Mining the Roles of Cucumber DUF966 Genes in Fruit Development and Stress Response

Identification of the SbDUF966 Gene Family in Sorghum and Investigation of It Role in Response to Abiotic Stresses

BACKGROUND

Sorghum (Sorghum bicolor L.) is an adversity-tolerant crop, but the function of the DUF966 gene family in its growth, development, and stress tolerance is unclear.

METHODS

The SbDUF966 gene was identified and analyzed using bioinformatics methods in this study. We also analyzed the expression pattern of SbDUF966 in different tissues and stress conditions using RNA-seq and RT-qPCR. We explored its post-transcriptional regulatory mechanism by combining it with miRNA analysis.

RESULTS

A total of six SbDUF966 genes were identified and categorized into two groups (Group I and Group II). Gene expression analysis showed that SbDUF966 exhibited specific expression in different tissues and developmental stages, and the expression response to abiotic stresses such as low temperature, high temperature, salinity, and flooding varied over time. In addition, 12 sorghum miRNAs were predicted as potential regulators of SbDUF966.

CONCLUSIONS

The SbDUF966 gene family likely regulates sorghum's growth, development, and stress tolerance.

Comprehensive analysis of Capsicum annuum CaLhcs uncovered the roles of CaLhca5.1 and CaLhcb1.7 in photosynthesis and stress tolerance

The light-harvesting chlorophyll a/b-binding proteins (Lhcs) are integral to plants' capture and transfer of light energy during photosynthesis. However, the Lhc gene family remains unexplored in pepper. In this study, 37 CaLhcs (Capsicum annuum Lhc) were identified from the reference genome and classified into five subfamilies (Lhca, Lhcb, CP24, CP26, and CP29) based on phylogenetic relationships and conserved domains, with members of each subfamily displaying similar conserved motifs and gene structures. Cis-element analysis revealed an enrichment of light-responsive elements within CaLhcs (46.1%). Transcriptome analysis showed that most CaLhcs are specifically expressed in leaves, flowers, and pericarp and are responsive to stressors, including NaCl, cold, heat, H2O2, and d-mannitol. Post-transcriptional regulation analysis identified 11 miRNAs that target nine CaLhcs through cleavage. RT-qPCR analysis validated the involvement of CaLhcs in response to NaCl stress. Localization studies confirmed that CaLhca4.1, CaLhcb1.1, CaLhca1.7, CaLhcb1.11, and CaLhcb6.1 are chloroplast-localized, whereas CaLhca5.1 localizes in the nucleus. Overexpression of CaLhcb1.7 and CaLhca5.1 increased chlorophyll content and net photosynthetic rate, enhancing photosynthesis. Additionally, CaLhcb1.7 and CaLhca5.1 reduced ROS accumulation, bolstering the plant's resistance to pathogens and salt stress. These findings provide a foundation for further exploration of CaLhcs in photosynthesis and stress tolerance mechanisms.

Insights into cucumber (Cucumis sativus) genetics: Genome-wide discovery and computational analysis of the Calreticulin Domain-Encoding gene (CDEG) family

Cucumber is an essential vegetable crop throughout the world. Cucumber development is vital for accomplishing both quality and productivity requirements. Meanwhile, numerous factors have resulted in substantial cucumber losses. However, the calreticulin domain-encoding genes (CDEGs) in cucumber were not well-characterized and had little function. In the genome-wide association study (GWAS), we recognized and characterized the CDEGs in Cucumis sativus (cucumber). Through a comprehensive study of C. sativus, our research has unveiled the presence of three unique genes, denoted as CsCRTb, CsCRT3, and CsCNX1, unevenly distributed on three chromosomes in the genome of C. sativus. In accordance to the phylogenetic investigation, these genes may be categorized into three subfamilies. Based on the resemblance with AtCDE genes, we reorganized the all CsCDE genes in accordance with international nomenclature. The expression analysis and cis-acting components revealed that each of CsCDE gene promoter region enclosed number of cis-elements connected with hormone and stress response. According to subcellular localization studies demonstrated that, they were found in deferent locations of the cell such as endoplasmic reticulum, plasma membrane, golgi apparatus, and vacuole, according to subcellular localization studies. Chromosomal distribution analysis and synteny analysis demonstrated the probability of segmental or tandem duplications within the cucumber CDEG gene family. Additionally, miRNAs displayed diverse modes of action, including mRNA cleavage and translational inhibition. We used the RNA seq data to analyze the expression of CDEG genes in response to cold stress and also improved cold tolerance, which was brought on by treating cucumber plants to an exogenous chitosan oligosaccharide spray. Our investigation revealed that these genes responded to this stress in a variety of ways, demonstrating that they may adapt quickly to environmental changes in cucumber plants. This study provides a base for further understanding in reference to CDE gene family and reveals that genes play significant functions in cucumber stress responses.

Double roles of light-harvesting chlorophyll a/b binding protein TaLhc2 in wheat stress tolerance and photosynthesis

Light-harvesting chlorophyll a/b binding proteins are encoded by nucleus genes and widely involve in capturing light energy, transferring energy, and responding to various stresses. However, their roles in wheat photosynthesis and stress tolerance are largely unknown. Here, Triticum aestivumlight-harvesting chlorophyll a/b binding protein TaLhc2 was identified. It showed subcellular localization in chloroplast, contained light responsive cis-elements, and highly expressed in green tissues and down-regulated by multiple stresses. TaLhc2 promoted the colonization of hemi-biotrophic pathogen; further analysis showed that TaLhc2 strengthened BAX-induced cell death, enhanced the ROS accumulation, and up-regulated pathogenesis-related genes; those results suggested that TaLhc2 has adverse influence on host immunity and function as a susceptible gene, thus host decreased its expression when faced with pathogen infection. RT-qPCR results showed that TaLhc2 was down-regulated by drought and salt stresses, while TaLhc2 improved the ROS accumulation under the two stresses, suggesting TaLhc2 may participate in wheat responding to abiotic stress. Additionally, TaLhc2 can increase the content of total chlorophyll and carotenoid by 1.3 % and 2.9 %, increase the net photosynthetic rate by 18 %, thus promote plant photosynthesis. Conclusively, we preliminarily deciphered the function of TaLhc2 in biotic/abiotic stresses and photosynthesis, which laid foundation for its usage in wheat breeding.

Genome-Wide Identification, Characterization and Expression Analysis of the TaDUF724 Gene Family in Wheat (Triticum aestivum)

Unknown functional domain (DUF) proteins constitute a large number of functionally uncharacterized protein families in eukaryotes. DUF724s play crucial roles in plants. However, the insight understanding of wheat TaDUF724s is currently lacking. To explore the possible function of TaDUF724s in wheat growth and development and stress response, the family members were systematically identified and characterized. In total, 14 TaDUF724s were detected from a wheat reference genome; they are unevenly distributed across the 11 chromosomes, and, according to chromosome location, they were named TaDUF724-1 to TaDUF724-14. Evolution analysis revealed that TaDUF724s were under negative selection, and fragment replication was the main reason for family expansion. All TaDUF724s are unstable proteins; most TaDUF724s are acidic and hydrophilic. They were predicted to be located in the nucleus and chloroplast. The promoter regions of TaDUF724s were enriched with the cis-elements functionally associated with growth and development, as well as being hormone-responsive. Expression profiling showed that TaDUF724-9 was highly expressed in seedings, roots, leaves, stems, spikes and grains, and strongly expressed throughout the whole growth period. The 12 TaDUF724 were post-transcription regulated by 12 wheat MicroRNA (miRNA) through cleavage and translation. RT-qPCR showed that six TaDUF724s were regulated by biological and abiotic stresses. Conclusively, TaDUF724s were systematically analyzed using bioinformatics methods, which laid a theoretical foundation for clarifying the function of TaDUF724s in wheat.