scholarly journals Phylogenetic and expression dynamics of tomato ClpB/Hsp100 gene under heat stress

PLoS ONE ◽  
2021 ◽  
Vol 16 (8) ◽  
pp. e0255847
Author(s):  
Sanober Gul ◽  
Kausar Nawaz Shah ◽  
Rashid Mehmood Rana ◽  
Muhammad Azam Khan ◽  
Ahmed M. El-Shehawi ◽  
...  
Keyword(s):  
Heat Stress ◽  
Gene Family ◽  
Cellular Localization ◽  
Pollen Viability ◽  
Functional Divergence ◽  
Evolutionary Relationship ◽  
Internal Stresses ◽  
Cell Membrane Stability ◽  
Functional Homology ◽  
Shock Proteins

Heat shock proteins (Hsps) are stress-responsive molecular chaperones, which uphold proper protein folding in response to external and internal stresses. The Hsp100 gene family plays a substantial role in thermos-tolerance of plants. This study investigated evolutionary relationship and expression of ClpB/Hsp100 gene family in tomato under heat stress. Six SlHsp100 genes were identified using bioinformatics tools. In silico sub-cellular localization indicated that of these 6 ClpB/Hsp100 members, 4 are found in chloroplast, 1 in mitochondria and 1 in the cytoplasm. For evolutionary study, 36 SlHsp100 genes were included in the phylogenetic tree showing a hierarchical clustering shared by the members of the kingdoms Plantae, Archaea, Chromista, Fungi and Bacteria. A total 4 pairs of orthologous and 5 pairs of paralogous genes were identified. Functional divergence between different Hsp100 clusters showed considerable functional homology. Thermo-tolerance measured in terms of cell viability, cell membrane stability and pollen viability indicated that it was paralleled by thermal resistance of Hsps. Reverse transcriptase polymerase chain reaction was used to analyze gene expression in leaves of five-week-old tomato seedlings following exposure to heat stress (45°C) and control (25°C). Chloroplastic LeHSP110/ClpB gene was upregulated in all tomato genotypes after exposure to heat stress highlighting the crucial role of this gene family in acquired thermo-tolerance.

scholarly journals A new insight into the evolution and functional divergence of FRK genes in Pyrus bretschneideri

2018 ◽  
Vol 5 (7) ◽  
pp. 171463 ◽  
Author(s):  
Yunpeng Cao ◽  
Shumei Li ◽  
Yahui Han ◽  
Dandan Meng ◽  
Chunyan Jiao ◽  
...  
Keyword(s):  
Gene Family ◽  
Gene Structure ◽  
Functional Divergence ◽  
Sugar Content ◽  
Expression Patterns ◽  
Evolutionary Relationship ◽  
World Market ◽  
Pear Fruit ◽  
Rosaceae Species ◽  
Chinese White

In plants, plant fructokinases (FRKs) are considered to be the main gateway of fructose metabolism as they can phosphorylate fructose to fructose-6-phosphate. Chinese white pears ( Pyrus bretschneideri ) are one of the popular fruits in the world market; sugar content is an important factor affecting the quality of the fruit. We identified 49 FRKs from four Rosaceae species; 20 of these sequences were from Chinese white pear. Subsequently, phylogenic relationship, gene structure and micro-collinearity were analysed. Phylogenetic and exon–intron analysis classified these FRK s into 10 subfamilies, and it was aimed to further reveal the variation of the gene structure and the evolutionary relationship of this gene family. Remarkably, gene expression patterns in different tissues or different development stages of the pear fruit suggested functional redundancy for PbFRKs derived from segmental duplication or genome-wide duplication and sub-functionalization for some of them. Additionally, PbFRK11 , PbFRK13 and PbFRK16 were found to play important roles in regulating the sugar content in the fruit. Overall, this study provided important insights into the evolution of the FRK gene family in four Rosaceae species, and highlighted its roles in both pear tissue and fruits. Results presented here provide the appropriate candidate of PbFRK s that might contribute to fructose efflux in the pear fruit.

Genome-wide Analysis of the Rice Mate Gene Family: Identification, Genomic Organization and Expression Profiles in Response to Abiotic Stresses

2020 ◽  
Author(s):  
Zhixuan Du ◽  
Qitao Su ◽  
Zheng Wu ◽  
Zhou Huang ◽  
Jianzhong Bao ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Family ◽  
Abiotic Stresses ◽  
Expression Profiles ◽  
Functional Divergence ◽  
Expression Patterns ◽  
Chemical Properties ◽  
Motif Analysis ◽  
Functional Homology ◽  
Exogenous Compounds

Abstract Background: Multidrug and toxic compound extrusion (MATE) proteins are involved in many physiological functions of plant growth and development. Although an increasing number of MATE proteins have been identified, the understanding of MATE proteins is still very limited in rice.Results: In this study, 46 MATE proteins were identified from the rice (Oryza sativa) genome by homology searches and domain prediction. In addition, physical and chemical properties of the encoded proteins, subcellular localization, chromosome localization, stress-related cis-elements in abiotic stresses were determined, and a phylogenetic analysis and conserved motif analysis were performed. The rice MATE family can be divided into four subfamilies. It is speculated that members of the rice MATE family have many potential functions, such as the transport and accumulation of flavonoids and alkaloids, the extrusion of plant or exogenous compounds, the regulation of disease resistance and the response to abiotic stress, based on the proteins and cis-acting elements with known functions in the same subfamily. Analysis of gene expression showed that most of the genes were constitutively expressed. Furthermore, eight MATE genes were chosen for qRT-PCR-based analysis and showed differential expression patterns in response to salt and drought stress. Conclusions: Phylogenetic analysis, element prediction, expression data and homology with other species provided strong evidence for functional homology of MATE gene in rice. The analysis results of this study provide comprehensive information on the MATE gene family in rice and will aid in understanding the functional divergence of MATE genes.

scholarly journals Genome-Wide Identification of Hsp70 Genes in the Large Yellow Croaker (Larimichthys crocea) and Their Regulated Expression Under Cold and Heat Stress

Genes ◽  
2018 ◽  
Vol 9 (12) ◽  
pp. 590 ◽  
Author(s):  
Kaida Xu ◽  
Hanxiang Xu ◽  
Zhiqiang Han
Keyword(s):  
Heat Stress ◽  
Gene Family ◽  
Environmental Changes ◽  
Expression Patterns ◽  
Cold Treatment ◽  
Large Yellow Croaker ◽  
Hsp70 Gene ◽  
Larimichthys Crocea ◽  
Stress Dependent ◽  
Shock Proteins

Heat shock proteins 70 (Hsp70) are required for key cellular processes and responses to environmental changes, however, there are an unknown number of hsp70 gene family members in the large yellow croaker (Larimichthys crocea). In the present study, 17 hsp70 genes were identified through the genome of the large yellow croaker. These genes are divided into seven evolutionarily distinct groups according to a phylogenetic tree. The orthologs of these hsp70 genes were found in humans and zebrafish. The expression patterns of the hsp70 gene family in the large yellow croaker under cold and heat stress were studied by examining transcriptome data. Six out of 17 genes were significantly unregulated or downregulated after cold or heat stress. There were two genes significantly upregulated and two genes downregulated in the liver after cold treatment, while after heat treatment, five genes were significantly upregulated, and no genes were significantly downregulated. Three expression patterns were detected: strictly heat-inducible hsp70, constitutively expressed and moderately heat-inducible hsp70, and constitutively expressed and less stress-dependent hsp70 genes. All the findings will contribute to a better understanding of the biological function of hsp70s in defending against thermal challenges.

scholarly journals Genome-wide identification of Hsp70/110 genes in rainbow trout and their regulated expression in response to heat stress

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10022
Author(s):  
Fang Ma ◽  
Lintong Luo
Keyword(s):  
Heat Stress ◽  
Rainbow Trout ◽  
Gene Family ◽  
Cold Water ◽  
Functional Characterization ◽  
Head Kidney ◽  
Rna Seq ◽  
Systematic Analysis ◽  
Heat Stress Response ◽  
Shock Proteins

Heat shock proteins (Hsps) play an important role in many biological processes. However, as a typical cold water fish, the systematic identification of Hsp70/110 gene family of rainbow trout (Oncorhynchus mykiss) has not been reported, and the role of Hsp70/110 gene in the evolution of rainbow trout has not been described systematically. In this study, bioinformatics methods were used to analyze the Hsp70/110 gene family of rainbow trout. A total of 16 hsp70/110 genes were identified and classified into ten subgroups. The 16 Hsp70/110 genes were all distributed on chromosomes 2, 4, 8 and 13. The molecular weight is ranged from 78.93 to 91.39 kD. Gene structure and motif composition are relatively conserved in each subgroup. According to RNA-seq analysis of rainbow trout liver and head kidney, a total of four out of 16 genes were significantly upregulated in liver under heat stress, and a total of seven out of 16 genes were significantly upregulated in head kidney. RT-qPCR was carried out on these gene, and the result were consistent with those of RNA-seq. The significantly regulated expressions of Hsp70/110 genes under heat stress indicats that Hsp70/110 genes are involved in heat stress response in rainbow trout. This systematic analysis provided valuable information about the diverse roles of Hsp70/110 in the evolution of teleost, which will contribute to the functional characterization of Hsp70/110 genes in further research.

scholarly journals Genome-Wide Identification and Characterization of Polygalacturonase Gene Family in Maize (Zea mays L.)

2021 ◽  
Vol 22 (19) ◽  
pp. 10722
Author(s):  
Lu Lu ◽  
Quancan Hou ◽  
Linlin Wang ◽  
Tianye Zhang ◽  
Wei Zhao ◽  
...  
Keyword(s):  
Zea Mays ◽  
Gene Family ◽  
Zea Mays L ◽  
Developmental Stages ◽  
Expression Profiles ◽  
Functional Divergence ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Evolutionary Relationship ◽  
Segmental Duplications

Polygalacturonase (PG, EC 3.2.1.15) is a crucial enzyme for pectin degradation and is involved in various developmental processes such as fruit ripening, pollen development, cell expansion, and organ abscission. However, information on the PG gene family in the maize (Zea mays L.) genome and the specific members involved in maize anther development are still lacking. In this study, we identified 55 PG family genes from the maize genome and further characterized their evolutionary relationship and expression patterns. Phylogenetic analysis revealed that ZmPGs are grouped into six Clades, and gene structures of the same Clade are highly conserved, suggesting their functional conservation. The ZmPGs are randomly distributed across maize chromosomes, and collinearity analysis showed that many ZmPGs might be derived from tandem duplications and segmental duplications, and these genes are under purifying selection. Furthermore, gene expression analysis provided insights into possible functional divergence among ZmPGs. Based on the RNA-seq data analysis, we found that many ZmPGs are expressed in various tissues while 18 ZmPGs are highly expressed in maize anther, and their detailed expression profiles in different anther developmental stages were further investigated by using RT-qPCR analysis. These results provide valuable information for further functional characterization and application of the ZmPGs in maize.

scholarly journals Evolutionary Divergence of Duplicated Hsf Genes in Populus

Cells ◽  
2019 ◽  
Vol 8 (5) ◽  
pp. 438 ◽  
Author(s):  
Bobin Liu ◽  
Jianjun Hu ◽  
Jin Zhang
Keyword(s):  
Heat Shock ◽  
Gene Family ◽  
Genome Duplication ◽  
Higher Plants ◽  
Function Analysis ◽  
Populus Trichocarpa ◽  
Functional Divergence ◽  
Evolutionary Divergence ◽  
Expression Divergence ◽  
Shock Proteins

Heat shock transcription factors (Hsfs), which function as the activator of heat shock proteins (Hsps), play multiple roles in response to environmental stress and the development of plants. The Hsf family had experienced gene expansion via whole-genome duplication from a single cell algae to higher plants. However, how the Hsf gene family went through evolutionary divergence after genome duplication is unknown. As a model wood species, Populus trichocarpa is widely distributed in North America with various ecological and climatic environments. In this study, we used P. trichocarpa as materials and identified the expression divergence of the PtHsf gene family in developmental processes, such as dormant bud formation and opening, catkins development, and in response to environments. Through the co-expression network, we further discovered the divergent co-expressed genes that related to the functional divergence of PtHsfs. Then, we studied the alternative splicing events, single nucleotide polymorphism distribution and tertiary structures of members of the PtHsf gene family. In addition to expression divergence, we uncovered the evolutionary divergence in the protein level which may be important to new function formations and for survival in changing environments. This study comprehensively analyzed the evolutionary divergence of a member of the PtHsf gene family after genome duplication, paving the way for further gene function analysis and genetic engineering.

scholarly journals New insights into the evolution and functional divergence of the CIPK gene family in Saccharum

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Weihua Su ◽  
Yongjuan Ren ◽  
Dongjiao Wang ◽  
Long Huang ◽  
Xueqin Fu ◽  
...  
Keyword(s):  
Gene Family ◽  
Gene Structure ◽  
Quantitative Polymerase Chain Reaction ◽  
Functional Divergence ◽  
Expression Patterns ◽  
Evolutionary Relationship ◽  
Functional Study ◽  
Last Common Ancestor ◽  
Duplicated Genes ◽  
Duplication Events

Abstract Background Calcineurin B-like protein (CBL)-interacting protein kinases (CIPKs) are the primary components of calcium sensors, and play crucial roles in plant developmental processes, hormone signaling transduction, and in the response to exogenous stresses. Results In this study, 48 CIPK genes (SsCIPKs) were identified from the genome of Saccharum spontaneum. Phylogenetic reconstruction suggested that the SsCIPK gene family may have undergone six gene duplication events from the last common ancestor (LCA) of SsCIPKs. Whole-genome duplications (WGDs) served as the driving force for the amplification of SsCIPKs. The Nonsynonymous to synonymous substitution ratio (Ka/Ks) analysis showed that the duplicated genes were possibly under strong purifying selection pressure. The divergence time of these duplicated genes had an average duplication time of approximately 35.66 Mya, suggesting that these duplication events occurred after the divergence of the monocots and eudicots (165 Mya). The evolution of gene structure analysis showed that the SsCIPK family genes may involve intron losses. Ten ScCIPK genes were amplified from sugarcane (Saccharum spp. hybrids). The results of real-time quantitative polymerase chain reaction (qRT-PCR) demonstrated that these ten ScCIPK genes had different expression patterns under abscisic acid (ABA), polyethylene glycol (PEG), and sodium chloride (NaCl) stresses. Prokaryotic expression implied that the recombinant proteins of ScCIPK3, − 15 and − 17 could only slightly enhance growth under salinity stress conditions, but the ScCIPK21 did not. Transient N. benthamiana plants overexpressing ScCIPKs demonstrated that the ScCIPK genes were involved in responding to external stressors through the ethylene synthesis pathway as well as to bacterial infections. Conclusions In generally, a comprehensive genome-wide analysis of evolutionary relationship, gene structure, motif composition, and gene duplications of SsCIPK family genes were performed in S. spontaneum. The functional study of expression patterns in sugarcane and allogenic expressions in E. coli and N. benthamiana showed that ScCIPKs played various roles in response to different stresses. Thus, these results improve our understanding of the evolution of the CIPK gene family in sugarcane as well as provide a basis for in-depth functional studies of CIPK genes in sugarcane.

scholarly journals Genome-wide identification and analysis of the heat shock transcription factor family in moso bamboo (Phyllostachys edulis)

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Bin Huang ◽  
Zhinuo Huang ◽  
Ruifang Ma ◽  
Jialu Chen ◽  
Zhijun Zhang ◽  
...  
Keyword(s):  
Heat Stress ◽  
Stress Response ◽  
Heat Shock ◽  
Gene Family ◽  
Regulatory Elements ◽  
Moso Bamboo ◽  
Naphthalene Acetic Acid ◽  
Plant Responses ◽  
Heat Stress Response ◽  
Regulatory Pathways

AbstractHeat shock transcription factors (HSFs) are central elements in the regulatory network that controls plant heat stress response. They are involved in multiple transcriptional regulatory pathways and play important roles in heat stress signaling and responses to a variety of other stresses. We identified 41 members of the HSF gene family in moso bamboo, which were distributed non-uniformly across its 19 chromosomes. Phylogenetic analysis showed that the moso bamboo HSF genes could be divided into three major subfamilies; HSFs from the same subfamily shared relatively conserved gene structures and sequences and encoded similar amino acids. All HSF genes contained HSF signature domains. Subcellular localization prediction indicated that about 80% of the HSF proteins were located in the nucleus, consistent with the results of GO enrichment analysis. A large number of stress response–associated cis-regulatory elements were identified in the HSF upstream promoter sequences. Synteny analysis indicated that the HSFs in the moso bamboo genome had greater collinearity with those of rice and maize than with those of Arabidopsis and pepper. Numerous segmental duplicates were found in the moso bamboo HSF gene family. Transcriptome data indicated that the expression of a number of PeHsfs differed in response to exogenous gibberellin (GA) and naphthalene acetic acid (NAA). A number of HSF genes were highly expressed in the panicles and in young shoots, suggesting that they may have functions in reproductive growth and the early development of rapidly-growing shoots. This study provides fundamental information on members of the bamboo HSF gene family and lays a foundation for further study of their biological functions in the regulation of plant responses to adversity.

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