Genome-wide analysis of the potato Hsp20 gene family: identification, genomic organization and expression profiles in response to heat stress

Genome-wide profile analysis of the Hsp20 family in lettuce and identification of its response to drought stress

Heat shock protein 20 (Hsp20) plays a very important role in response to abiotic stressors such as drought; however, in lettuce (Lactuca sativa L.), this gene family is poorly understood. This study used bioinformatics methods to identify 36 members of the lettuce Hsp20 family, which were named LsHsp20-1~LsHsp20-36. Subcellular localization results revealed that 26 members of the LsHsp20 protein family localized to the cytoplasm and nucleus. Additionally, 15 conserved domains were identified in the LsHsp20 protein family, with the number of amino acids ranging from 8 to 50. Gene structure analysis revealed that 15 genes (41.7%) had no introns, and 20 genes (55.5%) had one intron. The proportion of the LsHsp20 secondary structure was random coil > alpha helix > extended strand > beta turn. Chromosome positioning analysis indicated that 36 genes were unevenly distributed on nine chromosomes, and four pairs of genes were collinear. The Ka/Ks ratio of the collinear genes was less than 1, indicating that purifying selection dominated during L. sativa evolution. Thirteen pairs of genes were collinear in lettuce and Arabidopsis, and 14 pairs of genes were collinear in lettuce and tomato. A total of 36 LsHsp20 proteins were divided into 12 subgroups based on phylogenetic analysis. Three types of cis-acting elements, namely, abiotic and biotic stress-responsive, plant hormone-responsive, and plant development-related elements, were identified in the lettuce LsHsp20 family. qRT-PCR was used to analyze the expression levels of 23 LsHsp20 genes that were significantly upregulated on the 7th or 14th day of drought treatment, and the expression levels of two genes (LsHsp20-12 and LsHsp20-26) were significantly increased by 153-fold and 273-fold on the 14th and 7th days of drought treatment, respectively. The results of this study provide comprehensive information for research on the LsHsp20 gene family in lettuce and lay a solid foundation for further elucidation of Hsp20 biological functions, providing valuable information on the regulatory mechanisms of the LsHsp20 family in lettuce drought resistance.

Genome-Wide Identification of GRAS Transcription Factors and Their Functional Analysis in Salt Stress Response in Sugar Beet

GAI-RGA-and-SCR (GRAS) transcription factors can regulate many biological processes such as plant growth and development and stress defense, but there are few related studies in sugar beet. Salt stress can seriously affect the yield and quality of sugar beet (Beta vulgaris). Therefore, this study used bioinformatics methods to identify GRAS transcription factors in sugar beet and analyzed their structural characteristics, evolutionary relationships, regulatory networks and salt stress response patterns. A total of 28 BvGRAS genes were identified in the whole genome of sugar beet, and the sequence composition was relatively conservative. According to the topology of the phylogenetic tree, BvGRAS can be divided into nine subfamilies: LISCL, SHR, PAT1, SCR, SCL3, LAS, SCL4/7, HAM and DELLA. Synteny analysis showed that there were two pairs of fragment replication genes in the BvGRAS gene, indicating that gene replication was not the main source of BvGRAS family members. Regulatory network analysis showed that BvGRAS could participate in the regulation of protein interaction, material transport, redox balance, ion homeostasis, osmotic substance accumulation and plant morphological structure to affect the tolerance of sugar beet to salt stress. Under salt stress, BvGRAS and its target genes showed an up-regulated expression trend. Among them, BvGRAS-15, BvGRAS-19, BvGRAS-20, BvGRAS-21, LOC104892636 and LOC104893770 may be the key genes for sugar beet's salt stress response. In this study, the structural characteristics and biological functions of BvGRAS transcription factors were analyzed, which provided data for the further study of the molecular mechanisms of salt stress and molecular breeding of sugar beet.

Identification of key genes for triacylglycerol biosynthesis and storage in herbaceous peony (Paeonia lactifolra Pall.) seeds based on full-length transcriptome

BACKGROUND

The herbaceous peony (Paeonia lactiflora Pall.) is extensively cultivated in China due to its root being used as a traditional Chinese medicine known as 'Radix Paeoniae Alba'. In recent years, it has been discovered that its seeds incorporate abundant unsaturated fatty acids, thereby presenting a potential new oilseed plant. Surprisingly, little is known about the full-length transcriptome sequencing of Paeonia lactiflora, limiting research into its gene function and molecular mechanisms.

RESULTS

A total of 484,931 Reads of Inserts (ROI) sequences and 1,455,771 full-Length non-chimeric reads (FLNC) sequences were obtained for CDS prediction, TF analysis, SSR analysis and lncRNA identification. In addition, gene function annotation and gene structure analysis were performed. A total of 4905 transcripts were related to lipid metabolism biosynthesis pathway, belonging to 28 enzymes. We use these data to identify 10 oleosin (OLE) and 5 diacylglycerol acyltransferase (DGAT) gene members after de-redundancy. The analysis of physicochemical properties and secondary structure showed them similarity in gene family respectively. The phylogenetic analysis showed that the distribution of OLE and DGAT family members was roughly the same as that of Arabidopsis. Quantitative real-time polymerase chain reaction (qRT-PCR) analyses revealed expression changes in different seed development stages, and showed a trend of increasing and then decreasing.

CONCLUSION

In summary, these results provide new insights into the molecular mechanism of triacylglycerol (TAG) biosynthesis and storage during the seedling stage in Paeonia lactiflora. It provides theoretical references for selecting and breeding oil varieties and understanding the functions of oil storage as well as lipid synthesis related genes in Paeonia lactiflora.

The PPO family in Nicotiana tabacum is an important regulator to participate in pollination

Polyphenol oxidases (PPOs) are type-3 copper enzymes and are involved in many biological processes. However, the potential functions of PPOs in pollination are not fully understood. In this work, we have screened 13 PPO members in Nicotiana. tabacum (named NtPPO1-13, NtPPOs) to explore their characteristics and functions in pollination. The results show that NtPPOs are closely related to PPOs in Solanaceae and share conserved domains except NtPPO4. Generally, NtPPOs are diversely expressed in different tissues and are distributed in pistil and male gametes. Specifically, NtPPO9 and NtPPO10 are highly expressed in the pistil and mature anther. In addition, the expression levels and enzyme activities of NtPPOs are increased after N. tabacum self-pollination. Knockdown of NtPPOs would affect pollen growth after pollination, and the purines and flavonoid compounds are accumulated in self-pollinated pistil. Altogether, our findings demonstrate that NtPPOs potentially play a role in the pollen tube growth after pollination through purines and flavonoid compounds, and will provide new insights into the role of PPOs in plant reproduction.

Comprehensive investigation of BZR gene family in four dicots and the function of PtBZR9 and PtBZR12 under drought stress

Brassinazole-resistant (BZR) transcription factor plays an important role in plant growth and stress resistance through brassinosteroid (BR) signal transduction. However, systematic analysis of the BZR family in dicots remains limited. In this study, we conducted a genome-wide study of four typical dicots: Arabidopsis thaliana, Carica papaya, Vitis vinifera and Populus trichocarpa. Thirty-four BZR gene family members were identified and classified them into three subfamilies. Analysis of promoter and expression patterns revealed crucial role of a pair of homologous BZR genes, PtBZR9 and PtBZR12, in poplar may play a critical role under abiotic stress. PtBZR9 and PtBZR12 were localised in the nucleus and exhibited mutual interactions. Moreover, transient overexpression (OE) of PtBZR9 and PtBZR12 in poplar enhanced tolerance to drought stress. The phenotypic and physiological characteristics of PtBZR9 and PtBZR12 OE in Arabidopsis mirrored those of transient OE in the poplar. Additionally, PtBZR9 and PtBZR12 can bind to the E-box element. Under exogenous BR treatment, transgenic lines displayed a greater decrease in root length than the wild type. Thus, these findings provide a solid foundation for future research on the complex regulatory mechanisms of BZR genes.

Comprehensive analysis of Dendrobium catenatum HSP20 family genes and functional characterization of DcHSP20-12 in response to temperature stress

Heat shock proteins (HSPs) are a class of protective proteins in response to abiotic stress in plants, and HSP20 plays an essential role in response to temperature stress. However, there are few studies on HSP20 in Dendrobium catenatum. In this study, 18 DcHSP20 genes were identified from the D. catenatum genome. Phylogenetic analysis showed that DcHSP20s could be classified into six subgroups, each member of which has similar conserved motifs and gene structures. Gene expression analysis of 18 DcHSP20 genes revealed that they exhibited variable expression patterns in different plant tissues. Meanwhile, all 18 DcHSP20 genes were induced to be up-regulated under high temperature, while six genes (DcHSP20-2/9/10/12/16/17) were significantly up-regulated under low temperature. Moreover, combining gene expression under high and low temperature stress, the DcHSP20-12 gene was cloned for functional analysis. The germination ratios, fresh weights, root lengths of two DcHSP20-12-overexpressing transgenic Arabidopsis thaliana lines were significantly higher, but MDA contents were lower than that of wild-type (WT) plants under heat and cold stresses, displayed enhanced thermotolerance and cold-resistance. These results lay a foundation for the functional characterization of DcHSP20s and provide a candidate gene, DcHSP20-12, for improving the tolerance of D. catenatum to temperature stress in the future.

Heat and Wheat: Adaptation strategies with respect to heat shock proteins and antioxidant potential; an era of climate change

Extreme changes in weather including heat-wave and high-temperature fluctuations are predicted to increase in intensity and duration due to climate change. Wheat being a major staple crop is under severe threat of heat stress especially during the grain-filling stage. Widespread food insecurity underscores the critical need to comprehend crop responses to forthcoming climatic shifts, pivotal for devising adaptive strategies ensuring sustainable crop productivity. This review addresses insights concerning antioxidant, physiological, molecular impacts, tolerance mechanisms, and nanotechnology-based strategies and how wheat copes with heat stress at the reproductive stage. In this study stress resilience strategies were documented for sustainable grain production under heat stress at reproductive stage. Additionally, the mechanisms of heat resilience including gene expression, nanomaterials that trigger transcription factors, (HSPs) during stress, and physiological and antioxidant traits were explored. The most reliable method to improve plant resilience to heat stress must include nano-biotechnology-based strategies, such as the adoption of nano-fertilizers in climate-smart practices and the use of advanced molecular approaches. Notably, the novel resistance genes through advanced molecular approach and nanomaterials exhibit promise for incorporation into wheat cultivars, conferring resilience against imminent adverse environmental conditions. This review will help scientific communities in thermo-tolerance wheat cultivars and new emerging strategies to mitigate the deleterious impact of heat stress.

Genome-wide identification and characterization of the RZFP gene family and analysis of its expression pattern under stress in Populus trichocarpa

Forest trees face many abiotic stressors during their lifetime, including drought, heavy metals, high salinity, and chills, affecting their quality and yield. The RING-type ubiquitin ligase E3 is an invaluable component of the ubiquitin-proteasome system (UPS) and participates in plant growth and environmental interactions. Interestingly, only a few studies have explored the RING ZINC FINGER PROTEIN (RZFP) gene family. This study identified eight PtrRZFPs genes in the Populus genome, and their molecular features were analyzed. Gene structure analysis revealed that all PtrRZFPs genes contained >10 introns. Evolutionarily, the RZFPs were separated into four categories, and segmental replication events facilitated their amplification. Notably, many stress-related elements have been identified in the promoters of PtrRZFPs using Cis-acting element analysis. Moreover, some PtrRZFPs were significantly induced by drought and sorbitol, revealing their potential roles in regulating stress responses. Particularly, overexpression of the PtrRZFP1 gene in poplars conferred excellent drought tolerance; however, PtrRZFP1 knockdown plants were drought-sensitive. We identified the potential upstream transcription factors of PtrRZFPs and revealed the possible biological functions of RZFP1/4/7 in resisting osmotic and salt stress, laying the foundation for subsequent biological function studies and providing genetic resources for genetic engineering breeding for drought resistance in forest trees. This study offers crucial information for the further exploration of the functions of RZFPs in poplars.

Integrated analysis of HSP20 genes in the developing flesh of peach: identification, expression profiling, and subcellular localization

BACKGROUND

Plant HSP20s are not only synthesized in response to heat stress but are also involved in plant biotic and abiotic stress resistance, normal metabolism, development, differentiation, survival, ripening, and death. Thus, HSP20 family genes play very important and diverse roles in plants. To our knowledge, HSP20 family genes in peach have not yet been characterized in detail, and little is known about their possible function in the development of red flesh in peach.

RESULTS

In total, 44 PpHSP20 members were identified in the peach genome in this study. Forty-four PpHSP20s were classified into 10 subfamilies, CI, CII, CIII, CV, CVI, CVII, MII, CP, ER, and Po, containing 18, 2, 2, 10, 5, 1, 1, 2, 1, and 2 proteins, respectively. Among the 44 PpHSP20 genes, 6, 4, 4, 3, 7, 11, 5, and 4 PpHSP20 genes were located on chromosomes 1 to 8, respectively. In particular, approximately 15 PpHSP20 genes were located at both termini or one terminus of each chromosome. A total of 15 tandem PpHSP20 genes were found in the peach genome, which belonged to five tandemly duplicated groups. Overall, among the three cultivars, the number of PpHSP20 genes with higher expression levels in red flesh was greater than that in yellow or white flesh. The expression profiling for most of the PpHSP20 genes in the red-fleshed 'BJ' was higher overall at the S3 stage than at the S2, S4-1, and S4-2 stages, with the S3 stage being a very important period of transformation from a white color to the gradual anthocyanin accumulation in the flesh of this cultivar. The subcellular localizations of 16 out of 19 selected PpHSP20 proteins were in accordance with the corresponding subfamily classification and naming. Additionally, to our knowledge, Prupe.3G034800.1 is the first HSP20 found in plants that has the dual targets of both the endoplasmic reticulum and nucleus.

CONCLUSIONS

This study provides a comprehensive understanding of PpHSP20s, lays a foundation for future analyses of the unknown function of PpHSP20 family genes in red-fleshed peach fruit and advances our understanding of plant HSP20 genes.

Genome-wide identification of the OMT gene family in Cucumis melo L. and expression analysis under abiotic and biotic stress

Background

O-methyltransferase (OMT)-mediated O-methylation is a frequent modification that occurs during natural product biosynthesis, and it increases the diversity and stability of secondary metabolites. However, detailed genome-wide identification and expression analyses of OMT gene family members have not been performed in melons. In this study, we aimed to perform the genome-wide identification of OMT gene family members in melon to identify and clarify their actions during stress.

Methods

Genome-wide identification of OMT gene family members was performed using data from the melon genome database. The Cucumis melo OMT genes (CmOMTs) were then compared with the genes from two representative monocotyledons and three representative dicotyledons. The basic information, cis-regulatory elements in the promoter, predicted 3-D-structures, and GO enrichment results of the 21 CmOMTs were analyzed.

Results

In our study, 21 CmOMTs (named CmOMT1-21) were obtained by analyzing the melon genome. These genes were located on six chromosomes and divided into three groups composed of nine, six, and six CmOMTs based on phylogenetic analysis. Gene structure and motif descriptions were similar within the same classes. Each CmOMT gene contains at least one cis-acting element associated with hormone transport regulation. Analysis of cis-acting elements illustrated the potential role of CmOMTs in developmental regulation and adaptations to various abiotic and biotic stresses. The RNA-seq and quantitative real-time PCR (qRT-PCR) results indicated that NaCl stress significantly induced CmOMT6/9/14/18 and chilling and high temperature and humidity (HTH) stresses significantly upregulated CmOMT14/18. Furthermore, the expression pattern of CmOMT18 may be associated with Fusarium oxysporum f. sp. melonis race 1.2 (FOM1.2) and powdery mildew resistance. Our study tentatively explored the biological functions of CmOMT genes in various stress regulation pathways and provided a conceptual basis for further detailed studies of the molecular mechanisms.

A subfamily of the small heat shock proteins of the marine red alga Neopyropia yezoensis localizes in the chloroplast

Small heat shock proteins (sHSPs) play a crucial role under abiotic stress and are present in all organisms, from eukaryotes to prokaryotes. However, studies on the sHSP gene family in red alga are limited. In this study, we aimed to identify and characterize NysHSP genes from the genome of N. yezoensis, a marine red alga adapted to the stressful intertidal zone. We identified seven NysHSP genes distributed on all three chromosomes. Expression analysis revealed that all NysHSP genes responded to H2O2 and heat stress in the gametophytic thalli, but these genes responded only to heat stress in the sporophytic conchocelis. NysHSP20.3, which has an acidic isoelectric point (pI) and short N-terminal region, was localized as granules in the cytosol. Fluorescence imaging of the NysHSP25.8-GFP and NysHSP28.4-GFP fusion proteins revealed that these proteins were located in the chloroplast. Based on their characteristics and cellular localization, the NysHSPs are divided into two subfamilies. Subfamily I includes four sHSP genes that strongly respond to heat stress and encode a protein localized in the cytosol. The NysHSP gene of subfamily II encodes a polypeptide with a long N-terminal region located in the chloroplast. This study provides insights into the evolution and function of the sHSP gene family of the marine red alga N. yezoensis and how it adapts to the stressful intertidal zone.

The heat shock protein 20 gene family in large yellow croaker (Larimichthys crocea): Identification, phylogenetic relationships, expression analyses

Large yellow croaker (Larimichthys crocea) is an economically important fish in China, but its aquaculture industry has been threatened by both biotic and abiotic stressors such as hypoxia and pathogens. In the current study, hsp20 genes were identified and analyzed systematically for the first time from the genome of large yellow croaker, and their roles in hypoxia response and Aeromonas hydrophila, Pseudomonas plecoglossicida infection were investigated. Herein, 11 hsp20 genes were identified and annotated, phylogenetic analysis and selection pressure analysis showed that the hsp20 genes were evolutionarily-constrained and their function was conserved among fishes. Besides, we observed the expression patterns of the hsp20 genes under hypoxia and two pathogens' stress. In brief, seven, four, seven genes responded to hypoxia stress, A. hydrophila infection and P. plecoglossicida challenge, respectively, which indicated that they were involved in hypoxia and disease responses. Furthermore, pathogen- and time-specific pattern was observed after A. hydrophila and P. plecoglossicida infection whereas tissue-specific pattern was observed after hypoxia exposure, revealing that hsp20 genes showed differential functions in response to hypoxia and immune stress. Taken together, these results provided preliminary information for future analysis of the roles of hsp20 genes in both biotic and abiotic stress response in fish.

Identification of the Maize LEA Gene Family and Its Relationship with Kernel Dehydration

Maize, the most widely planted and highest yielding of the three major crops in the world, requires the development and breeding of new varieties to accommodate the shift towards mechanized harvesting. However, the moisture content of kernels during harvest poses a significant challenge to mechanized harvesting, leading to seed breakage and increased storage costs. Previous studies highlighted the importance of LEA (Late Embryogenesis Abundant) members in regulating kernel dehydration. In this study, we aimed to gain a better understanding of the relationship between the LEA family and grain dehydration in maize. Through expression pattern analysis of maize, we identified 52 LEA genes (ZmLEAs) distributed across 10 chromosomes, organized into seven subgroups based on phylogenetic analysis, gene structure, and conserved motifs. Evolutionary and selective pressure analysis revealed that the amplification of ZmLEA genes primarily resulted from whole-genome or fragment replication events, with strong purifying selection effects during evolution. Furthermore, the transcriptome data of kernels of two maize inbred lines with varying dehydration rates at different developmental stages showed that 14 ZmLEA genes were expressed differentially in the two inbreds. This suggested that the ZmLEA genes might participate in regulating the kernel dehydration rate (KDR) in maize. Overall, this study enhances our understanding of the ZmLEA family and provides a foundation for further research into its role in regulating genes associated with grain dehydration in maize.

Genome-Wide Analysis of Family I84 Protease Inhibitor Genes in Three Bivalves Reveals Important Information About the Protein Family's Evolution

Family I84 serine protease inhibitors are believed to be mollusk specific proteins involved in host defense. The molecular evolution of the family, however, remains to be understood. In this study, the genes of Family I84 protease inhibitors in 3 bivalves, Crassostrea gigas, Crassostrea virginica and Tegillarca granosa, were analyzed at the genomic level. A total of 66 Family I84 genes (22 in C. gigas, 28 in C. virginica and 16 in T. granosa) were identified from the 3 species. They distributed unevenly in the genomes involving 4 chromosomes in C. gigas and 5 chromosomes in C. virginica and T. granosa and some genes were tandemly duplicated. Most genes had 3 exons with 12 genes having 4 exons and 1 gene having 2 exons. All genes but 1 from C. gigas and 1 from T. granosa encoded peptides with a signal sequence at the N-terminus, and the properties of the predicted mature molecules were similar. Four conserved motifs were identified in the 66 amino acid sequences. Collinear analysis revealed higher collinearity between the 2 oyster species in general genes and in Family I84 genes. Phylogenetic analysis of the 66 genes with those previously reported from 3 other bivalves and 1 gastropod showed that Family I84 protease inhibitor genes from the same species tended to be grouped together in terminal branches of the constructed Maximum likelihood tree, but most internal nodes were poorly supported by the bootstrap values. In addition, differences in expression patterns between the genes of a same species were observed in the developmental stages and tissues of C. gigas and T. granosa. Moreover, the co-expression of genes within Family I84 and Family I84 genes with non-Family I84 were also detected in C. gigas and T. granosa. These results suggested that Family I84 protease inhibitor genes evolved by active duplications and structural and functional diversifications after the speciation of related mollusks, and the diversified protease inhibitor family was likely multifunctional.

AlignStatPlot: An R package and online tool for robust sequence alignment statistics and innovative visualization of big data

Multiple sequence alignment (MSA) is essential for understanding genetic variations controlling phenotypic traits in all living organisms. The post-analysis of MSA results is a difficult step for researchers who do not have programming skills. Especially those working with large scale data and looking for potential variations or variable sample groups. Generating bi-allelic data and the comparison of wild and alternative gene forms are important steps in population genetics. Customising MSA visualisation for a single page view is difficult, making viewing potential indels and variations challenging. There are currently no bioinformatics tools that permit post-MSA analysis, in which data on gene and single nucleotide scales could be combined with gene annotations and used for cluster analysis. We introduce "AlignStatPlot," a new R package and online tool that is well-documented and easy-to use for MSA and post-MSA analysis. This tool performs both traditional and cutting-edge analyses on sequencing data and generates new visualisation methods for MSA results. When compared to currently available tools, AlignStatPlot provides a robust ability to handle and visualise diversity data, while the online version will save time and encourage researchers to focus on explaining their findings. It is a simple tool that can be used in conjunction with population genetics software.

Integrated Transcriptome and Metabolome Analysis of Salinity Tolerance in Response to Foliar Application of β-Alanine in Cotton Seedlings

Salinity is amongst the serious abiotic stresses cotton plants face, impairing crop productivity. Foliar application of β-alanine is employed to improve salt tolerance in various crops, but the exact mechanism behind it is not yet completely understood. An advanced line SDS-01 of upland cotton Gossypium hirsutum L. was utilized to determine its salt tolerance. Foliar treatment with the β-alanine solution at different concentrations was applied to the seedlings stressed with 0.8% NaCl solution. On the 10th day of treatment, samples were collected for transcriptome and metabolome analyses. β-alanine solution at a concentration of 25 mM was found to be the best treatment with the lowest mortality rate and highest plant height and above-ground biomass under salt stress. Both differentially expressed genes and accumulated metabolites analyses showed improved tolerance of treated seedlings. The photosynthetic efficiency improved in seedlings due to higher expression of photosynthesis-antenna proteins and activation of hormones signal transduction after treatment with β-alanine. Highly expressed transcription factors observed were MYB, HD-ZIP, ARF, MYC, EREB, DELLA, ABF, H2A, H4, WRKY, and HK involved in the positive regulation of salinity tolerance in β-alanine-treated seedlings. Furthermore, compared to the control, the high accumulation of polyamines, coumarins, organic acids, and phenolic compounds in the β-alanine-treated seedlings helped regulate cellular antioxidant (glutathione and L-Cysteine) production. Hence, to improve salt tolerance and productivity in cotton, foliar application of β-alanine at the seedling stage can be a valuable management practice.

Integrative analysis of genome and transcriptome reveal the genetic basis of high temperature tolerance in pleurotus giganteus (Berk. Karun & Hyde)

BACKGROUND

Pleurotus giganteus is a commonly cultivated mushroom with notable high temperature resistance, making it significant for the growth of the edible fungi industry in the tropics. Despite its practical importance,, the genetic mechanisms underlying its ability to withstand high temperature tolerance remain elusive.

RESULTS

In this study, we performed high-quality genome sequencing of a monokaryon isolated from a thermotolerant strain of P. giganteus. The genome size was found to be 40.11 Mb, comprising 17 contigs and 13,054 protein-coding genes. Notably, some genes related to abiotic stress were identified in genome, such as genes regulating heat shock protein, protein kinase activity and signal transduction. These findings provide valuable insights into the genetic basis of P. giganteus' high temperature resistance. Furthermore, the phylogenetic tree showed that P. giganteus was more closely related to P. citrinopileatus than other Pleurotus species. The divergence time between Pleurotus and Lentinus was estimated as 153.9 Mya, and they have a divergence time with Panus at 168.3 Mya, which proved the taxonomic status of P. giganteus at the genome level. Additionally, a comparative transcriptome analysis was conducted between mycelia treated with 40 °C heat shock for 18 h (HS) and an untreated control group (CK). Among the 2,614 differentially expressed genes (DEGs), 1,303 genes were up-regulated and 1,311 were down-regulated in the HS group. The enrichment analysis showed that several genes related to abiotic stress, including heat shock protein, DnaJ protein homologue, ubiquitin protease, transcription factors, DNA mismatch repair proteins, and zinc finger proteins, were significantly up-regulated in the HS group. These genes may play important roles in the high temperature adaptation of P. giganteus. Six DEGs were selected according to fourfold expression changes and were validated by qRT-PCR, laying a good foundation for further gene function analysis.

CONCLUSION

Our study successfully reported a high-quality genome of P. giganteus and identified genes associated with high-temperature tolerance through an integrative analysis of the genome and transcriptome. This study lays a crucial foundation for understanding the high-temperature tolerance mechanism of P. giganteus, providing valuable insights for genetic modification of P. giganteus strains and the development of high-temperature strains for the edible fungus industry, particularly in tropical regions.

Comprehensive investigation of cucumber heat shock proteins under abiotic stress conditions: A multi-omics survey

Heat-shock proteins (Hsps) are a family of proteins essential in preserving the vitality and functionality of proteins under stress conditions. Cucumber (Cucumis sativus) is a widely grown plant with high nutritional value and is used as a model organism in many studies. This study employed a genomics, transcriptomics, and metabolomics approach to investigate cucumbers' Hsps against abiotic stress conditions. Bioinformatics methods were used to identify six Hsp families in the cucumber genome and to characterize family members. Transcriptomics data from the Sequence Read Archive (SRA) database was also conducted to select CsHsp genes for further study. Real-time PCR was used to evaluate gene expression levels under different stress conditions, revealing that CssHsp-08 was a vital gene for resistance to stress conditions; including drought, salinity, cold, heat stresses, and ABA application. Gas Chromatography-Mass Spectrometry (GC-MS) analysis of plant extracts revealed that amino acids accumulate in leaves under high temperatures and roots under drought, while sucrose accumulates in both tissues under applied most stress factors. The study provides valuable insights into the structure, organization, evolution, and expression profiles of the Hsp family and contributes to a better understanding of plant stress mechanisms. These findings have important implications for developing crops that can withstand environmental stress conditions better.

Hsp70 Gene Family in Sebastiscus marmoratus: The Genome-Wide Identification and Transcriptome Analysis under Thermal Stress

Heat shock protein 70 kDa (Hsp70) is a highly conserved heat stress protein that is important in biotic processes and responses to abiotic stress. Hsp70 genes may be important in Sebastiscus marmoratus, for it is a kind of nearshore reef fish, and habitat temperature change is more drastic during development. However, genome-wide identification and expression analysis in the Hsp70 gene family of S. marmoratus are still lacking. Here, a total of 15 Hsp70 genes in the genome of S. marmoratus are identified, and their expression patterns were investigated using transcriptomic data from thermal stress experiments. The expansion and gene duplication events of Hsp70 genes from the Hspa4, Hspa8, and Hspa12a subfamilies in S. marmoratus are revealed by phylogenetic analysis. qRT-PCR expression patterns demonstrated that seven Hsp70 genes were significantly up-regulated and none were significantly down-regulated after heat treatment. Only the hsp70 gene was significantly up-regulated after cold treatment. The selection test further showed a purifying selection on the duplicated gene pairs, suggesting that these genes underwent subfunctionalization. Our results add novel insight to aquaculture and biological research on S. marmoratus, providing important information on how Hsp70 genes are regulated in Scorpaeniformes under thermal stress.

Genome-wide analysis of the HSP20 gene family and its response to heat and drought stress in Coix (Coix lacryma-jobi L.)

BACKGROUND

Heat shock protein 20 (HSP20) is a member of the heat stress-related protein family, which plays critical roles in plant growth, development, and response to abiotic stresses. Although many HSP20 genes have been associated with heat stress in numerous types of plants, little is known about the details of the HSP20 gene family in Coix. To investigate the mechanisms of the ClHSP20 response to heat and drought stresses, the ClHSP20 gene family in Coix was identified and characterized based on genome-wide analysis.

RESULTS

A total of 32 putative ClHSP20 genes were identified and characterized in Coix. Phylogenetic analysis indicated that ClHSP20s were grouped into 11 subfamilies. The duplicated event analysis demonstrated that tandem duplication and segment duplication events played crucial roles in promoting the expansion of the ClHSP20 gene family. Synteny analysis showed that Coix shared the highest homology in 36 HSP20 gene pairs with wheat, followed by 22, 19, 15, and 15 homologous gene pairs with maize, sorghum, barley, and rice, respectively. The expression profile analysis showed that almost all ClHSP20 genes had different expression levels in at least one tissue. Furthermore, 22 of the 32 ClHSP20 genes responded to heat stress, with 11 ClHSP20 genes being significantly upregulated and 11 ClHSP20 genes being significantly downregulated. Furthermore, 13 of the 32 ClHSP20 genes responded to drought stress, with 6 ClHSP20 genes being significantly upregulated and 5 ClHSP20 genes being significantly downregulated.

CONCLUSIONS

Thirty-two ClHSP20 genes were identified and characterized in the genome of Coix. Tandem and segmental duplication were identified as having caused the expansion of the ClHSP20 gene family. The expression patterns of the ClHSP20 genes suggested that they play a critical role in growth, development, and response to heat and drought stress. The current study provides a theoretical basis for further research on ClHSP20s and will facilitate the functional characterization of ClHSP20 genes.

Structural and expression analysis of polyphenol oxidases potentially involved in globe artichoke (C. cardunculus var. scolymus L.) tissue browning

Globe artichoke capitula are susceptible to browning due to oxidation of phenols caused by the activity of polyphenol oxidases (PPOs), this reduces their suitability for fresh or processed uses. A genome-wide analysis of the globe artichoke PPO gene family was performed. Bioinformatics analyses identified eleven PPOs and their genomic and amino acidic features were annotated. Cis-acting element analysis identified a gene regulatory and functional profile associated to plant growth and development as well as stress response. For some PPOs, phylogenetic analyses revealed a structural and functional conservation with different Asteraceae PPOs, while the allelic variants of the eleven PPOs investigated across four globe artichoke varietal types identified several SNP/Indel variants, some of which having impact on gene translation. By RTqPCR were assessed the expression patterns of PPOs in plant tissues and in vitro calli characterized by different morphologies. Heterogeneous PPO expression profiles were observed and three of them (PPO6, 7 and 11) showed a significant increase of transcripts in capitula tissues after cutting. Analogously, the same three PPOs were significantly up-regulated in calli showing a brown phenotype due to oxidation of phenols. Our results lay the foundations for a future application of gene editing aimed at disabling the three PPOs putatively involved in capitula browning.

StMAPK1 functions as a thermos-tolerant gene in regulating heat stress tolerance in potato (Solanum tuberosum)

Background and aims

Mitogen-activated protein kinases (MAPKs) have been reported to respond to various stimuli including heat stress. This research aimed to investigate whether StMAPK1 is implicated in the transduction of the heat stress signal to adapt heat stress as a thermos-tolerant gene.

Materials and methods

Potato plants were cultivated under mild (30°C) and acute (35°C) heat stress conditions to analyze mRNA expression of StMAPKs and physiological indicators. StMAPK1 was up-regulated and down-regulated by transfection. Subcellular localization of StMAPK1 protein was observed by fluorescence microscope. The transgenic potato plants were assayed for physiological indexes, photosynthesis, cellular membrane integrity, and heat stress response gene expression.

Results

Heat stress altered the expression prolife of StMAPKs. StMAPK1 overexpression changed the physiological characteristics and phenotypes of potato plants under heat stresses. StMAPK1 mediates photosynthesis and maintains membrane integrity of potato plants in response to heat stress. Stress response genes (StP5CS, StCAT, StSOD, and StPOD) in potato plants were altered by StMAPK1 dysregulation. mRNA expression of heat stress genes (StHSP90, StHSP70, StHSP20, and StHSFA3) was affected by StMAPK1.

Conclusions

StMAPK1 overexpression increases the heat-tolerant capacity of potato plants at the morphological, physiological, molecular, and genetic levels.

Genome-Wide Analysis of the FBA Subfamily of the Poplar F-Box Gene Family and Its Role under Drought Stress

F-box proteins are important components of eukaryotic SCF E3 ubiquitin ligase complexes, which specifically determine protein substrate proteasomal degradation during plant growth and development, as well as biotic and abiotic stress. It has been found that the FBA (F-box associated) protein family is one of the largest subgroups of the widely prevalent F-box family and plays significant roles in plant development and stress response. However, the FBA gene family in poplar has not been systematically studied to date. In this study, a total of 337 F-box candidate genes were discovered based on the fourth-generation genome resequencing of P. trichocarpa. The domain analysis and classification of candidate genes revealed that 74 of these candidate genes belong to the FBA protein family. The poplar F-box genes have undergone multiple gene replication events, particularly in the FBA subfamily, and their evolution can be attributed to genome-wide duplication (WGD) and tandem duplication (TD). In addition, we investigated the P. trichocarpa FBA subfamily using the PlantGenIE database and quantitative real-time PCR (qRT-PCR); the results showed that they are expressed in the cambium, phloem and mature tissues, but rarely expressed in young leaves and flowers. Moreover, they are also widely involved in the drought stress response. At last, we selected and cloned PtrFBA60 for physiological function analysis and found that it played an important role in coping with drought stress. Taken together, the family analysis of FBA genes in P. trichocarpa provides a new opportunity for the identification of P. trichocarpa candidate FBA genes and elucidation of their functions in growth, development and stress response, thus demonstrating their utility in the improvement of P. trichocarpa.

Genome-Wide Identification and Characterization of the PPO Gene Family in Cotton (Gossypium) and Their Expression Variations Responding to Verticillium Wilt Infection

Polyphenol oxidases (PPOs) are copper-binding metalloproteinases encoded by nuclear genes, ubiquitously existing in the plastids of microorganisms, plants, and animals. As one of the important defense enzymes, PPOs have been reported to participate in the resistant processes that respond to diseases and insect pests in multiple plant species. However, PPO gene identification and characterization in cotton and their expression patterns under Verticillium wilt (VW) treatment have not been clearly studied. In this study, 7, 8, 14, and 16 PPO genes were separately identified from Gossypium arboreum, G. raimondii, G. hirsutum, and G. barbadense, respectively, which were distributed within 23 chromosomes, though mainly gathered in chromosome 6. The phylogenetic tree manifested that all the PPOs from four cotton species and 14 other plants were divided into seven groups, and the analyses of the conserved motifs and nucleotide sequences showed highly similar characteristics of the gene structure and domains in the cotton PPO genes. The dramatically expressed differences were observed among the different organs at various stages of growth and development or under the diverse stresses referred to in the published RNA-seq data. Quantitative real-time PCR (qRT-PCR) experiments were also performed on the GhPPO genes in the roots, stems, and leaves of VW-resistant MBI8255 and VW-susceptible CCRI36 infected with Verticillium dahliae V991, proving the strong correlation between PPO activity and VW resistance. A comprehensive analysis conducted on cotton PPO genes contributes to the screening of the candidate genes for subsequent biological function studies, which is also of great significance for the in-depth understanding of the molecular genetic basis of cotton resistance to VW.

Identification of histone acetyltransferase genes responsible for cannabinoid synthesis in hemp

BACKGROUND

Histone acetyltransferases (HATs) play an important role in plant growth and development, stress response, and regulation of secondary metabolite biosynthesis. Hemp (Cannabis sativa L.) is famous for its high industrial, nutritional, and medicinal value. It contains non-psychoactive cannabinoid cannabidiol (CBD) and cannabinol (CBG), which play important roles as anti-inflammatory and anti-anxiety. At present, the involvement of HATs in the regulation of cannabinoid CBD and CBG synthesis has not been clarified.

METHODS

The members of HAT genes family in hemp were systematically analyzed by bioinformatics analysis. In addition, the expression level of HATs and the level of histone acetylation modification were analyzed based on transcriptome data and protein modification data. Real-time quantitative PCR was used to verify the changes in gene expression levels after inhibitor treatment. The changes of CBD and CBG contents after inhibitor treatment were verified by HPLC-MS analysis.

RESULTS

Here, 11 HAT genes were identified in the hemp genome. Phylogenetic analysis showed that hemp HAT family genes can be divided into six groups. Cannabinoid synthesis genes exhibited spatiotemporal specificity, and histones were acetylated in different inflorescence developmental stages. The expression of cannabinoid synthesis genes was inhibited and the content of CBD and CBG declined by 10% to 55% in the samples treated by HAT inhibitor (PU139). Results indicated that CsHAT genes may regulate cannabinoid synthesis through altering histone acetylation.

CONCLUSIONS

Our study provides genetic information of HATs responsible for cannabinoid synthesis, and offers a new approach for increasing the content of cannabinoid in hemp.

Genomic Survey of Heat Shock Proteins in Liriodendron chinense Provides Insight into Evolution, Characterization, and Functional Diversities

Heat shock proteins (HSPs) are conserved molecular chaperones whose main role is to facilitate the regulation of plant growth and stress responses. The HSP gene family has been characterized in most plants and elucidated as generally stress-induced, essential for their cytoprotective roles in cells. However, the HSP gene family has not yet been analyzed in the Liriodendron chinense genome. In current study, 60 HSP genes were identified in the L. chinense genome, including 7 LchiHSP90s, 23 LchiHSP70s, and 30 LchiHSP20s. We investigated the phylogenetic relationships, gene structure and arrangement, gene duplication events, cis-acting elements, 3D-protein structures, protein-protein interaction networks, and temperature stress responses in the identified L. chinense HSP genes. The results of the comparative phylogenetic analysis of HSP families in 32 plant species showed that LchiHSPs are closely related to the Cinnamomum kanehirae HSP gene family. Duplication events analysis showed seven segmental and six tandem duplication events that occurred in the LchiHSP gene family, which we speculated to have played an important role in the LchiHSP gene expansion and evolution. Furthermore, the Ka/Ks analysis indicated that these genes underwent a purifying selection. Analysis in the promoter region evidenced that the promoter region LchiHSPs carry many stress-responsive and hormone-related cis-elements. Investigations in the gene expression patterns of the LchiHSPs using transcriptome data and the qRT-PCR technique indicated that most LchiHSPs were responsive to cold and heat stress. In total, our results provide new insights into understanding the LchiHSP gene family function and their regulatory mechanisms in response to abiotic stresses.

Genome-Wide Identification and Expression Profiling of Heat Shock Protein 20 Gene Family in Sorbus pohuashanensis (Hance) Hedl under Abiotic Stress

Small heat shock proteins (HSP20s) are a significant factor in plant growth and development in response to abiotic stress. In this study, we investigated the role of HSP20s' response to the heat stress of Sorbus pohuashanensis introduced into low-altitude areas. The HSP20 gene family was identified based on the genome-wide data of S. pohuashanensis, and the expression patterns of tissue specificity and the response to abiotic stresses were evaluated. Finally, we identified 38 HSP20 genes that were distributed on 16 chromosomes. Phylogenetic analysis of HSP20s showed that the closest genetic relationship to S. pohuashanensis (SpHSP20s) is Malus domestica, followed by Populus trichocarpa and Arabidopsis thaliana. According to phylogenetic analysis and subcellular localization prediction, the 38 SpHSP20s belonged to 10 subfamilies. Analysis of the gene structure and conserved motifs indicated that HSP20 gene family members are relatively conserved. Synteny analysis showed that the expansion of the SpHSP20 gene family was mainly caused by segmental duplication. In addition, many cis-acting elements connected with growth and development, hormones, and stress responsiveness were found in the SpHSP20 promoter region. Analysis of expression patterns showed that these genes were closely related to high temperature, drought, salt, growth, and developmental processes. These results provide information and a theoretical basis for the exploration of HSP20 gene family resources, as well as the domestication and genetic improvement of S. pohuashanensis.

Mechanistic Concept of Physiological, Biochemical, and Molecular Responses of the Potato Crop to Heat and Drought Stress

Most cultivated potatoes are tetraploid, and the tuber is the main economic part that is consumed due to its calorific and nutritional values. Recent trends in climate change led to the frequent occurrence of heat and drought stress in major potato-growing regions worldwide. The optimum temperature for tuber production is 15-20 °C. High-temperature and water-deficient conditions during the growing season result in several morphological, physiological, biochemical, and molecular alterations. The morphological changes under stress conditions may affect the process of stolon formation, tuberization, and bulking, ultimately affecting the tuber yield. This condition also affects the physiological responses, including an imbalance in the allocation of photoassimilates, respiration, water use efficiency, transpiration, carbon partitioning, and the source-sink relationship. The biochemical responses under stress conditions involve maintaining ionic homeostasis, synthesizing heat shock proteins, achieving osmolyte balance, and generating reactive oxygen species, ultimately affecting various biochemical pathways. Different networks that include both gene regulation and transcription factors are involved at the molecular level due to the combination of hot and water-deficient conditions. This article attempts to present an integrative content of physio-biochemical and molecular responses under the combined effects of heat and drought, prominent factors in climate change. Taking into account all of these aspects and responses, there is an immediate need for comprehensive screening of germplasm and the application of appropriate approaches and tactics to produce potato cultivars that perform well under drought and in heat-affected areas.

Genome-wide identification, characterization and expression of HSP 20 gene family in dove

Davidia involucrata is a significant living fossil with high abiotic stress tolerance. Although heat shock protein 20 (HSP20) has already been linked to heat stress, nothing is known about HSP20 family protein activities in D. involucrata. The functional dynamics of the D. involucrata HSP20 (DiHSP20) gene family were identified and characterized using a thorough genome-wide investigation. From the genome of D. involucrata, a total of 42 HSP20 genes were identified, which are distributed across 16 chromosomes. The DiHSP20 proteins were grouped into seven separate subfamilies by our phylogenetic analysis, which was validated by the conserved motif composition and gene structure studies. Segmental duplication events were shown to play a crucial role in the expansion of the DiHSP20 gene family. Synteny analysis revealed that 19 DiHSP20 genes of D. involucrata shared a syntenic connection with Arabidopsis genes, 39 with C. acuminata genes, and just 6 with O. sativa genes. Additionally, heat stress differently enhanced the expression levels of D. involucrata HSP20 genes. After 1 hour of heat treatment, the expression levels of most DiHSP20 genes, particularly DiHSP20-7, DiHSP20-29, DiHSP20-30, DiHSP20-32, and DiHSP20-34, were dramatically increased, suggestted that they might be employed as heat tolerance candidate genes. Overall, these findings add to our knowledge of the HSP20 family genes and provide helpful information for breeding heat stress resistance in D. involucrata.

Genome-Wide Identification and Salt Stress Response Analysis of the bZIP Transcription Factor Family in Sugar Beet

As one of the largest transcription factor families in plants, bZIP transcription factors play important regulatory roles in different biological processes, especially in the process of stress response. Salt stress inhibits the growth and yield of sugar beet. However, bZIP-related studies in sugar beet (Beta vulgaris L.) have not been reported. This study aimed to identify the bZIP transcription factors in sugar beet and analyze their biological functions and response patterns to salt stress. Using bioinformatics, 48 BvbZIP genes were identified in the genome of sugar beet, encoding 77 proteins with large structural differences. Collinearity analysis showed that three pairs of BvbZIP genes were fragment replication genes. The BvbZIP genes were grouped according to the phylogenetic tree topology and conserved structures, and the results are consistent with those reported in Arabidopsis. Under salt stress, the expression levels of most BvbZIP genes were decreased, and only eight genes were up-regulated. GO analysis showed that the BvbZIP genes were mainly negatively regulated in stress response. Protein interaction prediction showed that the BvbZIP genes were mainly involved in light signaling and ABA signal transduction, and also played a certain role in stress responses. In this study, the structures and biological functions of the BvbZIP genes were analyzed to provide foundational data for further mechanistic studies and for facilitating the efforts toward the molecular breeding of stress-resilient sugar beet.

Phylogenetic and Transcriptional Analyses of the HSP20 Gene Family in Peach Revealed That PpHSP20-32 Is Involved in Plant Height and Heat Tolerance

The heat shock protein 20 (HSP20) proteins comprise an ancient, diverse, and crucial family of proteins that exists in all organisms. As a family, the HSP20s play an obvious role in thermotolerance, but little is known about their molecular functions in addition to heat acclimation. In this study, 42 PpHSP20 genes were detected in the peach genome and were randomly distributed onto the eight chromosomes. The primary modes of gene duplication of the PpHSP20s were dispersed gene duplication (DSD) and tandem duplication (TD). PpHSP20s in the same class shared similar motifs. Based on phylogenetic analysis of HSP20s in peach, Arabidopsis thaliana, Glycine max, and Oryza sativa, the PpHSP20s were classified into 11 subclasses, except for two unclassified PpHSP20s. cis-elements related to stress and hormone responses were detected in the promoter regions of most PpHSP20s. Gene expression analysis of 42 PpHSP20 genes revealed that the expression pattern of PpHSP20-32 was highly consistent with shoot length changes in the cultivar 'Zhongyoutao 14', which is a temperature-sensitive semi-dwarf. PpHSP20-32 was selected for further functional analysis. The plant heights of three transgenic Arabidopsis lines overexpressing PpHSP20-32 were significantly higher than WT, although there was no significant difference in the number of nodes. In addition, the seeds of three over-expressing lines of PpHSP20-32 treated with high temperature showed enhanced thermotolerance. These results provide a foundation for the functional characterization of PpHSP20 genes and their potential use in the growth and development of peach.

Genome-Wide Identification and Characterization of Heat Shock Protein 20 Genes in Maize

Maize is an important cereal crop worldwide and is sensitive to abiotic stresses in fluctuant environments that seriously affect its growth, yield, and quality. The small heat shock protein (HSP20) plays a crucial role in protecting plants from abiotic stress. However, little is known about HSP20 in maize (ZmHSP20). In this study, 44 ZmHSP20s were identified, which were unequally distributed over 10 chromosomes, and 6 pairs of ZmHSP20s were tandemly presented. The gene structure of ZmHSP20s was highly conserved, with 95% (42) of the genes having no more than one intron. The analysis of the cis-element in ZmHSP20s promoter demonstrated large amounts of elements related to hormonal and abiotic stress responses, including abscisic acid (ABA), high temperature, and hypoxia. The ZmHSP20s protein had more than two conserved motifs that were predictably localized in the cytoplasm, nucleus, endoplasmic reticulum, peroxisome, mitochondria, and plasma. Phylogenetic analysis using HSP20s in Arabidopsis, rice, maize, and Solanum tuberosum indicated that ZmHSP20s were classified into 11 categories, of which each category had unique subcellular localization. Approximately 80% (35) of ZmHSP20 were upregulated under heat stress at the maize seedling stage, whereas the opposite expression profiling of 10 genes under 37 and 48 °C was detected. A total of 20 genes were randomly selected to investigate their expression under treatments of ABA, gibberellin (GA), ethylene, low temperature, drought, and waterlogging, and the results displayed that more than half of these genes were downregulated while ZmHSP20-3, ZmHSP20-7, ZmHSP20-24, and ZmHSP20-44 were upregulated under 1 h treatment of ethylene. A yeast-one-hybrid experiment was conducted to analyze the binding of four heat stress transcription factors (ZmHSFs) with eight of the ZmHSP20s promoter sequences, in which ZmHSF3, ZmHSF13, and ZmHSF17 can bind to most of these selected ZmHSP20s promoters. Our results provided a valuable resource for studying HSP20s function and offering candidates for genetic improvement under abiotic stress.

Genome-wide identification and characterization of the C2 domain family in Sorghum bicolor (L.) and expression profiles in response to saline-alkali stress

The C2 domain family proteins in plants has been recently shown to be involved in the response to abiotic stress such as salt and drought stress. However, less information on C2 domain family members has been reported in Sorghum bicolor (L.), which is a tolerant cereal crop. To elaborate the mechanism of C2 domain family members in response to abiotic stress, bioinformatic methods were used to analyze this family. The results indicated that 69 C2 domain genes belonging to 5 different groups were first identified within the sorghum genome, and each group possessed various gene structures and conserved functional domains. Second, those C2 family genes were localized on 10 chromosomes 3 tandem repeat genes and 1 pair of repeat gene fragments were detected. The family members further presented a variety of stress responsive cis-elements. Third, in addition to being the major integral component of the membrane, sorghum C2 domain family proteins mainly played roles in response to abiotic and biotic stress with their organic transport and catalytic activity by specific location in the cell on the basis of gene ontology analysis. C2 family genes were differentially expressed in root, shoot or leaf, and shown different expression profiling after saline-alkali stress, which indicated that C2 family members played an important role in response to saline-alkali stress based on the transcription profiles of RNA-seq data and expression analysis by quantitative real-time polymerase chain reaction. Besides, most C2 family members were mainly located in cytoplasmi and nucleus. Weighted gene co-expression network analysis revealed three modules (turquoise, dark magenta and pink) that were associated with stress resistance, respectively. Therefore, the present research provides comprehensive information for further analysis of the molecular function of C2 domain family genes in sorghum.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-022-01222-3.

Genome-wide analysis of HSP20 gene family and expression patterns under heat stress in cucumber (Cucumis sativus L.)

Cucumber is an important vegetable in China, and its yield and cultivation area are among the largest in the world. Excessive temperatures lead to high-temperature disorder in cucumber. Heat shock protein 20 (HSP20), an essential protein in the process of plant growth and development, is a universal protective protein with stress resistance. HSP20 plays crucial roles in plants under stress. In this study, we characterized the HSP20 gene family in cucumber by studying chromosome location, gene duplication, phylogenetic relationships, gene structure, conserved motifs, protein-protein interaction (PPI) network, and cis-regulatory elements. A total of 30 CsHSP20 genes were identified, distributed across 6 chromosomes, and classified into 11 distinct subgroups based on conserved motif composition, gene structure analyses, and phylogenetic relationships. According to the synteny analysis, cucumber had a closer relationship with Arabidopsis and soybean than with rice and maize. Collinearity analysis revealed that gene duplication, including tandem and segmental duplication, occurred as a result of positive selection and purifying selection. Promoter analysis showed that the putative promoters of CsHSP20 genes contained growth, stress, and hormone cis-elements, which were combined with protein-protein interaction networks to reveal their potential function mechanism. We further analyzed the gene expression of CsHSP20 genes under high stress and found that the majority of the CsHSP20 genes were upregulated, suggesting that these genes played a positive role in the heat stress-mediated pathway at the seedling stage. These results provide comprehensive information on the CsHSP20 gene family in cucumber and lay a solid foundation for elucidating the biological functions of CsHSP20. This study also provides valuable information on the regulation mechanism of the CsHSP20 gene family in the high-temperature resistance of cucumber.

Genome-wide identification and expression analysis of the Hsp20, Hsp70 and Hsp90 gene family in Dendrobium officinale

Dendrobium officinale, an important orchid plant with great horticultural and medicinal values, frequently suffers from abiotic or biotic stresses in the wild, which may influence its well-growth. Heat shock proteins (Hsps) play essential roles in the abiotic stress response of plants. However, they have not been systematically investigated in D. officinale. Here, we identified 37 Hsp20 genes (DenHsp20s), 43 Hsp70 genes (DenHsp70s) and 4 Hsp90 genes (DenHsp90s) in D. officinale genome. These genes were classified into 8, 4 and 2 subfamilies based on phylogenetic analysis and subcellular predication, respectively. Sequence analysis showed that the same subfamily members have relatively conserved gene structures and similar protein motifs. Moreover, we identified 33 pairs of paralogs containing 30 pairs of tandem duplicates and 3 pairs of segmental duplicates among these genes. There were 7 pairs in DenHsp70s under positive selection, which may have important functions in helping cells withstand extreme stress. Numerous gene promoter sequences contained stress and hormone response cis-elements, especially light and MeJA response elements. Under MeJA stress, DenHsp20s, DenHsp70s and DenHsp90s responded to varying degrees, among which DenHsp20-5,6,7,16 extremely up-regulated, which may have a strong stress resistance. Therefore, these findings could provide useful information for evolutional and functional investigations of Hsp20, Hsp70 and Hsp90 genes in D. officinale.

Characteristics and molecular identification of glyceraldehyde-3-phosphate dehydrogenases in poplar

Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), an essential enzyme of the glycolysis metabolic pathway, plays a vital role in carbon metabolism, plant development, and stress resistance. As a kind of woody plant, poplars are widely cultivated for afforestation. Although the whole genome data of poplars have been published, little information is known about the GAPDH family of genes in poplar. This study performed a genome-wide identification of the poplar GAPDH family, and 13 determined PtGAPDH genes were identified from poplar genome. Phylogenetic tree showed that the PtGAPDH members were divided into PtGAPA/B, PtGAPC, PtGAPCp, and PtGAPN groups. A total of 13 PtGAPDH genes were distributed on eight chromosomes, 13 gene pairs belonging to segmented replication events were detected in poplar, and 23 collinearity gene pairs were determined between poplar and willow. The PtGAPDHcis-acting elements associated with growth and development as well as stress resistance revealed that PtGAPDHs might be involved in these processes. The phosphoglycerate kinase (PGK) and triose-phosphate isomerase (TPI) were predicted as the putative interaction proteins of PtGAPDHs. Gene ontology (GO) analysis showed that PtGAPDHs play a crucial role in the oxidation and reduction processes. PtGAPDH expression levels were induced by NaCl and PEG treatments, which implied that PtGAPDHs might be involved in stress response. Overexpression of PtGAPC1 significantly changed the contents of lipid and carbohydrate metabolites, which indicated that PtGAPC1 plays an essential role in metabolic regulation. This study highlights the characterizations and profiles of PtGAPDHs and reveals that PtGAPC1 is involved in the loop of lipid and carbohydrate metabolisms.

Identification of OSCA gene family in Solanum habrochaites and its function analysis under stress

Background

OSCA (hyperosmolality-gated calcium-permeable channel) is a calcium permeable cation channel protein that plays an important role in regulating plant signal transduction. It is involved in sensing changes in extracellular osmotic potential and an increase in Ca²⁺ concentration. S. habrochaites is a good genetic material for crop improvement against cold, late blight, planthopper and other diseases. Till date, there is no report on OSCA in S. habrochaites. Thus, in this study, we performed a genome-wide screen to identify OSCA genes in S. habrochaites and characterized their responses to biotic and abiotic stresses.

Results

A total of 11 ShOSCA genes distributed on 8 chromosomes were identified. Subcellular localization analysis showed that all members of ShOSCA localized on the plasma membrane and contained multiple stress-related cis acting elements. We observed that genome-wide duplication (WGD) occurred in the genetic evolution of ShOSCA5 (Solhab04g250600) and ShOSCA11 (Solhab12g051500). In addition, repeat events play an important role in the expansion of OSCA gene family. OSCA gene family of S. habrochaites used the time lines of expression studies by qRT-PCR, do indicate OSCAs responded to biotic stress (Botrytis cinerea) and abiotic stress (drought, low temperature and abscisic acid (ABA)). Among them, the expression of ShOSCAs changed significantly under four stresses. The resistance of silencing ShOSCA3 plants to the four stresses was reduced.

Conclusion

This study identified the OSCA gene family of S. habrochaites for the first time and analyzed ShOSCA3 has stronger resistance to low temperature, ABA and Botrytis cinerea stress. This study provides a theoretical basis for clarifying the biological function of OSCA, and lays a foundation for tomato crop improvement.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08675-6.

The heat shock protein 20 gene editing suppresses mycelial growth of Botryosphaeria dothidea and decreases its pathogenicity to postharvest apple fruits

Apple ring rot caused by Botryosphaeria dothidea is an essential and prevalent disease in the apple orchard in China. Our previous study demonstrated that dimethyl trisulfide (DT) from Chinese leek (Allium tuberosum) significantly suppressed the mycelial growth of B. dothidea and inhibited the incidence of apple ring rot postharvest. However, the mechanism underlying the inhibitory role of DT against B. dothidea is not fully understood. Comparing the control and the DT-treated B. dothidea mycelial transcriptomes revealed that heat shock protein 20 (Hsp20) strongly responded to DT treatment. This study identified four Hsp20 genes throughout the B. dothidea genome (BdHsp20_1-4). Each BdHsp20 gene had a conserved ACD with a variable N-terminal region and a short C-terminal extension. The segmental duplication event has contributed to the expansion of the BdHsp20 gene family. Compared to the wild-type strain, the CRISPR/Cas9 gene-edited BdHsp20 mutant (ΔBdHsp20) decreased the mycelial growth by 55.95% and reduced the disease symptom in postharvest apple fruit by 96.34%. However, the BdHsp20 complemented strain (ΔBdHsp20_C) significantly restored the growth and pathogenicity, which suggested that the BdHsp20 gene was closely involved in the growth and pathogenicity of B. dothidea. This study would accelerate the exploration of the molecular mechanism of the inhibitory effect of DT against B. dothidea and also provide new insights for the management of apple ring rot disease.

Effect of Developmental Stages on Genes Involved in Middle and Downstream Pathway of Volatile Terpene Biosynthesis in Rose Petals

Terpenoids are economically and ecologically important compounds, and they are vital constituents in rose flower fragrance and rose essential oil. The terpene synthase genes (TPSs), trans-prenyltransferases genes (TPTs), NUDX1 are involved in middle and downstream pathway of volatile terpene biosynthesis in rose flowers. We identified 7 complete RcTPTs, 49 complete RcTPSs, and 9 RcNUDX1 genes in the genome of Rosachinensis. During the flower opening process of butterfly rose (Rosachinensis ‘Mutabilis’, MU), nine RcTPSs expressed in the petals of opening MU flowers exhibited two main expression trends, namely high and low, in old and fresh petals. Five short-chain petal-expressed RcTPTs showed expression patterns corresponding to RcTPSs. Analysis of differential volatile terpenes and differential expressed genes indicated that higher emission of geraniol from old MU petals might be related to the RcGPPS expression. Comprehensive analysis of volatile emission, sequence structure, micro-synteny and gene expression suggested that RcTPS18 may encode (E,E)-α-farnesene synthase. These findings may be useful for elucidating the molecular mechanism of terpenoid metabolism in rose and are vital for future studies on terpene regulation.

Physiological and Molecular Approaches for Developing Thermotolerance in Vegetable Crops: A Growth, Yield and Sustenance Perspective

Vegetables are a distinct collection of plant-based foods that vary in nutritional diversity and form an important part of the healthy diet of the human being. Besides providing basic nutrition, they have great potential for boosting human health. The balanced consumption of vegetables is highly recommended for supplementing the human body with better nutrition density, dietary fiber, minerals, vitamins, and bioactive compounds. However, the production and quality of fresh vegetables are influenced directly or indirectly by exposure to high temperatures or heat stress (HS). A decline in quality traits and harvestable yield are the most common effects of HS among vegetable crops. Heat-induced morphological damage, such as poor vegetative growth, leaf tip burning, and rib discoloration in leafy vegetables and sunburn, decreased fruit size, fruit/pod abortion, and unfilled fruit/pods in beans, are common, often rendering vegetable cultivation unprofitable. Further studies to trace down the possible physiological and biochemical effects associated with crop failure reveal that the key factors include membrane damage, photosynthetic inhibition, oxidative stress, and damage to reproductive tissues, which may be the key factors governing heat-induced crop failure. The reproductive stage of plants has extensively been studied for HS-induced abnormalities. Plant reproduction is more sensitive to HS than the vegetative stages, and affects various reproductive processes like pollen germination, pollen load, pollen tube growth, stigma receptivity, ovule fertility and, seed filling, resulting in poorer yields. Hence, sound and robust adaptation and mitigation strategies are needed to overcome the adverse impacts of HS at the morphological, physiological, and biochemical levels to ensure the productivity and quality of vegetable crops. Physiological traits such as the stay-green trait, canopy temperature depression, cell membrane thermostability, chlorophyll fluorescence, relative water content, increased reproductive fertility, fruit numbers, and fruit size are important for developing better yielding heat-tolerant varieties/cultivars. Moreover, various molecular approaches such as omics, molecular breeding, and transgenics, have been proved to be useful in enhancing/incorporating tolerance and can be potential tools for developing heat-tolerant varieties/cultivars. Further, these approaches will provide insights into the physiological and molecular mechanisms that govern thermotolerance and pave the way for engineering "designer" vegetable crops for better health and nutritional security. Besides these approaches, agronomic methods are also important for adaptation, escape and mitigation of HS protect and improve yields.

Genome Wide Identification and Expression Profiling Indicate Expansion of Family I84 Protease Inhibitor via Gene Tandem Duplication and Divergence in Razor Clam Sinonovacula constricta

Family I84 protease inhibitors represent a novel family in the MEROPS peptidase database and are likely unique for molluscan host defense. Two Family I84 members, scSI-1 and scSI-2, were reported from the razor clam Sinonovacula constricta in a previous research. In the present study, 12 additional genes, named scSI-3 to scSI-14, were identified via genome wide sequence analyses. Among them, 10 genes were predicted to have a signal sequence, but one (scSI-7) was not. Besides, one sequence (scSI-14) was likely to encode a prematurely terminated peptide. The predicted mature peptides shared characteristics including 12 conserved cysteine residues, isoelectric points of 4.98 to 6.11, and molecular weights of 7.1 to 9.3 kDa with previously reported family members. Four motifs were characterized in 13 predicted mature peptides (with exception of scSI-14), which shared two to four conserved cysteine residues, are possibly to form two functional domain comprised 6 cysteine residues, respectively. At genomic level, all the 14 razor clam Family I84 genes were organized into 3 exons and 2 introns; 13 of them clustered in 3 regions of 100 kb on 3 separate chromosomes, suggesting tandem duplications of related genes. The promoter region of all the 14 genes was predicted to share some transcription factor binding sites, in particular those responsive to pathological and physiological stimuli, but no shared motifs were identified. Analyses also revealed differences in expression patterns among the genes. One gene in a tandem duplicated gene pairs usually showed a higher expression level than the other whereas non-tandem duplicated genes exhibited a higher degree of correlation in expression level. In addition, 8 of the 14 genes demonstrated higher level of expression in Vibrio tolerant clams than in non-tolerant clams following challenges with Vibrio parahaemolyticus. These results generated important information about the evolution of Family I84 protease inhibitors in S. constricta.

Comprehensive Analysis of the Hsp20 Gene Family in Canavalia rosea Indicates Its Roles in the Response to Multiple Abiotic Stresses and Adaptation to Tropical Coral Islands

Heat shock protein 20 (Hsp20) is a major family of heat shock proteins that mainly function as molecular chaperones and are markedly accumulated in cells when organisms are subjected to environmental stress, particularly heat. Canavalia rosea is an extremophile halophyte with good adaptability to environmental high temperature and is widely distributed in coastal areas or islands in tropical and subtropical regions. In this study, we identified a total of 41 CrHsp20 genes in the C. rosea genome. The gene structures, phylogenetic relationships, chromosome locations, and conserved motifs of each CrHsp20 or encoding protein were analyzed. The promoters of CrHsp20s contained a series of predicted cis-acting elements, which indicates that the expression of different CrHsp20 members is regulated precisely. The expression patterns of the CrHsp20 family were analyzed by RNA sequencing both at the tissue-specific level and under different abiotic stresses, and were further validated by quantitative reverse transcription PCR. The integrated expression profiles of the CrHsp20s indicated that most CrHsp20 genes were greatly upregulated (up to dozens to thousands of times) after 2 h of heat stress. However, some of the heat-upregulated CrHsp20 genes showed completely different expression patterns in response to salt, alkaline, or high osmotic stresses, which indicates their potential specific function in mediating the response of C. rosea to abiotic stresses. In addition, some of CrHsp20s were cloned and functionally characterized for their roles in abiotic stress tolerance in yeast. Taken together, these findings provide a foundation for functionally characterizing Hsp20s to unravel their possible roles in the adaptation of this species to tropical coral reefs. Our results also contribute to the understanding of the complexity of the response of CrHsp20 genes to other abiotic stresses and may help in future studies evaluating the functional characteristics of CrHsp20s for crop genetic improvement.

Genome-wide identification and characterization of superoxide dismutases in four oyster species reveals functional differentiation in response to biotic and abiotic stress

Background

Oysters inhabit in the intertidal zone and may be suffered from environmental stresses, which can increase the production of reactive oxygen species (ROS), resulting in mass mortality. Superoxide dismutases (SODs) protect oysters from ROS damage through different mechanisms compared with vertebrates. However, the molecular and functional differentiation in oyster SODs were rarely analyzed.

Result

In this study, a total of 13, 13, 10, and 8 candidate SODs were identified in the genome of Crassostrea gigas, Crassostrea virginica, Crassostrea hongkongensis, and Saccostrea glomerata respectively. The domain composition, gene structure, subcellular locations, conserved ligands, and cis-elements elucidated the SODs into five groups (Mn-SODs, Cu-only-SODs, Cu/Zn ion ligand Cu/Zn-SOD with enzyme activity, Zn-only-SODs, and no ligand metal ions Cu/Zn-SODs). For single domain Cu/Zn-SODs, only one cytosolic Cu/Zn-SOD (cg_XM_034479061.1) may conserve enzymatic activity while most extracellular Cu/Zn-SOD proteins appeared to lose SOD enzyme activity according to conserved ligand amino acid analysis and expression pattern under biotic and abiotic stress in C. gigas. Further, multi-domain-SODs were identified and some of them were expressed in response to biotic and abiotic stressors in C. gigas. Moreover, the expression patterns of these genes varied in response to different stressors, which may be due to the cis-elements in the gene promoter.

Conclusion

These findings revealed the most extracellular Cu/Zn-SOD proteins appeared to lose SOD enzyme activity in oysters. Further, our study revealed that only one cytosolic Cu/Zn-SOD (cg_XM_034479061.1) may conserve enzymatic activity of SOD. Moreover, the expression patterns of these genes varied in response to different stressors, which may be due to the cis-elements in the promoter. This study provides important insights into the mechanisms through which oysters adapt to harsh intertidal conditions, as well as potential biomarkers of stress response in related species.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08610-9.

Effects of Elevated Temperature and Salicylic Acid on Heat Shock Response and Growth of Potato Microplants

Potato is a globally important, highly heat-susceptible crop species. We investigated the effects of prolonged exposure to elevated temperatures and exogenous salicylic acid (SA) on microplant growth and heat-shock response (HSR) in three unrelated potato genotypes/cultivars. Long-term exposure to 29 °C (mild heat stress) caused a significant reduction in the number of surviving explants and shoot morphometric parameters in heat-sensitive genotypes, while exposure to 26 °C (warming) caused only a decline in shoot growth. Interestingly, 26 °C-temperature treatment stimulated root growth in some investigated genotypes, indicating a difference between favorable temperatures for potato shoot and root growth. SA showed a protective effect regarding potato shoot growth at 26 °C. At 29 °C, this effect was genotype-dependent. SA did not affect the number of roots and inhibited root elongation at all temperature treatments, indicating the difference between shoot and root responses to applied SA concentration. Although HSR is mainly considered rapid and short-lived, elevated transcript levels of most investigated HSFs and HSPs were detected after three weeks of heat stress. Besides, two StHSFs and StHSP21 showed elevated expression at 26 °C, indicating extreme potato heat-susceptibility and significance of HSR during prolonged warming. SA effects on HSFs and HSPs expression were minor and alterable.

Characterization of the wheat VQ protein family and expression of candidate genes associated with seed dormancy and germination

BACKGROUND

Seed dormancy and germination determine wheat resistance to pre-harvest sprouting and thereby affect grain yield and quality. Arabidopsis VQ genes have been shown to influence seed germination; however, the functions of wheat VQ genes have not been characterized.

RESULTS

We identified 65 TaVQ genes in common wheat and named them TaVQ1-65. We identified 48 paralogous pairs, 37 of which had Ka/Ks values greater than 1, suggesting that most TaVQ genes have experienced positive selection. Chromosome locations, gene structures, promoter element analysis, and gene ontology annotations of the TaVQs showed that their structures determined their functions and that structural changes reflected functional diversity. Transcriptome-based expression analysis of 62 TaVQ genes and microarray analysis of 11 TaVQ genes indicated that they played important roles in diverse biological processes. We compared TaVQ gene expression and seed germination index values among wheat varieties with contrasting seed dormancy and germination phenotypes and identified 21 TaVQ genes that may be involved in seed dormancy and germination.

CONCLUSIONS

Sixty-five TaVQ proteins were identified for the first time in common wheat, and bioinformatics analyses were used to investigate their phylogenetic relationships and evolutionary divergence. qRT-PCR data showed that 21 TaVQ candidate genes were potentially involved in seed dormancy and germination. These findings provide useful information for further cloning and functional analysis of TaVQ genes and introduce useful candidate genes for the improvement of PHS resistance in wheat.

In Silico Characterization and Expression Analysis of GIGANTEA Genes in Potato

GIGANTEA (GI) genes are ubiquitous in the plant kingdom and are involved in diverse processes from flowering during stress responses to tuberization; the latter occurs in potato (Solanum tuberosum L.). GI genes have a diurnal cycle of expression; however, no details on the regulation of GI gene expression in potato have been reported thus far. The aim of our work was the analysis of the GI promoter sequence and studying GI expression in different organs and under abiotic stress conditions in potato. Two GI genes homologous to Arabidopsis GI located on chromosomes 4 and 12 (StGI.04 and StGI.12) were identified in the genome-sequenced potato S. phureja. The GI promoter regions of the commercial potato cultivar ‘Désirée’ were cloned and found to be almost identical to the S. phureja GI promoter sequence. More than ten TF families binding to the GI promoters were predicted. EVENING ELEMENT and ABSCISIC ACID RESPONSE ELEMENT LIKE elements related to circadian regulation and a binding site for POTATO HOMEOBOX 20 presumably involved in tuber initiation were detected in both GI promoters. However, the locations of these elements and several other cis-acting regulatory elements as well as the organ-specific expression and responses of the genes to abiotic stresses and abscisic acid were different. Thus, we presume that the function of StGI.04 and StGI.12 are at least partially different. This study lays foundation for further investigation of the roles of GI genes in potato.

Genome-Wide Analysis of HSP70s in Hexaploid Wheat: Tandem Duplication, Heat Response, and Regulation

HSP70s play crucial roles in plant growth and development, as well as in stress response. Knowledge of the distribution and heat response of HSP70s is important to understand heat adaptation and facilitate thermotolerance improvement in wheat. In this study, we comprehensively analyzed the distribution of HSP70s in hexaploid wheat (TaHSP70s) and its relatives, and we found an obvious expansion of TaHSP70s in the D genome of hexaploid wheat. Meanwhile, a large portion of tandem duplication events occurred in hexaploid wheat. Among the 84 identified TaHSP70s, more than 64% were present as homeologs. The expression profiles of TaHSP70s in triads tended to be expressed more in non-stressful and heat stress conditions. Intriguingly, many TaHSP70s were especially heat responsive. Tandem duplicated TaHSP70s also participated in heat response and growth development. Further HSE analysis revealed divergent distribution of HSEs in the promoter regions of TaHSP70 homeologs, which suggested a distinct heat regulatory mechanism. Our results indicated that the heat response of TaHSP70s may experience a different regulation, and this regulation, together with the expression of tandem duplicated TaHSP70s, may help hexaploid wheat to adapt to heat conditions.

Salinity responses and tolerance mechanisms in underground vegetable crops: an integrative review

The present review gives an insight into the salinity stress tolerance responses and mechanisms of underground vegetable crops. Phytoprotectants, agronomic practices, biofertilizers, and modern biotechnological approaches are crucial for salinity stress management. Underground vegetables are the source of healthy carbohydrates, resistant starch, antioxidants, vitamins, mineral, and nutrients which benefit human health. Soil salinity is a serious threat to agriculture that severely affects the growth, development, and productivity of underground vegetable crops. Salt stress induces several morphological, anatomical, physiological, and biochemical changes in crop plants which include reduction in plant height, leaf area, and biomass. Also, salinity stress impedes the growth of the underground organs, which ultimately reduces crop yield. Moreover, salt stress is detrimental to photosynthesis, membrane integrity, nutrient balance, and leaf water content. Salt tolerance mechanisms involve a complex interplay of several genes, transcription factors, and proteins that are involved in the salinity tolerance mechanism in underground crops. Besides, a coordinated interaction between several phytoprotectants, phytohormones, antioxidants, and microbes is needed. So far, a comprehensive review of salinity tolerance responses and mechanisms in underground vegetables is not available. This review aims to provide a comprehensive view of salt stress effects on underground vegetable crops at different levels of biological organization and discuss the underlying salt tolerance mechanisms. Also, the role of multi-omics in dissecting gene and protein regulatory networks involved in salt tolerance mechanisms is highlighted, which can potentially help in breeding salt-tolerant underground vegetable crops.

Genome wide identification and characterization of small heat shock protein gene family in pigeonpea and their expression profiling during abiotic stress conditions

Small heat shock proteins as large multigene family are present ubiquitously among Archaea to Eukaryota. The sHSPs are molecular chaperones that maintain the proper protein folding and disaggregation of denatured proteins during stress conditions. In the present study, out of identified 38 sHSPs in the pigeonpea genome, the 20 are distributed across seven chromosomes while the remaining are located on unassembled scaffolds. These Cc_sHSPs are classified into 16 subfamilies. The cytoplasmic class-II is the largest sub-family with five Cc_sHSPs. The gene structure analysis revealed that Cc_sHSP genes specifically containing no or very few introns. The promoter analysis revealed the presence of various cis-acting elements responsible for developmental, biotic, and abiotic stress specific-induction of Cc_sHSPs. A total of one segmental duplication and four tandem duplication events are identified for Cc_sHSPs. The qRT-PCR based expression analysis of all 38 Cc_sHSP genes was conducted for diverse abiotic stress conditions. The Cc_sHSP genes are highly induced by heat, drought, cold, and salt stresses indicating a key role in mitigating the various abiotic stress responses. The divergence time of paralogous Cc_sHSPs ranged from 8.66 to 191.82 MYA. The present study can be a strong basis for the functional characterization of Cc_sHSPs.

Chromosome-level genome assembly of Bactrocera dorsalis reveals its adaptation and invasion mechanisms

Bactrocera dorsalis is an invasive polyphagous pest causing considerable ecological and economic damage worldwide. We report a high-quality chromosome-level genome assembly and combine various transcriptome data to explore the molecular mechanisms of its rapid adaptation to new environments. The expansions of the DDE transposase superfamily and key gene families related to environmental adaptation and enrichment of the expanded and unique gene families in metabolism and defence response pathways explain its environmental adaptability. The relatively high but not significantly different expression of heat-shock proteins, regardless of the environmental conditions, suggests an intrinsic mechanism underlying its adaptation to high temperatures. The mitogen-activated protein kinase pathway plays a key role in adaptation to new environments. The prevalence of duplicated genes in its genome explains the diversity in the B. dorsalis complex. These findings provide insights into the genetic basis of the invasiveness and diversity of B. dorsalis, explaining its rapid adaptation and expansion.

Jiang et al. sequence the genome of Bactrocera dorsalis, a destructive and invasive agricultural pest. Insights from this chromosome-level assembly shed light on molecular adaptations that allow for the global invasion and expansion of this pest.