Genomes of cultivated and wild Capsicum species provide insights into pepper domestication and population differentiation.

Pepper (Capsicum spp.) is one of the earliest cultivated crops and includes five domesticated species, C. annuum var. annuum, C. chinense, C. frutescens, C. baccatum var. pendulum and C. pubescens. Here, we report a pepper graph pan-genome and a genome variation map of 500 accessions from the five domesticated Capsicum species and close wild relatives. We identify highly differentiated genomic regions among the domesticated peppers that underlie their natural variations in flowering time, characteristic flavors, and unique resistances to biotic and abiotic stresses. Domestication sweeps detected in C. annuum var. annuum and C. baccatum var. pendulum are mostly different, and the common domestication traits, including fruit size, shape and pungency, are achieved mainly through the selection of distinct genomic regions between these two cultivated species. Introgressions from C. baccatum into C. chinense and C. frutescens are detected, including those providing genetic sources for various biotic and abiotic stress tolerances.

Corrigendum: Genome-wide identification and capsaicinoid biosynthesis-related expression analysis of the R2R3-MYB gene family in Capsicum annuum L.

[This corrects the article DOI: 10.3389/fgene.2020.598183.].

Analysis of the response regulatory network of pepper genes under hydrogen peroxide stress.

Hydrogen peroxide (H2O2) is a regulatory component related to plant signal transduction. To better understand the genome-wide gene expression response to H2O2 stress in pepper plants, a regulatory network of H2O2 stress-gene expression in pepper leaves and roots was constructed in the present study. We collected the normal tissues of leaves and roots of pepper plants after 40 days of H2O2 treatment and obtained the RNA-seq data of leaves and roots exposed to H2O2 for 0.5-24 h. By comparing the gene responses of pepper leaves and roots exposed to H2O2 stress for different time periods, we found that the response in roots reached the peak at 3 h, whereas the response in leaves reached the peak at 24 h after treatment, and the response degree in the roots was higher than that in the leaves. We used all datasets for K-means analysis and network analysis identified the clusters related to stress response and related genes. In addition, CaEBS1, CaRAP2, and CabHLH029 were identified through a co-expression analysis and were found to be strongly related to several reactive oxygen species-scavenging enzyme genes; their homologous genes in Arabidopsis showed important functions in response to hypoxia or iron uptake. This study provides a theoretical basis for determining the dynamic response process of pepper plants to H2O2 stress in leaves and roots, as well as for determining the critical time and the molecular mechanism of H2O2 stress response in leaves and roots. The candidate transcription factors identified in this study can be used as a reference for further experimental verification.

Transcriptome data reveal gene clusters and key genes in pepper response to heat shock.

Climate change and global warming pose a great threat to plant growth and development as well as crop productivity. To better study the genome-wide gene expression under heat, we performed a time-course (0.5 to 24 h) transcriptome analysis in the leaf and root of 40-day-old pepper plants under 40°C as well as in control plants. Clustering analysis (K-means) showed that the expression of 29,249 genes can be grouped into 12 clusters with distinct expression dynamics under stress. Gene ontology (GO) enrichment analysis and transcription factor (TF) identification were performed on the clusters with certain expression patterns. Comparative analysis between the heat-treated and control plants also identified differentially expressed genes (DEGs), which showed the largest degree of change at 24 h. Interestingly, more DEGs were identified in the root than in the leaf. Moreover, we analyzed the gene expression of 25 heat shock factor genes (HSFs) in pepper after heat stress, identified five of these HSFs that responded to heat stress, and characterized the role of these genes in heat-tolerant (17CL30) and heat-susceptible (05S180) pepper lines. The findings of this study improve our understanding of the genome-wide heat stress response in pepper.

Evolution and functional diversification of catalase genes in the green lineage.

BACKGROUND: Catalases (CATs) break down hydrogen peroxide into water and oxygen to prevent cellular oxidative damage, and play key roles in the development, biotic and abiotic stresses of plants. However, the evolutionary relationships of the plant CAT gene family have not been systematically reported. RESULTS: Here, we conducted genome-wide comparative, phylogenetic, and structural analyses of CAT orthologs from 29 out of 31 representative green lineage species to characterize the evolution and functional diversity of CATs. We found that CAT genes in land plants were derived from core chlorophytes and detected a lineage-specific loss of CAT genes in Fabaceae, suggesting that the CAT genes in this group possess divergent functions. All CAT genes were split into three major groups (group α, ß1, and ß2) based on the phylogeny. CAT genes were transferred from bacteria to core chlorophytes and charophytes by lateral gene transfer, and this led to the independent evolution of two types of CAT genes: α and ß types. Ten common motifs were detected in both α and ß groups, and ß CAT genes had five unique motifs, respectively. The findings of our study are inconsistent with two previous hypotheses proposing that (i) new CAT genes are acquired through intron loss and that (ii) the Cys-343 residue is highly conserved in plants. We found that new CAT genes in most higher plants were produced through intron acquisition and that the Cys-343 residue was only present in monocots, Brassicaceae and Pp_CatX7 in P. patens, which indicates the functional specificity of the CATs in these three lineages. Finally, our finding that CAT genes show high overall sequence identity but that individual CAT genes showed developmental stage and organ-specific expression patterns suggests that CAT genes have functionally diverged independently. CONCLUSIONS: Overall, our analyses of the CAT gene family provide new insights into their evolution and functional diversification in green lineage species.

Analysis of the Expression and Function of Key Genes in Pepper Under Low-Temperature Stress.

The mechanism of resistance of plants to cold temperatures is very complicated, and the molecular mechanism and related gene network in pepper are largely unknown. Here, during cold treatment, we used cluster analysis (k-means) to classify all expressed genes into 15 clusters, 3,680 and 2,405 differentially expressed genes (DEGs) were observed in the leaf and root, respectively. The DEGs associated with certain important basic metabolic processes, oxidoreductase activity, and overall membrane compositions were most significantly enriched. In addition, based on the homologous sequence alignment of Arabidopsis genes, we identified 14 positive and negative regulators of the ICE-CBF-COR module in pepper, including CBF and ICE, and compared their levels in different data sets. The correlation matrix constructed based on the expression patterns of whole pepper genes in leaves and roots after exposure to cold stress showed the correlation between 14 ICE-CBF-COR signaling module genes, and provided insight into the relationship between these genes in pepper. These findings not only provide valuable resources for research on cold tolerance, but also lay the foundation for the genetic modification of cold stress regulators, which would help us achieve improved crop tolerance. To our knowledge, this is the first study to demonstrate the relationship between positive and negative regulators related to the ICE-CBF-COR module, which is of great significance to the study of low-temperature adaptive mechanisms in plants.

Genome-Wide Identification and Capsaicinoid Biosynthesis-Related Expression Analysis of the R2R3-MYB Gene Family in Capsicum annuum L.

Capsaicinoids are naturally specialized metabolites in pepper and are the main reason that Capsicum fruits have a pungent smell. During the synthesis of capsaicin, MYB transcription factors play key regulatory roles. In particular, R2R3-MYB subfamily genes are the most important members of the MYB family and are critical candidate factors in capsaicinoid biosynthesis. The 108 R2R3-MYB genes in pepper were identified in this study and all are shown to have two highly conserved MYB binding domains. Phylogenetic and structural analyses clustered CaR2R3-MYB genes into seven groups. Interspecies collinearity analysis found that the R2R3-MYB family contains 16 duplicated gene pairs and the highest gene density is on chromosome 00 and 03. The expression levels of CaR2R3-MYB differentially expressed genes (DEGs) and capsaicinoid-biosynthetic genes (CBGs) in fruit development stages were obtained via RNA-seq and quantitative polymerase chain reaction (qRT-PCR). Co-expression analyses reveal that highly expressed CaR2R3-MYB genes are co-expressed with CBGs during early stages of pericarp and placenta development processes. It is speculated that six candidate CaR2R3-MYB genes are involved in regulating the synthesis of capsaicin and dihydrocapsaicin. This study is the first systematic analysis of the CaR2R3-MYB gene family and provided references for studying their molecular functions. At the same time, these results also laid the foundation for further research on the capsaicin characteristics of CaR2R3-MYB genes in pepper.

Genome-Wide Identification and Characterization of the Mitochondrial Transcription Termination Factors (mTERFs) in Capsicum annuum L.

Mitochondrial transcription termination factors (mTERFs) regulate the expression of mitochondrial genes and are closely related to the function of the mitochondrion and chloroplast. In this study, the mTERF gene family in capsicum (Capsicum annuum L.) was identified and characterized through genomic and bioinformatic analyses. Capsicum was found to possess at least 35 mTERF genes (CamTERFs), which were divided into eight major groups following phylogenetic analysis. Analysis of CamTERF promoters revealed the presence of many cis-elements related to the regulation of cellular respiration and photosynthesis. In addition, CamTERF promoters contained cis-elements related to phytohormone regulation and stress responses. Differentially expressed genes in different tissues and developmental phases were identified using RNA-seq data, which revealed that CamTERFs exhibit various expression and co-expression patterns. Gene ontology (GO) annotations associated CamTERFs primarily with mitochondrion and chloroplast function and composition. These results contribute towards understanding the role of mTERFs in capsicum growth, development, and stress responses. Moreover, our data assist in the identification of CamTERFs with important functions, which opens avenues for future studies.

Decreased circulating levels of oxytocin in obesity and newly diagnosed type 2 diabetic patients.

CONTEXT AND OBJECTIVE: Oxytocin can affect energy homeostasis and has interesting potential as a metabolic disease therapeutic. We detected serum oxytocin levels in obese (OB) and type 2 diabetes mellitus (T2DM) subjects and investigated the relationships between serum oxytocin levels and glycolipid metabolism, insulin resistance, pancreatic ß-cell function, and inflammation. PATIENTS AND METHODS: A total of 176 subjects were enrolled in the study, including 88 patients with newly diagnosed T2DM and 88 subjects with normal glucose tolerance (NGT). NGT and T2DM groups were divided into normal-weight (NW) and OB subgroups. We analyzed the concentrations of oxytocin by ELISA. Oral glucose tolerance testing was done, and hemoglobin A1c (HbA1c), blood lipids, and highly sensitive C-reactive protein (hs-CRP) were also measured. Insulin resistance and pancreatic ß-cell function were assessed by homeostasis model assessment (HOMA). RESULTS: Serum oxytocin levels were lower in the T2DM group than in the NGT group (P < .01). The levels of serum oxytocin in OB subjects were also lower than those in NW subjects (P < .01). Serum oxytocin levels were negatively correlated with body mass index (BMI), waist circumference (WC), waist-to-hip ratio (WHR), HbA1c, fasting plasma glucose (FPG), 2-hour plasma glucose, fasting insulin (FINS), 2-h insulin, total cholesterol (TC), triglycerides (TG), low-density lipoprotein cholesterol (LDL-C), HOMA of insulin resistance (HOMA-IR), and hs-CRP and positively correlated with HOMA of ß-cell function (HOMA-ß) (P < .05). Multiple stepwise regression analysis showed that 2-hour plasma glucose, BMI, and TC were associated with serum oxytocin levels (P < .05). Logistic regression analyses demonstrated that serum oxytocin was significantly associated with T2DM (P < .01). CONCLUSIONS: Serum oxytocin levels were decreased in T2DM as well as OB subjects.

Increased circulating levels of betatrophin in newly diagnosed type 2 diabetic patients.

OBJECTIVE: Betatrophin, a newly identified hormone, has been recently characterized as a potent stimulator that increases the production and expansion of insulin-secreting ß-cells in mice, but the physiological role of betatrophin remains poorly understood. This study measured for the first time serum betatrophin levels in newly diagnosed patients with type 2 diabetes (T2DM) and explored the correlations between its serum levels and various metabolic parameters in T2DM. RESEARCH DESIGN AND METHODS: We analyzed the concentrations of betatrophin by ELISA in blood samples of 166 well-characterized individuals in whom anthropometric parameters, oral glucose tolerance test (OGTT), glycosylated hemoglobin, blood lipids, insulin sensitivity (1/homeostasis model assesment of insulin resistance [1/HOMA-IR] and Matsuda index [ISIM]), and insulin secretion were measured. The participants were divided into newly diagnosed T2DM patients (n = 83) and age-, sex- and BMI-matched healthy control subjects (n = 83). RESULTS: Serum betatrophin levels were significantly higher in T2DM patients than in healthy control subjects (613.08 [422.19-813.08] vs. 296.57 [196.53-509.46] pg/mL; P < 0.01). Serum betatrophin positively correlated with age, 2-h post-OGTT glucose (2hPG), and postprandial serum insulin (PSI), but negatively with 1/HOMA-IR and ISIM in T2DM patients. In the control group, betatrophin was only positively associated with age. In T2DM subjects, multivariate regression analyses showed that age, 2hPG, and PSI were independent factors influencing serum betatrophin levels. CONCLUSIONS: Circulating concentrations of betatrophin are significantly increased in T2DM patients. Our results suggest that betatrophin may play a role in the pathogenesis of T2DM.

Safety and efficacy of sitagliptin in combination with transient continuous subcutaneous insulin infusion (CSII) therapy in patients with newly diagnosed type 2 diabetes.

Sitagliptin was used as monotherapy or in combination with metformin, thiazolidinedione or sulfonylurea. It is not clear whether effects are enhanced or unique when in combination with transient continuous subcutaneous insulin infusion (CSII) therapy. The aim of this study was to assess the safety and efficacy of sitagliptin in combination with transient CSII therapy in patients with newly diagnosed type 2 diabetes. Eighty patients with newly diagnosed type 2 diabetes from July 2011 to May 2013 were recruited into the study. These patients were randomly divided into a CSII monotherapy group (group A, n = 40) or a sitagliptin in combination with CSII therapy group (group B, n = 40) and received insulin intensive therapy. Treatments were maintained for 2 weeks. 75g oral glucose tolerance test (OGTT) was performed before and after treatments, and the levels of glucose, insulin and C-peptide were examined. The results indicated that, compared with CSII therapy group, the level of plasma glucose significantly decreased, the levels of insulin and C-peptide strikingly increased and homeostasis model assessment for beta-cell function (HOMA-ß) and Insulinogenic index (Ins index) were improved in the group of sitagliptin in combination with CSII therapy. Above all, the incidence of hypoglycemia was lower, insulin doses were less and the rate of recovery to normal glucose tolerance (NGT) or impaired glucose tolerance (IGT) determined by 75gOGTT was higher in the latter. So, Sitagliptin in combination with CSII therapy can be a new safe and effective therapy in patients with newly diagnosed type 2diabetes.