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.

The bHLH1-DTX35/DFR module regulates pollen fertility by promoting flavonoid biosynthesis in Capsicum annuum L.

High pollen fertility can ensure the yield and efficiency of breeding work, but factors that affect the fertility of pepper pollen have not been studied extensively. In this work, we screened the reduced pollen fertility 1 (rpf1) mutant of Capsicum annuum with reduced pollen fertility and yellow anthers from an EMS (ethyl methanesulfonate)-mutagenized pepper population. Through construction of an F 2 population followed by BSA (bulked segregant analysis) mapping and KASP genotyping, we identified CabHLH1 as a candidate gene for control of this trait. A G â†’ A mutation at a splice acceptor site in CabHLH1 causes a frameshift mutation in the mutant, and the translated protein is terminated prematurely. Previous studies on CabHLH1 have focused on the regulation of flavonoid synthesis. Here, we found that CabHLH1 also has an important effect on pollen fertility. Pollen vigor, anther flavonoid content, and seed number were lower in CabHLH1-silenced pepper plants, whereas anther H2O2 and MDA (malondialdehyde) contents were higher. RNA-seq analyses showed that expression of the flavonoid synthesis genes DFR, ANS, and RT was significantly reduced in anthers of CabHLH1-silenced plants and rpf1 plants, as was the expression of DTX35, a gene related to pollen fertility and flavonoid transport. Yeast one-hybrid and dual-luciferase reporter assays showed that CabHLH1 can directly bind to the promoters of DTX35 and DFR and activate their expression. These results indicate that CabHLH1 regulates reactive oxygen species homeostasis by promoting the synthesis of anther flavonoids and acts as a positive regulator of pepper pollen fertility.

Comprehensive Proteome and Lysine Acetylome Analysis Reveals the Widespread Involvement of Acetylation in Cold Resistance of Pepper (Capsicum annuum L.).

Pepper is a typical warmth-loving vegetable that lacks a cold acclimation mechanism and is sensitive to cold stress. Lysine acetylation plays an important role in diverse cellular processes, but limited knowledge is available regarding acetylation modifications in the resistance of pepper plants to cold stress. In this study, the proteome and acetylome of two pepper varieties with different levels of cold resistance were investigated by subjecting them to cold treatments of varying durations followed by recovery periods. In total, 6,213 proteins and 4,574 lysine acetylation sites were identified, and this resulted in the discovery of 3,008 differentially expressed proteins and 768 differentially expressed acetylated proteins. A total of 1,988 proteins were identified in both the proteome and acetylome, and the functional differences in these co-identified proteins were elucidated through GO enrichment. KEGG analysis showed that 397 identified acetylated proteins were involved in 93 different metabolic pathways. The dynamic changes in the acetylated proteins in photosynthesis and the "carbon fixation in the photosynthetic organisms" pathway in pepper under low-temperature stress were further analyzed. It was found that acetylation of the PsbO and PsbR proteins in photosystem II and the PsaN protein in photosystem I could regulate the response of pepper leaves to cold stress. The acetylation levels of key carbon assimilation enzymes, such as ribulose bisphosphate carboxylase, fructose-1,6-bisphosphatase, sedoheptulose-1,7-bisphosphatase, glyceraldehyde 3-phosphate dehydrogenase, phosphoribulokinase, and triosephosphate isomerase decreased, leading to decreases in carbon assimilation capacity and photosynthetic efficiency, reducing the cold tolerance of pepper leaves. This study is the first to identify the acetylome in pepper, and it greatly expands the catalog of lysine acetylation substrates and sites in Solanaceae crops, providing new insights for posttranslational modification studies.

Coexpression Network Analysis of Genes Related to the Characteristics of Tumor Stemness in Triple-Negative Breast Cancer.

Cancer stem cells (CSCs) are subsets of cells with the ability of self-renewal and differentiation in neoplasm, which are considered to be related to tumor heterogeneity. It has been reported that CSCs act on tumorigenesis and tumor biology of triple-negative breast cancer (TNBC). However, the key genes that cause TNBC showing stem cell characteristics are still unclear. We combined the RNA sequencing (RNA-seq) data from The Cancer Genome Atlas (TCGA) database and mRNA expression-based stemness index (mRNAsi) to further analyze mRNAsi with regard to molecular subtypes, tumor depth, and pathological staging characteristics of breast cancer (BC). Secondly, we extract the differential gene expression of tumor vs. normal group and TNBC vs. other subtypes of BC group, respectively, and intersect them to achieve precise results. We used a weighted gene coexpression network analysis (WGCNA) to screen significant gene modules and the functions of selected genes including BIRC5, CDC25A, KIF18B, KIF2C, ORC1, RAD54L, and TPX2 were carried out through gene ontology (GO) functional annotation. The Oncomine, bc-GenExMiner v4.4, GeneMANIA, Kaplan-Meier Plotter (KM-plotter), and GEPIA were used to verify the expression level and functions of key genes. In this study, we found that TNBC had the highest stem cell characteristics in BC compared with other subtypes. The lower the mRNAsi score, the better the overall survival and treatment outcome. Seven key genes of TNBC were screened and functional annotation indicated that there were strong correlations between them, relating to nuclear division, organelle fission, mitotic nuclear division, and other events that determine cell fate. Among these genes, we found four genes that were highly associated with adverse survival events. Seven key genes identified in this study were found to be closely related to the maintenance of TNBC stemness, and the overexpression of four showed earlier recurrence. The overall survival (OS) curves of all key genes between differential expression level crossed at around nine-year follow-up, which was consistent with the trend of the OS curve related to mRNAsi. These findings may provide new ideas for screening therapeutic targets in order to depress TNBC stemness.

Nomogram for predicting the risk of bone metastasis in breast cancer: a SEER population-based study.

BACKGROUND: Bone is the most common metastasis site of breast cancer. The prognosis of bone metastasis is better than other distant metastases, but patients with skeletal related events (SREs) have a poor quality of life, high healthcare costs and low survival rates. This study aimed to establish an effective nomogram for predicting risk of bone metastasis of breast cancer. METHODS: The nomogram was built on 4,895 adult/female/primary invasive breast cancer patients with complete clinicopathologic information, captured by the Surveillance, Epidemiology, and End Results (SEER) database from 2010 to 2015. Five biological factors (age, grade, histologic type, surgery of breast lesions and subtypes) were assessed with logistic regression to predict the risk of bone metastases. The predictive accuracy and discriminative ability of the nomogram were determined by the Receiver Operating Characteristic (ROC) curves and the calibration plot. Results were validated on a separate 2,093 cohort using bootstrap resampling from 2010 to 2015 as an internal group and a retrospective study on 120 patients in the First Affiliated Hospital of China Medical University from 2010 to 2014 at the same situation as an external group. RESULTS: On multivariate logistic regression of the primary cohort, independent factors for bone metastases were age, grade, histologic type, surgery of breast lesions and subtypes, which were all selected into the nomogram. The calibration plot for probability of incidence showed good agreement between prediction by nomogram and two observations. The ROC curves presented a good statistical model for risk of bone metastasis, and the corresponding AUC value of the development group, internal validation group and external validation group were 0.678, 0.689 and 0.704 respectively. CONCLUSIONS: The proposed nomogram resulted in more-accurate prognostic prediction for breast cancer patients with bone metastases.