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Key message: Twenty-five VvIAA genes and eighteen VaIAA genes were identified from Pinot Noir and Shanputao, respectively. The overexpression of VaIAA3 in transgenic Arabidopsis increased cold tolerance by regulating auxin, ABA and ethylene signaling. Aux/IAA genes are key genes involved in regulating auxin signal transduction in plants. Although IAA genes have been characterized in various plant species, the role of IAA genes in grape cold resistance is unclear. To further explore the members of the Aux/IAA gene family in grape and their functions, in this study, using genomic data for Pinot Noir (Vitis vinifera cv. ‘Pinot Noir’) and Shanputao (Vitis amurensis), 25 VvIAA genes and 18 VaIAA genes were identified. The VaIAA genes presented different expression patterns at five different temperatures (28 ± 1 °C, 5 ± 1 °C, 0 ± 1 °C, -5 ± 1 °C, and -10 ± 1 °C) according to qRT‑PCR results. VaIAA3 was selected as a candidate gene for further functional analysis because of its high expression level under low-temperature stress. Subcellular localization experiments revealed that VaIAA3 was localized in the nucleus. Additionally, under 4 °C treatment for 24 h, relative expression level of VaIAA3, antioxidant enzyme activity, survival rate, and cold-responsive gene expression in three transgenic lines (OE-1, OE-2, OE-3) were greater, whereas relative electrolytic conductivity (REC), malondialdehyde (MDA) content and hydrogen peroxide (H2O2) content were lower than those of the wild type (WT). Transcriptome sequencing analysis revealed that VaIAA3 regulated cold stress resistance in Arabidopsis thaliana (Arabidopsis) through pathways involving auxin, ABA, JA, or ethylene. Importantly, heterologous overexpression of VaIAA3 increased the resistance of Arabidopsis to cold stress, which provides a theoretical basis for the further use of VaIAA3 to improve cold resistance in grape. [ABSTRACT FROM AUTHOR]

Sugarcane (Saccharum officinarum) is a plant with high economic value because it can produce sugar. Shoot borer Scircophaga excerptalis (Lepidoptera: Pyralidae) and stem borer Chilo sacchariphagus (Lepidoptera: Pyralidae) attacks are one of the issues that limit sugarcane productivity. Establishing transgenic sugarcane is one of the most efficient ways to prevent borer damage. Previously, Cry1Ab and Cry1Ac genes were successfully used to create transgenic sugarcane plants. This study aimed to detect the presence of transgenes and analyze the expression level of the Cry1Ab-Cry1Ac gene fusion in transgenic sugarcane using RT-PCR. The methods used in this study are transgene detection with PCR and gene expression analysis in normalized expression (2-ΔΔCq) with RT-PCR. The Cry1Ab-Cry1Ac gene has been integrated into all lines with varied expression levels. In 311 GV and 333 GV lines, the Cry1Ab-Cry1Ac gene was expressed in the leaf but not in the stem. Shoot and stem borer attack percentage values showed that all lines were lower than the control, with 222 EH as the lowest and 311 GV as the highest. Leaf and stem borer attack levels were compared to gene expression values of Cry1Ab-Cry1Ac. Results may indicate that the 222 EH line was resistant, but the 311 GV and 333 GV lines were not. [ABSTRACT FROM AUTHOR]

Copyright of Acta Prataculturae Sinica is the property of Acta Prataculturae Sinica Editorial Office and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Main conclusion: This study identified 82 wheat BRD genes, revealing both conserved evolutionary and functional characteristics across plant species and novel features specific to wheat. GTE8-12 cluster TaBRDs were found as positive response to salt stress. Bromodomain-containing proteins (BRDs) are crucial in histone acetylation “reading” and chromatin remodeling in eukaryotes. Despite some of their members showing importance in various biological processes in plants, our understanding of the BRD family in wheat (Triticum aestivum) remains limited. This study comprehensively analyzes the T. aestivum BRD (TaBRD) family. We identified 82 TaBRD genes in wheat genome encoding hydrophobic proteins with a conserved pocket structure. Phylogenetic analysis classified these genes into 16 distinct clusters, with conserved protein motifs and gene structures within clusters but diverse patterns across clusters. Gene duplication analysis revealed that whole-genome or segmental duplication events were the primary expansion mechanism for the TaBRD family, with purifying selection acting on these genes. Subcellular localization and Gene Ontology (GO) analyses indicated that TaBRD proteins are predominantly nuclear-localized and involved in transcription regulation and RNA metabolism. Promoter analysis and interaction network prediction suggested diverse regulatory mechanisms for TaBRDs. Notably, TaBRDs from the GTE8-12 cluster were enriched with cis-elements responsive to abscisic acid (ABA), methyl jasmonate (MeJA), and light, implying their involvement in physiological functions and abiotic stress responses. Expression analysis confirmed tissue-specific patterns and responsiveness to salinity stress. This comprehensive study enhances our understanding of the BRD family in higher plants and provides a foundation for developing salt-tolerant wheat varieties. [ABSTRACT FROM AUTHOR]

Introduction: NAC (NAM, ATAF, and CUC) transcription factor family, one of the important switches of transcription networks in plants, functions in plant growth, development, and stress resistance. Night lily (Hemerocallis citrina) is an important horticultural perennial monocot plant that has edible, medicinal, and ornamental values. However, the NAC gene family of night lily has not yet been analyzed systematically to date. Methods: Therefore, we conducted a genome-wide study of the HcNAC gene family and identified a total of 113 HcNAC members from the Hemerocallis citrina genome. Results: We found that 113 HcNAC genes were unevenly distributed on 11 chromosomes. Phylogenetic analysis showed that they could be categorized into 16 instinct subgroups. Proteins clustering together exhibited similar conserved motifs and intron-exon structures. Collinearity analysis indicated that segmental and tandem duplication might contribute to the great expansion of the NAC gene family in night lily, whose relationship was closer with rice than Arabidopsis. Additionally, tissue-specific pattern analysis indicated that most HcNAC genes had relatively higher expression abundances in roots. RNA-Seq along with RT-qPCR results jointly showedHcNACgenesexpresseddifferentlyunder drought andsalinity stresses. Interestingly, HcNAC35 was overexpressed in watermelon, and the stress resilience of transgenic lines was much higher than that of wild-type watermelon, which revealed its wide participation in abiotic stress response. Conclusion: In conclusion, our findings provide a new prospect for investigating the biological roles of NAC genes in night lily. [ABSTRACT FROM AUTHOR]

The WRKY transcription factors are integral to plant biology, serving essential functions in growth, development, stress responses, and the control of secondary metabolism. Through the use of bioinformatics techniques, this research has effectively characterized 207 members of the WRKY family (LaWRKY) present in the entire genome of Lavandula angustifolia. Phylogenetic analysis classified LaWRKYs into three distinct categories based on conserved domains. Collinearity analysis revealed tandem repeats, segmental duplications, and whole genome duplications in LaWRKYs, especially for segmental duplication playing a significant role in gene family expansion. LaWRKYs displayed distinct tissue-specific expression profiles across six different tissues of L. angustifolia. Particularly noteworthy were 12 genes exhibiting high expression in flower buds and calyx, the primary sites of volatile terpenoid production, indicating their potential role in terpenoid biosynthesis in L. angustifolia. RT-qPCR analysis revealed a notable increase in the expression levels of most examined LaWRKY genes in flower buds in response to both intense light and low-temperature conditions, whereas the majority of these genes in leaves were primarily induced by drought stress. However, all genes exhibited downregulation following GA treatment in both flower buds and leaves. Overexpression of LaWRKY57 (La13G01665) and LaWRKY75 (La16G00030) in tobacco led to a reduction in the density of glandular trichomes on leaf surfaces, resulting in changes to the volatile terpenoid composition in the leaves. Specifically, the content of Neophytadiene was significantly elevated compared to wild-type tobacco, while compounds such as eucalyptol, cis-3-Hexenyl isobutyrate, and D-Limonene were produced, which were absent in the wild type. These findings provide a valuable reference for future investigations into the biological functions of the WRKY gene family in L. angustifolia. [ABSTRACT FROM AUTHOR]

Introduction: Neuropeptides and their receptors constitute diverse and abundant signal molecules in insects, primarily synthesized and released primarily from neurosecretory cells within the central nervous system Neuropeptides act as neurohormones and euromodulators, regulating insect behavior, lifecycle, and physiology by binding to receptors on cell surface. As a typical natural predator of agricultural pests, the lady beetle, Coccinella septempunctata, has been commercially mass-cultured and widely employed in pest management. Insect diapause is a physiological and ecological adaptative strategy acquired in adverse environments. In biological control programs, knowledge about diapause regulation in natural enemy insects provides important insight for improving long-term storage, transportation, and field adoption of these biological control agents. However, little is known about the function of neuropeptides and their receptors in controlling reproductive diapause of C. septempunctata. It is unclear which neuropeptides affect diapause of C. septempunctata. Methods: In this study, RNA-seq technology and bioinformatics were utilized to investigate genes encoding neuropeptides and their receptors in female adults of C. septempunctata. Quantitative real-time PCR (qRT-PCR) analysis was employed to examine gene expression across different development/diapause stages. Results: A total of 17 neuropeptide precursor genes and 9 neuropeptide receptor genes were identified, implicated in regulating various behaviors such as feeding, reproduction, and diapause. Prediction of partial mature neuropeptides from precursor sequences was also performed using available information about these peptides from other species, conserved domains and motifs. During diapause induction, the mRNA abundance of AKH was notably higher on the 10th day compared to non-diapause females, but decreased by the 20th day. In contrast, GPHA showed lower expression levels on the 5th day of diapause induction compared to non-diapause females, but increased significantly by the 15th and 20th days. NPF was higher expressed in head and midgut while DH showed higher expression in the fat body and midgut. Additionally, NPF expression remained consistently lower throughout all stages of diapause induction compared to nondiapause conditions in females. Discussion: This study represents the first sequencing, identification, and expression analysis of neuropeptides and neuropeptide receptor genes in C. septempunctata. Our results could provide a foundational framework for further investigations into the presence, functions, and potential targets of neuropeptides and their receptors, particularly in devising novel strategies for diapause regulation in C. septempunctata. [ABSTRACT FROM AUTHOR]

Cyclic nucleotide-gated ion channels (CNGCs) are cell membrane channel proteins for calcium ions. They have been reported to play important roles in survival and in the responses to environmental factors in various plants. However, little is known about the CNGC family and its functions in luffa (Luffa cylindrica L.). In this study, a bioinformatics-based method was used to identify members of the CNGC gene family in L. cylindrica. In total, 20 LcCNGCs were detected, and they were grouped into five subfamilies (I, II, Ⅲ, IV-a, and IV-b) in a phylogenetic analysis with CNGCs from Arabidopsis thaliana (20 AtCNGCs) and Momordica charantia (17 McCNGCs). The 20 LcCNGC genes were unevenly distributed on 11 of the 13 chromosomes in luffa, with none on Chromosomes 1 and 5. The members of each subfamily encoded proteins with highly conserved functional domains. An evolutionary analysis of CNGCs in luffa revealed three gene losses and a motif deletion. An examination of gene replication events during evolution indicated that two tandemly duplicated gene pairs were the primary driving force behind the evolution of the LcCNGC gene family. PlantCARE analyses of the LcCNGC promoter regions revealed various cis-regulatory elements, including those responsive to plant hormones (abscisic acid, methyl jasmonate, and salicylic acid) and abiotic stresses (light, drought, and low temperature). The presence of these cis-acting elements suggested that the encoded CNGC proteins may be involved in stress responses, as well as growth and development. Transcriptome sequencing (RNA-seq) analyses revealed tissue-specific expression patterns of LcCNGCs in various plant parts (roots, stems, leaves, flowers, and fruit) and the upregulation of some LcCNGCs under low-temperature stress. To confirm the accuracy of the RNA-seq data, 10 cold-responsive LcCNGC genes were selected for verification by quantitative real-time polymerase chain reaction (RT-qPCR) analysis. Under cold conditions, LcCNGC4 was highly upregulated (>50-fold increase in its transcript levels), and LcCNGC3, LcCNGC6, and LcCNGC13 were upregulated approximately 10-fold. Our findings provide new information about the evolution of the CNGC family in L. cylindrica and provide insights into the functions of the encoded CNGC proteins. [ABSTRACT FROM AUTHOR]

Peanut (Arachis hypogaea L.) is one of the most important oil and food legume crops worldwide. ASR (abscisic acid, stress, ripening) plays extremely important roles in plant growth and development, fruit ripening, pollen development, and stress. Here, six ASR genes were identified in peanut. Structural and conserved motif analyses were performed to identify common ABA/WDS structural domains. The vast majority of ASR genes encoded acidic proteins, all of which are hydrophilic proteins and localized on mitochondria and nucleus, respectively. The cis-element analysis revealed that some cis-regulatory elements were related to peanut growth and development, hormone, and stress response. Under normal growth conditions, AhASR4 and AhASR5 were expressed in all tissues of peanut plants. Quantitative real-time PCR (qRT-PCR) results indicated that peanut ASR genes exhibited complex expression patterns in response to abiotic stress. Notably, under drought and cadmium (Cd) stress, the expression levels of AhASR4 and AhASR5 were significantly upregulated, suggesting that these genes may play a crucial role in the peanut plant's resistance to such stressors. These results provide a theoretical basis for studying the evolution, expression, and function of the peanut ASR gene family and will provide valuable information in the identification and screening of genes for peanut stress tolerance breeding. [ABSTRACT FROM AUTHOR]

Drought stress poses a critical threat to global crop yields and sustainable agriculture. The GASA genes are recognized for their pivotal role in stress tolerance and plant growth, but little is known about how they function in sunflowers. The investigation aimed to identify and elucidate the role of HaGASA genes in conferring sunflowers with drought tolerance. Twenty-seven different HaGASA gene family members were found in this study that were inconsistently located across eleven sunflower chromosomes. Phylogeny analysis revealed that the sunflower HaGASA genes were divided into five subgroups by comparing GASA genes with those from Arabidopsis, peanut, and soybean, with members within each subgroup displaying similar conserved motifs and gene structures. In-silico evaluation of cis-regulatory elements indicated the existence of specific elements associated with stress-responsiveness being the most abundant, followed by hormone, light, and growth-responsive elements. Transcriptomic data from the NCBI database was utilized to assess the HaGASA genes expression profile in different sunflower varieties under drought conditions. The HaGASA genes expression across ten sunflower genotypes under drought stress, revealed 14 differentially expressed HaGASA genes, implying their active role in the plant's stress response. The expression in different organs revealed that HaGASA2, HaGASA11, HaGASA17, HaGASA19, HaGASA21 and HaGASA26 displayed maximum expression in the stem. Our findings implicate HaGASA genes in mediating sunflower growth maintenance and adaptation to abiotic stress, particularly drought. The findings, taken together, provided a basic understanding of the structure and potential functions of HaGASA genes, setting the framework for further functional investigations into their roles in drought stress mitigation and crop improvement strategies. [ABSTRACT FROM AUTHOR]

Calcium-Dependent Protein Kinases (CDPKs) are a class of serine/threonine protein kinases encoded by several gene families that play key roles in biotic and abiotic stresses response and plant growth and development. However, snow lotus (Saussurea involucrata kar L.) CDPKs has rarely been reported. In this study, 20 CDPK genes in snow lotus were identified based on transcriptome data and classified into four groups (I-IV) based on their structural features and phylogenetic analyses. Among them, the transcript levels of SikCDPK1 were significantly induced by low temperature and multiple hormone treatments, and SikCDPK1 gene was found to have different expression in snow lotus seeds, leaves, stems and roots. The full-length promoter activity of SikCDPK1 gene was higher than that of the 5’ end deletion fragment, and the promoter fragment containing the low temperature inducing element had increased activation after low temperature treatment. The promoter activity of SikCDPK1 gene was mainly expressed in roots and rosette leaves. In addition, overexpressing plants of SikCDPK1 were more tolerant compared to the wild type after being subjected to low temperature stress. Physiological analyses indicated that SikCDPK1 improved plant tolerance to low temperature stress by maintaining cell membrane stability and reducing the accumulation of reactive oxygen species (ROS). These findings provided insights into CDPK gene families in snow lotus and broaden our understanding of the biological role of SikCDPK1 and the mechanism of low temperature stress tolerance in snow lotus. [ABSTRACT FROM AUTHOR]

Copyright of South China Fisheries Science is the property of South China Fisheries Science Editorial Department and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Pectin is a vital component of plant cell walls and its methylation process is regulated by pectin methylesterase inhibitors (PMEIs). PMEIs regulate the structural and functional modifications of cell walls in plants and play an important role in plant processes such as seed germination, fruit ripening, and stress response. Although the PMEI gene family has been well characterized in model plants, the understanding of its molecular evolution and biological functions in watermelon remains limited. In this study, 60 ClPMEI genes were identified and characterized, revealing their dispersion on multiple chromosomes. Based on a systematic developmental analysis, these genes were classified into three subfamilies, which was further supported by the exon, intron, and conserved motif distribution. Analysis of cis-elements and expression patterns indicated that ClPMEIs might be involved in regulating the tolerance of watermelon to various abiotic stresses. Moreover, distinct ClPMEI genes exhibit specific functions under different abiotic stresses. For example, ClPMEI51 and ClPMEI54 showed a significant upregulation in expression levels during the late stage of drought treatments, whereas ClPMEI3 and ClPMEI12 displayed a significant downregulation under low-temperature induction. Subcellular localization prediction and analysis revealed that the ClPMEI family member proteins were localized to the cell membrane. This study provided an important foundation for the further exploration of the functions of ClPMEI genes in watermelon. [ABSTRACT FROM AUTHOR]

Dihydroflavonol 4-reductase (DFR) significantly influences the modification of flower color. To explore the role of DFR in the synthesis of strawberry anthocyanins, in this study, we downloaded the CDS sequences of the DFR gene family from the Arabidopsis genome database TAIR; the DFR family of forest strawberry was compared; then, a functional domain screen was performed using NCBI; the selected strawberry DFR genes were analyzed; and the expression characteristics of the family members were studied by qRT-PCR. The results showed that there are 57 members of the DFR gene family in strawberry, which are mainly expressed in the cytoplasm and chloroplast; most of them are hydrophilic proteins; and the secondary structure of the protein is mainly composed of α-helices and random coils. The analysis revealed that FvDFR genes mostly contain light, hormone, abiotic stress, and meristem response elements. From the results of the qRT-PCR analysis, the relative expression of each member of the FvDFR gene was significantly different, which was expressed throughout the process of fruit coloring. Most genes had the highest expression levels in the full coloring stage (S4). The expression of FvDFR30, FvDFR54, and FvDFR56 during the S4 period was 8, 2.4, and 2.4 times higher than during the S1 period, indicating that the DFR gene plays a key role in regulating the fruit coloration of strawberry. In the strawberry genome, 57 members of the strawberry DFR gene family were identified. The higher the DFR gene expression, the higher the anthocyanin content, and the DFR gene may be the key gene in anthocyanin synthesis. Collectively, the DFR gene is closely related to fruit coloring, which lays a foundation for further exploring the function of the DFR gene family. [ABSTRACT FROM AUTHOR]

The calmodulin-binding transcriptional activator (CAMTA) is a small, conserved gene family in plants that plays a crucial role in regulating growth, development, and responses to various abiotic stress. Given the significance of the CAMTA gene family, various studies have been dedicated to uncovering its functional characteristics. In this study, genome-wide identification and bioinformatics analysis were conducted to explore CAMTAs in Phoebe bournei. A total of 17 CAMTA genes, each containing at least one domain from CG-1, TIG, ANK, or IQ, were identified in the P. bournei genome. The diversity of PbCAMTAs could be varied depending on their subcellular localization. An analysis of protein motifs, domains, and gene structure revealed that members within the same subgroup exhibited similar organization, supporting the results of the phylogenetic analysis. Gene duplications occurred among members of the PbCAMTA gene family. According to the cis-regulatory element prediction and protein–protein interaction network analysis, eight genes were subjected to qRT-PCR under drought, heat, and light stresses. The expression profiles indicated that PbCAMTAs, particularly PbCAMTA2, PbCAMTA12, and PbCAMTA16, were induced by abiotic stress. This study provides profound insights into the functions of CAMTAs in P. bournei. [ABSTRACT FROM AUTHOR]

Bone morphogenetic proteins (BMPs) play an important biological role in pearl biomineralization in pearl mussels. In this study, based on the genome data of the triangular sail mussel (Hyriopsis cumingii), the genome-wide identification and bioinformatic analysis of BMP gene family were performed, and the expression pattern of the BMP genes was investigated by the insertion experiments. The results showed that a total of 12 BMP gene family members (BMP2a/2b, BMP3, BMP5a/5b, BMP7a/7b/7c, BMP9, BMP10a/10b, and BMP11) were identified, which were unevenly distributed on chromosome 3/14/18, encoding 169-- 583 amino acids, with molecular weights ranging from 19.32 to 65.99 kDa. BMP2a, BMP7b, and BMP10a were distributed, respectively, in the cytoplasm, endoplasmic reticulum and mitochondria, others were distributed in the nucleus. qRT-PCR results showed the significant tissue specificity in BMPs gene expression. The HcBMPs were differentially expressed in the mantle and visceral mass, and the expression level was higher in the visceral mass. The expressing trends of HcBMPs were not consistent between the mantle and visceral mass insertion, suggesting that HcBMPs may perform different functions. We also found that insertion surgery in the mantle and visceral mass significantly alters the expression profiling of the BMP gene family. Insertion of the mantle induced the biomineralization function of BMP2a, BMP7a, and BMP7b, while BMP3 and BMP10b played opposite roles in visceral mass insertion. Visceral mass insertion could suppress BMP9 expression at 5 d and BMP5b expression at 90 d after insertion This work lays the foundation and data support for the preliminary elucidation of regulatory role and mechanism of HcBMPs in the pearl-cultivating process of mantle and visceral mass. [ABSTRACT FROM AUTHOR]

【Objective】Glucose-6-phosphate dehydrogenase（G6PDH）plays an important role in plant response to abiotic stress. Identification of the G6PDH gene family in potato and analysis of its expression pattern in damaged tubers would provide a reference for the subsequent in-depth study of the role of potato G6PDH genes in damage stress. 【Method】We used bioinformatics methods to identify the G6PDH gene family members of the potato w, and to analyze the chromosomal distribution, protein physicochemical properties, secondary structure, evolutionary relationships, gene structure, conserved motifs, and promoter cis-acting elements of proteins encoded by members of the gene family, as well as the expression pattern in different organs and damaged tubers of potato.【Result】A total of 4 G6PDH family members in potato genome were identified and distributed on 4 chromosomes, named StG6PDH1-StG6PDH4. Based on the subcellular localization and phylogenetic analysis, StG6PDH1, StG6PDH3 and StG6PDH4 were located in the chloroplasts and belonged to the plastidic type, StG6PDH2 was located in the cytoplasm and belonged to the cytoplasmic type. The number of amino acids of potato G6PDH proteins ranged from 511 to 596 aa, molecular weights from 58.48 to 66.65 kD, isoelectric points from 5.83 to 8.57, and instabilities coefficient from 39.79 to 47.53. The secondary structure of protein showed the highest percentage of α-helices and irregular coils and the least of β-turns. In addition, the promoters of StG6PDHs contained a large number of phytohormone, light, and stress response elements. The four StG6PDHs were expressed in the roots, stems, leaves and tubers of potato, and the expression in the leaves was higher than in other organs. The members of StG6PDHs were involved in the responses of potato tubers to injury stress. The expressions of StG6PDH1, StG6PDH2 and StG6PDH3 were upregulated within 36 h after tubers injured, and StG6PDH4 was down-regulated in injured potato tubers. 【Conclusion】A total of four potato StG6PDHs gene family members are identified, unevenly distributed on four chromosomes, of which one is cytoplasmic and three are plastidic. The promoter region of StG6PDHs includes light, hormone, and stress response elements. The expression of StG6PDHs in wounded tubers is differential, and the members synergistically regulate the responses of potato tubers to damage stress. [ABSTRACT FROM AUTHOR]

【Objective】The structure and function of UGT gene family members in pepper were identified and analyzed, laying the foundation for subsequent research.【Method】BioEdit, BLASTP and Pfam were used to align and search for UGT members in pepper. CDD and HMMER databases were used to verify conserved domains. ExPASy, Cell PLOC, MAGA X, MG2C, GSDS, and STRING were used to analyze and predict protein physicochemical properties, phylogeny, chromosome localization, gene structure and protein interaction. Transcriptome data and real-time PCR were used to analyze the expression pattern of UGT gene in various organs during the development of various organs.【Result】The prediction results showed that the 140 CaUGTs family members identified from the pepper gene family encoded amino acids in the range of 253-534 and the isoelectric point in the range of 4.7-8.45, most of the CaUGTs were located outside the cell, and a few were located in the plasma membrane and chloroplasts, and were distributed in 17 groups and mapped on 13 chromosomes, of which 25 members were located in chrom12, and all members contained the conserved domains motif 1 and motif 3. They responded to the action elements related to plant growth and development, stress. Real-time quantitative PCR analysis of the expression patterns of UGT gene in pepper under different tissues, stress and hormone response showed that UGT gene was of tissue-specific expression differences, and the expression of UGT gene significantly increased or decreased under the conditions of ABA, GA3, high and low temperature stress, and CaUGTs members might play different roles in specific stages of development, and may be involved in regulating the defense response under stress in pepper. 【Conclusion】The distribution and structure of the 140 pepper UGT members are diverse, while the members within the group are highly similar, indicating that the CaUGTs gene may respond to abiotic stress during the growth and development of pepper plants. [ABSTRACT FROM AUTHOR]

【Objective】 Serine acetyltransferase (SAT) is a critical enzyme in assimilating sulfur into cysteine (Cys), participating in various biological processes in plants, especially in plant response to abiotic stress. However, analyses on the potato SAT gene family (StSAT) has not yet be reported. This study systematically and comprehensively identified the potato SAT gene family, providing a theoretical basis for further understanding the characteristics of the StSAT gene family and further analysis of their functions in potato resistance to abiotic stress. 【Method】HMM was used to identify the StSAT gene family in potatoes and analyze their chromosomal distribution, gene structure, protein-conserved motifs, and collinearity across species. Additionally, RNA-seq data downloaded from PGSC were used to analyze the expression patterns of StSATs in different tissue parts of doubled-monoploid (DM) potatoes under abiotic stress and exogenous hormone treatments. qPCR (quantitative real-time PCR) was to analyze the relative expressions of StSATs in tetraploid potatoes under NaCl and PEG treatment (0, 1, 3, and 24 h) 【Result】Four StSATs were identified in potatoes, and they were distributed across four chromosomes. Based on phylogenetic characteristics, these four StSATs were classified into three subfamilies. According to synteny analysis, there were 4 orthologous SAT genes to Arabidopsis, 4 to tomato (Solanum lycopersicum), 2 to cabbage (Brassica oleracea), 1 to rice (Oryza sativa), and 1 to corn (Zea mays) . Expression analysis showed that the expressions of all four StSATs significantly increased over time under NaCl and PEG treatments compared to 0 h, indicating their likely involvement in the potato's response to salt and osmotic stress.【Conclusion】 StSAT gene family members play an essential role in potato responses to salt and osmotic stress. [ABSTRACT FROM AUTHOR]

【Objective】Aquaporins (AQPs) are crucial in physiological processes such as plant growth and development, water transport and stress response under abiotic stress in plants, and the present study was aimed to reveal the properties and functions of the potato StAQP family. 【Method】The potato's StAQP gene family was identified by genome-wide, and their gene structures, conserved motifs, cis-acting progenitors, chromosomal localization, and gene collinearity were analyzed using bioinformatics, and the gene expression patterns were verified by combining transcriptome data and RT-qPCR. 【Result】The 44 members of the potato StAQP gene family were distributed in five subfamilies: PIP, TIP, NIP, SIP and XIP. The gene structures and conserved motifs of the members in the same subfamily were basically the same, and the most of the members of the potato AQP family were distributed in the plasma membrane; the members of the potato StAQP family contained a large number of cis-acting progenitors related to light and stress response. The results of collinearity analysis showed that there were a large number of homologous gene pairs in AQP family between the potato and Arabidopsis thaliana, Nicotiana attenuata, Solanum lycopersicu and Capsicum annuum. The results of transcriptome and RT-qPCR validation showed that the potato's StAQP family members were highly expressed under drought and salt stress, and that there was a difference in the expressions of different members under different stresses. Differences in the expression of the same genes under different stresses also existed, three of these genes, StAQP7, StAQP28 and StAQP31, were the key genes of the StAQP family in response to abiotic stresses. 【Conclusion】StAQPs genes play an important role in the growth and development of potato and in the response to abiotic stresses. [ABSTRACT FROM AUTHOR]

Glutaredoxins (GRXs) are widely distributed oxidoreductase enzymes that play important roles in plant growth, development, and responses to various stresses. In this study, bioinformatics methods were used to identify and analyze the wheat GRX gene family and predict their properties and potential functions. RNA-seq and RT-qPCR expression analyses were used to investigate their regulatory functions under hormone treatment and fungal diseases. In this study, 86 GRX genes were identified in wheat and classified into CC-type, CGFS-type, and CPYC-type categories with no TaGRX located on chromosome 4B. The results show that TaGRXs regulate wheat transcriptional responses and have an integrative role in biotic and abiotic stress responses. TaGRXs are involved in wheat responses to Fusarium graminearum, Puccinia striiformis, and Erysiphe graminis diseases. TaGRX73-7D, TaGRX20-3A, and TaGRX29-3B play a negative regulatory role in E. graminis infection but a positive regulatory role in F. graminearum and P. striiformis infection. These TaGRXs play potential regulatory functions in wheat responses to the plant hormones and signaling molecules, including IAA, ABA, H2O2, and SA. The findings of this study lay the groundwork for further investigation of the functions of wheat GRX genes and their potential use as candidate genes for molecular breeding of stress-resistant wheat varieties. [ABSTRACT FROM AUTHOR]

In response to various stressors, the calmodulin-binding transcription activator (CAMTA) can regulate downstream genes involved in calcium (Ca2+)/calmodulin signaling after binding to calmodulin (CAM) or calmodulin-like (CML) proteins. We previously reported seven OsCAMTA genes available throughout the rice (Oryza sativa) genome and their docking with the best probable interactors. This refined study demonstrated the evolutionary conservation of OsCAMTA motif structure and its correlation with 41 different plant species through phylogenetic tree construction along with the detailed molecular docking study focusing specifically on the calmodulin-binding domain (CaMBD) of each CAMTA protein with all available CAM/CML proteins across the rice genome. More insights regarding these were obtained from gene duplication studies through synteny analysis. Protein–protein interactions by STRING database analysis were conducted to know the involvement of OsCAMTA proteins in various development and stress-dependent pathways by identifying probable interactors. Tissue-specific expression analysis through qRT-PCR revealed that all the OsCAMTA genes except OsCAMTA7a and OsCAMTA7b were abundantly expressed in the roots of rice plants. Transcript expressions of rice CAMTAs under differential salt concentrations have depicted their participation in salt stress activity. Gene expression analysis in various temperatures indicated the most up-regulation of OsCAMTA7b, OsCAMTA4 and OsCAMTA3b at 4 ºC, 37 ºC and 42 ºC, respectively. In comparison to earlier research on OsCAMTA genes, this study is the most comprehensive fine-tuned and well-honed research conducted through tissue-specific expression study, followed by spatio-temporal expression analysis under different stresses with protein–protein interaction studies, molecular docking and prediction of microRNA to target each of the OsCAMTAs. [ABSTRACT FROM AUTHOR]

Glycoside hydrolases (GHs) are important in metabolic processes involving diverse carbohydrate-based substances found inside plant tissues. Potatoes (Solanum tuberosum) are rich in starchy carbohydrates, suggesting the role of GHs in their metabolic pathways. In this study, we examine the GH superfamily in potato where 366 potential GHs were identified using a similarity search method. Genes were subjected to further characterisation to gain insights into their structural composition, functional properties and distribution patterns across tissue types. Several in silico methodologies were also employed to investigate the physicochemical features, conserved motifs, chromosomal mapping, duplication events, syntenic links with tomato (Solanum lycopersicum), subcellular localisations, secondary structures and phylogenetic relationships. Cis -elements in StGHs revealed that the promoters of StGHs contain cis -elements that are responsive to phytohormones that are involved in plant growth and development, and are associated with stress responses. RNA-seq data identified significant changes in expression levels of GH16, GH17 , GH18 , GH19 and GH28 members under stress conditions. Expression patterns of several GHs were confirmed using real time quantitative PCR in response to stress. StGH16.24 expression increased after 3 days of drought stress, whereas StGH16.30 continuously increased under salt stress. Potential interactions between potato miRNAs and StGH revealed 393 and 627 interactions under drought and salt stress, respectively. Our findings offer insights into specific functions of GHs in diverse developmental stages and stress-related challenges in potato and other plants. Glycoside hydrolases (GHs) are involved in plant defence, cell wall metabolism and stress response. A total of 366 GH superfamily genes were identified in potato (Solanum tuberosum). Differential expression analysis indicated the involvement of GHs in various tissues, abiotic stress and biotic stresses, with specific genes showing significant changes in expression levels under drought and salt stress. Real time qPCR analysis revealed that StGH16.24 expression increased significantly after 3 days of drought stress, validating the presence of ABRE, MYB and MYC cis -regulatory elements. This article belongs to the Collection Functional Genomics for Developing Climate Resilient Crops. [ABSTRACT FROM AUTHOR]

An important family of transcription factors (TFs) in plants known as NAC (NAM, ATAF1/2, and CUC2) is crucial for the responses of plants to environmental stressors. In this study, we mined the NAC TF family members of tree peony (Paeonia suffruticosa Andrews) from genome-wide data and analyzed their response to heat and waterlogging stresses in conjunction with transcriptome data. Based on tree peony's genomic information, a total of 48 PsNAC genes were discovered. Based on how similar their protein sequences were, these PsNAC genes were divided into 14 branches. While the gene structures and conserved protein motifs of the PsNAC genes within each branch were largely the same, the cis-acting elements in the promoter region varied significantly. Transcriptome data revealed the presence of five PsNAC genes (PsNAC06, PsNAC23, PsNAC38, PsNAC41, PsNAC47) and one PsNAC gene (PsNAC37) in response to heat and waterlogging stresses, respectively. qRT-PCR analysis reconfirmed the response of these five PsNAC genes to heat stress and one PsNAC gene to waterlogging stress. This study lays a foundation for the study of the functions and regulatory mechanisms of NAC TFs in tree peony. Meanwhile, the NAC TFs of tree peony in response to heat and waterlogging stress were excavated, which is of great significance for the selection and breeding of new tree peony varieties with strong heat and waterlogging tolerance. [ABSTRACT FROM AUTHOR]

Rubisco small subunit (RbcS), a core component with crucial effects on the structure and kinetic properties of the Rubisco enzyme, plays an important role in response to plant growth, development, and various stresses. Although Rbcs genes have been characterized in many plants, their muti-functions in soybeans remain elusive. In this study, a total of 11 GmRbcS genes were identified and subsequently divided into three subgroups based on a phylogenetic relationship. The evolutionary analysis revealed that whole-genome duplication has a profound effect on GmRbcSs. The cis-acting elements responsive to plant hormones, development, and stress-related were widely found in the promoter region. Expression patterns based on the RT-qPCR assay exhibited that GmRbcS genes are expressed in multiple tissues, and notably Glyma.19G046600 (GmRbcS8) exhibited the highest expression level compared to other members, especially in leaves. Moreover, differential expressions of GmRbcS genes were found to be significantly regulated by exogenous plant hormones, demonstrating their potential functions in diverse biology processes. Finally, the function of GmRbcS8 in enhancing soybean resistance to soybean mosaic virus (SMV) was further determined through the virus-induced gene silencing (VIGS) assay. All these findings establish a strong basis for further elucidating the biological functions of RbcS genes in soybeans. [ABSTRACT FROM AUTHOR]

Brassica rapa L. is an important overwintering oilseed crop in Northwest China. Histone acetyltransferases (HATs) play an important role in epigenetic regulation, as well as the regulation of plant growth, development, and responses to abiotic stresses. To clarify the role of histone acetylation in the low-temperature response of B. rapa L., we identified 29 HAT genes in B. rapa L. using bioinformatics tools. We also conducted a comprehensive analysis of the physicochemical properties, gene structure, chromosomal localization, conserved structural domains and motifs, cis-acting regulatory elements, and evolutionary relationships of these genes. Using transcriptome data, we analyzed the expression patterns of BrHAT family members and predicted interactions between proteins; the results indicated that BrHATs play an important role in the low-temperature response of B. rapa L. HAT inhibitor (curcumin; CUR) and histone deacetylase inhibitor (Trichostatin A; TSA) were applied to four B. rapa L. varieties varying in cold resistance under the same low-temperature conditions, and changes in the physiological indexes of these four varieties were analyzed. The inhibitor treatment attenuated the effect of low temperature on seed germination, and curcumin treatment was most effective, indicating that the germination period was primarily regulated by histone acetylase. Both inhibitor treatments increased the activity of protective enzymes and the content of osmoregulatory substances in plants, suggesting that histone acetylation and deacetylation play a significant role in the response of B. rapa L. to low-temperature stress. The qRT-PCR analyses showed that the expression patterns of BrHATs were altered under different inhibitor treatments and low-temperature stress; meanwhile, we found three significantly differentially expressed genes. In sum, the process of histone acetylation is involved in the cold response and the BrHATs gene plays a role in the cold stress response. [ABSTRACT FROM AUTHOR]

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The cystathionine-β-synthase (CBS) domain is present in the proteins of all living organisms and functions as an energy sensor, regulating protein activity through the binding capacity of its adenosine ligands. The role of the CBS gene in plant growth and development, as well as tolerance to abiotic stresses, remains largely unknown, especially in grapevine. In our study, 32 members of the CBS gene family were obtained that were distributed on 15 chromosomes. The results of the structural and evolutionary tree analyses indicated that the VvCBS gene family exhibits diverse intron-exon patterns and highly conserved motifs. Furthermore, the phylogenetic classification of the VvCBS genes revealed the presence of three subfamilies. Subcellular localization analyses showed that the VvCBS genes are mainly located in the plasma membrane region. The secondary structure of the VvCBS protein mainly consists of α-helices, extended strands, β-turns, and random coils. The VvCBS gene family exhibited four co-linear gene pairs, while the numbers for Arabidopsis thaliana and rice were 21 and 7, respectively. The promoter cis-acting element analysis revealed the presence of light-responsive, hormone-responsive, stress-responsive, and growth- and development-related elements in the VvCBS family. The expression characterization demonstrated that 12 VvCBS genes exhibited high expression levels in all grape tissues. Additionally, the RT-qPCR expression analyses showed that the 32 VvCBS exhibited different responses to a variety of abiotic stresses (cold, drought, salt), suggesting that they were functionally differentiated. VvCBS27 was cloned from 'Pinot Noir' of grapevine with a coding sequence of 624 bp. Subcellular localization showed that VvCBS27 protein was mainly located in the cytoplasm, cell membrane, and nucleus. This study lays a foundation for elucidating the function of grape CBS protein. [ABSTRACT FROM AUTHOR]

Drought is a significant environmental limiting factor that restricts the growth of Quercus wutaishanica Mayr. The MYB transcription factor plays a wide role in controlling the growth of plants. In this study, the QwMYB108 gene was cloned and the bioinformatics was analyzed, and we examined how QwMYB108 responded to various gradient drought stresses. The results demonstrated that QwMYB108 encoded 275 amino acids using an 828 bp open reading frame. Subcellular localization indicated that the gene was located in the nucleus. Phylogenetic analysis showed that QwMYB108 was close to Q. robur, and that the highest level of expression was found in leaves, which was significantly different from other tissues. The expression of QwMYB108 increased as the stress degree rose when drought stress was present, and there was a significant difference between severe drought stress and other gradient stress. In this study, the function of QwMYB108 in drought stress response was investigated, and the drought response function gene of Q. wutaishanica was further explored to provide a theoretical basis. [ABSTRACT FROM AUTHOR]

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Histone modification plays a crucial role in chromatin remodeling and regulating gene expression, and participates in various biological processes, including plant development and responses to stress. Several gene families related to histone modification have been reported in various plant species. However, the identification of members and their functions in the rice (Oryza sativa L.) histone modification gene family (OsHM) at the whole-genome level remains unclear. In this study, a total of 130 OsHMs were identified through a genome-wide analysis. The OsHM gene family can be classified into 11 subfamilies based on a phylogenetic analysis. An analysis of the genes structures and conserved motifs indicates that members of each subfamily share specific conserved protein structures, suggesting their potential conserved functions. Molecular evolutionary analysis reveals that a significant number of OsHMs proteins originated from gene duplication events, particularly segmental duplications. Additionally, transcriptome analysis demonstrates that OsHMs are widely expressed in various tissues of rice and are responsive to multiple abiotic stresses. Fourteen OsHMs exhibit high expression in rice anthers and peaked at different pollen developmental stages. RT-qPCR results further elucidate the expression patterns of these 14 OsHMs during different developmental stages of anthers, highlighting their high expression during the meiosis and tetrad stages, as well as in the late stage of pollen development. Remarkably, OsSDG713 and OsSDG727 were further identified to be nucleus-localized. This study provides a fundamental framework for further exploring the gene functions of HMs in plants, particularly for researching their functions and potential applications in rice anthers' development and male sterility. [ABSTRACT FROM AUTHOR]

Alfin-like proteins (ALs) form a plant-specific transcription factor (TF) gene family involved in the regulation of plant growth and development, and abiotic stress response. In this study, 30 ALs were identified in Brassica napus ecotype 'Zhongshuang 11' genome (BnaALs), and unevenly distributed on 15 chromosomes. Structural characteristic analysis showed that all of the BnaALs contained two highly conserved domains: the N terminal DUF3594 domain and the C-terminal PHD-finger domain. The BnaALs were classified into four groups (Group I-IV), supported by conserved intron–exon and protein motif structures in each group. The allopolyploid event between B. oleracea and B. rapa ancestors and the small-scale duplication events in B. napus both contributed to the large BnaALs expansion. The promoter regions of BnaALs contained multiple abiotic stress cis-elements. The BnaALs in I-IV groups were mainly expressed in cotyledon, petal, root, silique, and seed tissues, and the duplicated gene pairs shared highly similar expression patterns. RNA-seq and RT-qPCR analysis showed that BnaALs were obviously induced by low nitrogen (LN) and low phosphorus (LP) treatments in roots. Overexpressing BnaAL02 and BnaAL28 in Arabidopsis demonstrated their functions in response to LN and LP stresses. BnaAL28 enhanced primary roots' (PRs) length and lateral roots' (LRs) number under LP and LN conditions, where BnaAL02 can inhibit LR numbers under the two conditions. They can promote root hair (RH) elongation under LP conditions; however, they suppressed RH elongation under LN conditions. Our result provides new insight into the functional dissection of this family in response to nutrient stresses in plants. [ABSTRACT FROM AUTHOR]

Pyrabactin resistance 1-like (PYL) proteins are abscisic acid (ABA) receptors that play a crucial role in the plant's response to adverse environmental conditions. However, as of yet, there is limited research on the role of PYL proteins in potato. In this study, a potato PYL gene, StPYL8-like, was identified through transcriptome analysis under drought stress. Molecular characterization revealed that the StPYL8-like protein possesses a highly conserved PYL family domain. Evolutionary analysis demonstrated that StPYL8-like protein clusters with various PYL proteins are involved in stress responses across different species. Functional assays showed that StPYL8-like robustly responds to different abiotic stresses, including drought and ABA treatment. Furthermore, the transient and stable expressions of StPYL8-like in tobacco enhanced their drought resistance, leading to increased plant height, leaf number, and fresh weight, as well as an improved root system. Transgenic tobacco carrying the StPYL8-like gene exhibited lower malondialdehyde (MDA) levels and higher proline accumulation and antioxidant enzyme activity compared to wild-type plants under drought conditions. Moreover, StPYL8-like upregulated the expression of stress-responsive genes (NtRD29A, NtLEA5, NtP5CS, NtPOD, NtSOD, and NtCAT) in transgenic plants subjected to drought stress. Collectively, these findings highlight the positive regulatory role of the StPYL8-like gene in enhancing potato plants' response to drought stress. [ABSTRACT FROM AUTHOR]

Abstract Drought stress poses a critical threat to global crop yields and sustainable agriculture. The GASA genes are recognized for their pivotal role in stress tolerance and plant growth, but little is known about how they function in sunflowers. The investigation aimed to identify and elucidate the role of HaGASA genes in conferring sunflowers with drought tolerance. Twenty-seven different HaGASA gene family members were found in this study that were inconsistently located across eleven sunflower chromosomes. Phylogeny analysis revealed that the sunflower HaGASA genes were divided into five subgroups by comparing GASA genes with those from Arabidopsis, peanut, and soybean, with members within each subgroup displaying similar conserved motifs and gene structures. In-silico evaluation of cis-regulatory elements indicated the existence of specific elements associated with stress-responsiveness being the most abundant, followed by hormone, light, and growth-responsive elements. Transcriptomic data from the NCBI database was utilized to assess the HaGASA genes expression profile in different sunflower varieties under drought conditions. The HaGASA genes expression across ten sunflower genotypes under drought stress, revealed 14 differentially expressed HaGASA genes, implying their active role in the plant’s stress response. The expression in different organs revealed that HaGASA2, HaGASA11, HaGASA17, HaGASA19, HaGASA21 and HaGASA26 displayed maximum expression in the stem. Our findings implicate HaGASA genes in mediating sunflower growth maintenance and adaptation to abiotic stress, particularly drought. The findings, taken together, provided a basic understanding of the structure and potential functions of HaGASA genes, setting the framework for further functional investigations into their roles in drought stress mitigation and crop improvement strategies.

Abstract [Objective] The study aims to clone the fructokinase (FRK ) gene of red pitaya (Hylocereus polyrhizus), detect its expression and enzyme activity, and analyze its physiological function in soluble sugar accumulation during fruit development. [Methods] HpFRK1 gene was cloned from ‘Zihonglong’ fruits, and bioinformatics and subcellular localization analysis were carried out. Gene expression was detected by qRT-PCR. Recombinant protein was obtained by E.coli induction and enzyme activity was detected. [Results] The open reading frame (ORF) of HpFRK1 was 993 bp in length, encoding 330 amino acids with a phosphofructokinase type B (pfkB) domain. HpFRK1 had the closest genetic relationship with sugar beet BvFRK, both of which belonged to cytoplasm localized FRKs. HpFRK1 was expressed in different developmental stages of mature stems and fruits. The expression level of HpFRK1 was the highest at 20 days after flowering and the lowest at 30 days after flowering (fruit ripening), and was gradually decreased with fruit development. Subcellular localization assay showed that HpFRK1 was mainly localized in the nucleus and cytoplasm. HpFRK1 recombinant protein specifically catalyzed fructose phosphorylation (K m=11.01 mmol/L). [Conclusion] HpFRK1 specifically catalyzes fructose phosphorylation in the cytoplasm and negatively regulates fruit soluble sugar accumulation during the development of red-fleshed pitaya fruits

[Objective] This study aims to explore the characteristics of PvGH3 family members in kidney bean and their roles in abiotic stress, to provide reference for further study of gene function, as well as provides new gene resources for breeding stress tolerant varieties of kidney bean. [Methods] Genome-wide identification of the GH3 gene family in kidney bean was carried out by a bioinformatics approach, and qRT-PCR was used to detect the expression of the PvGH3 gene under abiotic stresses. [Results] 19 PvGH3 genes were identified in kidney bean, of which 17 genes were unevenly distributed on eight chromosomes, and the remaining two genes were localized on scafford and could not be precisely located. These genes could be classified into three subfamilies, with members of each subfamily sharing similar gene structure and conserved motif. There were three paralogous pairs among the members, and 15 orthologous pairs with Arabidopsis. The 19 PvGH3 were up-regulated in response to drought (6% PEG), salt (100 mmol/L NaCl), and low temperature (4 ℃). [Conclusion] 19 PvGH3 genes were identified in kidney bean. qRT-PCR assays showed that these PvGH3 genes respond to abiotic stresses to different degrees, which provided basis for the analysis of stress tolerance of PvGH3.

Eukaryotic gene expression is regulated by RNA interference (RNAi). Dicer-like (DCL), Argonaute (AGO), and RNA-dependent RNA polymerase (RDR) are essential elements involved in the process of RNAi. However, Jatropha (J.) curcas, an oil-producing plant, has not undergone any previous systematic analysis or expression profiling of these genes. In this study, a total of four JcDCL, nine JcAGO, and seven JcRDR genes were identified in the J. curcas genome. Based on phylogenetic analysis, each gene family was classified into four clades and randomly distributed on nine J. curcas chromosomes. Protein sequence alignment revealed that the classical PAZ, Piwi, and RdRP domains were present in all JcDCLs, JcAGOs, and JcRDRs, respectively. Comprehensive expression pattern analysis using RNA-seq data showed various expression patterns in different organs and under different abiotic stresses. In addition, special attention should be paid to JcDCL1, JcAGO1, JcAGO4, and JcRDR5, which play important roles in response to various stresses. [ABSTRACT FROM AUTHOR]

Lodging, being the major problem in barley, affects both grain yield and quality and can be mediated through the exploitation of GA homeostatic genes, nonetheless. HvGA20ox, HvGA3ox and HvGA2ox genes play an important role in the Gibberellic Acid (GA) homeostasis that improves plant architecture especially plant height. In the current study, eight lines and five testers with different expression levels of HvGA20ox, HvGA3ox and HvGA2ox transcripts with lodging resistance and sensitivity were hybridized using Line × Tester mating design. Forty F1 hybrids were generated and the next year all F1 along with their parents were sown in filed under RCBD split plot in three replications and two treatments (normal and water deficit). Variance due to general combining ability (σ2 gca) was lower than the variance due to specific combining ability (σ2 sca) which indicates non-additive gene action. Line 3 was found with higher GCA estimates for the number of tillers/plant, grain yield, photosynthesis and water use efficiency. Cross 6, 11 and 21 were observed with twofold upregulation of HvGA2ox.2 transcript and downregulation of HvGA20ox.1 transcript at third node. These hybrids also showed a significant decrease in plant height (18–20%), lodging (< 10%) and increased grain yield (15–18%). The results proposed that the best-performing combinations may be utilized in breeding programs for the development of barley varieties with increased grain yield and lodging resistance. [ABSTRACT FROM AUTHOR]

Abstract Background Salt Overly Sensitive 1 (SOS1), a plasma membrane Na+/H+ exchanger, is essential for plant salt tolerance. Salt damage is a significant abiotic stress that impacts plant species globally. All living organisms require copper (Cu), a necessary micronutrient and a protein cofactor for many biological and physiological processes. High Cu concentrations, however, may result in pollution that inhibits the growth and development of plants. The function and production of mangrove ecosystems are significantly impacted by rising salinity and copper contamination. Results A genome-wide analysis and bioinformatics techniques were used in this study to identify 20 SOS1 genes in the genome of Kandelia obovata. Most of the SOS1 genes were found on the plasma membrane and dispersed over 11 of the 18 chromosomes. Based on phylogenetic analysis, KoSOS1s can be categorized into four groups, similar to Solanum tuberosum. Kandelia obovata's SOS1 gene family expanded due to tandem and segmental duplication. These SOS1 homologs shared similar protein structures, according to the results of the conserved motif analysis. The coding regions of 20 KoSOS1 genes consist of amino acids ranging from 466 to 1221, while the exons include amino acids ranging from 3 to 23. In addition, we found that the 2.0 kb upstream promoter region of the KoSOS1s gene contains several cis-elements associated with phytohormones and stress responses. According to the expression experiments, seven randomly chosen genes experienced up- and down-regulation of their expression levels in response to copper (CuCl2) and salt stressors. Conclusions For the first time, this work systematically identified SOS1 genes in Kandelia obovata. Our investigations also encompassed physicochemical properties, evolution, and expression patterns, thereby furnishing a theoretical framework for subsequent research endeavours aimed at functionally characterizing the Kandelia obovata SOS1 genes throughout the life cycle of plants.

Abstract Cytokinin oxidase/dehydrogenase (CKX) is the key enzyme that has been observed to catalyze irreversible inactivation of cytokinins and thus modulate cytokinin levels in plants. CKX gene family is known to have few members which are, expanded in the genome mainly due to duplication events. A total of nine MiCKXs were identified in Morus indica cv K2 with almost similar gene structures and conserved motifs and domains. The cis-elements along with expression analysis of these MiCKXs revealed their contrasting and specific role in plant development across different developmental stages. The localization of these enzymes in ER and Golgi bodies signifies their functional specification and property of getting modified post-translationally to carry out their activities. The overexpression of MiCKX4, an ortholog of AtCKX4, displayed longer primary root and higher number of lateral roots. Under ABA stress also the transgenic lines showed higher number of lateral roots and tolerance against drought stress as compared to wild-type plants. In this study, the CKX gene family members were analyzed bioinformatically for their roles under abiotic stresses.

Abstract Background Sterol side-chain reductase 2 (SSR2) is a key enzyme in the synthesis of plant cholesterol pathway. Despite the importance of watermelon as a horticultural cash crop, the SSR2 gene in watermelon has not been previously studied or reported. Results In this study, 28 SSR2 genes were identified in the watermelon genome. The physicochemical properties of 28 ClaSSR proteins were predicted by bioinformatics methods, and the gene structure, conserved motif, chromosome localization, phylogenetic analysis, cis-acting elements, expression patterns, promoter activity analysis and subcellular localization of ClaSSRs were studied. The 28 ClaSSRs were unevenly distributed on 11 chromosomes, and phylogenetic analysis showed that they could be grouped into 4 groups with other related Cucurbitaceae homologous genes. Analysis of gene structure and motifs revealed similarities in exons/introns and motifs between members of the same group, further supporting phylogenetic results. The RT–qPCR results showed variations in ClaSSRs expression during watermelon fruit development. The analysis of promoter activity for ClaSSR25 showed strong activity. Subcellular localization studies confirmed that ClaSSR25 is mainly located in the cytoplasm, which aligns with the predicted outcomes. We additionally estimated the network of protein–protein interactions for ClaSSR25 and analyzed proteins that could potentially interact with ClaSSR25 in melon and Arabidopsis thaliana. Conclusions We conducted bioinformatics analysis and expression analysis of members of the watermelon SSR2 gene family in this work, and the outcomes set the stage for further investigations into the watermelon SSR2 gene. Graphical Abstract

Abstract Background The dirigent (DIR) genes encode proteins that act as crucial regulators of plant lignin biosynthesis. In Solanaceae species, members of the DIR gene family are intricately related to plant growth and development, playing a key role in responding to various biotic and abiotic stresses. It will be of great application significance to analyze the DIR gene family and expression profile under various pathogen stresses in Solanaceae species. Results A total of 57 tobacco NtDIRs and 33 potato StDIRs were identified based on their respective genome sequences. Phylogenetic analysis of DIR genes in tobacco, potato, eggplant and Arabidopsis thaliana revealed three distinct subgroups (DIR-a, DIR-b/d and DIR-e). Gene structure and conserved motif analysis showed that a high degree of conservation in both exon/intron organization and protein motifs among tobacco and potato DIR genes, especially within members of the same subfamily. Total 8 pairs of tandem duplication genes (3 pairs in tobacco, 5 pairs in potato) and 13 pairs of segmental duplication genes (6 pairs in tobacco, 7 pairs in potato) were identified based on the analysis of gene duplication events. Cis-regulatory elements of the DIR promoters participated in hormone response, stress responses, circadian control, endosperm expression, and meristem expression. Transcriptomic data analysis under biotic stress revealed diverse response patterns among DIR gene family members to pathogens, indicating their functional divergence. After 96 h post-inoculation with Ralstonia solanacearum L. (Ras), tobacco seedlings exhibited typical symptoms of tobacco bacterial wilt. The qRT-PCR analysis of 11 selected NtDIR genes displayed differential expression pattern in response to the bacterial pathogen Ras infection. Using line 392278 of potato as material, typical symptoms of potato late blight manifested on the seedling leaves under Phytophthora infestans infection. The qRT-PCR analysis of 5 selected StDIR genes showed up-regulation in response to pathogen infection. Notably, three clustered genes (NtDIR2, NtDIR4, StDIR3) exhibited a robust response to pathogen infection, highlighting their essential roles in disease resistance. Conclusion The genome-wide identification, evolutionary analysis, and expression profiling of DIR genes in response to various pathogen infection in tobacco and potato have provided valuable insights into the roles of these genes under various stress conditions. Our results could provide a basis for further functional analysis of the DIR gene family under pathogen infection conditions.

【Objective】As one of the four major nutrients required by plants, sulfur is a crucial for plant growth and development, playing a pivotal role in enhancing plant resistance against both biotic and abiotic stresses. Sulfate transporters (SULTR) serve as primary regulators in the absorption and transport of sulfate in plants, playing an irreplaceable role in this process. The understanding of the fundamental characteristics and expression patterns of CaSULTR genes could help to provide theoretical support for advancing researches on SULTR in peppers.【Method】Based on the pepper genome, members of the epper CaSULTR gene family were identified at the whole-genome level. A comprehensive analysis of their physicochemical properties, conserved Motifs and gene structures was conducted. By utilizing publicly available transcriptome data and qPCR technology, the expression patterns of CaSULTR genes under various hormone stress conditions were analyzed. Additionally, differentially expressed genes were cloned for further investigation.【Result】A total of 13 CaSULTR genes were identified and designated as CaSULTR1;1~1;3, CaSULTR2;1~2;2, CaSULTR3;1~3;7 and CaSULTR4;1. These genes were distributed on seven chromosomes in pepper, with amino acid lengths ranging from 641 to 947 aa, molecular weights from 69.65 to 104.36 kD, and isoelectric points between 8.42 to 9.62. Characterized by the hydrophobicity, CaSULTR proteins were classified into four subgroups (Ⅰ-Ⅳ), with subgroup Ⅲ containing the highest number of members. Within the same subgroup, members exhibited relatively small differences in physicochemical properties, and Motifs and gene structures were relatively conserved. With the exception of CaSULTR2;1 and CaSULTR2;2, all members possessed Motif 5. Tissue expression analysis indicated that CaSULTR genes may be involved in the development of organs such as leaves, fruits and flowers, with CaSULTR4;1 exhibiting expression in leaves, roots and stems. Expression profile analysis under hormone stress, coupled with qPCR results, revealed significant up-regulation of CaSULTR1;1 and CaSULTR3;4 under hormone induction.【Conclusion】The expression patterns of CaSULTR genes under hormone stress are identified, suggesting that of CaSULTR1;1 and CaSULTR3;4 may be involved in the regulation of sulfur metabolism by exogenous hormones.

In order to clarify the molecular bioinformatics characteristics and tissue expression patterns of the COBRA gene family members of Huperzia serrata, the physicochemical properties, domains, conserved motifs, cis-acting elements, and genes expression of the family members (HsCOBRAs) were analyzed by bioinformatics techniques, based on the full-length transcriptome data of the H. serrata. The results were as follows: (1) A total of 24 HsCOBRAs family members were screened in the full-length transcriptome of H. serrata, including 9 acidic proteins, 11 stabilizing proteins, 5 hydrophobic proteins, 7 proteins with transmembrane structures, and 3 proteins with signal peptides. (2) Subcellular localization was found in the cell wall, chloroplast, nucleus, and cell membrane. (3) Structural analysis revealed that HsCOBRAs had 7 domains and 6 conserved motifs, and partial members had a highly conserved CCVS structure. (4) HsCOBRAs had 45 cis-acting elements such as CAAT-box and TATA-box. (5) HsCOBRA2 had the highest expressions in leaves, spores, stems and gemma. The study results can provide theoretical basis for further research and biological function verification of HsCOBRAs.

Abstract Background Jasmonate ZIM-domain (JAZ) proteins, which act as negative regulators in the jasmonic acid (JA) signalling pathway, have significant implications for plant development and response to abiotic stress. Results Through a comprehensive genome-wide analysis, a total of 20 members of the JAZ gene family specific to alfalfa were identified in its genome. Phylogenetic analysis divided these 20 MsJAZ genes into five subgroups. Gene structure analysis, protein motif analysis, and 3D protein structure analysis revealed that alfalfa JAZ genes in the same evolutionary branch share similar exon‒intron, motif, and 3D structure compositions. Eight segmental duplication events were identified among these 20 MsJAZ genes through collinearity analysis. Among the 32 chromosomes of the autotetraploid cultivated alfalfa, there were 20 MsJAZ genes distributed on 17 chromosomes. Extensive stress-related cis-acting elements were detected in the upstream sequences of MsJAZ genes, suggesting that their response to stress has an underlying function. Furthermore, the expression levels of MsJAZ genes were examined across various tissues and under the influence of salt stress conditions, revealing tissue-specific expression and regulation by salt stress. Through RT‒qPCR experiments, it was discovered that the relative expression levels of these six MsJAZ genes increased under salt stress. Conclusions In summary, our study represents the first comprehensive identification and analysis of the JAZ gene family in alfalfa. These results provide important information for exploring the mechanism of JAZ genes in alfalfa salt tolerance and identifying candidate genes for improving the salt tolerance of autotetraploid cultivated alfalfa via genetic engineering in the future.

Color pattern plays a vital role in animal survival and communication. The type, distribution, and pigment state of pigment cells, and the reflective ability of iridophores determines body color. It varies adaptively in response to external environmental changes and physiological states. The skin pigmentation pattern reflects the number and arrangement of chromatophores. Some fish with rich color patterns, including egg spot patterns, blotch patterns, melanism, horizontal stripe patterns, and vertical bar patterns, have been studied increasingly. This study observed the formation, distribution, and main pattern of chromatophores in 1–60-day-old Misgurnus anguillicaudatus after hatching. Larval melanocytes were first observed in the yolk sac of loach larvae at 3 h post-hatching. From the larval to juvenile stage at 21 days, larval melanocytes appeared on the loach body surface. From the juvenile stage at 22 days to the adult stage, adult melanocytes appeared on the loach body surface. Iridocytes were first observed in the eyes of one-day-old larvae but not on the body surface until they were 12 days old. Xanthophores appeared on the body surface of seven-day-old juveniles. At 2–21 days post-hatching, the melanocytes in the loaches were larval, and their shape changed from star-to snowflake-shaped before forming a black spot. From 22 days, different morphological adult melanocytes formed on the body surface of the loaches with three types of black spots. Chrysanthemum-shaped melanocytes regularly aggregated into large black spots on large black spot loaches. Round and dendritic melanocytes gathered to form small black spots on small black spot loaches. Dendritic melanocytes were evenly distributed on non-black spot loaches. The pigmentation-related mitfa gene was obtained from M. anguillicaudatus using the rapid amplification of cDNA ends (RACE) approach with the SMARTer RACE 5´/3´ Kit User Manual according to the manufacturer's recommendations and was analyzed using bioinformatics and quantitative methods. The results showed that the mitfa gene encoded a protein with 408 amino acids with a calculated molecular mass of 45.68 kDa and an estimated isoelectric point of 7.16. MITFa contained MITF_TFEB_C_3_N, bHLH-Zip, and DUF 3371 domains. MITFa was well-conserved compared to MITF of various species with a higher degree of sequence similarity with other fishes (58.8%–83.2%). The qRT-PCR results showed that the mitfa mRNA was expressed at all stages of embryonic development and reached a peak value at the fertilization stage. mitfa expression was detected in all examined tissues of the three types of loaches, and the highest level of expression was detected in both muscle and dorsal skin (P < 0.01). This study explored pigmentation formation and mitfa expression, serving as a foundation for gaining further insight into the genetic mechanism of body color formation in M. anguillicaudatus.

Abstract Background Broussonetia papyrifera is an economically significant tree with high utilization value, yet its cultivation is often constrained by soil contamination with heavy metals (HMs). Effective scientific cultivation management, which enhances the yield and quality of B. papyrifera, necessitates an understanding of its regulatory mechanisms in response to HM stress. Results Twelve Metallothionein (MT) genes were identified in B. papyrifera. Their open reading frames ranged from 186 to 372 bp, encoding proteins of 61 to 123 amino acids with molecular weights between 15,473.77 and 29,546.96 Da, and theoretical isoelectric points from 5.24 to 5.32. Phylogenetic analysis classified these BpMTs into three subclasses: MT1, MT2, and MT3, with MT2 containing seven members and MT3 only one. The expression of most BpMT genes was inducible by Cd, Mn, Cu, Zn, and abscisic acid (ABA) treatments, particularly BpMT2e, BpMT2d, BpMT2c, and BpMT1c, which showed significant responses and warrant further study. Yeast cells expressing these BpMT genes exhibited enhanced tolerance to Cd, Mn, Cu, and Zn stresses compared to control cells. Yeasts harboring BpMT1c, BpMT2e, and BpMT2d demonstrated higher accumulation of Cd, Cu, Mn, and Zn, suggesting a chelation and binding capacity of BpMTs towards HMs. Site-directed mutagenesis of cysteine (Cys) residues indicated that mutations in the C domain of type 1 BpMT led to increased sensitivity to HMs and reduced HM accumulation in yeast cells; While in type 2 BpMTs, the contribution of N and C domain to HMs’ chelation possibly corelated to the quantity of Cys residues. Conclusion The BpMT genes are crucial in responding to diverse HM stresses and are involved in ABA signaling. The Cys-rich domains of BpMTs are pivotal for HM tolerance and chelation. This study offers new insights into the structure-function relationships and metal-binding capabilities of type-1 and − 2 plant MTs, enhancing our understanding of their roles in plant adaptation to HM stresses.

Background: Salt Overly Sensitive 1 (SOS1), a plasma membrane Na+/H+ exchanger, is essential for plant salt tolerance. Salt damage is a significant abiotic stress that impacts plant species globally. All living organisms require copper (Cu), a necessary micronutrient and a protein cofactor for many biological and physiological processes. High Cu concentrations, however, may result in pollution that inhibits the growth and development of plants. The function and production of mangrove ecosystems are significantly impacted by rising salinity and copper contamination. Results: A genome-wide analysis and bioinformatics techniques were used in this study to identify 20 SOS1 genes in the genome of Kandelia obovata. Most of the SOS1 genes were found on the plasma membrane and dispersed over 11 of the 18 chromosomes. Based on phylogenetic analysis, KoSOS1s can be categorized into four groups, similar to Solanum tuberosum. Kandelia obovata's SOS1 gene family expanded due to tandem and segmental duplication. These SOS1 homologs shared similar protein structures, according to the results of the conserved motif analysis. The coding regions of 20 KoSOS1 genes consist of amino acids ranging from 466 to 1221, while the exons include amino acids ranging from 3 to 23. In addition, we found that the 2.0 kb upstream promoter region of the KoSOS1s gene contains several cis-elements associated with phytohormones and stress responses. According to the expression experiments, seven randomly chosen genes experienced up- and down-regulation of their expression levels in response to copper (CuCl2) and salt stressors. Conclusions: For the first time, this work systematically identified SOS1 genes in Kandelia obovata. Our investigations also encompassed physicochemical properties, evolution, and expression patterns, thereby furnishing a theoretical framework for subsequent research endeavours aimed at functionally characterizing the Kandelia obovata SOS1 genes throughout the life cycle of plants. [ABSTRACT FROM AUTHOR]

Simple Summary: Intensive aquaculture decreases immunity and increases diseases that occur in grass carp, which increases economic loss. Hence, improving grass carp immunity is an important strategy for solving the problem of intensive aquaculture. It has been reported that akirin takes part in immune responses. However, the role of akirin in grass carp is unclear. In this study, the akirin gene was isolated from grass carp spleen. The tissue-specific expression of akirin was analyzed. Akirin expression was detected by treatment with LPS, poly (I:C), and A. hydrophila. The immunologic function of akirin proteins was evaluated in HKLs. The findings showed that akirin expression was widely detected in grass carp tissues. Akirin levels were markedly induced via LPS, poly (I:C), and A. hydrophila stimulation in vitro and in vivo. Recombinant grass carp akirin proteins were produced by E. coli. The immune-related genes in HKLs were increased by treatment with recombinant akirin proteins. Intensive aquaculture of grass carp often leads to decreased immunity and increased disease prevalence, resulting in economic losses. Improving grass carp immunity is therefore a critical strategy for addressing these challenges. Akirin reportedly participates in myogenesis, growth, and immune responses. However, its role in grass carp remains unclear. Herein, we isolated akirins from the spleen of grass carp and analyzed their tissue-specific expression. Akirin expression was detected following treatment with poly (I:C), LPS, and Aeromonas hydrophila (A. hydrophila). The immunological function of the akirin protein was evaluated in head kidney leukocytes (HKLs). The results revealed that the coding sequence (CDS) of akirin1 is 570 bp, encoding 189 amino acids. There was one predicted nuclear localization signal (NLS) and two predicted α- helix domains. The CDS of akirin2 is 558 bp, encoding 185 amino acids. There were two predicted NLSs and two predicted α-helix domains. Tissue-specific expression analysis showed that akirins are widely detected in grass carp tissues. akirin1 was highly detected in the brain, kidneys, heart, spleen, and gonads, while akirin2 was highly detected in the brain, liver, gonads, kidneys, spleen, and heart. The mRNA levels of akirins were promoted after treatment with poly (I:C), LPS, and A. hydrophila. Recombinant akirin proteins were produced in Escherichia coli (E. coli). il-1β, ifnγ, il-6, tnfα, il-4, iκbα, and nfκb were markedly increased in grass carp HKLs by treatment with the akirin protein. These results suggest that akirins play a role in the immunological regulation of grass carp. [ABSTRACT FROM AUTHOR]

PYR/PYL/RCAR proteins are abscisic acid (ABA) receptors that play a crucial role in plant responses to abiotic stresses. However, there have been no research reports on potato PYL so far. In this study, a potato PYL gene named StPYL16 was identified based on transcriptome data under drought stress. Molecular characteristics analysis revealed that the StPYL16 protein possesses an extremely conserved PYL family domain. The tissue expression results indicated that the StPYL16 is predominantly expressed at high levels in the underground parts, particularly in tubers. Abiotic stress response showed that StPYL16 has a significant response to drought treatment. Further research on the promoter showed that drought stress could enhance the activation activity of the StPYL16 promoter on the reporter gene. Then, transient and stable expression of StPYL16 in tobacco enhanced the drought resistance of transgenic plants, resulting in improved plant height, stem thickness, and root development. In addition, compared with wild-type plants, StPYL16 transgenic tobacco exhibited lower malondialdehyde (MDA) content, higher proline accumulation, and stronger superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) activities. Meanwhile, StPYL16 also up-regulated the expression levels of stress-related genes (NtSOD, NtCAT, NtPOD, NtRD29A, NtLEA5, and NtP5CS) in transgenic plants under drought treatment. These findings indicated that the StPYL16 gene plays a positive regulatory role in potato responses to drought stress. [ABSTRACT FROM AUTHOR]