Evolution of cytosolic and organellar invertases empowered the colonization and thriving of land plants.

The molecular innovation underpinning efficient carbon and energy metabolism during evolution of land plants remains largely unknown. Invertase-mediated sucrose cleavage into hexoses is central to fuel growth. Why some cytoplasmic invertases (CINs) function in the cytosol, whereas others operate in chloroplasts and mitochondria, is puzzling. We attempted to shed light on this question from an evolutionary perspective. Our analyses indicated that plant CINs originated from a putatively orthologous ancestral gene in cyanobacteria and formed the plastidic CIN (α1 clade) through endosymbiotic gene transfer, while its duplication in algae with a loss of its signal peptide produced the ß clade CINs in the cytosol. The mitochondrial CINs (α2) were derived from duplication of the plastidic CINs and coevolved with vascular plants. Importantly, the copy number of mitochondrial and plastidic CINs increased upon the emergence of seed plants, corresponding with the rise of respiratory, photosynthetic, and growth rates. The cytosolic CIN (ß subfamily) kept expanding from algae to gymnosperm, indicating its role in supporting the increase in carbon use efficiency during evolution. Affinity purification mass spectrometry identified a cohort of proteins interacting with α1 and 2 CINs, which points to their roles in plastid and mitochondrial glycolysis, oxidative stress tolerance, and the maintenance of subcellular sugar homeostasis. Collectively, the findings indicate evolutionary roles of α1 and α2 CINs in chloroplasts and mitochondria for achieving high photosynthetic and respiratory rates, respectively, which, together with the expanding of cytosolic CINs, likely underpin the colonization of land plants through fueling rapid growth and biomass production.

Molecular Evolution and Functional Divergence of Stress-Responsive Cu/Zn Superoxide Dismutases in Plants.

Superoxide dismutases (SODs), a family of antioxidant enzymes, are the first line of defense against oxidative damage and are ubiquitous in every cell of all plant types. The Cu/Zn SOD, one of three types of SODs present in plant species, is involved in many of the biological functions of plants in response to abiotic and biotic stresses. Here, we carried out a comprehensive analysis of the Cu/Zn SOD gene family in different plant species, ranging from lower plants to higher plants, and further investigated their organization, sequence features, and expression patterns in response to biotic and abiotic stresses. Our results show that plant Cu/Zn SODs can be divided into two subfamilies (group I and group II). Group II appeared to be conserved only as single- or low-copy genes in all lineages, whereas group I genes underwent at least two duplication events, resulting in multiple gene copies and forming three different subgroups (group Ia, group Ib, and group Ic). We also found that, among these genes, two important events-the loss of introns and the loss of and variation in signal peptides-occurred over the long course of their evolution, indicating that they were involved in shifts in subcellular localization from the chloroplast to cytosol or peroxisome and underwent functional divergence. In addition, expression patterns of Cu/Zn SOD genes from Arabidopsis thaliana and Solanum lycopersicum were tested in different tissues/organs and developmental stages and under different abiotic stresses. The results indicate that the Cu/Zn SOD gene family possesses potential functional divergence and may play vital roles in ROS scavenging in response to various stresses in plants. This study will help establish a foundation for further understanding these genes' function during stress responses.

The SlWRKY81 transcription factor inhibits stomatal closure by attenuating nitric oxide accumulation in the guard cells of tomato under drought.

The WRKY transcription factors (TFs) play multifaceted roles in plant growth, development, and stress response. Previously, we found that SlWRKY81 negatively regulates tomato tolerance to drought; however, the mechanisms of stomatal regulation in response to drought remain largely unclear. Here, we showed that drought-induced upregulation in the SlWRKY81 transcripts induced photoinhibition and reduced the net photosynthetic rate in tomato leaves. However, silencing SlWRKY81 alleviated those inhibitions and minimized the drought-induced damage. A time-course of water loss showed that SlWRKY81 silencing significantly and consistently reduced leaf water loss, suggesting a role for SlWRKY81 in stomatal movement. Further analysis using light microscopy revealed that SlWRKY81 silencing significantly decreased stomatal aperture and increased the ratio of length to width of stomata under drought. Both biochemical assay and confocal laser scanning microscopy demonstrated that drought-induced upregulation in SlWRKY81 expression inhibited the nitric oxide (NO) accumulation in the guard cells, which was attributed to the simultaneous declines in the activity of nitrate reductase (NR) and NR expression in tomato leaves. The inspection of 3-kb sequences upstream of the predicted transcriptional start site of the NR identified three copies of the core W-box (TTGACC/T) sequence in the promoter region, indicating possible targets of SlWRKY81. Taken together, these data suggest that SlWRKY81 potentially represses NR transcription and thus reduces NO accumulation to attenuate stomatal closure and subsequent drought tolerance. These findings provide an improved understanding of the mechanism of WRKY-induced regulation of stomatal closure, which can be exploited in the future to enhance drought tolerance in crops.

Genetic Diversity and Identification of Wilt and Root Rot Pathogens of Tomato in China.

Fungal wilt and root rot diseases affecting tomato have become prevalent in China in recent years and have caused considerable damage. In 2016 to 2018, symptoms of putative wilt and root rot diseases were observed in several locations in tomato cultivars with resistance to Fusarium oxysporum f. sp. lycopersici races 1 and 2. The objective of this study was to identify the causative agents of wilt and root rot of tomato in China and provide a basis for disease prevention and resistance breeding programs. Based on DNA sequence analyses of the internal transcribed spacer (ITS) region, 91 isolates from the roots of tomato plants showing symptoms of wilt and root rot were identified, including F. oxysporum (64 isolates), Fusarium solani (11 isolates), Fusarium proliferatum (2 isolates), Fusarium graminearum (2 isolates), Fusarium equiseti (1 isolate), Pythium aphanidermatum (6 isolates), Ascomycota sp. (2 isolates), and Plectosphaerella cucumerina (3 isolates). F. oxysporum accounted for 70.33% of the isolates obtained. In this case, using PCR-based methods for differentiation of F. oxysporum, we identified several formae speciales and races of F. oxysporum: 7 isolates were identified as F. oxysporum f. sp. lycopersici race 1, 2 isolates as F. oxysporum f. sp. lycopersici race 2, 35 isolates as F. oxysporum f. sp. lycopersici race 3, and 13 isolates as F. oxysporum f. sp. radicis-lycopersici. Pathogenicity tests revealed 55 isolates of tomato wilt and root rot pathogens to be virulent. This study demonstrated that F. oxysporum f. sp. lycopersici race 3 was the most widespread and highly virulent race among these tomato pathogens in China, followed by F. oxysporum f. sp. radicis-lycopersici. Therefore, the development of resistant varieties of tomato against F. oxysporum f. sp. lycopersici race 3 and F. oxysporum f. sp. radicis-lycopersici would aid efforts to develop effective disease management strategies.

The Tryptophan Decarboxylase in Solanum lycopersicum.

Melatonin plays an important role in plant growth, development, and environmental stress. In this study, a systematic analysis of tomato tryptophan decarboxylase (SlTrpDC), which is the first enzyme of melatonin biosynthesis, was conducted by integrating structural features, phylogenetic relationships, an exon/intron feature, and a divergent expression profile. The results determined that the tomato genome encoded five members (SlTrpDC1-SlTrpDC5). The phylogenetic relationships indicated that gene expansion was proposed as the major mode of evolution of the TrpDC genes from the different plant algae species to the higher plants species. The analyses of the exon/intron configurations revealed that the intron loss events occurred during the structural evolution of the TrpDCs in plants. Additionally, the RNA-seq and qRT-PCR analysis revealed that the expression of the SlTrpDC3 was high in all of the tested tissues, while the SlTrpDC4 and SlTrpDC5 were not expressed. The expression patterns of the remaining two (SlTrpDC1 and SlTrpDC2) were tissue-specific, which indicated that these genes may play important roles within the different tissues. No expression difference was observed in the tomato plants in response to the biotic stresses. This study will expand the current knowledge of the roles of the TrpDC genes in tomato growth and development.

Upregulation of the long non-coding RNA PlncRNA-1 promotes esophageal squamous carcinoma cell proliferation and correlates with advanced clinical stage.

BACKGROUND: Recent studies revealed that long noncoding RNAs (lncRNAs) play critical regulatory roles in cancer biology. PlncRNA-1 is one of lncRNAs that is associated with cell apoptosis and proliferation of prostate cancer. AIM: This study aimed to assess the potential role of PlncRNA-1 in the pathogenesis of esophageal squamous cell carcinoma (ESCC). MATERIALS AND METHODS: Quantitative real-time polymerase chain reaction (qRT-PCR) was used to detect the expression level of PlncRNA-1 in 73 pairs of ESCC and their matched normal tissues. The correlation of PlncRNA-1 with clinicopathological features and clinical stages was also analyzed. Cancer cell proliferation and apoptosis were assessed following knock-down of PlncRNA-1 by MTT, colony formation assay, and flow cytometry. RESULTS: The expression of PlncRNA-1 was significantly higher in human ESCC compared with the adjacent noncancerous tissues (69.8 %, p < 0.05), and the high level of PlncRNA-1 expression was significantly correlated with advanced clinical stage (p < 0.01) and lymph node metastasis (p < 0.05). Furthermore, knockdown of PlncRNA-1 reduced cell proliferation and increased the apoptosis in vitro. CONCLUSIONS: PlncRNA-1 plays an important role in ESCC cell proliferation. Overexpression of PlncRNA-1 is correlated with advanced tumor stage and lymph node metastasis, and may serve as a potential prognostic marker and therapeutic target for ESCC.

[Genome-wide identification and analysis of heat shock protein 90 in tomato].

Heat shock proteins 90 (Hsp90) are a kind of specific proteins in plant which were produced under environmental stresses. By referring to the tomato genome database, we identified and analyzed Hsp90 gene family members using bioinformatics methods. Results indicated that the tomato genome contained at least 7 Hsp90 genes, which were distributed unevenly on 6 chromosomes. Amino acid sequence length of these proteins ranged from 267 to 794aa. Numbers of intron ranged from 2 to 19. Microsynteny analysis showed that two pairs of Hsp90 genes (Hsp90-1and Hsp90-3, Hsp90-5 and Hsp90-7) were identified by segment duplication. In addition, multiple conservation motifs were found in Hsp90 proteins. Phylogenetic analysis revealed that Hsp90 genes from tomato, rice and Arabidopsis can be divided into 5 groups. Three pair of orthologous genes and four pairs of homologous genes were found. Expression analysis based on RNA-seq showed that the expression of three genes (Hsp90-5, Hsp90-6 and Hsp90-7) was high in vegetable and reproductive organs, while the expression of other four genes (Hsp90-1, Hsp90-2, Hsp90-3 and Hsp90-4) was relatively low except for its expression at the breaking stage of fruit. Analysis of promoter regions of Hsp90 genes showed that multiple cis-elements were involved in plant responses to biotic and abiotic stresses. The expression of 7 genes under heat stress was also detected by qRT-PCR. Expression of all Hsp90 genes in tomato leaf was enhanced. The results indicated that these genes could be participated in tomato leaf response to heat stresses. Together, these results will lay a foundation for analyzing Hsp90 gene function and molecular evolution in the future.

Detection and Analysis of VOCs in Cherry Tomato Based on GC-MS and GC×GC-TOF MS Techniques.

Volatile organic compounds (VOCs) play a significant role in influencing the flavor quality of cherry tomatoes (Solanum lycopersicum var. cerasiforme). The scarcity of systematic analysis of VOCs in cherry tomatoes can be attributed to the constraints imposed by detection technology and other contributing factors. In this study, the cherry tomato cultivar var. 'Zheyingfen1' was chosen due to its abundant fruit flavor. Two detection technology platforms, namely the commonly employed headspace solid-phase microextraction-gas chromatography-mass spectrometry (HS-SPME-GC-MS) and the most advanced headspace solid-phase microextraction-full two-dimensional gas chromatography-time-of-flight mass spectrometry (HS-SPME-GC×GC-TOFMS), were employed in the analysis. The VOCs of cherry tomato cultivar var. 'Zheyingfen1' fruits at red ripening stage were detected. A combined total of 1544 VOCs were detected using the two aforementioned techniques. Specifically, 663 VOCs were identified by through the HS-SPME-GC-MS method, 1026 VOCs were identified by through the HS-SPME-GC×GC-TOFMS, and 145 VOCs were identified by both techniques. The identification of ß-ionone and (E)-2-nonenal as the principal VOCs was substantiated through the application of the relative odor activity value (rOAV) calculation and subsequent analysis. Based on the varying contribution rates of rOAV, the analysis of sensory flavor characteristics revealed that cherry tomato cultivar var. 'Zheyingfen1' predominantly exhibited green and fatty attributes, accompanied by elements of fresh and floral flavor characteristics. In conclusion, our study conducted a comprehensive comparison of the disparities between these two methodologies in detecting VOCs in cherry tomato fruits. Additionally, we systematically analyzed the VOC composition and sensory flavor attributes of the cherry tomato cultivar var. 'Zheyingfen1'. This research serves as a significant point of reference for investigating the regulatory mechanisms underlying the development of volatile flavor quality in cherry tomatoes.

Upregulation of the long non-coding RNA HOTAIR promotes esophageal squamous cell carcinoma metastasis and poor prognosis.

Recent studies of the individual functionalities of long non-coding RNAs (lncRNAs) in the development and progression of cancer have suggested that HOX transcript antisense RNA (HOTAIR) is capable of reprogramming chromatin organization and promoting cancer cell metastasis. In order to ascertain the expression pattern of the lncRNA HOTAIR and assess its biological role in the development and progression of esophageal squamous cell carcinoma (ESCC), HOTAIR expression in ESCC tissues and adjacent noncancerous tissues were collected from 78 patients and measured by real-time reverse transcription-polymerase chain reaction (RT-PCR). HOTAIR correlation with clinicopathological features and prognosis was also analyzed. Suppression of HOTAIR using siRNA treatment was performed in order to explore its role in tumor progression. Notably elevated HOTAIR expression levels were observed in cancerous tissues compared to adjacent noncancerous tissues (96%, P < 0.01), showing a high correlation with cancer metastasis (P < 0.01), elevated TNM (2009) stage classification (P < 0.01), and lowered overall survival rates (P = 0.003). Multivariate analysis revealed that HOTAIR expression (P = 0.003) is also an independent prognostic factor for comparison of TNM stage (P = 0.024) and lymph node metastasis (P = 0.010). Furthermore, in vitro assays of the ESCC cell line KYSE30 demonstrated that knockdown of HOTAIR reduced cell invasiveness and migration while increasing the response of cells to apoptosis. Thus, HOTAIR is a novel molecule involved in both ESCC progression and prognosis. Full elucidation of HOTAIR functionality relevant to ESCC may open avenues for the use of lncRNAs in identification of novel drug targets and therapies for ESCC and other prevalent cancers.

Effects of Storage Temperature at the Early Postharvest Stage on the Firmness, Bioactive Substances, and Amino Acid Compositions of Chili Pepper (Capsicum annuum L.).

The commercial and nutritional quality of chili peppers deteriorates rapidly after harvest. So far, little is known about the effect of temperature on postharvest chili pepper quality. This study elucidated the effects of two temperatures (20 °C and 30 °C) on chili peppers' postharvest firmness, flavor, and nutritional attributes. We found that compared to 20 °C, 30 °C escalated the decline in fruit firmness, capsaicin content, and dihydrocapsaicin content, while enhancing the increment in water loss and electrical conductivity, as well as total carotenoids and ascorbic acid content. The contents of most amino acids (AAs) decreased significantly during postharvest storage compared to their initial values, whether stored at 20 °C or 30 °C; however, 30 °C had a more substantial impact than 20 °C. Meanwhile, as for soluble protein and amino acid compositions, the effect of storage temperature was genotype-dependent, as reflected by differential changes in total AA contents, single AA contents, essential AA ratio, delicious AA ratio, etc., under the 20 °C or 30 °C treatments. In conclusion, our findings reveal the influence of temperature on pepper quality, showing that the storage temperature of 20 °C was better for maintaining chili quality than 30 °C from the perspective of overall commercial attributes.

Comprehensive identification of glutathione peroxidase (GPX) gene family in response to abiotic stress in pepper (Capsicum annuum L.).

Plant glutathione peroxidase (GPX) plays an important role in the maintenance of cell homeostasis and in the antioxidant response in plants. In this study, the peroxidase (GPX) gene family was identified in the whole genome of pepper using bioinformatic method. As a result, a total of 5 CaGPX genes were identified, which were unevenly distributed on 3 of the 12 chromosomes of pepper genome. Based on phylogenetic analysis, 90 GPX genes in 17 species from lower plants to higher plants can be divided into 4 groups (GroupⅠ, Group Ⅱ, Group Ⅲ, Group Ⅳ). The MEME Suite analysis of GPX proteins shows that all these proteins contain four highly conserved motifs, as well as other conserved sequences and amino acid residues. Gene structure analysis revealed the conservative exon-intron organization pattern of these genes. In the promoter region of CaGPX genes, many cis elements of plant hormone and abiotic stress response were identified in each of CaGPX proteins. In addition, expression patterns of CaGPX genes in different tissues, developmental stages and responses to abiotic stress were also performed. The results of qRT-PCR showed that the transcripts of CaGPX genes varied greatly under abiotic stress at different time points. There results suggest that the GPX gene family of pepper may play a role in plant development andstress response. In conclusion, our research provides new insights into the evolution of pepper GPX gene family, and understanding for functional of these genes in response to abiotic stresses.

Divergent Retention of Sucrose Metabolism Genes after Whole Genome Triplication in the Tomato (Solanum lycopersicum).

Sucrose, the primary carbon transport mode and vital carbohydrate for higher plants, significantly impacts plant growth, development, yield, and quality formation. Its metabolism involves three key steps: synthesis, transport, and degradation. Two genome triplication events have occurred in Solanaceae, which have resulted in massive gene loss. In this study, a total of 48 and 65 genes from seven sucrose metabolism gene families in Vitis vinifera and Solanum lycopersicum were identified, respectively. The number of members comprising the different gene families varied widely. And there were significant variations in the pattern of gene duplication and loss in the tomato following two WGD events. Tandem duplication is a major factor in the expansion of the SWEET and Acid INV gene families. All the genes are irregularly distributed on the chromosomes, with the majority of the genes showing collinearity with the grape, particularly the CIN family. And the seven gene families were subjected to a purifying selection. The expression patterns of the different gene families exhibited notable variations. This study presents basic information about the sucrose metabolism genes in the tomato and grape, and paves the way for further investigations into the impact of SCT events on the phylogeny, gene retention duplication, and function of sucrose metabolism gene families in the tomato or Solanaceae, and the adaptive evolution of the tomato.

Analysis of TIR- and non-TIR-NBS-LRR disease resistance gene analogous in pepper: characterization, genetic variation, functional divergence and expression patterns.

BACKGROUND: Pepper (Capsicum annuum L.) is one of the most important vegetable crops worldwide. However, its yield and fruit quality can be severely threatened by several pathogens. The plant nucleotide-binding site (NBS)-leucine-rich repeat (LRR) gene family is the largest class of known disease resistance genes (R genes) effective against such pathogens. Therefore, the isolation and identification of such R gene homologues from pepper will provide a critical foundation for improving disease resistance breeding programs. RESULTS: A total of 78 R gene analogues (CaRGAs) were identified in pepper by degenerate PCR amplification and database mining. Phylogenetic tree analysis of the deduced amino acid sequences for 51 of these CaRGAs with typically conserved motifs ( P-loop, kinase-2 and GLPL) along with some known R genes from Arabidopsis and tomato grouped these CaRGAs into the non-Toll interleukin-1 receptor (TIR)-NBS-LRR (CaRGAs I to IV) and TIR-NBS-LRR (CaRGAs V to VII) subfamilies. The presence of consensus motifs (i.e. P-loop, kinase-2 and hydrophobic domain) is typical of the non-TIR- and TIR-NBS-LRR gene subfamilies. This finding further supports the view that both subfamilies are widely distributed in dicot species. Functional divergence analysis provided strong statistical evidence of altered selective constraints during protein evolution between the two subfamilies. Thirteen critical amino acid sites involved in this divergence were also identified using DIVERGE version 2 software. Analyses of non-synonymous and synonymous substitutions per site showed that purifying selection can play a critical role in the evolutionary processes of non-TIR- and TIR-NBS-LRR RGAs in pepper. In addition, four specificity-determining positions were predicted to be responsible for functional specificity. qRT-PCR analysis showed that both salicylic and abscisic acids induce the expression of CaRGA genes, suggesting that they may primarily be involved in defence responses by activating signaling pathways. CONCLUSION: The identified CaRGAs are a valuable resource for discovering R genes and developing RGA molecular markers for genetic map construction. They will also be useful for improving disease resistance in pepper. The findings of this study provide a better understanding of the evolutionary mechanisms that drive the functional diversification of non-TIR- and TIR-NBS-LRR R genes in pepper.

The hsa_circ_0007396-miR-767-3p-CHD4 axis is involved in the progression and carcinogenesis of gastric cancer.

Background: Circular RNAs (circRNAs) have been linked to numerous human cancers, including gastric cancer (GC), in numerous recent investigations. The expression of circRNA and the mechanisms involved in GC are still unknown. Methods: In this work, Gene Expression Omnibus 2R (GEO2R) online tool was first used to screen 6 candidates of differentially expressed circRNAs in 2 datasets, GSE83521 and GSE89143. Then, using Cancer-Specific CircRNA Database (CSCD), the structural loop diagrams of these circRNAs were generated. After combining the Circular RNA Interactome (CRI) and CSCD databases for miRNA co-prediction, a candidate circRNA-miRNA sub-network was successfully created. The expression of these miRNAs was further examined using Cytoscape software, and 2 miRNAs, miR-767-5p and miR-767-3p. Results: We used GEO2R to analyze the differential expression of GSE83521 and GSE89143 datasets in GEO database. Through the construction of the structural ring diagram of CSCD database, we found that hsa_circRNA_100571, hsa_circRNA_103102, hsa_circRNA_100754, hsa_circRNA_100737, hsa_circRNA_100269, hsa_circRNA_102476, hsa_circRNA_101287 is the final candidate circRNA in GC. MiR-767-5p and miR-767-3p were found to be important miRNAs in GC. The miRNet database indicated their downstream target genes. In various studies, namely central gene screening, correlation analysis, and protein-protein interaction (PPI), we detected chromodomain helicase DNA binding protein 4 (CHD4) as a key potential candidate of hsa-mir-767-3p. Next, we conducted validation of clinical data. We included the clinical data of 100 patients with GC, and found that patients with low CHD4 expression had significantly higher OS and PFS than those with high CHD4 expression (P<0.001, P=0.005). Cox regression analysis showed that low CHD4 expression was an independent risk factor for tumor progression (P=0.001). At the same time, tumor differentiation and chemotherapy also had a certain impact on the progression of GC (all P<0.05). Therefore, CHD4 may provide a promising therapeutic target for the future treatment of GC. Conclusions: We identified an important hsa_circ_0007396-miR-767-3p-CHD4 axis, which is associated with GC proliferation and carcinogenesis, and may represent a promising therapeutic target for the future cure of GC.

The PAP Gene Family in Tomato: Comprehensive Comparative Analysis, Phylogenetic Relationships and Expression Profiles.

Purple acid phosphatase (PAP) plays a vital role in plant phosphate acquisition and utilization, as well as cell wall synthesis and redox reactions. In this study, comprehensive comparative analyses of PAP genes were carried out using the integration of phylogeny, chromosomal localization, intron/exon structural characteristics, and expression profiling. It was shown that the number of introns of the PAP genes, which were distributed unevenly on 12 chromosomes, ranged from 1 to 12. These findings pointed to the existence of complex structures. Phylogenetic analyses revealed that PAPs from tomato, rice, and Arabidopsis could be divided into three groups (Groups I, II, and III). It was assumed that the diversity of these PAP genes occurred before the monocot-dicot split. RNA-seq analysis revealed that most of the genes were expressed in all of the tissues analyzed, with the exception of SlPAP02, SlPAP11, and SlPAP14, which were not detected. It was also found that expression levels of most of the SlPAP gene family of members were changed under phosphorus stress conditions, suggesting potential functional diversification. The findings of this work will help us to achieve a better insight into the function of SlPAP genes in the future, as well as enhance our understanding of their evolutionary relationships in plants.

Deep Learning and Hyperspectral Images Based Tomato Soluble Solids Content and Firmness Estimation.

Cherry tomato (Solanum lycopersicum) is popular with consumers over the world due to its special flavor. Soluble solids content (SSC) and firmness are two key metrics for evaluating the product qualities. In this work, we develop non-destructive testing techniques for SSC and fruit firmness based on hyperspectral images and the corresponding deep learning regression model. Hyperspectral reflectance images of over 200 tomato fruits are derived with the spectrum ranging from 400 to 1,000 nm. The acquired hyperspectral images are corrected and the spectral information are extracted. A novel one-dimensional (1D) convolutional ResNet (Con1dResNet) based regression model is proposed and compared with the state of art techniques. Experimental results show that, with a relatively large number of samples our technique is 26.4% better than state of art technique for SSC and 33.7% for firmness. The results of this study indicate the application potential of hyperspectral imaging technique in the SSC and firmness detection, which provides a new option for non-destructive testing of cherry tomato fruit quality in the future.

Post-Harvest LED Light Irradiation Affects Firmness, Bioactive Substances, and Amino Acid Compositions in Chili Pepper (Capsicum annum L.).

Chili pepper is an important vegetable and spice crop with high post-harvest deteriorations in terms of commercial and nutritional quality. Light-emitting diodes (LEDs) are eco-friendly light sources with various light spectra that have been demonstrated to improve the shelf-life of various vegetables by manipulating light quality; however, little is known about their effects on the post-harvest nutritional quality of chili peppers. This study investigated the effects of different LED lightings on the post-harvest firmness and nutritional quality of chili peppers. We found that red and blue light could increase the content of capsaicinoids, whereas white and red light could increase the essential and aromatic amino acid (AA) content in pepper. Nonetheless, the influence of light treatments on AA contents and compositions depends strongly on the pepper genotype, which was reflected by total AA content, single AA content, essential AA ratio, delicious AA ratio, etc., that change under different light treatments. Additionally, light affected fruit firmness and the content of nutrients such as chlorophyll, vitamin C, and total carotenoids, to varying degrees, depending on pepper genotypes. Thus, our findings indicate that LED-light irradiation is an efficient and promising strategy for preserving or improving the post-harvest commercial and nutritional quality of pepper fruit.

Identification of reference genes for reverse transcription quantitative real-time PCR normalization in pepper (Capsicum annuum L.).

Reverse transcription quantitative real-time polymerase chain reaction (qRT-PCR) is a commonly used technology for gene expression and transcriptome analysis. Normalization is a process that is necessary to accurately analyze qRT-PCR data. Stability of reference gene expression is required for this process. Due to the large variation in expression levels of reference genes obtained from different experimental conditions, gene expression stabilities must be evaluated and identified in all experimental systems. In the present paper, the stability of the expression levels of seven potential reference genes in pepper are assessed using qRT-PCR analysis to determine optimal reference genes. These reference genes are evaluated in different pepper tissues, abiotic stress, and hormonal treatment samples. Three common statistical algorithms, geNorm, NormFinder, and BestKeeper, are used to identify expression stability and provide an accurate selection of reference genes. Two reference genes, beta tubulin and ubiquitin-conjugating protein (UBI-3), showed high stability in sample pools with abiotic stress and hormonal treatments. Among the sample pools tested, UBI-3 and glyceraldehyde-3-phosphate dehydrogenase expression levels were the most stable in different tissues. Therefore, these reference genes are selected for qRT-PCR analysis under the experimental conditions tested in pepper. In contrast, ubiquitin-conjugating enzyme and actin genes are identified as the least stable reference genes in all the groups tested, confirming that they are not suitable for normalization. Validation of these candidate genes could provide useful guidelines for reference gene selection in qRT-PCR studies in pepper.

Evolutionary Origin of the Carotenoid Cleavage Oxygenase Family in Plants and Expression of Pepper Genes in Response to Abiotic Stresses.

Plant carotenoid cleavage oxygenase (CCO) is an enzyme that catalyzes the synthesis of carotenoids and participates in many important physiological functions. The plant CCOs exist in two forms, namely carotenoid cleavage dioxygenase (CCD) and nine-cis epoxide carotenoid dioxygenase (NCED). Although studies have shown that this gene family has been identified in many species, such as Arabidopsis, grape, and tomato, the evolutionary origin of the CCO family and the expression pattern of pepper genes in response to H2O2 and other abiotic stresses are still unclear. In this study, we used the bioinformatics method to identify and analyze the members of the CCO gene family from pepper and other 13 plants from lower to higher plant species based on the whole genome sequence. A total of 158 CCO genes were identified in different plant species and further divided into two groups (e.g., groups I and II). The former was subdivided into CCD7 and CCD8 and have independent evolutionary origins, respectively, while the latter was subdivided into CCD1, CCD4, CCD-like, and NCED, which may have come from a common ancestor. In addition, the results of RNA-seq showed that the expression patterns of pepper CaCCO genes were different in the tissues tested, and only few genes were expressed at high levels such as CaCCD1a, CaCCD4a, CaNCED3, and CaCCD1b. For hydrogen peroxide (H2O2) and other abiotic stresses, such as plant hormones, heat, cold, drought, and NaCl treatments, induction of about half of the CaCCO genes was observed. Moreover, the expression patterns of CaCCOs were further investigated under heat, cold, drought, and NaCl treatments using quantitative real-time PCR (qRT-PCR), and most members were responsive to these stresses, especially some CaCCOs with significant expression changes were identified, such as CaCCD4c, CaCCD-like1, CaCCD8, and CaCCD1b, suggesting the important roles of CaCCOs in abiotic stress responses. All these results will provide a valuable analytical basis for understanding the evolution and functions of the CCO family in plants.

Genomic Organization and Comparative Phylogenic Analysis of NBS-LRR Resistance Gene Family in Solanum pimpinellifolium and Arabidopsis thaliana.

NBS-LRR (nucleotide-binding site and leucine-rich repeat) is one of the largest resistance gene families in plants. The completion of the genome sequencing of wild tomato Solanum pimpinellifolium provided an opportunity to conduct a comprehensive analysis of the NBS-LRR gene superfamily at the genome-wide level. In this study, gene identification, chromosome mapping, and phylogenetic analysis of the NBS-LRR gene family were analyzed using the bioinformatics methods. The results revealed 245 NBS-LRRs in total, similar to that in the cultivated tomato. These genes are unevenly distributed on 12 chromosomes, and ~59.6% of them form gene clusters, most of which are tandem duplications. Phylogenetic analysis divided the NBS-LRRs into 2 subfamilies (CNL-coiled-coil NBS-LRR and TNL-TIR NBS-LRR), and the expansion of the CNL subfamily was more extensive than the TNL subfamily. Novel conserved structures were identified through conserved motif analysis between the CNL and TNL subfamilies. Compared with the NBS-LRR sequences from the model plant Arabidopsis thaliana, wide genetic variation occurred after the divergence of S. pimpinellifolium and A thaliana. Species-specific expansion was also found in the CNL subfamily in S. pimpinellifolium. The results of this study provide the basis for the deeper analysis of NBS-LRR resistance genes and contribute to mapping and isolation of candidate resistance genes in S. pimpinellifolium.