Genome-wide identification and characterization of HSP70 gene family in four species of cotton

Comparative proteomic analysis of seed germination between allotetraploid cotton Gossypium hirsutum and Gossypium barbadense

Seed germination, a key initial event in the plant life cycle, directly affects cotton yield and quality. Gossypium barbadense and Gossypium hirsutum gradually evolved through polyploidization, resulting in different characteristics, and this interspecific variation lacks genetic and molecular explanation. This work aimed to compare the proteomes between G. barbadense and G. hirsutum during seed germination. Here, we identified 2740 proteins for G. barbadense and 3758 for G. hirsutum. In the initial state, proteins in two cotton involved similar bioprocess, such as sugar metabolism, DNA repairing, and ABA signaling pathway. However, in the post-germination stage, G. hirsutum expressed more protein related to redox homeostasis, peroxidase activity, and pathogen interactions. Analyzing the different expression patterns of 915 single-copy orthogroups between the two kinds of cotton indicated that most of the differentially expressed proteins in G. barbadense were related to carbon metabolism. In contrast, most proteins in G. hirsutum were associated with stress response. Besides that, by proteogenomic analysis, we found 349 putative non-canonical peptides, which may be involved in plant development. These results will help to understand the different characteristics of these two kinds of cotton, such as fiber quality, yield, and adaptability. SIGNIFICANCE STATEMENT: Cotton is the predominant natural fiber crop worldwide; Gossypium barbadense and Gossypium hirsutum have evolved through polyploidization to produce differing traits. However, given their specific features, the divergence of mechanisms underlying seed germination between G. hirsutum and G. barbadense has not been discussed. Here, we explore what protein contributes to interspecific differences between G. barbadense and G. hirsutum during the seed germination period. This study helps to elucidate the evolution and domestication history of cotton polyploids and may allow breeders to understand their domestication history better and improve fiber quality and adaptability.

Development and identification of molecular markers of GhHSP70-26 related to heat tolerance in cotton

Heat stress significantly affect plant growth and development, which is an important factor contributing to crop yield loss. However, heat shock proteins (HSPs) in plants can effectively alleviate cell damage caused by heat stress. In order to rapidly and accurately cultivate heat-tolerant cotton varieties, this study conducted correlation analysis between heat tolerance index and insertion/deletion (In/Del) sites of GhHSP70-26 promoter in 39 cotton materials, so as to find markers related to heat tolerance function of cotton, which can be used in molecular marker-assisted breeding. The results showed the natural variation allele (Del22 bp) type at -1590 bp upstream of GhHSP70-26 promoter (haplotype2, Hap2) in cotton (Gossypium spp.) promoted GhHSP70-26 expression under heat stress. The relative expression level of GhHSP70-26 of M-1590-Del22 cotton materials were significantly higher than that of M-1590-In type cotton materials under heat stress (40 ℃). Also, M-1590-Del22 material had lower conductivity and less cell damage after heat stress, indicating that it is a heat resistant cotton material. The Hap1 (M-1590-In) promoter was mutated into Hap1^del22, and Hap1 and Hap1^del22 were fused with GUS to transform Arabidopsis thaliana. Furthermore, Hap1^del22 promoter had higher induction activity than Hap1 under heat stress and abscisic acid (ABA) treatment in transgenic Arabidopsis thaliana. Further analysis confirmed that M-1590-Del22 was the dominant heat-resistant allele. In summary, these results identify a key and previously unknown natural variation in GhHSP70-26 with respect to heat tolerance, providing a valuable functional molecular marker for genetic breeding of cotton and other crops with heat tolerance.

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 Analysis of Heat Shock Protein 70 (HSP70) Gene Family in Pumpkin (Cucurbita moschata) Rootstock under Drought Stress Suggested the Potential Role of these Chaperones in Stress Tolerance

Heat shock protein 70s (HSP70s) are highly conserved proteins that are involved in stress responses. These chaperones play pivotal roles in protein folding, removing the extra amounts of oxidized proteins, preventing protein denaturation, and improving the antioxidant system activities. This conserved family has been characterized in several crops under drought stress conditions. However, there is no study on HSP70s in pumpkin (Cucurbita moschata). Therefore, we performed a comprehensive analysis of this gene family, including phylogenetic relationship, motif and gene structure analysis, gene duplication, collinearity, and promoter analysis. In this research, we found 21 HSP70s that were classified into five groups (from A to E). These genes were mostly localized in the cytoplasm, chloroplast, mitochondria, nucleus, and endoplasmic reticulum (ER). We could observe more similarity in closely linked subfamilies in terms of motifs, the number of introns/exons, and the corresponding cellular compartments. According to the collinearity analysis, gene duplication had occurred as a result of purifying selection. The results showed that the occurrence of gene duplication for all nine gene pairs was due to segmental duplication (SD). Synteny analysis revealed a closer relationship between pumpkin and cucumber than pumpkin and Arabidopsis. Promoter analysis showed the presence of various cis-regulatory elements in the up-stream region of the HSP70 genes, such as hormones and stress-responsive elements, indicating a potential role of this gene family in stress tolerance. We furtherly performed the gene expression analysis of the HSP70s in pumpkin under progressive drought stress. Pumpkin is widely used as a rootstock to improve stress tolerance, as well as fruit quality of cucumber scion. Since stress-responsive mobile molecules translocate through vascular tissue from roots to the whole plant body, we used the xylem of grafted materials to study the expression patterns of the HSP70 (potentially mobile) gene family. The results indicated that all CmoHSP70s had very low expression levels at 4 days after stress (DAS). However, the genes showed different expression patterns by progressing he drought period. For example, the expression of CmoHSP70-4 (in subgroup E) and CmoHSP70-14 (in subgroup C) sharply increased at 6 and 11 DAS, respectively. However, the expression of all genes belonging to subgroup A did not change significantly in response to drought stress. These findings indicated the diverse roles of this gene family under drought stress and provided valuable information for further investigation on the function of this gene family, especially under stressful conditions.

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.

Identification of C2H2 subfamily ZAT genes in Gossypium species reveals GhZAT34 and GhZAT79 enhanced salt tolerance in Arabidopsis and cotton

Soil salinization is a vital factor that restricts the efficient and sustainable development of global agriculture. Studies enlightened that the C₂H₂ zinc finger proteins (C₂H₂-ZFP) were involved in regulating the stress response in plants. However, knowledge of the C₂H₂-ZFP subfamily C1 (ZAT; Zinc finger of Arabidopsis thaliana) in cotton is still a mystery. In this study, 47, 45, 94, and 88 ZAT genes were obtained from diploid A2, D5 and tetraploid AD1, AD2 cotton genomes, respectively. The function of hybridization and allopolyploidy in the evolutionary linkage of allotetraploid cotton was explained by the family of ZAT gene in 4 species. Duplication of gene activities indicates that the family of ZAT gene of cotton evolution was under strong purifying selection. The integration of previous transcriptome data related to NaCl stress, strongly suggests the GhZAT34 and GhZAT79 may interact with salt resistance in upland cotton. The expression level of certain ZAT genes, higher seed germination rate of transgenic Arabidopsis and gene- silenced cotton revealed that both genes were involved in the salt tolerance of upland cotton. This study may pave the substantial understandings into the role of ZATs genes in plants as well as suggest appropriate candidate genes for breeding of cotton varieties against salinity tolerance.

Genome wide analysis of IQD gene family in diploid and tetraploid species of cotton (Gossypium spp.)

Calmodulin (CaM) is considered as the most significant Ca²⁺ signaling messenger that mediate various biochemical and physiological reactions. IQ domain (IQD) proteins are plant specific CML/CaM calcium binding which are characterized by domains of 67 amino acids. 50, 50, 94, and 99 IQD genes were detected from G. arboreum (A2), G. raimondii (D5), G. barbadense (AD2) and G. hirsutum (AD1) respectively. Existence of more orthologous genes in cotton species than Arabidopsis, advocated that polyploidization produced new cotton specific orthologous gene clusters. Duplication of gene events depicts that IQD gene family of cotton evolution was under strong purifying selection. G. hirsutum exhibited high level synteny. GarIQD25 exhibited high expression in stem, root, flower, ovule and fiber in G. arboreum. In G. raimondii, GraIQD03 demonstrated upregulation across stem, ovule, fiber and seed. GbaIQD11 and GbaIQD62 exhibited upregulation in fiber development in G. barbadense. GhiIQD69 recognized as main candidate genes for plant parts, floral tissues, fiber and ovule development. Promotor analysis identified cis-regulatory elements were involved in plant growth and development. Overwhelmingly, present study paves the way to better understand the evolution of cotton IQD genes and lays a foundation for future investigation of IQD in cotton.

Genome wide identification, classification and functional characterization of heat shock transcription factors in cultivated and ancestral cottons (Gossypium spp.)

Heat shock transcription factors (HSF) have been demonstrated to play a significant transcriptional regulatory role in plants and considered as an integral part of signal transduction pathways against environmental stresses especially heat stress. Despite of their importance, HSFs have not yet been identified and characterized in all cotton species. In this study, we report the identification of 42, 39, 67, and 79 non-redundant HSF genes from diploid cottons G. arboreum (A2) and G. raimondii (D5), and tetraploid cottons G. barbadense (AD2) and G. hirsutum (AD1) respectively. The chromosome localization of identified HSFs revealed their random distribution on all the 13 chromosomes of A and D genomes of cotton with few regions containing HSFs in clusters. The genes structure and conserved domain analysis revealed the family-specific conservation of intron/exon organization and conserved domains in HSFs. Various abiotic stress-related cis-regulatory elements were identified from the putative promoter regions of cotton HSFs suggesting their possible role in mediating abiotic stress tolerance. The combined phylogenetic analysis of all the cotton HSFs grouped them into three subfamilies; with 145 HSFs belong to class A, 85 to class B, and 17 to class C subfamily. Moreover, a detailed analysis of HSF gene family in four species of cotton elucidated the role of allopolyploid and hybridization during evolutionary cascade of allotetraploid cotton. Comparatively, existence of more orthologous genes in cotton species than Arabidopsis, advocated that polyploidization produced new cotton specific orthologous gene clusters. Phylogenetic, collinearity and multiple synteny analyses exhibited dispersed, segmental, proximal, and tandem gene duplication events in HSF gene family. Duplication of gene events suggests that HSF gene family of cotton evolution was under strong purifying selection. Expression analysis revealed that GarHSF04 were found to be actively involved in PEG and salinity tolerance in G. arboreum. GhiHSF14 upregulated in heat and downregulated in salinity whilst almost illustrated similar behavior under cold and PEG treatments and GhiHSF21 exhibited down regulation almost across all the stresses in G. hirsutum. Overwhelmingly, present study paves the way to better understand the evolution of cotton HSF TFs and lays a foundation for future investigation of HSFs in improving abiotic stress tolerance in cotton.