Genetic analysis from multiple cohorts implies causality between 2200 druggable genes, telomere length, and leukemia.

BACKGROUND: Clinical therapeutic targets for leukemia remain to be identified and the causality between leukemia and telomere length is unclear. METHODS: This work employed cis expression quantitative trait locus (eQTL) for 2,200 druggable genes from the eQTLGen Consortium and genome-wide association studies (GWAS) summary data for telomere length in seven blood cell types from the UK Biobank, Netherlands Cohort as exposures. GWAS data for lymphoid leukemia (LL) and myeloid leukemia (ML) from FinnGen and Lee Lab were used as outcomes for discovery and replication cohorts, respectively. Robust Mendelian randomization (MR) findings were generated from seven MR models and a series of sensitivity analyses. Summary-data-based MR (SMR) analysis and transcriptome-wide association studies (TWAS) were further implemented to verify the association between identified druggable genes and leukemia. Single-cell type expression analysis was employed to identify the specific expression of leukemia casual genes on human bone marrow and peripheral blood immune cells. Multivariable MR analysis, linkage disequilibrium score regression (LDSC), and Bayesian colocalization analysis were performed to further validate the relationship between telomere length and leukemia. Mediation analysis was used to assess the effects of identified druggable genes affecting leukemia via telomere length. Phenome-wide MR (Phe-MR) analysis for assessing the effect of leukemia causal genes and telomere length on 1,403 disease phenotypes. RESULTS: Combining the results of the meta-analysis for MR estimates from two cohorts, SMR and TWAS analysis, we identified five LL causal genes (TYMP, DSTYK, PPIF, GDF15, FAM20A) and three ML causal genes (LY75, ADA, ABCA2) as promising drug targets for leukemia. Univariable MR analysis showed genetically predicted higher leukocyte telomere length increased the risk of LL (odds ratio [OR] = 2.33, 95 % confidence interval [95 % CI] 1.70-3.18; P = 1.33E-07), and there was no heterogeneity and horizontal pleiotropy. Evidence from the meta-analysis of two cohorts strengthened this finding (OR = 1.88, 95 % CI 1.06-3.05; P = 0.01). Multivariable MR analysis showed the causality between leukocyte telomere length and LL without interference from the other six blood cell telomere length (OR = 2.72, 95 % CI 1.88-3.93; P = 1.23E-07). Evidence from LDSC supported the positive genetic correlation between leukocyte telomere length and LL (rg = 0.309, P = 0.0001). Colocalization analysis revealed that the causality from leukocyte telomere length on LL was driven by the genetic variant rs770526 in the TERT region. The mediation analysis via two-step MR showed that the causal effect from TYMP on LL was partly mediated by leukocyte telomere length, with a mediated proportion of 12 %. CONCLUSION: Our study identified several druggable genes associated with leukemia risk and provided new insights into the etiology and drug development of leukemia. We also found that genetically predicted higher leukocyte telomere length increased LL risk and its potential mechanism of action.

Syphilitic proctitis: review of the literature.

Syphilitic proctitis is a rare sexually transmitted disease caused by spirochete pallidum infecting the rectal mucosa. It usually has no specific clinical manifestations and is easily misdiagnosed with other rectal and anal diseases such as rectal cancer, malignant lymphoma, inflammatory bowel disease, etc.. Therefore, diagnosis of the disease is difficult and treatment options are often unreasonable. A case of syphilitic proctitis in our hospital with "rectal mass" as the main manifestation is reported as follows and relevant literature is reviewed. At the same time, we studied and analyzed the clinical and histological characteristics and differential diagnosis of syphilitic proctitis to further deepen the understanding of this disease.

The role of Shenqi Fuzheng injection as adjuvant therapy for breast cancer: an overview of systematic reviews and meta-analyses.

BACKGROUND: Breast cancer (BC) is the most frequent malignancy in the world. Chemotherapy (CT) is a common treatment for BC but is accompanied by toxicity and side effects. Shenqi Fuzheng Injection (SFI) is an adjuvant therapy with promising results in improving efficacy and reducing toxicity in clinical studies. This overview of systematic reviews and meta-analysis (SRs/MAs) aimed to summarize the benefits and evaluate the quality of evidence supporting SFI adjuvant as CT for BC. METHODS: A systematic search for SRs/MAs of randomized controlled trials (RCTs) on SFI treatment for BC was performed by searching PubMed, Web of Science, EMbase, Cochrane Library, CNKI, Wanfang, VIP, and SinoMed databases from inception to October 1, 2022. The quality of SRs/MAs was evaluated using AMSTAR-2, PRISMA 2020, ROBIS, and GRADE by two reviewers. The corrected covered area (CCA) was used to quantify the degree of duplication of the original SRs/MAs. Finally, quantitative analysis of RCTs was conducted using RevMan 5.4 software. This study was registered with PROSPERO, CRD42022377290. RESULTS: Six SRs/MAs including 61 RCTs with 5593 patients were included in this study. Studies were published between 2015 and 2019, the original RCTs ranged from 7-49, with sample sizes ranging from 336-1989. The quantitative meta-analysis found that adjuvant CT of SFI improved the clinical response rate (RR=1.37, 95% CI=1.28, 1.46; P<0.00001) and the KPS score (RR=1.66, 95% CI 1.54, 1.79, P<0.00001) of patients with BC. In terms of immune function, CD3+ (SMD=1.51, 95% CI 0.91, 2.10; P<0.00001), CD4+ (SMD=1.87, 95% CI 1.18, 2.56; P<0.00001), CD4+/CD8+ (SMD=0.86, 95% CI 0.48, 1.23; P<0.00001), and NK cell levels (SMD=0.94, 95% CI 0.63, 1.24; P<0.00001) in the adjuvant CT group SFI were better than those with CT alone. Adverse reactions following SFI adjuvant CT showed reduced incidence of leukopenia (RR=0.53, 95% CI 0.46, 0.62; P<0.00001) and gastrointestinal reactions (RR=0.48, 95% CI 0.39, 0.58; P<0.00001). However, the GRADE results showed 'very low' to 'moderate' evidence for the 42 outcomes, without high-quality evidence supporting them, limited mainly by deficiencies in the design of RCTs (42/42, 100.00%), inconsistency (19/42, 45.24%), publication bias (41/42, 97.62%), and inaccuracy (3/42, 7.14%). The unsatisfactory results of AMSTAR-2, PRISMA 2020, and ROBIS were limited to lack of registration of study protocols, explanation of inclusion basis of RCTs, description of funding sources for the included studies, incomplete search strategy and screening process, addressing heterogeneity and sensitivity, and reporting potential conflicts of interest. CONCLUSION: Adjuvant CT with SFI for BC had better benefits and a lower risk of adverse events. The methodology and quality of the evidence are generally low, highlighting a need of greater attention during study implementation. More objective and high-quality studies are needed to verify the efficacy of adjuvant CT with SFI in clinical decision-making for BC.

Transanal local excision for mucosal prolapse syndrome.

A 46-year-old male visited our hospital with blood stool and constipation. Colonoscopy revealed a broad-based protruded lesion in the rectum.The endoscopic ultrasonography showed the lesion invaded the submucosa, and the boundary between the local and intrinsic muscular layer was not clear. Transanal local excision was conducted, the pathology showed a rare case of mucosal prolapse syndrome merging chronic suppurative inflammation.

Shenqi Fuzheng Injection Combined With Chemotherapy for Gastric Cancer: An Overview of Systematic Reviews and Meta-Analyses.

BACKGROUND: Gastric cancer (GC) is a prevalent malignant tumor of the digestive tract. Chemotherapy (CT) is the primary treatment for GC, but it is accompanied by toxic side effects. Several systematic reviews and meta-analyses (SRs/MAs) on the combination of Shenqi Fuzheng injection (SFI) with CT for GC have been published; however, the conclusions have been inconsistent. This overview of SRs/MAs aims to assess the effectiveness and safety of SFI for GC, establishing a dependable foundation for its clinical application. METHODS: We utilized 7 databases, namely PubMed, Embase, Cochrane Library, CNKI, Wanfang, VIP, and SinoMed, to conduct our search. The retrieval period spanned from inception to August 2023. The methodological quality, bias risk, reporting quality, and evidence quality of the SRs/MAs were assessed using the evaluation tools AMSTAR-2, ROBIS, PRISMA 2020, and GRADE, respectively. Subsequently, the randomized controlled trials (RCTs) included in the SRs/MAs were quantitatively analyzed through the implementation of RevMan 5.4 software. RESULTS: Eleven SRs/MAs were included in this study, comprising 54 RCTs involving a total of 9539 patients with GC. The studies covered the period from 2012 to 2021, with the number of original RCTs per study ranging from 3 to 20 and sample sizes ranging from 159 to 1413. The methodological quality of all 11 SRs/MAs was assessed as low or very low, and the quality of evidence was determined to range from moderate to very low. The comprehensive quantitative meta-analysis revealed that the combination of SFI with CT improved the objective response rate (ORR) (RR = 1.30, 95% CI = [1.21, 1.41], P < .00001) and disease control rate (DCR) (RR = 1.13, 95% CI = [1.09, 1.18], P < .00001) in GC patients, without heterogeneity observed among the studies. In comparison with CT alone, SFI combined with CT also demonstrated improvements in the Karnofsky performance status (KPS) (RR = 1.36, 95% CI = [1.25, 1.49], P < .00001) and CD4+/CD8+ level (RR = 1.16, 95% CI = [0.87, 1.46], P < .00001) of patients. In terms of adverse reactions, the combination therapy of SFI with CT was associated with a reduced incidence of gastrointestinal reactions (RR = 0.67, 95% CI = [0.58, 0.78], P < .00001) and neurotoxicity (RR = 0.64, 95% CI = [0.50, 0.81], P = .0002). CONCLUSIONS: SFI combined with CT can enhance the clinical effectiveness and enhance the quality of life in patients with GC, while minimizing adverse reactions. Nonetheless, the evaluation of overall quality remains deficient, thus restricting the reliability and stability of the conclusions. High-quality, large-sample RCTs remain crucial for establishing dependable clinical evidence. SYSTEMATIC REVIEW REGISTRATION: INPLASY20239004.

Genome-Wide Identification of 5-HT Receptor Gene Family in Razor Clam Sinonovacula constricta and Their Circadian Rhythm Expression Analysis.

Serotonin (5-HT) is primarily distributed in the gastrointestinal and central nervous systems, where it plays a crucial role in regulating various physiological functions such as digestion, reproduction and establishing animal emotions. 5-HT is an effective oxytocin widely used in molluscan aquaculture, and its physiological functions are performed by binding to corresponding 5-HT receptors (5-HTRs). In this study, seven 5-HTR genes of Sinonovacula constricta (Sc5-HTRs) were identified and analyzed, and they were designated as Sc5-HT1A, Sc5-HT1D, Sc5-HT2-1, Sc5-HT2-2, Sc5-HT2-3, Sc5-HT4 and Sc5-HT6. Phylogenetic analysis showed that the seven Sc5-HTRs were conserved among mollusks, and the Sc5-HTRs were all transmembrane proteins. The seven Sc5-HTR genes were distributed on chromosome 1, 2, 13 and 14. After injecting 5-HT, there was a significant increase in mRNA expression levels of Sc5-HT1A (p < 0.05) and Sc5-HT2-3 (p < 0.01), while Sc5-HT4 decreased significantly (p < 0.01) compared to control groups which might be effective 5-HT receptors. Furthermore, two of the receptors (Sc5-HT2-3 and Sc5-HT4) were expressed in the circadian rhythm patterns, indicating their potential influence on the nocturnal spawning of S. constricta. Overall, these findings provide a theoretical basis for understanding the structures and functions of 5-HTR gene family members, and may facilitate the artificial propagation of mollusks.

Expression and Functional Analysis of AMT1 Gene Responding to High Ammonia Stress in Razor Clam (Sinonovacula constricta).

Ammonium transporter 1 (AMT1), a member of ammonia (NH3/NH4+) transport proteins, has been found to have ammonia transport activity in plants and microorganisms. However, the functional characteristics and molecular mechanisms of AMT1 in mollusks remain unclear. The razor clam (Sinonovacula constricta) is a suitable model species to explore the molecular mechanism of ammonia excretion because of the high concentration of ambient ammonia it is exposed to in the clam-fish-shrimp polyculture system. Here, the expression of AMT1 in S. constricta (Sc-AMT1) in response to high ammonia (12.85 mmol/L NH4Cl) stress was identified by real-time quantitative PCR (qRT-PCR), Western blotting, RNA interference, and immunofluorescence analysis. Additionally, the association between the SNP_g.15211125A > T linked with Sc-AMT1 and ammonia tolerance was validated by kompetitive allele-specific PCR (KASP). A significant upregulated expression of Sc-AMT1 was observed during ammonia exposure, and Sc-AMT1 was found to be localized in the flat cells of gill. Moreover, the interference with Sc-AMT1 significantly upregulated the hemolymph ammonia levels, accompanied by the increased mRNA expression of Rhesus glycoprotein (Rh). Taken together, our findings imply that AMT1 may be a primary contributor to ammonia excretion in S. constricta, which is the basis of their ability to inhabit benthic water with high ammonia levels.

Genome-wide characterization of the cytosolic sulfotransferase 1B member 1 (SULT1B1) family and its expression responses to sulfide stress in the razor clam Sinonovacula constricta.

The razor clam (Sinonovacula constricta), a typical burrowing organism in the intertidal zones, is often exposed to sulfide environment and shows strong sulfide tolerance. Located downstream of the sulfur metabolism pathway, cytosolic sulfotransferase family 1B member 1 (SULT1B1) is a key enzyme catalysing the sulfonation reaction, and plays an important role in the biotransformation of endogenous substances such as thyroid hormones (THs). To investigate their roles in sulfide resistance, a systematic analysis of S. constricta SULT1B1s (ScSULT1B1s), including genomic distribution, phylogenetic relationships, gene structure, conserved motifs, and expression profiles under sulfide stress, was performed. A total of 10 ScSULT1B1 genes were found in the S. constricta genome. Sequence analysis showed that ScSULT1B1 gene family encoded 155-425 amino acids, containing four catalytic active sites (K, N, H, and S), one PAPS binding domain at the N-terminus, and one PAPS binding and dimerization domain at the C-terminus. The spatial-temporal expression patterns of ScSULT1B1s were further estimated by quantitative real-time PCR (qRT-PCR). Among them, partial ScSULT1B1s showed significantly high expression in the gill, hepatopancreas, and siphon. Furthermore, the response expression of certain ScSULT1B1s significantly fluctuated under sulfide stress. Together, our results suggest that ScSULT1B1s, by mediating the sulfonation reaction, may regulate THs levels to maintain basic metabolic and immune functions, making S. constricta highly sulfide tolerant.

A high-density genetic linkage map for Chinese perch (Siniperca chuatsi) using 2.3K genotyping-by-sequencing SNPs.

Chinese perch, Siniperca chuatsi (Basilewsky), is one of the most commercially important cultured fishes in China. In the present study, a high-density genetic linkage map of Chinese perch was constructed by genotyping-by-sequencing technique with an F1 mapping panel containing 190 progenies. A total of 2328 SNPs were assigned to 24 linkage groups (LGs), agreeing with the chromosome haploid number in this species (n = 24). The sex-averaged map covered 97.9% of the Chinese perch genome, with the length of 1694.3 cM and a marker density of 0.7 cM/locus. The number of markers per LG ranged from 57 to 222, with a mean of 97. The length of LGs varied from 43.2 to 108.2 cM, with a mean size of 70.6 cM. The recombination rate of females was 1.5:1, which was higher than that of males. To better understand the distribution pattern of segregation distortion between the two sexes of Chinese perch, the skewed markers were retained and used to reconstruct the sex-specific maps. The 16 segregation distortion regions were identified on 10 LGs of the female map, while 12 segregation distortion regions on eight LGs of the male map. Among these LGs, six LGs matched between the sex-specific maps. This high-density linkage map could provide a solid basis for identifying QTL associated with economically important traits, and for implementing marker-assisted selection breeding of Chinese perch.

Genomic Insights into the Origin and Evolution of Molluscan Red-Bloodedness in the Blood Clam Tegillarca granosa.

Blood clams differ from their molluscan kins by exhibiting a unique red-blood (RB) phenotype; however, the genetic basis and biochemical machinery subserving this evolutionary innovation remain unclear. As a fundamental step toward resolving this mystery, we presented the first chromosome-level genome and comprehensive transcriptomes of the blood clam Tegillarca granosa for an integrated genomic, evolutionary, and functional analyses of clam RB phenotype. We identified blood clam-specific and expanded gene families, as well as gene pathways that are of RB relevant. Clam-specific RB-related hemoglobins (Hbs) showed close phylogenetic relationships with myoglobins (Mbs) of blood clam and other molluscs without the RB phenotype, indicating that clam-specific Hbs were likely evolutionarily derived from the Mb lineage. Strikingly, similar to vertebrate Hbs, blood clam Hbs were present in a form of gene cluster. Despite the convergent evolution of Hb clusters in blood clam and vertebrates, their Hb clusters may have originated from a single ancestral Mb-like gene as evidenced by gene phylogeny and synteny analysis. A full suite of enzyme-encoding genes for heme synthesis was identified in blood clam, with prominent expression in hemolymph and resembling those in vertebrates, suggesting a convergence of both RB-related Hb and heme functions in vertebrates and blood clam. RNA interference experiments confirmed the functional roles of Hbs and key enzyme of heme synthesis in the maintenance of clam RB phenotype. The high-quality genome assembly and comprehensive transcriptomes presented herein serve new genomic resources for the super-diverse phylum Mollusca, and provide deep insights into the origin and evolution of invertebrate RB.

Mandarin fish (Sinipercidae) genomes provide insights into innate predatory feeding.

Mandarin fishes (Sinipercidae) are piscivores that feed solely on live fry. Unlike higher vertebrates, teleosts exhibit feeding behavior driven mainly by genetic responses, with no modification by learning from parents. Mandarin fishes could serve as excellent model organisms for studying feeding behavior. We report a long-read, chromosomal-scale genome assembly for Siniperca chuatsi and genome assemblies for Siniperca kneri, Siniperca scherzeri and Coreoperca whiteheadi. Positive selection analysis revealed rapid adaptive evolution of genes related to predatory feeding/aggression, growth, pyloric caeca and euryhalinity. Very few gill rakers are observed in mandarin fishes; analogously, we found that zebrafish deficient in edar had a gill raker loss phenotype and a more predatory habit, with reduced intake of zooplankton but increased intake of prey fish. Higher expression of bmp4, which could inhibit edar expression and gill raker development through binding of a Xvent-1 site upstream of edar, may cause predatory feeding in Siniperca.

Effect of agmatine on food intake in mandarin fish (Siniperca chuatsi).

Agmatine, an endogenous biogenic amine, is considered to be a central neurotransmitter. And it plays an important role in mammal feeding behavior. However, there were few studies on the effect of agmatine on feeding behavior in fishes. Here, we investigated the impact of intracerebroventricular (ICV) injections of agmatine (1.25-20 nmol/fish) on food intake in mandarin fish (Siniperca chuatsi). At 1-h post-injection, food intake showed a significant decrease in agmatine-treated fishes compared with the saline treated. Furthermore, the food intake in agmatine treatment mostly did not differ from that in saline treatment at 4--24-h post-injection as well as the results of genes expression of neuropeptide Y (NPY), agouti-regulated peptide (AgRP), and anorexigenic melanocortin 4 receptor (MC4R). In accordance with the insulin level increasing in liver, the gene expression of insulin receptor substrate (IRS2) was significantly higher in agmatine treatment compared to saline treatment at 1-h post-injection. Thus, the anorexigenic effect of agmatine is likely to decrease NPY and AgRP expression levels and increase MC4R and IRS2 levels which was coupled with stimulation of insulin secretion. Although these initial findings are limited in dose, the data firstly provides evidence for the anorectic effects of agmatine in fish.

Genome-Wide Identification and Characterization of Olfactory Receptor Genes in Chinese Perch, Siniperca chuatsi.

Olfaction, which is mediated by olfactory receptor (OR) genes, is essential in the daily life of fish, especially in foraging. However, Chinese perch (Siniperca chuatsi) is believed to prey with reliance on vision and lateral sensation, but not on olfaction. Therefore, understanding the evolutionary dynamics of the Chinese perch OR repertoire could provide insights into genetic evidence for adapting to a decreasing reliance on olfaction. Here, we reported a whole-genome analysis of the Chinese perch OR repertoire. Our analysis identified a total of 152 OR genes, including 123 functional genes and 29 pseudogenes, and showed their genomic organization. A phylogenetic tree was constructed, and the phylogenetic relationships of teleosts ORs was illustrated. The dN/dS (global ratios of non-synonymous to synonymous) analysis demonstrated that OR groups all appeared to be under purifying selection. Among the five Percomorpha fishes, Chinese perch only had 22 subfamilies, suggesting a decrease in OR diversities. The species-specific loss of subfamily 56 and 66 in Chinese perch, of which the genes belonged to subfamily 66, were orthologs of OR51E2, which recognized the plant odorant ß-ionone, indicating that extremely piscivorous fish which might lose those receptors responded to plant-related odors. Finally, the expression profiles of OR genes in the olfactory epithelium at different developmental stages were investigated using RNA-seq data. From the aforementioned results, the evolution of the OR repertoire may be shaped by the adaption of vision-dependent specializations for foraging in Chinese perch. The first systematic study of OR genes in Chinese perch could provide valuable genomic resources for the further investigation of olfactory function in teleosts.

Curcumin ameliorates dextran sulfate sodium-induced colitis in mice via regulation of autophagy and intestinal immunity.

BACKGROUND/AIMS: Inflammatory bowel disease (IBD) is regarded as a kind of chronic and unspecific intestinal inflammatory disorder. Its exact pathogenesis has not been elucidated. Curcumin, as an herbal drug, has been used in the treatment of IBD due to its immunoregulation. Autophagy has been reported to play an important role in the mechanism of IBD. In the present study, we focused on the autophagic regulation role of curcumin in the murine model of dextran sulfate sodium (DSS)-induced colitis. MATERIALS AND METHODS: We investigated the effects of curcumin on the progress of DSS-induced acute colitis in mice by evaluating the disease activity index (DAI) and histopathological score. Meanwhile, the mRNA and protein expression of autophagy-related key genes from colon tissues comprising autophagy-related 5 (ATG5), LC3-phosphatidylethanolamine conjugate (LC-3II), beclin-1, and B cell lymphoma 2 (bcl-2) was examined by quantitative reverse transcription polymerase chain reaction and Western blot. Furthermore, the mRNA and protein expression of cytokines, including tumor necrosis factor (TNF)-α, interleukin (IL) 6, IL-10, and IL-17A, was examined. Autophagosome was also examined under transmission electron microscopy. RESULTS: Both DAI and histopathological score increased in mice with DSS-induced colitis and obviously decreased after curcumin intervention. The expression levels of TNF-α, IL-6, IL-17, ATG5, LC-3II, and beclin-1 were significantly higher in mice with colitis than in normal ones, whereas those of IL-10 and bcl-2 decreased accordingly. However, curcumin intervention adjusted the expression level of those factors toward normal level. The number of autophagosome in the colon epithelia increased after DSS stimulation and decreased after curcumin administration. CONCLUSION: Curcumin could prevent the development of DSS-induced colitis through the inhibition of excessive autophagy and regulation of following cytokine networks.

Effects of fasting, temperature, and photoperiod on preproghrelin mRNA expression in Chinese perch.

Preproghrelin, a gut/brain peptide, plays an important role in the regulation of food intake and energy homeostasis in teleost and mammals. In the present study, we obtained the full-length preproghrelin cDNA in Chinese perch. The preproghrelin messenger RNA (mRNA) tissue expression showed that level was much higher in stomach and pituitary than in other tissues. The fasting study showed, after gastric emptying (3-6 h), short-term fasting (6-12 h) increased preproghrelin expression in the stomach. While in the pituitary, fasting reduced preproghrelin expression at 1, 3, 12, and 48 h, presenting state fluctuation of self-adjustment. The temperature study showed that the mRNA expression of preproghrelin was the highest in the brain at 26 °C and highest in the stomach at 32 °C, respectively, with different optimum temperature in these two tissues, reflecting spatiotemporal differences of regulation by central nervous system and peripheral organs. The photoperiod study showed that normal light (11 h of lightness and 13 h of darkness) led to highest preproghrelin expression, both in the brain and in the stomach, than continuous light or continuous dark, proving food intake is adapted to natural photoperiod or normal light in this study. These results all indicated that tissue-specific preproghrelin expression of Chinese perch could be significantly affected by environmental factors. Short-term fasting of 6 h after gastric emptying, 26 °C, and normal light led to higher preproghrelin expression, which indicated potential appetite increase in Chinese perch.

Identification of differentially expressed genes associated with differential body size in mandarin fish (Siniperca chuatsi).

Body size is an obvious and important characteristic of fish. Mandarin fish Siniperca chuatsi (Basilewsky) is one of the most valuable perciform species widely cultured in China. Individual differences in body size are common in mandarin fish and significantly influence the aquaculture production. However, little is currently known about its genetic control. In this study, digital gene expression profiling and transcriptome sequencing were performed in mandarin fish with differential body size at 30 and 180 days post-hatch (dph), respectively. Body weight, total length and body length of fish with big-size were significantly higher than those with small-size at both 30 and 180 dph (P < 0.05). 2171 and 2014 differentially expressed genes were identified between small-size and big-size fish at 30 and 180 dph, respectively. RT quantitative PCR (qPCR) analysis showed that the differential expression of 10 selected genes in mandarin fish that went through the same training procedure. The genes were involved in the growth hormone-insulin-like growth factor axis, cell proliferation and differentiation, appetite control, glucose metabolism, reproduction and sexual size dimorphism pathways. This study will help toward a comprehensive understanding of the complexity of regulation of body size in mandarin fish individuals and provide valuable information for future research.

Construction and characterization of a bacterial artificial chromosome library for mandarin fish Siniperca chuatsi (Basilewsky).

Siniperca chuatsi (Basilewsky), a demersal piscivore, is an endemic freshwater fish species in China. For the purpose of genomics research, we have constructed the first bacterial artificial chromosome (BAC) library for S. chuatsi. The BAC library comprised a total of 84,480 clones with an average insert size of 124.6 kb and less than 2.5% empty clones, corresponding to a 10.5-fold coverage of the S. chuatsi genome. The probability of isolating genes of interest was more than 99%. To validate the library, we screened 220 superpools and found that 1-19 were positive for six SSR markers, while none was positive for two mitochondrial gene markers. Therefore, the S. chuatsi BAC library will provide useful genomics resources and tools for cloning, functional genomics research and identification of economically important genes in this species.

The complete mitochondrial genome of the hybrid of Siniperca chuatsi (♀) × Siniperca kneri (♂).

In this study, we reported the complete mitochondrial DNA sequence of the hybrid of Siniperca chuatsi (♀)×Siniperca kneri (♂). The total length of the mitochondrial genome is 16,493 bp, with the base composition of 28.61% A, 29.21% C, 16.21% G, and 25.97% T. It contains 2 rRNA genes, 13 protein-coding genes, 22 tRNA genes, and a major non-coding control region (D-loop region). The composition and order of these genes are identical to most of other vertebrates. All the protein initiation codons are ATG, except for COX1 that begins with GTG. The complete mitogenome of the hybrid of Siniperca chuatsi (♀) × Siniperca kneri (♂) provides an important data set for the study in genetic mechanism.