881 circRNAs were significantly dysregulated in BCa tissues compared to normal tissues. circST6GALNAC6(hsa_circ_0088708) was downregulated in BCa tissues and cells. Overexpression of circST6GALNAC6 effectively inhibited the cell proliferation, migration, invasion and epithelial-mesenchymal transition (EMT) in vitro and suppressed BCa metastasis in vivo. Mechanistically, we showed that the SP1 transcription factor, which binds to the circST6GALNAC6 mRNA transcript, activates circST6GALNAC6 transcription. Next, we verified that circST6GALNAC6 serves as a sponge that directly binds miR-200a-3p to regulate stathmin (STMN1) expression. Furthermore, we found that STMN1 is involved in circST6GALNAC6/miR-200a-3p axis-regulated BCa EMT and metastasis. Thus, our findings indicate an important underlying mechanism in BCa metastasis by which SP1-induced circST6GALNAC6 sponges miR-200a-3p to promote STMN1/EMT signalling. This mechanism could provide pivotal potential prognostic biomarkers and therapeutic targets for BCa.

LncRNA ZNF503-AS1 acts as a tumor suppressor in bladder cancer by up-regulating Ca2+ concentration via transcription factor GATA6.

PURPOSE: Ca2+ homeostasis plays a pivotal role in regulating proliferation and apoptosis during cancer development. This study intended to examine the potential tumor-suppressing role of ZNF503 antisense RNA 1 (ZNF503-AS1) in bladder cancer, which may be implicated in the regulation of Ca2+ homeostasis. METHODS: Differentially expressed long non-coding RNAs (lncRNAs) related to bladder cancer were identified using microarray analysis, followed by the verification of transcription factors to which they bind. The relationship between ZNF503-AS1, GATA6 and SLC8A1 was assessed using dual luciferase reporter, RIP and ChIP assays. The expression levels of ZNF503-AS1, GATA6 and SLC8A1 were modulated to examine their effects on the tumorigenic potential, intracellular Ca2+ concentration and Ca2+-ATPase activity in bladder cancer cells. The in vivo tumorigenic ability was validated in nude mice. RESULTS: Microarray-based expression profile analysis of the GEO GSE61615 dataset revealed that the expression of ZNF503-AS1 was decreased in bladder cancer. Subsequently, we found that ZNF503-AS1 can bind to the transcription factor GATA6 to up-regulate the expression of SLC8A1. ZNF503-AS1 and SLC8A1 were found to be down-regulated in both primary bladder cancer tissues and cells. Exogenous overexpression of ZNF503-AS1 or SLC8A1 attenuated bladder cancer cell proliferation, invasion and migration, but promoted their apoptosis, accompanied by decreased Ca2+-ATPase activities and increased intracellular Ca2+ concentrations. Additional in vivo experiments validated the inhibitory effect of ZNF503-AS1 overexpression on the tumorigenic capacity of bladder cancer cells in nude mice. CONCLUSION: ZNF503-AS1 can recruit transcription factor GATA6 to up-regulate SLC8A1 expression, thereby increasing the intracellular Ca2+ concentration and repressing the proliferation, invasion and migration, and enhancing the apoptosis of bladder cancer cells.

The circ_0004463/miR-380-3p/FOXO1 axis modulates mitochondrial respiration and bladder cancer cell apoptosis.

Bladder cancer is one of the most commonly diagnosed and fatal malignancies of the urinary tract. Noncoding RNAs have been reported to be new biomarkers and effective treatment targets for bladder cancer. In the present study, we identified a novel bladder cancer-related circRNA-miRNA-mRNA network, the circ_0004463/miR-380-3p/FOXO1 axis. circ_0004463 is significantly downregulated, whereas miR-380-3p is upregulated in bladder carcinoma tissue samples and cells. circ_0004463 acts as a tumor suppressor by inhibiting bladder cancer cell proliferation. Genes that negatively correlated with miR-380-3p and genes that miR-380-3p might target are enriched in mitochondrial respiration chain-related pathways. miR-380-3p promotes the proliferation of bladder cancer cells and mitochondrial respiration by acting as an oncogenic miRNA. circ_0004463 competes with FOXO1 for miR-380-3p binding to counteract miR-380-3p-mediated repression of FOXO1. Circ_0004463 overexpression inhibits cancer cell proliferation and mitochondrial respiration in bladder cancer cell lines, while miR-380-3p overexpression dramatically reverses the roles of circ_0004463 overexpression. In conclusion, the circ_0004463/miR-380-3p/FOXO1 axis could regulate mitochondrial respiration and bladder cancer cell apoptosis via FOXO1 signaling.

The long noncoding RNA LINC01140/miR-140-5p/FGF9 axis modulates bladder cancer cell aggressiveness and macrophage M2 polarization.

MIBC (muscle invasive bladder cancer) only accounts for only a minority of bladder cancers, however, the disease-specific and overall survival rates of patients with MIBC are low. Macrophage M2 polarization has been reported to be associated with poorer prognosis in bladder cancer. Through cancer bioinformatics and experimental analyses, FGF9 was found to be upregulated in MIBC tissues. FGF9 knockdown in T24 cells strongly suppressed the viability, migratory capacity, and invasive capacity of cells; culture with medium from FGF9 knockdown T24 cells (si-FGF9-CM) significantly inhibited macrophage M2 polarization, while promoting M1 polarization. The long noncoding RNA (lncRNA) LINC01140 was positively correlated with FGF9 and was significantly upregulated in MIBC tissues. LINC01140 knockdown inhibited the viability, migratory capacity and invasive capacity of T24 cells; culture in si-LINC01140-CM also inhibited macrophage M2 polarization, while promoting M1 polarization. LINC01140 targeted miR-140-5p, while miR-140-5p targeted FGF9 to form a lncRNA-miRNA-mRNA axis. The effects of miR-140-5p inhibition on bladder cancer aggressiveness and macrophage M2 polarization were opposite to those of LINC01140 or FGF9 knockdown; additionally, miR-140-5p inhibition partially reversed the effects of LINC01140 knockdown on FGF9 protein levels, bladder cancer phenotype, and macrophage M2 polarization. In conclusion, LINC01140, miR-140-5p, and FGF9 form a lncRNA-miRNA-mRNA axis that modulates the bladder cancer phenotype, affects macrophage M2 polarization through the tumor microenvironment, and in turn affects bladder cancer cell aggressiveness.

Serum omentin-1 level in patients with benign prostatic hyperplasia.

BACKGROUD: To evaluate the relationship between omentin-1 and benign prostatic hyperplasia (BPH). BPH is the most common urological disease in elderly men worldwide. Lower serum omentin-1 levels were reported to be negatively associated with the incidence of inflammation, diabetes, obesity and metabolic syndrome, which all play a role in the development of BPH. To the best of our knowledge, the relationship between omentin-1 and BPH has not been investigated previously. METHODS: A total of 70 males participated in this study, including forty patients diagnosed with BPH and thirty healthy males. The anthropometric measurements and the biochemical parameters were measured in this study. We evaluated serum omentin-1 levels and the correlation with those data. We also test the gene expression of IL-8, IL-18 in BPH group using the TURP tissues. RESULTS: The serum omentin-1 levels were lower in the BPH patients than in the control group (27.95 ± 4.18 versus 32.03 ± 5.46, p < 0.001). The general characteristics and biochemical parameters were investigated, and a negative correlation was found between serum omentin-1 levels and BMI in the BPH group (r = - 0.391, p = 0.013) as well as the whole group (r = - 0.457, p < 0.001). Multiple-factor binary regression analysis revealed that serum omentin-1was a protective factor of BPH development. Furthermore, lower serum omentin-1 levels were associated with higher mRNA expression of IL-8 or IL-18 in the BPH group. CONCLUSION: Omentin-1 may suppress the development of BPH and Lower serum omentin-1 levels in BPH patients might associated with higher prostate volume and higher IL-8 and IL-18 expression levels in their prostatic cells.

A multi-omic analysis of orange-spotted grouper larvae infected with nervous necrosis virus identifies increased adhesion molecules and collagen synthesis in the persistent state.

Grouper (Epinephelus coioides) is an important commercial maricultural fish, which suffers from nervous necrosis virus (NNV) infection. The molecular mechanisms underlying the pathogenesis of the viral infection are not clear. In this study, we combined deep RNA sequencing and label-free mass spectrum for the first time to analyze the transcriptomic and proteomic profiles in infected/dead, infected/survival (persistent), and infection-free (control)orange-spotted groupers in the larval stage. Further analyses showed that the transcriptome and proteome changed dramatically among the three distinct groups, especially differentially-expressed genes in the infected/dead and infected/survival larvae enriched for pathways related to immune response. Notably, the overlapped genes between transcriptomes and proteomes identified that genes related to collagen synthesis and adhesion molecules were enhanced in the persistent (infected/survival) stage, which might contribute to suppressing the acute and lethal immune responses upon NNV infection. These transcriptomic and proteomic datasets enable the investigation of molecular mechanisms underlying NNV infection, thus may help further development of molecular breeding in marine fishery.

The complete mitochondrial genome of the Picasso clownfish: genomic comparisons and phylogenetic inference among Amphiprioninae.

Picasso clownfish belong to the subfamily Amphiprioninae and are considered a variant of the genus Amphiprion. In this study, we first sequenced the complete mitochondrial genome of the Picasso clownfish by Illumina next-generation sequencing technology. The length of the whole mitogenome is 16,727 bp long, with a gene arrangement and composition similar to those of two other Amphiprion species (Amphiprion ocellaris and Amphiprion percula). The topological structure of the phylogenetic tree shows that the Picasso clownfish is more closelyrelated to A. percula than it is to A. ocellaris, suggesting that the Picasso clownfish may be a variant of A. percula.

An SNP-Based Genetic Map and QTL Mapping for Growth Traits in the Red-Spotted Grouper (Epinephelus akaara).

The red-spotted grouper (Epinephelus akaara) is one of the most commercially important aquatic species in China. However, its seedstock has low larval survival rates, and its stability is confronted with the danger of overexploitation. In this study, a high-density genetic map was constructed using 3435 single nucleotide polymorphisms (SNPs) from 142 first generation (F1) full-sib offspring and two parents of a red-spotted grouper population. The total genetic length of the map was 2300.12 cM with an average intermarker distance of 0.67 cM. Seventeen genome-wide significant quantitative trait loci (QTLs) for growth-related traits were detected on 24 linkage groups, including 5 QTLs for full length, 7 QTLs for body length, and 5 QTLs for body weight. The contribution values of explained phenotypic variance ranged from 10.7% to 12.9%. Moreover, 13 potential candidate genes for growth-related traits were identified. Collectively, these findings will be useful for conducting marker-assisted selection of the red-spotted grouper in future studies.

De novo assembly of a chromosome-level reference genome of red-spotted grouper (Epinephelus akaara) using nanopore sequencing and Hi-C.

The red-spotted grouper Epinephelus akaara (E. akaara) is one of the most economically important marine fish in China, Japan and South-East Asia and is a threatened species. The species is also considered a good model for studies of sex inversion, development, genetic diversity and immunity. Despite its importance, molecular resources for E. akaara remain limited and no reference genome has been published to date. In this study, we constructed a chromosome-level reference genome of E. akaara by taking advantage of long-read single-molecule sequencing and de novo assembly by Oxford Nanopore Technology (ONT) and Hi-C. A red-spotted grouper genome of 1.135 Gb was assembled from a total of 106.29 Gb polished Nanopore sequence (GridION, ONT), equivalent to 96-fold genome coverage. The assembled genome represents 96.8% completeness (BUSCO) with a contig N50 length of 5.25 Mb and a longest contig of 25.75 Mb. The contigs were clustered and ordered onto 24 pseudochromosomes covering approximately 95.55% of the genome assembly with Hi-C data, with a scaffold N50 length of 46.03 Mb. The genome contained 43.02% repeat sequences and 5,480 noncoding RNAs. Furthermore, combined with several RNA-seq data sets, 23,808 (99.5%) genes were functionally annotated from a total of 23,923 predicted protein-coding sequences. The high-quality chromosome-level reference genome of E. akaara was assembled for the first time and will be a valuable resource for molecular breeding and functional genomics studies of red-spotted grouper in the future.