The powerful Solanaceae: Food and nutraceutical applications in a sustainable world

Vegetable and fruit wastes: Valuable source for organic fertilizer for effective growth of short-term crops: Solanum lycopersicum and Capsicum annum

Agriculture plays a vital role in the food security and economies of Asian countries. Annually, numerous metric tons of vegetable and fruit wastes are disposed of. This research aimed to convert the food wastes encompassing the vegetable and fruit wastes into solid and liquid organic fertilizer and to evaluate their influence on the growth (germination, phytochemicals, and biomolecules) of Solanum lycopersicum and Capsicum annum. Solanum lycopersicum, known as tomato, and Capsicum annum, known as bell pepper or chili pepper, are globally significant crops valued for their medicinal properties and economic importance. The pot experiment was performed with organic fertilizers (solid and liquid organic fertilizer) and compared with the influence of chemical fertilizer and control soil without fertilizers. Interestingly, the liquid organic fertilizer effectively enhanced the biometric profile and chlorophyll content of S. lycopersicum and C. annum Viz., 1.23 mg g-1 and 0.89 mg g-1, respectively. The results of a 30-days pot experiment with various fertilizer treatments showed significant influence of liquid organic fertilizer on the fresh and dry weight biomass of both S. lycopersicum and C. annum. Subsequently, the solid organic fertilizer showed considerable influence on test crops, and the influence of these organic fertilizers was more significant than the chemical fertilizer on crop growth in 30-days experiment. These results suggest that the sustainable approach can effectively convert vegetables and fruit waste into valuable organic fertilizer enriched with plant growth supporting essential nutritional elements.

Genome-wide identification and characterization of SPXdomain-containing genes family in eggplant

Phosphorus is one of the lowest elements absorbed and utilized by plants in the soil. SPX domain-containing genes family play an important role in plant response to phosphate deficiency signaling pathway, and related to seed development, disease resistance, absorption and transport of other nutrients. However, there are no reports on the mechanism of SPX domain-containing genes in response to phosphorus deficiency in eggplant. In this study, the whole genome identification and functional analysis of SPX domain-containing genes family in eggplant were carried out. Sixteen eggplant SPX domain-containing genes were identified and divided into four categories. Subcellular localization showed that these proteins were located in different cell compartments, including nucleus and membrane system. The expression patterns of these genes in different tissues as well as under phosphate deficiency with auxin were explored. The results showed that SmSPX1, SmSPX5 and SmSPX12 were highest expressed in roots. SmSPX1, SmSPX4, SmSPX5 and SmSPX14 were significantly induced by phosphate deficiency and may be the key candidate genes in response to phosphate starvation in eggplant. Among them, SmSPX1 and SmSPX5 can be induced by auxin under phosphate deficiency. In conclusion, our study preliminary identified the SPX domain genes in eggplant, and the relationship between SPX domain-containing genes and auxin was first analyzed in response to phosphate deficiency, which will provide theoretical basis for improving the absorption of phosphorus in eggplants through molecular breeding technology.

Chromosome-scale assembly and gene editing of Solanum americanum genome reveals the basis for thermotolerance and fruit anthocyanin composition

Solanum americanum serves as a promising source of resistance genes against potato late blight and is considered as a leafy vegetable for complementary food and nutrition. The limited availability of high-quality genome assemblies and gene annotations has hindered the exploration and exploitation of stress-resistance genes in S. americanum. Here, we present a chromosome-level genome assembly of a thermotolerant S. americanum ecotype and identify a crucial heat-inducible transcription factor gene, SaHSF17, essential for heat tolerance. The CRISPR/Cas9 system-mediated knockout of SaHSF17 results in remarkably reduced thermotolerance in S. americanum, exhibiting a significant suppression of multiple HSP gene expressions under heat treatment. Furthermore, our transcriptome analysis and anthocyanin component investigation of fruits indicated that delphinidins are the major anthocyanins accumulated in the mature dark-purple fruits. The accumulation of delphinidins and other pigment components during fruit ripening in S. americanum coincides with the transcriptional regulation of key genes, particularly the F3'5'H and F3'H genes, in the anthocyanin biosynthesis pathway. By integrating existing knowledge, the development of this high-quality reference genome for S. americanum will facilitate the identification and utilization of novel abiotic and biotic stress-resistance genes for improvement of Solanaceae and other crops.

Carboxypeptidase inhibitors from Solanaceae as a new subclass of pathogenesis related peptide aiming biotechnological targets for plant defense

Background: Plant protease inhibitors play a crucial role in inhibiting proteases produced by phytopathogens and exhibiting inhibitory effects on nematodes, fungi, and insects, making them promising candidates for crop protection. Specifically, carboxypeptidase inhibitors, a subset of proteinase inhibitors, have been extensively studied in potato and tomato of Solanaceae plant family. However, further research is needed to fully understand the functions and biotechnological potential of those inhibitors in plants. This work aimed to in silico characterize carboxypeptidase inhibitors from Solanaceae as potential antimicrobial and defense agents focused on biotechnological targets. Methods: The methodology employed involved search in UniProt, PDB, KNOTTIN, NCBI, and MEROPS databases for solanaceous carboxypeptidase inhibitors, phylogenetic relationships and conservation patterns analyzes using MEGA-X software and Clustal Omega/MView tools, physicochemical properties and antimicrobial potential prediction using ProtParam, ToxinPred, iAMPred, and APD3 tools, and structural features prediction using PSIPRED. Results and discussion: A systematic literature search was conducted to identify relevant studies on Solanaceae carboxypeptidase inhibitors and their activities against pathogens. The selected studies were reviewed and the main findings compiled. The characterization of Solanaceae carboxypeptidase inhibitors proposed for the first time the global sequence consensus motif CXXXCXXXXDCXXXXXCXXC, shedding light on carboxypeptidase inhibitors distribution, sequence variability, and conservation patterns. Phylogenetic analysis showed evolutionary relationships within the Solanaceae family, particularly in Capsicum, Nicotiana, and Solanum genera. Physicochemical characteristics of those peptides indicated their similarity to antimicrobial peptides. Predicted secondary structures exhibited variations, suggesting a broad spectrum of action, and studies had been demonstrated their activities against various pathogens. Conclusion: Carboxypeptidase inhibitors are being proposed here as a new subclass of PR-6 pathogenesis-related proteins, which will aid in a focused understanding of their functional roles in plant defense mechanisms. These findings confirm the Solanaceae carboxypeptidase inhibitors potential as defense agents and highlight opportunities for their biotechnological applications in pathogen control.

Systematic Investigation of TCP Gene Family: Genome-Wide Identification and Light-Regulated Gene Expression Analysis in Pepino (Solanum Muricatum)

Plant-specific transcription factors such as the TCP family play crucial roles in light responses and lateral branching. The commercial development of S. muricatum has been influenced by the ease with which its lateral branches can be germinated, especially under greenhouse cultivation during the winter with supplemented LED light. The present study examined the TCP family genes in S. muricatum using bioinformatics analysis (whole-genome sequencing and RNA-seq) to explore the response of this family to different light treatments. Forty-one TCP genes were identified through a genome-wide search; phylogenetic analysis revealed that the CYC/TB1, CIN and Class I subclusters contained 16 SmTCP, 11 SmTCP and 14 SmTCP proteins, respectively. Structural and conserved sequence analysis of SmTCPs indicated that the motifs in the same subcluster were highly similar in structure and the gene structure of SmTCPs was simpler than that in Arabidopsis thaliana; 40 of the 41 SmTCPs were localized to 12 chromosomes. In S. muricatum, 17 tandem repeat sequences and 17 pairs of SmTCP genes were found. We identified eight TCPs that were significantly differentially expressed (DETCPs) under blue light (B) and red light (R), using RNA-seq. The regulatory network of eight DETCPs was preliminarily constructed. All three subclusters responded to red and blue light treatment. To explore the implications of regulatory TCPs in different light treatments for each species, the TCP regulatory gene networks and GO annotations for A. thaliana and S. muricatum were compared. The regulatory mechanisms suggest that the signaling pathways downstream of the TCPs may be partially conserved between the two species. In addition to the response to light, functional regulation was mostly enriched with auxin response, hypocotyl elongation, and lateral branch genesis. In summary, our findings provide a basis for further analysis of the TCP gene family in other crops and broaden the functional insights into TCP genes regarding light responses.

Genome-Wide Analysis of the Mads-Box Transcription Factor Family in Solanum melongena

The MADS-box transcription factors are known to be involved in several aspects of plant growth and development, especially in floral organ specification. However, little is known in eggplant. Here, 120 eggplant MADS-box genes were identified and categorized into type II (MIKCC and MIKC*) and type I (Mα, Mβ, and Mγ) subfamilies based on phylogenetic relationships. The exon number in type II SmMADS-box genes was greater than that in type I SmMADS-box genes, and the K-box domain was unique to type II MADS-box TFs. Gene duplication analysis revealed that segmental duplications were the sole contributor to the expansion of type II genes. Cis-elements of MYB binding sites related to flavonoid biosynthesis were identified in three SmMADS-box promoters. Flower tissue-specific expression profiles showed that 46, 44, 38, and 40 MADS-box genes were expressed in the stamens, stigmas, petals, and pedicels, respectively. In the flowers of SmMYB113-overexpression transgenic plants, the expression levels of 3 SmMADS-box genes were co-regulated in different tissues with the same pattern. Correlation and protein interaction predictive analysis revealed six SmMADS-box genes that might be involved in the SmMYB113-regulated anthocyanin biosynthesis pathway. This study will aid future studies aimed at functionally characterizing important members of the MADS-box gene family.