[Clinical features of primary sclerosing cholangitis and inflammatory bowel disease]

Objective: To explore disease characteristics of primary sclerosing cholangitis (PSC) and inflammatory bowel disease (IBD) and compare the differences between PSC with and without IBD. Methods: Study design was cross sectional. Forty-two patients with PSC who were admitted from January 2000 to January 2021 were included. We analyzed their demographic characteristics, clinical manifestations, concomitant diseases, auxiliary examination, and treatment. Results: The 42 patients were 11-74(43±18) years of age at diagnosis. The concordance rate of PSC with IBD was 33.3%, and the age at PSC with IBD diagnosis was 12-63(42±17) years. PSC patients with IBD had higher incidences of diarrhea and lower incidences of jaundice and fatigue than in those without IBD (all P<0.05). Alanine aminotransferase, total bilirubin, direct bilirubin, total bile acid and carbohydrate antigen 19-9 levels were higher in PSC patients without IBD than in those with IBD (all P<0.05). The positive rates for antinuclear antibodies and fecal occult blood were higher in PSC patients with IBD than in those without IBD (all P<0.05). Patients with PSC complicated with ulcerative colitis mainly experienced extensive colonic involvement. The proportion of 5-aminosalicylic acid and glucocorticoid application in PSC patients with IBD was significantly increased compared with that of PSC patients without IBD (P=0.025). Conclusions: The concordance rate of PSC with IBD is lower at Peking Union Medical College Hospital than in Western countries. Colonoscopy screening may benefit PSC patients with diarrhea or fecal occult blood-positive for early detection and diagnosis of IBD.

[Status of HVPG clinical application in China in 2021]

Objective: The investigation and research on the application status of Hepatic Venous Pressure Gradient (HVPG) is very important to understand the real situation and future development of this technology in China. Methods: This study comprehensively investigated the basic situation of HVPG technology in China, including hospital distribution, hospital level, annual number of cases, catheters used, average cost, indications and existing problems. Results: According to the survey, there were 70 hospitals in China carrying out HVPG technology in 2021, distributed in 28 provinces (autonomous regions and municipalities directly under the central Government). A total of 4 398 cases of HVPG were performed in all the surveyed hospitals in 2021, of which 2 291 cases (52.1%) were tested by HVPG alone. The average cost of HVPG detection was (5 617.2±2 079.4) yuan. 96.3% of the teams completed HVPG detection with balloon method, and most of the teams used thrombectomy balloon catheter (80.3%). Conclusion: Through this investigation, the status of domestic clinical application of HVPG has been clarified, and it has been confirmed that many domestic medical institutions have mastered this technology, but it still needs to continue to promote and popularize HVPG technology in the future.

[Value of the monocyte-to-lymphocyte ratio in the prognostic evaluation of hepatitis B-related acute-on-chronic liver failure]

Objective: To investigate the predictive value of the monocyte-to-lymphocyte ratio (MLR) for survival in patients with hepatitis B-related acute-on-chronic liver failure (HBV-ACLF). Methods: 92 cases with HBV-ACLF who were admitted to the General Hospital of Western Theater Command from October 2014 to October 2017 were selected. Clinical indicators were retrospectively collected, and their survival condition was followed up for 90 days, with the end point as death or liver transplantation. MLR levels predictive value among patients after 90 days of involvement was compared by analyzing the differences between the survival and death groups and its correlation with various indicators of liver function for prognosis. Results: 92 cases were included in this study, with a 90-day survival rate of 52% (48/92), and a mortality rate of 48% (44/92). MLR for survival and death groups were 0.520 (0.310, 0.828) and 0.740 (0.440, 1.120), respectively. MLR level was significantly higher in the death than survival group (P<0.05). Receiver operating characteristic curve (ROC) analysis showed that the area under the ROC curve (AUC) and 95% confidence interval for the survival group was 0.640 (0.527-0.754). The cutoff value for MLR was 0.399 at which the sensitivity and specificity were 0.864 and 0.396, respectively. Survival analysis showed that the 90-day survival rate was significantly lower in the high MLR group than corresponding low MLR group (P=0.011). Logistic multivariate regression analysis showed that after adjusting for other factors, MLR level was an independent prognostic factor in patients with HBV-ACLF. Conclusions: MLR can be used as a potential prognostic indicator for patients with HBV-ACLF, and its clinical value needs to be verified by large-scale prospective randomized trials.

[The 494th case: acute pancreatitis, acute acalculous cholecystitis and anaphylaxis]

A young male patient with abdominal pain and fever was diagnosed as acute hyper-triglyceridemicpancreatitis is clear. During the recovery of pancreatitis, the patient developed acute acalculous cholecystitis, as well as carbapenem-resistant Enterobacter infection and Cytomegaloviremia, and had anaphylaxis for several times after the use of antibiotics, which cannot be completely explained by drug allergy. This paper analyzes the possible causes of multiple diseases in the same patient in detail.

Detection performance of PCR for Legionella pneumophila in environmental samples: a systematic review and meta-analysis

Background

Legionellosis remains a public health problem. The most common diagnostic method to detect Legionella pneumophila (L. pneumophila) is culture. Polymerase chain reaction (PCR) is a fast and accurate method for this detection in environmental samples.

Methods

Four databases were searched for studies that evaluated the detection efficiency of PCR in L. pneumophila. The quality evaluation was conducted using Review Manager 5.3. We used Meta-DiSc 1.4 software and the Stata 15.0 software to create forest plots, a meta-regression, a bivariate boxplot and a Deeks’ funnel plot.

Results

A total of 18 four-fold tables from 16 studies were analysed. The overall pooled sensitivity and specificity of PCR was 94% and 72%, respectively. The positive likelihood ratio (RLR) and negative likelihood ratio (NLR) was 2.73 and 0.12, respectively. The result of the diagnostic odds ratio (DOR) was 22.85 and the area under the curve (AUC) was 0.7884.

Conclusion

Establishing a laboratory diagnostic tool for L. pneumophila detection is important for epidemiological studies. In this work, PCR demonstrated a promising diagnostic accuracy for L. pneumophila.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12941-022-00503-9.

Residual SYNTAX score in relation to culprit-plaque characteristics and cardiovascular risk in acute myocardial infarction:an optical coherence tomography study

Introduction

The residual SYNTAX score (rSS) as the SYNTAX remaining after completion of percutaneous coronary intervention (PCI) was proved to be related to poor outcomes.

Purpose

This study aimed to investigate the association of culprit-plaque morphology with rSS and the predictive value of rSS for major adverse cardiac events (MACE) in patients with ST-segment elevation myocardial infarction (STEMI).

Methods

A total of 274 STEMI patients undergoing preintervention optical coherence tomography examination were included and divided into 3 groups – rSS=0 (n=72), 0&lt;rss≤8&gt;8 (n=68). Baseline clinical data and culprit-plaque characteristics were compared. MACE was defined as the composite of all-cause death, recurrence of myocardial infarction (MI), stroke and unplanned revascularization of any coronary artery.

Results

There was a significant difference in the prevalence of plaque ruptures, lipid-rich plaques, and calcification among the three groups (plaque rupture: 44.4% versus 59.0% versus 64.7%, lowest to highest rSS, p=0.04; lipid-rich plaque: 40.3% versus 54.5% versus 69.1%, lowest to highest rSS, p=0.003; calcification: 38.9% versus 52.5% versus 61.8%, lowest to highest rSS, p=0.024). Multivariate logistic regression analysis indicated that rSS&gt;8 was an independent predictor for plaque rupture (OR: 2.21, 95% CI: 1.19–4.19, P=0.013). During a mean follow-up of 2.2 years, MACE occurred in 47 (17.2%) patients. In fully adjusted analyses, rSS was independently associated with MACE (HR: 1.06, 95% CI: 1.02–1.10, P=0.005); patients with rSS &gt;8 had higher MACE risk compared to rSS=0 (HR: 2.68, 95% CI: 1.11–6.5, P=0.029).

Conclusion

In STEMI patients, culprit-plaque morphology was significantly correlated with rSS, and elevated rSS was independently associated with cardiovascular risk.&lt;/rss≤8&gt;

Funding Acknowledgement

Type of funding sources: Public Institution(s). Main funding source(s): Chinese Academy of Medical Sciences Innovation Fund for Medical Sciences OCT findingsSurvival curves according to rSS

[Clinicopathological characteristics of rectal neuroendocrine neoplasms]

Objective: Clinicopathological characteristics of neuroendocrine neoplasms are highly heterogeneous based on variable origins.Our study aims to explore the clinical features of rectal neuroendocrine neoplasm (RNEN). Methods: Patients with histologically diagnosed rectal neuroendocrine neoplasms were retrospectively analyzed between January 2012 and December 2020. Epidemiological characteristics, clinical manifestations, complete blood count, endoscopy findings, and pathological features were recorded and analyzed. T-test was used for measurement data analysis, Chi-square test was performed for classification data analysis, and Binary logistic regression was applied for analyzing risk factors of metastasis. Results: Among 172 patients, the male to female ratio was 107 to 65 with an average age of (52±12) years (16-77 years). Altered bowel habit was the most common initial symptom (58/172, 33.7%), followed by abdominal pain (36/172, 20.9%) and loss of body weight (27/172, 15.7%). One hundred and sixty-one cases were neuroendocrine tumors, 9 were neuroendocrine carcinomas and 2 were mixed neuroendocrine-non-neuroendocrine neoplasms. Most endoscopic presentations were polypoid lesions (147/172, 85.5%), mainly limited to mucosa (48/172, 27.9%) and submucosa (96/172, 55.8%). Twenty-nine patients developed lymph node invasion or distant metastasis at diagnosis. There were statistical difference of neutrophil-to-lymphocyte ratios (NLR) among groups with different tumor size (<10 mm vs. 10-20 mm vs.>20 mm, mean NLR 1.79±0.55 vs. 2.27±1.23 vs. 2.95±0.66, P<0.01. Compared with non-metastatic group, the metastatic group presented higher NLR(2.61±0.81 vs. 1.89±0.80, P<0.01). Tumor size (<10 mm vs. 10-20 mm vs.>20 mm, OR 1.00 vs. 2.10 vs. 5.25×10⁹, P =0.001), invasion to bowel wall (mucosa vs. submucosa vs. muscularis vs. serosa invasion,OR 1.00 vs. 3.26 vs. 14.11 vs. 39.42, P=0.008), and NLR (NLR<2.25 vs. NLR≥2.25, OR 1.00 vs. 5.19, P =0.024) were risk factors for metastasis. Conclusion: Metastasis of RNEN is related with tumor size, degree of bowel invasion and NLR. High NLR is a poor prognostic factor of RNEN.

[The incidence risk of elevated fasting blood glucose in people with fatty liver disease: a cohort study of 40 000 people over the past 10 years]

Objective: To analyze the time point when patients with fatty liver disease had a significantly higher risk of elevated fasting blood glucose than those without in the physical examination group in Karamay Central Hospital, factors affecting the incidence of elevated blood glucose in patients with fatty liver disease, and the influence of the number of influencing factors on it. Methods: Physical examination data from Karamay Central Hospital during September 2008 to April 2017 were retrospectively analyzed. Combined with the survival analysis, the 1-,3-, 5-, and 7-year prevalence rates of elevated fasting glucose occurs in people with and without fatty liver disease were analyzed. Z-test was used to compare the survival rate difference at each time point. Cox regression model was used for multivariate analysis. Results: 10 802 people were in the fatty liver group. The elevated fasting blood glucose incidence density was 61/1 000 person-years, and the 1-, 3-, 5-, and 7-year prevalence rates were 2%, 16%, 28%, and 38%, respectively. 29 579 people were in the non-fatty liver group. The elevated fasting blood glucose incidence density was 23/1000 person-years, and the 1-, 3-, 5-, and 7-year prevalence rates were 1%, 7%, 11%, and 16%, respectively. The short-term and long-term elevated fasting blood glucose incidence risk were significantly higher in fatty liver group than non-fatty liver group(P < 0.001). The elevated fasting blood glucose incidence risk was apparently higher in fatty liver group than that of non-fatty liver group from the first year onward (P < 0.001). Age≥50 year's old (HR = 1.954, 95% CI :1.792-2.132), elevated body mass index (HR = 1.397, 95% CI : 1.198-1.629), blood pressure (HR = 1.284, 95% CI : 1.181-1.397), triglycerides (HR = 1.171, 95% CI: 1.077-1.274) were independent risk factors, which promoted the elevated fasting blood glucose incidence risk in patients with fatty liver disease. Fatty liver combined with the above 2, 3, and 4 risk factors had apparently increased the incidence risk of elevated fasting blood glucose (P < 0.001). Conclusion: People with fatty liver disease had a higher risk of elevated fasting blood glucose from the first year than those without. Age≥50 year's old, elevated blood pressure, body mass index and triglyceride might increase risk of elevated fasting blood glucose in patients with fatty liver disease, combined with the above 2,3 or 4 risk factors can increase the risk of elevated fasting blood glucose.

[The Chinese guidelines for the diagnosis and treatment of pancreatic neuroendocrine neoplasms (2020)]

Pancreatic neuroendocrine neoplasms (pNENs) are highly heterogeneous, and the management of pNENs patients can be intractable. To address this challenge, an expert committee was established on behalf of the Group of Pancreatic Surgery, Chinese Society of Surgery, Chinese Medical Association, which consisted of surgical oncologists, gastroenterologists, medical oncologists, endocrinologists, radiologists, pathologists, and nuclear medicine specialists. By reviewing the important issues regarding the diagnosis and treatment of pNENs, the committee concluded evidence-based statements and recommendations in this article, in order to further improve the management of pNENs patients in China.

[The variation of serum uric acid levels among patients with myocardial infarction treated with ticagrelor and the association between serum uric acid and platelet reactivity]

Objectives: To compare the impact of ticagrelor or clopidogrel on serum uric acid levels among patients with ST-segment elevation myocardial infarction (STEMI) who underwent primary percutaneous coronary intervention (PCI) and further evaluate the effects of variation of serum uric acid levels on platelet reactivity. Methods: STEMI patients who admitted to Fuwai Hospital from April 2017 to January 2020, and underwent primary PCI and discharged alive with aspirin and ticagrelor or clopidogrel were included in this study. Patients were divided into ticagrelor group and clopidogrel group. The baseline clinical data were collected. Serum uric acid and creatinine levels at baseline and 30 days post-PCI were measured. Light transmittance aggregometry was used to assess maximum aggregation rate induced by adenosine diphosphate and arachidonic acid. The changes of serum uric acid and creatinine were compared between the two groups. Multivariate logistic regression was performed to evaluate independent related factors for rise in the uric acid levels, and the effect of variation of serum uric acid level on platelet reactivity was analyzed. Results: A total of 967 patients were included, the age was (59.4±12.1) years, and 163 case were female. There were 550 cases in ticagrelor group (56.9%) and 417 cases in clopidogrel group (43.1%). Baseline serum uric acid and creatinine levels were similar between the 2 groups. At 30 days, the serum uric acid level [(347.2±96.5) mmol/L vs. (341.2±105.3) mmol/L, P=0.009] and absolute [46.4 (-2.4, 88.1) mmol/L vs. 25.0 (-21.9, 73.0) mmol/L, P=0.001] and percentage [13.2 (-0.01, 29.0) % vs. 7.9 (-5.7, 25.0) %, P=0.007] increase in the serum uric acid levels were significantly higher in ticagrelor group than in clopidogrel group. The level of serum creatinine at 30 days was significantly lower in ticagrelor group than in clopidogrel group [(89.7±21.3) μmol/L vs. (94.4±43.9) μmol/L, P<0.05], whereas there were no differences in absolute [8.0 (-1.4, 16.6) μmol/L vs. 7.8 (-2.0, 16.6) μmol/L] and percentage [10.5 (-1.7%, 22.6%) vs. 9.8 (-2.4%, 22.1%)] change in the serum creatinine between the 2 groups (all P>0.05). Logistic regression analysis showed that, after adjusting for confounding factors, ticagrelor therapy was an independent related factor of serum uric acid elevation (OR=1.582, 95% CI:1.023-2.447, P=0.039). The variation of the serum uric acid levels did not affect platelet aggregation and the percentage of high platelet reactivity in both groups. Conclusions: Ticagrelor use is related to a significant increase in the serum uric acid levels at 30 days post-PCI in this patient cohort. The variations in the uric acid levels do not increase the percentage of high platelet reactivity in STEMI patients treated with ticagrelor or clopidogrel.

Genome-Wide Survey and Expression Analysis of the KT/HAK/KUP Family in Brassica napus and Its Potential Roles in the Response to K+ Deficiency

The KT/HAK/KUP (HAK) family is the largest potassium (K⁺) transporter family in plants, which plays key roles in K⁺ uptake and homeostasis, stress resistance, and root and embryo development. However, the HAK family has not yet been characterized in Brassica napus. In this study, 40 putative B. napus HAK genes (BnaHAKs) are identified and divided into four groups (Groups I–III and V) on the basis of phylogenetic analysis. Gene structure analysis revealed 10 conserved intron insertion sites across different groups. Collinearity analysis demonstrated that both allopolyploidization and small-scale duplication events contributed to the large expansion of BnaHAKs. Transcription factor (TF)-binding network construction, cis-element analysis, and microRNA prediction revealed that the expression of BnaHAKs is regulated by multiple factors. Analysis of RNA-sequencing data further revealed extensive expression profiles of the BnaHAKs in groups II, III, and V, with limited expression in group I. Compared with group I, most of the BnaHAKs in groups II, III, and V were more upregulated by hormone induction based on RNA-sequencing data. Reverse transcription-quantitative polymerase reaction analysis revealed that the expression of eight BnaHAKs of groups I and V was markedly upregulated under K⁺-deficiency treatment. Collectively, our results provide valuable information and key candidate genes for further functional studies of BnaHAKs.

Genome-wide characterization, expression analyses, and functional prediction of the NPF family in Brassica napus

Background

NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER (NRT1/PTR) family (NPF) members are essential transporters for many substrates in plants, including nitrate, hormones, peptides, and secondary metabolites. Here, we report the global characterization of NPF in the important oil crop Brassica napus, including that for phylogeny, gene/protein structures, duplications, and expression patterns.

Results

A total of 199 B. napus (BnaNPFs) NPF-coding genes were identified. Phylogenetic analyses categorized these genes into 11 subfamilies, including three new ones. Sequence feature analysis revealed that members of each subfamily contain conserved gene and protein structures. Many hormone−/abiotic stress-responsive cis-acting elements and transcription factor binding sites were identified in BnaNPF promoter regions. Chromosome distribution analysis indicated that BnaNPFs within a subfamily tend to cluster on one chromosome. Syntenic relationship analysis showed that allotetraploid creation by its ancestors (Brassica rapa and Brassica oleracea) (57.89%) and small-scale duplication events (39.85%) contributed to rapid BnaNPF expansion in B. napus. A genome-wide spatiotemporal expression survey showed that NPF genes of each Arabidopsis and B. napus subfamily have preferential expression patterns across developmental stages, most of them are expressed in a few organs. RNA-seq analysis showed that many BnaNPFs (32.66%) have wide exogenous hormone-inductive profiles, suggesting important hormone-mediated patterns in diverse bioprocesses. Homologs in a clade or branch within a given subfamily have conserved organ/spatiotemporal and hormone-inductive profiles, indicating functional conservation during evolution. qRT-PCR-based comparative expression analysis of the 12 BnaNPFs in the NPF2–1 subfamily between high- and low-glucosinolate (GLS) content B. napus varieties revealed that homologs of AtNPF2.9 (BnaNPF2.12, BnaNPF2.13, and BnaNPF2.14), AtNPF2.10 (BnaNPF2.19 and BnaNPF2.20), and AtNPF2.11 (BnaNPF2.26 and BnaNPF2.28) might be involved in GLS transport. qRT-PCR further confirmed the hormone-responsive expression profiles of these putative GLS transporter genes.

Conclusion

We identified 199 B. napus BnaNPFs; these were divided into 11 subfamilies. Allopolyploidy and small-scale duplication events contributed to the immense expansion of BnaNPFs in B. napus. The BnaNPFs had preferential expression patterns in different tissues/organs and wide hormone-induced expression profiles. Four BnaNPFs in the NPF2–1 subfamily may be involved in GLS transport. Our results provide an abundant gene resource for further functional analysis of BnaNPFs.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-020-07274-7.

Genome-wide identification and expression profiling of the carotenoid cleavage dioxygenase (CCD) gene family in Brassica napus L

Carotenoid cleavage dioxygenase (CCD), a key enzyme in carotenoid metabolism, cleaves carotenoids to form apo-carotenoids, which play a major role in plant growth and stress responses. CCD genes had not previously been systematically characterized in Brassica napus (rapeseed), an important oil crop worldwide. In this study, we identified 30 BnCCD genes and classified them into nine subgroups based on a phylogenetic analysis. We identified the chromosomal locations, gene structures, and cis-promoter elements of each of these genes and performed a selection pressure analysis to identify residues under selection. Furthermore, we determined the subcellular localization, physicochemical properties, and conserved protein motifs of the encoded proteins. All the CCD proteins contained a retinal pigment epithelial membrane protein (RPE65) domain. qRT-PCR analysis of expression of 20 representative BnCCD genes in 16 tissues of the B. napus cultivar Zhong Shuang 11 ('ZS11') revealed that members of the BnCCD gene family possess a broad range of expression patterns. This work lays the foundation for functional studies of the BnCCD gene family.

[Associations between postprocedural D-dimer, hs-CRP, LDL-C levels and prognosis of acute myocardial infarction patients treated by percutaneous coronary intervention]

Objective: To investigate the association between postprocedural D-dimer, high sensitivity C-reactive protein(hs-CRP) and low-density lipoprotein-cholesterol(LDL-C) and outcomes of acute myocardial infarction (AMI) patients treated by percutaneous coronary intervention(PCI), in order to clarify the impacts of thrombotic, inflammatory and cholesterol risks on long-term prognosis. Methods: Patients with AMI who underwent emergency PCI from January 2010 to June 2017 in Fuwai Hospital with complete baseline data were enrolled. Patients were stratified into four groups according to quartiles of D-dimer, hs-CRP and LCL-C. Cox regression was used to analyze the relationship between these biomarkers and prognosis. Restricted cubic spline (RCS) was used to characterize the continuous association between risk of all-cause death and biomarkers. The primary outcome was all-cause death. Results: A total of 3 614 patients were included in the analysis. The age was (59.2±12.0) years old, and 2 845 (78.7%) were male and 3 161 (87.5%) patients were diagnosed as ST-segment elevation myocardial infarction. The follow-up time was 652 (414, 1 880) days. Survival analysis showed that postprocedural D-dimer and hs-CRP were significantly associated with all-cause mortality (all P<0.05). Cox regression with multiple adjustments showed that patients with D-dimer≥580 μg/L presented higher risk of all-cause death (HR=2.03, 95%CI 1.22-3.38, P=0.006), compared to patients with D-dimer<220 μg/L. RCS analysis showed that risk of all-cause death was stably high when D-dimer reached 500 μg/L. Multivariable Cox regression also showed that patients with hs-CRP<2.74 mg/L (HR=1.86, 95%CI 1.10-3.15, P=0.020)or hs-CRP≥11.99 mg/L (HR=2.14, 95%CI 1.35-3.40, P=0.001) presented higher mortality compared to patients whose hs-CRP was 2.74-7.18 mg/L. RCS analysis indicated a J-shaped relation between hs-CRP and mortality, as greater risk of death was observed when hs-CRP was lower than 2 mg/L or higher than 10 mg/L. LDL-C was not associated with outcomes (all P>0.05). Conclusions: Postprocedural D-dimer is significantly associated with long-term prognosis of AMI patients treated by PCI. Patients with extremely high or low levels of hs-CRP presents worse outcomes. Intensive and tailored antithrombotic or anti-inflammatory therapies should be considered for patients with increased thrombotic risk and those with extremely high or low inflammatory risk.

Genome-wide survey of the bHLH super gene family in Brassica napus

BACKGROUND

The basic helix-loop-helix (bHLH) gene family is one of the largest transcription factor families in plants and is functionally characterized in diverse species. However, less is known about its functions in the economically important allopolyploid oil crop, Brassica napus.

RESULTS

We identified 602 potential bHLHs in the B. napus genome (BnabHLHs) and categorized them into 35 subfamilies, including seven newly separated subfamilies, based on phylogeny, protein structure, and exon-intron organization analysis. The intron insertion patterns of this gene family were analyzed and a total of eight types were identified in the bHLH regions of BnabHLHs. Chromosome distribution and synteny analyses revealed that hybridization between Brassica rapa and Brassica oleracea was the main expansion mechanism for BnabHLHs. Expression analyses showed that BnabHLHs were widely in different plant tissues and formed seven main patterns, suggesting they may participate in various aspects of B. napus development. Furthermore, when roots were treated with five different hormones (IAA, auxin; GA3, gibberellin; 6-BA, cytokinin; ABA, abscisic acid and ACC, ethylene), the expression profiles of BnabHLHs changed significantly, with many showing increased expression. The induction of five candidate BnabHLHs was confirmed following the five hormone treatments via qRT-PCR. Up to 246 BnabHLHs from nine subfamilies were predicted to have potential roles relating to root development through the joint analysis of their expression profiles and homolog function.

CONCLUSION

The 602 BnabHLHs identified from B. napus were classified into 35 subfamilies, and those members from the same subfamily generally had similar sequence motifs. Overall, we found that BnabHLHs may be widely involved in root development in B. napus. Moreover, this study provides important insights into the potential functions of the BnabHLHs super gene family and thus will be useful in future gene function research.

Global Survey and Expressions of the Phosphate Transporter Gene Families in Brassica napus and Their Roles in Phosphorus Response

Phosphate (Pi) transporters play critical roles in Pi acquisition and homeostasis. However, currently little is known about these genes in oil crops. In this study, we aimed to characterize the five Pi transporter gene families (PHT1-5) in allotetraploid Brassica napus. We identified and characterized 81 putative PHT genes in B. napus (BnaPHTs), including 45 genes in PHT1 family (BnaPHT1s), four BnaPHT2s, 10 BnaPHT3s, 13 BnaPHT4s and nine BnaPHT5s. Phylogenetic analyses showed that the largest PHT1 family could be divided into two groups (Group I and II), while PHT4 may be classified into five, Groups I-V. Gene structure analysis revealed that the exon-intron pattern was conservative within the same family or group. The sequence characteristics of these five families were quite different, which may contribute to their functional divergence. Transcription factor (TF) binding network analyses identified many potential TF binding sites in the promoter regions of candidates, implying their possible regulating patterns. Collinearity analysis demonstrated that most BnaPHTs were derived from an allopolyploidization event (~40.7%) between Brassica rapa and Brassica oleracea ancestors, and small-scale segmental duplication events (~39.5%) in the descendant. RNA-Seq analyses proved that many BnaPHTs were preferentially expressed in leaf and flower tissues. The expression profiles of most colinearity-pairs in B. napus are highly correlated, implying functional redundancy, while a few pairs may have undergone neo-functionalization or sub-functionalization during evolution. The expression levels of many BnaPHTs tend to be up-regulated by different hormones inductions, especially for IAA, ABA and 6-BA treatments. qRT-PCR assay demonstrated that six BnaPHT1s (BnaPHT1.11, BnaPHT1.14, BnaPHT1.20, BnaPHT1.35, BnaPHT1.41, BnaPHT1.44) were significantly up-regulated under low- and/or rich- Pi conditions in B. napus roots. This work analyzes the evolution and expression of the PHT family in Brassica napus, which will help further research on their role in Pi transport.