Genome-wide identification and characterization of the Hsp70 gene family in allopolyploid rapeseed (Brassica napus L.) compared with its diploid progenitors

Genome-wide identification of 1R-MYB transcription factors family and functional characterization of TrMYB130 under drought stresses in Trifolium repens (L.)

White clover (Trifolium repens L.) is a high-quality leguminous forage, but its short rooting habit, poor transpiration tolerance, and drought tolerance, have become a key factor restricting its growth and cultivation. 1R-MYB transcription factors (TFs) are a significant subfamily of TFs in plants, playing a vital role in regulating plant responses to drought stress, however, knowledge about the role of 1R-MYB transcription factors in white clover is still limited. We identified 134 1R-MYB members, which were unevenly designated onto 16 chromosomes and divided phylogenetically into five subgroups. The members of the same subgroup had conserved motifs. Collinearity analysis revealed that segmental and tandem duplications significantly contributed to the expansion of the Tr1R-MYBs. Tr1R-MYBs promoter region enriched with potential drought cis-acting regulatory elements. The RT-qPCR results show that the five Tr1R-MYB genes (TrMYB41, TrMYB49, TrMYB94, TrMYB125, TrMYB130) have a certain degree of response under drought stress conditions but exhibited different expression profiles. Furthermore, subcellular localization analysis showed that the TrMYB130 protein is primarily located in the nucleus. Overexpression of this protein in transgenic Arabidopsis (Arabidopsis thaliana L.) was found to impair drought tolerance. Our findings will establish a basis for deeper investigation into the characteristics and functions of 1R-MYB TFs, as well as for employing genetic engineering techniques to improve white clover.

Genome-Wide Identification and Characterization of HSP70 Gene Family in Tausch's Goatgrass (Aegilops tauschii)

BACKGROUND

Aegilops tauschii, a winter annual grass weed native to Eastern Europe and Western Asia, has become a widespread invasive species in the wheat-growing regions of China due to its high environmental adaptability. This study aims to explore the molecular mechanisms underlying the stress resistance of Tausch's goatgrass, focusing on the HSP70 gene family.

METHODS

A genome-wide analysis was conducted to identify and characterize the HSP70 gene family in A. tauschii. Afterward, their physicochemical properties, phylogenetic relationships, gene structures, and chromosomal distributions were analyzed. Additionally, cis-acting regulatory elements were predicted to understand their potential role in stress resistance.

RESULTS

A total of 19 identified HSP70 family genes were classified into four subfamilies and distributed across all chromosomes. The syntenic analysis revealed extensive homology between Tausch's goatgrass and wheat HSP70 genes. Segmental duplication was found to play a crucial role in the expansion of the HSP70 gene family. The prediction of cis-acting elements suggested that these genes are involved in stress resistance to various environmental conditions.

CONCLUSIONS

This study provides a comprehensive overview of the HSP70 gene family in A. tauschii, offering insights into their role in stress resistance and their potential application in understanding invasive species behavior and improving wheat resilience. Further research is needed to validate their functional roles in stress adaptation.

Insights into the Heat Shock Protein 70 (Hsp70) Family in Camelina sativa and Its Roles in Response to Salt Stress

Hsp70s, a group of heat shock proteins, are ancient proteins that play a crucial part in maintaining the stability of cells when faced with various internal and external stresses. In this research, there are 72 CsHSP70 genes present and verified in Camelina sativa, all of which exhibit a wide range of physicochemical characteristics. Through evolutionary analysis, the Hsp70 family was categorized into five primary groups, and numerous segmental duplications were anticipated among the CsHSP70 genes. The GO enrichment analysis of co-expression network elements revealed a significant association between key signaling terms, such as phosphorelay signal transduction, and MAPK cascade with the function of CsHsp70. An analysis of transcriptome data exposed to cold, drought, salinity, and cadmium stress demonstrated the varied expression profiles of CsHsp70 genes. The expression levels of CsHSP70 genes varied across various organs and stages of development in camelina, although some of them illustrated tissue-specific expression. qRT-PCR analysis further disclosed that CsHsp70-60, -52, and -13 were up-regulated and CsHsp70-03, -58, and -09 showed down-regulation in response to salinity. Furthermore, CsHsp70 genes are categorized as late-responsive elements to salinity stress. Through docking analysis, the current research revealed that CsHsp70 proteins interacted with ABA, BR, and MeJA.

Heat shock responsive genes in Brassicaceae: genome-wide identification, phylogeny, and evolutionary associations within and between genera

Heat stress affects the growth and development of Brassicaceae crops. Plant breeders aim to mitigate the effects of heat stress by selecting for heat stress tolerance, but the genes responsible for heat stress in Brassicaceae remain largely unknown. During heat stress, heat shock proteins (HSPs) function as molecular chaperones to aid in protein folding, and heat shock transcription factors (HSFs) serve as transcriptional regulators of HSP expression. We identified 5002 heat shock related genes, including HSPs and HSFs, across 32 genomes in Brassicaceae. Among these, 3347 genes were duplicated, with segmented duplication primarily contributing to their expansion. We identified 466 physical gene clusters, including 240 homogenous clusters and 226 heterogeneous clusters, shedding light on the organization of heat shock related genes. Notably, 37 genes were co-located with published thermotolerance quantitative trait loci, which supports their functional role in conferring heat stress tolerance. This study provides a comprehensive resource for the identification of functional Brassicaceae heat shock related genes, elucidates their clustering and duplication patterns and establishes the genomic foundation for future heat tolerance research. We hypothesise that genetic variants in HSP and HSF genes in certain species have potential for improving heat stress tolerance in Brassicaceae crops.

Systematic analysis of Heat Shock Protein 70 (HSP70) gene family in radish and potential roles in stress tolerance

The 70 kD heat shock proteins (HSP70s) represent a class of molecular chaperones that are widely distributed in all kingdoms of life, which play important biological roles in plant growth, development, and stress resistance. However, this family has not been systematically characterized in radish (Raphanus sativus L.). In this study, we identified 34 RsHSP70 genes unevenly distributed within nine chromosomes of R. sativus. Phylogenetic and multiple sequence alignment analyses classified the RsHSP70 proteins into six distinct groups (Group A-F). The characteristics of gene structures, motif distributions, and corresponding cellular compartments were more similar in closely linked groups. Duplication analysis revealed that segmental duplication was the major driving force for the expansion of RsHSP70s in radish, particularly in Group C. Synteny analysis identified eight paralogs (Rs-Rs) in the radish genome and 19 orthologs (Rs-At) between radish and Arabidopsis, and 23 orthologs (Rs-Br) between radish and Chinese cabbage. RNA-seq analysis showed that the expression change of some RsHSP70s were related to responses to heat, drought, cadmium, chilling, and salt stresses and Plasmodiophora brassicae infection, and the expression patterns of these RsHSP70s were significantly different among 14 tissues. Furthermore, we targeted a candidate gene, RsHSP70-23, the product of which is localized in the cytoplasm and involved in the responses to certain abiotic stresses and P. brassicae infection. These findings provide a reference for further molecular studies to improve yield and stress tolerance of radish.

Comprehensive Evolution and Expression anaLysis of PHOSPHATE 1 Gene Family in Allotetraploid Brassica napus and Its Diploid Ancestors

The members of PHOSPHATE 1 (PHO1) family play important roles in plant phosphate (Pi) transport and adaptation to Pi deficiency. The functions of PHO1 family proteins have been reported in several plant species, with the exception of Brassica species. Here, we identified 23, 23, and 44 putative PHO1 family genes in Brassica rapa, Brassica oleracea, and Brassica napus by whole genome analysis, respectively. The phylogenetic analysis divided PHO1 family proteins into eight groups, which represented the orthologous relationships among PHO1 members. The gene structure and the conserved motif analysis indicated that the most PHO1 family genes had similar gene structures and the PHO1 proteins shared mutual conserved motifs. The chromosome distribution analysis showed that the majority of BnPHO1 family genes distributed analogously at chromosomes with BrPHO1 and BoPHO1 family genes. The data showed that PHO1 family genes were highly conserved during evolution from diploid to tetraploid. Furthermore, the expression analysis showed that PHO1 family genes had different expression patterns in plant tissues, suggesting the diversity of gene functions in Brassica species. Meanwhile, the expression analysis also revealed that some PHO1 family genes were significantly responsive to Pi deficiency, suggesting that PHO1 family genes play critical roles in Pi uptake and homeostasis under low Pi stress. Altogether, the characteristics of PHO1 family genes provide a reliable groundwork for further dissecting their functions in Brassica species.

HSP70 Gene Family in Brassica rapa: Genome-Wide Identification, Characterization, and Expression Patterns in Response to Heat and Cold Stress

Heat shock proteins protect plants from abiotic stress, such as salt, drought, heat, and cold stress. HSP70 is one of the major members of the heat shock protein family. To explore the mechanism of HSP70 in Brassica rapa, we identified 28 putative HSP70 gene family members using state-of-the-art bioinformatics-based tools and methods. Based on chromosomal mapping, HSP70 genes were the most differentially distributed on chromosome A03 and the least distributed on chromosome A05. Ka/Ks analysis revealed that B. rapa evolution was subjected to intense purifying selection of the HSP70 gene family. RNA-sequencing data and expression profiling showed that heat and cold stress induced HSP70 genes. The qRT-PCR results verified that the HSP70 genes in Chinese cabbage (Brassica rapa ssp. pekinensis) are stress-inducible under both cold and heat stress. The upregulated expression pattern of these genes indicated the potential of HSP70 to mitigate environmental stress. These findings further explain the molecular mechanism underlying the responses of HSP70 to heat and cold stress.

The activation of gene expression and alternative splicing in the formation and evolution of allopolyploid Brassica napus

Allopolyploids contain two or more sets of subgenomes. To establish a compatible relationship between subgenomes, a series of gene expression changes occurred in allopolyploids. What evolutionary changes of transcripts have taken place in Brassica napus during the early establishment and subsequent evolution was a fascinating scientific question. Here, we study this issue using a set of materials (natural, resynthesized B. napus and their progenitors/parents) by long-read RNA sequencing technology. The results showed that more genes were up-regulated in resynthesized B. napus compared with its two parents, and more up-regulated expressed genes were observed in natural B. napus compared with resynthesized B. napus. The presence of up-regulation genes in organism may help it adapt to the influence of "genomic shock" and cope with natural environment. Isoforms are produced from precursor mRNAs by alternative splicing (AS) events, and more than 60% of novel isoforms were identified in all materials, which could improve the reference genome information of B. napus. We found that the isoform numbers, the number of genes potentially involved in AS and alternative polyadenylation increased in B. napus after evolution, which may involve in the adaptation of plants to natural environment. In addition, all identified isoforms were functional annotated by searching 7 databases. In general, this study could improve our overall understanding of the full-length transcriptome of B. napus, and help us recognize the significant gene expression changes and isoform abundance changes occurred in allopolyploid B. napus during evolution.

Genetic and Physiological Responses to Heat Stress in Brassica napus

Given the current rise in global temperatures, heat stress has become a major abiotic challenge affecting the growth and development of various crops and reducing their productivity. Brassica napus, the second largest source of vegetable oil worldwide, experiences a drastic reduction in seed yield and quality in response to heat. This review outlines the latest research that explores the genetic and physiological impact of heat stress on different developmental stages of B. napus with a special attention to the reproductive stages of floral progression, organogenesis, and post flowering. Several studies have shown that extreme temperature fluctuations during these crucial periods have detrimental effects on the plant and often leading to impaired growth and reduced seed production. The underlying mechanisms of heat stress adaptations and associated key regulatory genes are discussed. Furthermore, an overview and the implications of the polyploidy nature of B. napus and the regulatory role of alternative splicing in forming a priming-induced heat-stress memory are presented. New insights into the dynamics of epigenetic modifications during heat stress are discussed. Interestingly, while such studies are scarce in B. napus, opposite trends in expression of key genetic and epigenetic components have been identified in different species and in cultivars within the same species under various abiotic stresses, suggesting a complex role of these genes and their regulation in heat stress tolerance mechanisms. Additionally, omics-based studies are discussed with emphasis on the transcriptome, proteome and metabolome of B. napus, to gain a systems level understanding of how heat stress alters its yield and quality traits. The combination of omics approaches has revealed crucial interactions and regulatory networks taking part in the complex machinery of heat stress tolerance. We identify key knowledge gaps regarding the impact of heat stress on B. napus during its yield determining reproductive stages, where in-depth analysis of this subject is still needed. A deeper knowledge of heat stress response components and mechanisms in tissue specific models would serve as a stepping-stone to gaining insights into the regulation of thermotolerance that takes place in this important crop species and support future breeding of heat tolerant crops.

Heat Shock Protein 70 Family in Response to Multiple Abiotic Stresses in the Silkworm

Simple Summary

Heat shock protein 70 family is widely distributed in all the organisms, which plays important roles in protein folding and preventing protein denaturation. Heat or cold stress response has been studied in some insects, but there is a lack of systematic investigation on the response of the same species to multiple stressors. Here, we performed genome-wide identification of heat shock protein 70 family in the silkworm, Bombyx mori. Using the silkworm as a model, the transcription profiles of all the genes against heat, cold, and pesticides were studied. Our findings would provide insights into the functional diversification of heat shock proteins 70 in insects.

Abstract

The 70 kDa heat shock proteins play important roles in protecting organisms against environmental stresses, which are divided into stress-inducible forms (HSP70s) and heat shock cognates (HSC70s). In this study, heat shock protein 70 family was identified in the whole genome of the silkworm. Based on the known nomenclature and phylogenetic analysis, four HSP70s and five HSC70s were classified. Relatively, heat shock cognates were more conservative and were constitutively expressed in various tissues of the silkworm larvae. Under thermal (37 °C and 42 °C) and cold (2 °C) stresses, the expressions of HSP70–1, HSP70–2, and HSP70–3 were up-regulated, and the highest induction reached 4147.3, 607.1, and 1987.3 times, respectively. Interestingly, HSC70–1, HSC70–4, and HSC70–5 also showed slight induced expressions in the fat body and/or midgut under thermal stresses. In addition, the expression of HSP70–1 was induced by dichlorvos and phoxim insecticides, while most HSC70 genes were inhibited. The results suggested that stress-inducible forms play more important roles in adaptation to various stresses than HSC70s.

Genome-Wide Identification and Analysis of the Valine-Glutamine Motif-Containing Gene Family in Brassica napus and Functional Characterization of BnMKS1 in Response to Leptosphaeria maculans

Proteins containing valine-glutamine (VQ) motifs play important roles in plant growth and development as well as in defense responses to both abiotic and biotic stresses. Blackleg disease, which is caused by Leptosphaeria maculans, is the most important disease in canola (Brassica napus) worldwide; however, the identification of Brassica napus VQs and their functions in response to blackleg disease have not yet been reported. In this study, we conducted a genome-wide identification and characterization of the VQ gene family in Brassica napus, including chromosome location, phylogenetic relations, gene structure, motif domain, synteny analysis, and cis-elements categorization of their promoter regions. To understand Brassica napus VQ gene function in response to blackleg disease, we overexpressed BnVQ7 (BnaA01g36880D, also known as the mitogen-activated protein kinase 4 substrate 1 [MKS1] gene) in a blackleg-susceptible canola variety, Westar. Overexpression of BnMKS1 in canola did not improve its resistance to blackleg disease at the seedling stage; however, transgenic canola plants overexpressing BnMKS1 displayed an enhanced resistance to L. maculans infection at the adult plant stage. Expression levels of downstream and defense marker genes in cotyledons increased significantly at the necrotrophic stage of L. maculans infection in the overexpression line of BnMKS1, suggesting that the salicylic acid- and jasmonic acid-mediated signaling pathways were both involved in the defense responses. Together, these results suggest that BnMKS1 might play an important role in defense against L. maculans.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Genome-wide identification, and phylogenetic and expression profiling analyses, of XTH gene families in Brassica rapa L. and Brassica oleracea L

BACKGROUND

Xyloglucan endotransglucosylase/hydrolase genes (XTHs) are a multigene family and play key roles in regulating cell wall extensibility in plant growth and development. Brassica rapa and Brassica oleracea contain XTHs, but detailed identification and characterization of the XTH family in these species, and analysis of their tissue expression profiles, have not previously been carried out.

RESULTS

In this study, 53 and 38 XTH genes were identified in B. rapa and B. oleracea respectively, which contained some novel members not observed in previous studies. All XTHs of B. rapa, B. oleracea and Arabidopsis thaliana could be classified into three groups, Group I/II, III and the Early diverging group, based on phylogenetic relationships. Gene structures and motif patterns were similar within each group. All XTHs in this study contained two characteristic conserved domains (Glyco_hydro and XET_C). XTHs are located mainly in the cell wall but some are also located in the cytoplasm. Analyses of the mechanisms of gene family expansion revealed that whole-genome triplication (WGT) events and tandem duplication (TD) may have been the major mechanisms accounting for the expansion of the XTH gene family. Interestingly, TD genes all belonged to Group I/II, suggesting that TD was the main reason for the largest number of genes being in these groups. B. oleracea had lost more of the XTH genes, the conserved domain XET_C and the conserved active-site motif EXDXE compared with B. rapa, consistent with asymmetrical evolution between the two Brassica genomes. A majority of XTH genes exhibited different tissue-specific expression patterns based on RNA-seq data analyses. Moreover, there was differential expression of duplicated XTH genes in the two species, indicating that their functional differentiation occurred after B. rapa and B. oleracea diverged from a common ancestor.

CONCLUSIONS

We carried out the first systematic analysis of XTH gene families in B. rapa and B. oleracea. The results of this investigation can be used for reference in further studies on the functions of XTH genes and the evolution of this multigene family.