scholarly journals Genome-Wide Identification and Expansion Patterns of SULTR Gene Family in Gramineae Crops and Their Expression Profiles under Abiotic Stress in Oryza sativa

Genes ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 634
Author(s):  
Zhengqing Yuan ◽  
Weixiong Long ◽  
Haifei Hu ◽  
Ting Liang ◽  
Xiaoyun Luo ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Stress Responses ◽  
Expression Profiles ◽  
Functional Differentiation ◽  
Rice Seedling ◽  
Oryza Rufipogon ◽  
Evolutionary Patterns ◽  
Duplication Events ◽  
High Selenium ◽  
Low Selenium

Sulfate transporters (SULTRs), also known as H+/SO42− symporters, play a key role in sulfate transport, plant growth and stress responses. However, the evolutionary relationships and functional differentiation of SULTRs in Gramineae crops are rarely reported. Here, 111 SULTRs were retrieved from the genomes of 10 Gramineae species, including Brachypodium disachyon, Hordeum vulgare, Setaria italica, Sorghum bicolor, Zea mays, Oryza barthii, Oryza rufipogon, Oryza glabbermia and Oryza sativa (Oryza sativa ssp. indica and Oryza sativa ssp. japonica). The SULTRs were clustered into five clades based on a phylogenetic analysis. Syntheny analysis indicates that whole-genome duplication/segmental duplication and tandem duplication events were essential in the SULTRs family expansion. We further found that different clades and orthologous groups of SULTRs were under a strong purifying selective force. Expression analysis showed that rice SULTRs with high-affinity transporters are associated with the functions of sulfate uptake and transport during rice seedling development. Furthermore, using Oryza sativa ssp. indica as a model species, we found that OsiSULTR10 was significantly upregulated under salt stress, while OsiSULTR3 and OsiSULTR12 showed remarkable upregulation under high temperature, low-selenium and drought stresses. OsiSULTR3 and OsiSULTR9 were upregulated under both low-selenium and high-selenium stresses. This study illustrates the expression and evolutionary patterns of the SULTRs family in Gramineae species, which will facilitate further studies of SULTR in other Gramineae species.

scholarly journals Genome-Wide Characterization of the sHsp Gene Family in Salix suchowensis Reveals Its Functions under Different Abiotic Stresses

2018 ◽  
Vol 19 (10) ◽  
pp. 3246 ◽  
Author(s):  
Jianbo Li ◽  
Jin Zhang ◽  
Huixia Jia ◽  
Zhiqiang Yue ◽  
Mengzhu Lu ◽  
...  
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Purifying Selection ◽  
Molecular Characteristics ◽  
Specific Expression ◽  
Cis Acting ◽  
Shsp Gene ◽  
Duplication Events

Small heat shock proteins (sHsps) function mainly as molecular chaperones that play vital roles in response to diverse stresses, especially high temperature. However, little is known about the molecular characteristics and evolutionary history of the sHsp family in Salix suchowensis, an important bioenergy woody plant. In this study, 35 non-redundant sHsp genes were identified in S. suchowensis, and they were divided into four subfamilies (C, CP, PX, and MT) based on their phylogenetic relationships and predicted subcellular localization. Though the gene structure and conserved motif were relatively conserved, the sequences of the Hsp20 domain were diversified. Eight paralogous pairs were identified in the Ssu-sHsp family, in which five pairs were generated by tandem duplication events. Ka/Ks analysis indicated that Ssu-sHsps had undergone purifying selection. The expression profiles analysis showed Ssu-Hsps tissue-specific expression patterns, and they were induced by at least one abiotic stress. The expression correlation between two paralogous pairs (Ssu-sHsp22.2-CV/23.0-CV and 23.8-MT/25.6-MT) were less than 0.6, indicating that they were divergent during the evolution. Various cis-acting elements related to stress responses, hormone or development, were detected in the promoter of Ssu-sHsps. Furthermore, the co-expression network revealed the potential mechanism of Ssu-sHsps under stress tolerance and development. These results provide a foundation for further functional research on the Ssu-sHsp gene family in S. suchowensis.

scholarly journals Expansion and Evolutionary Patterns of Glycosyltransferase Family 8 in Gramineae Crop Genomes and Their Expression under Salt and Cold Stresses in Oryza sativa ssp. japonica

Biomolecules ◽  
2019 ◽  
Vol 9 (5) ◽  
pp. 188 ◽  
Author(s):  
Weilong Kong ◽  
Ziyun Gong ◽  
Hua Zhong ◽  
Yue Zhang ◽  
Gangqing Zhao ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Gene Family ◽  
Plant Cell ◽  
Plant Cell Wall ◽  
Brachypodium Distachyon ◽  
Expression Patterns ◽  
Evolutionary Relationship ◽  
Oryza Rufipogon ◽  
Potential Candidate ◽  
Evolutionary Patterns

Plant cell walls play a fundamental role in several ways, providing structural support for cells, resistance against pathogens and facilitating the communication between cells. The glycosyltransferase family 8 (GT8) is involved in the formation of the plant cell wall. However, the evolutionary relationship and the functional differentiation of this important gene family remain obscure in Gramineae crop genomes. In the present investigation, we identified 269 GT8 genes in the seven Gramineae representative crop genomes, namely, 33 in Hordeum vulgare, 37 in Brachypodium distachyon, 40 in Oryza sativa ssp. japonica, 41 in Oryza rufipogon, 36 in Setaria italica, 37 in Sorghum bicolor, and 45 in Zea mays. Phylogenetic analysis suggested that all identified GT8 proteins belonged to seven subfamilies: galacturonosyltransferase (GAUT), galacturonosyltransferase-like (GATL), GATL-related (GATR), galactinol synthase (GolS), and plant glycogenin-like starch initiation proteins A (PGSIP-A), PGSIP-B, and PGSIP-C. We estimated that the GAUT subfamily might be further divided into four subgroups (I–IV) due to differentiation of gene structures and expression patterns. Our orthogroup analysis identified 22 orthogroups with different sizes. Of these orthogroups, several orthogroups were lost in some species, such as S. italica and Z. mays. Moreover, lots of duplicate pairs and collinear pairs were discovered among these species. These results indicated that multiple duplication modes led to the expansion of this important gene family and unequal loss of orthogroups and subfamilies might have happened during the evolutionary process. RNA-seq, microarray analysis, and qRT-PCR analyses indicated that GT8 genes are critical for plant growth and development, and for stresses responses. We found that OsGolS1 was significantly up-regulated under salt stress, while OsGAUT21, OsGATL2, and OsGATL5 had remarkable up-regulation under cold stress. The current study highlighted the expansion and evolutionary patterns of the GT8 gene family in these seven Gramineae crop genomes and provided potential candidate genes for future salt- and cold- resistant molecular breeding studies in O. sativa.

scholarly journals Gene Expression Profiles Deciphering the Pathways of Coronatine Alleviating Water Stress in Rice (Oryza sativa L.) Cultivar Nipponbare (Japonica)

2019 ◽  
Vol 20 (10) ◽  
pp. 2543 ◽  
Author(s):  
Wei Gao ◽  
Chunxin Yu ◽  
Lin Ai ◽  
Yuyi Zhou ◽  
Liusheng Duan
Keyword(s):  
Gene Expression ◽  
Oryza Sativa ◽  
Water Stress ◽  
Drought Stress ◽  
Oryza Sativa L ◽  
Expression Profiles ◽  
Radical Scavenging Activity ◽  
Radical Scavenging ◽  
Gene Expression Profiles ◽  
Rice Seedling

Coronatine (COR) is a structural and functional analog of methyl jasmonic acid (MeJA), which can alleviate stress on plant. We studied the effects of COR on the drought stress of rice (Oryza sativa L.). Pre-treatment with COR significantly increased the biomass, relative water and proline content, and DPPH (1,1-diphenyl-2-picrylhydrazyl)-radical scavenging activity, decreased the electrolyte leakage and MDA (Malondialdehyde) content in order to maintain the stability of cell membrane. Meanwhile, we determined how COR alleviates water stress by Nipponbare gene expression profiles and cDNA microarray analyses. Seedlings were treated with 0.1 μmol L−1 COR at the three leafed stage for 12 h, followed with 17.5% polyethylene glycol (PEG). Whole genome transcript analysis was determined by employing the Rice Gene Chip (Affymetrix), a total of 870 probe sets were identified to be up or downregulated due to COR treatment under drought stress. Meanwhile, the real-time quantitative PCR (RT-qPCR) method was used to verify some genes; it indicated that there was a good agreement between the microarray data and RT-qPCR results. Our data showed that the differentially expressed genes were involved in stress response, signal transduction, metabolism and tissue structure development. Some important genes response to stress were induced by COR, which may enhance the expression of functional genes implicated in many kinds of metabolism, and play a role in defense response of rice seedling to drought stress. This study will aid in the analysis of the expressed gene induced by COR.

scholarly journals Effect of Caffeine on the Expression Pattern of Water-Soluble Proteins in Rice (Oryza sativa) Seedlings

2015 ◽  
Vol 10 (5) ◽  
pp. 1934578X1501000 ◽  
Author(s):  
Wei-Wei Deng ◽  
Hamako Sasamoto ◽  
Hiroshi Ashihara
Keyword(s):  
Oryza Sativa ◽  
Malate Dehydrogenase ◽  
Rna Binding ◽  
Expression Profiles ◽  
Time Of Flight ◽  
Rice Seedling ◽  
Water Soluble ◽  
Flight Mass Spectrometry ◽  
Germination And Growth ◽  
Alanyl Aminopeptidase

It has been suggested that caffeine acts as an allelochemical which influences the germination and growth of plants. The effect of caffeine on the expression profiles of proteins was investigated in shoot-root axes of rice (Oryza sativa) seedlings. Two-dimensional difference gel electrophoresis combined with Matrix-Assisted Laser Desorption/Ionization Time of Flight/Time of Flight Mass Spectrometry was employed for the separation and identification of proteins. The results indicated that amounts of 51 protein spots were reduced and 14 were increased by treatment with 1 mM caffeine. Twelve rice seedling proteins were identified. Down-regulated proteins were β-tubulin, sucrose synthase, glyceraldehyde-3-phosphate dehydrogenase, reversibly glycosylated polypeptide/α-1,4-glucan protein synthase and cytoplasmic malate dehydrogenase. In contrast, up-regulated proteins were alanyl-aminopeptidase, acetyl-CoA carboxylase, adenine phosphoribosyltransferase, NAD-malate dehydrogenase, ornithine carbamoyltransferase, glucose-6-phosphate isomerase and nuclear RNA binding protein. Possible alternation of metabolism caused by caffeine is discussed with the protein expression data.

scholarly journals Evolutionary Analysis of GH3 Genes in Six Oryza Species/Subspecies and Their Expression under Salinity Stress in Oryza sativa ssp. japonica

Plants ◽  
2019 ◽  
Vol 8 (2) ◽  
pp. 30 ◽  
Author(s):  
Weilong Kong ◽  
Hua Zhong ◽  
Xiaoxiao Deng ◽  
Mayank Gautam ◽  
Ziyun Gong ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Gene Family ◽  
Salinity Stress ◽  
Common Ancestor ◽  
Oryza Rufipogon ◽  
Oryza Species ◽  
Evolutionary Analysis ◽  
Wild Rice Species ◽  
Oryza Punctata ◽  
Duplication Events

Glycoside Hydrolase 3 (GH3), a member of the Auxin-responsive gene family, is involved in plant growth, the plant developmental process, and various stress responses. The GH3 gene family has been well-studied in Arabidopsis thaliana and Zea mays. However, the evolution of the GH3 gene family in Oryza species remains unknown and the function of the GH3 gene family in Oryza sativa is not well-documented. Here, a systematic analysis was performed in six Oryza species/subspecies, including four wild rice species and two cultivated rice subspecies. A total of 13, 13, 13, 13, 12, and 12 members were identified in O. sativa ssp. japonica, O. sativa ssp. indica, Oryza rufipogon, Oryza nivara, Oryza punctata, and Oryza glumaepatula, respectively. Gene duplication events, structural features, conserved motifs, a phylogenetic analysis, chromosome locations, and Ka/Ks ratios of this important family were found to be strictly conservative across these six Oryza species/subspecies, suggesting that the expansion of the GH3 gene family in Oryza species might be attributed to duplication events, and this expansion could occur in the common ancestor of Oryza species, even in common ancestor of rice tribe (Oryzeae) (23.07~31.01 Mya). The RNA-seq results of different tissues displayed that OsGH3 genes had significantly different expression profiles. Remarkably, the qRT-PCR result after NaCl treatment indicated that the majority of OsGH3 genes play important roles in salinity stress, especially OsGH3-2 and OsGH3-8. This study provides important insights into the evolution of the GH3 gene family in Oryza species and will assist with further investigation of OsGH3 genes’ functions under salinity stress.

scholarly journals In silico identification, characterization expression profile of WUSCHEL-Related Homeobox (WOX) gene family in two species of kiwifruit

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12348
Author(s):  
Chen Feng ◽  
Shuaiyu Zou ◽  
Puxin Gao ◽  
Zupeng Wang
Keyword(s):  
Gene Family ◽  
Expression Profiles ◽  
Gene Families ◽  
Functional Differentiation ◽  
Element Analysis ◽  
Evolutionary Patterns ◽  
Stem Cell Maintenance ◽  
Systematic Identification ◽  
Identification And Characterization

The WUSCHEL (WUS)-related homeobox (WOX) gene family is a class of plant-specific transcriptional factors and plays a crucial role in forming the shoot apical meristem and embryonic development, stem cell maintenance, and various other developmental processes. However, systematic identification and characterization of the kiwifruit WOX gene family have not been studied. This study identified 17 and 10 WOX genes in A. chinensis (Ac) and A. eriantha (Ae) genomes, respectively. Phylogenetic analysis classified kiwifruit WOX genes from two species into three clades. Analysis of phylogenetics, synteny patterns, and selection pressure inferred that WOX gene families in Ac and Ae had undergone different evolutionary patterns after whole-genome duplication (WGD) events, causing differences in WOX gene number and distribution. Ten conserved motifs were identified in the kiwifruit WOX genes, and motif architectures of WOXs belonging to different clades highly diverged. The cis-element analysis and expression profiles investigation indicated the functional differentiation of WOX genes and identified the potential WOXs in response to stresses. Our results provided insight into general characters, evolutionary patterns, and functional diversity of kiwifruit WOXs.

scholarly journals Genome-Wide Identification and Characterization of Apple P3A-Type ATPase Genes, with Implications for Alkaline Stress Responses

Forests ◽  
2020 ◽  
Vol 11 (3) ◽  
pp. 292
Author(s):  
Baiquan Ma ◽  
Meng Gao ◽  
Lihua Zhang ◽  
Haiyan Zhao ◽  
Lingcheng Zhu ◽  
...  
Keyword(s):  
Stress Responses ◽  
Draft Genome ◽  
Chemical Properties ◽  
Purifying Selection ◽  
Molecular Characteristics ◽  
Alkaline Stress ◽  
Evolutionary Patterns ◽  
Atpase Gene ◽  
Alkaline Conditions ◽  
Duplication Events

The P3A-type ATPases play crucial roles in various physiological processes via the generation of a transmembrane H+ gradient (∆pH). However, the P3A-type ATPase superfamily in apple remains relatively uncharacterized. In this study, 15 apple P3A-type ATPase genes were identified based on the new GDDH13 draft genome sequence. The exon-intron organization of these genes, the physical and chemical properties, and conserved motifs of the encoded enzymes were investigated. Analyses of the chromosome localization and ω values of the apple P3A-type ATPase genes revealed the duplicated genes were influenced by purifying selection pressure. Six clades and frequent old duplication events were detected. Moreover, the significance of differences in the evolutionary rates of the P3A-type ATPase genes were revealed. An expression analysis indicated that all of the P3A-type ATPase genes were specifically expressed in more than one tissue. The expression of one P3A-type ATPase gene (MD15G1108400) was significantly upregulated in response to alkaline stress. Furthermore, a subcellular localization assay indicated that MD15G1108400 is targeted to the plasma membrane. These results imply that MD15G1108400 may be involved in responses to alkaline stress. Our data provide insights into the molecular characteristics and evolutionary patterns of the apple P3A-type ATPase gene family and provide a theoretical foundation for future in-depth functional characterizations of P3A-type ATPase genes under alkaline conditions.

scholarly journals Genome-wide characterization of WRKY gene family in Helianthus annuus L. and their expression profiles under biotic and abiotic stresses

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0241965
Author(s):  
Juanjuan Li ◽  
Faisal Islam ◽  
Qian Huang ◽  
Jian Wang ◽  
Weijun Zhou ◽  
...  
Keyword(s):  
Helianthus Annuus ◽  
Stress Responses ◽  
Expression Profiles ◽  
Phylogenetic Analyses ◽  
Expression Patterns ◽  
Gene Families ◽  
Biotic Stresses ◽  
Gene Pairs ◽  
Duplication Events ◽  
Species Specific

WRKY transcription factors play important roles in various physiological processes and stress responses in flowering plants. Sunflower (Helianthus annuus L.) is one of the important vegetable oil supplies in the world. However, the information about WRKY genes in sunflower is limited. In this study, ninety HaWRKY genes were identified and renamed according to their locations on chromosomes. Further phylogenetic analyses classified them into four main groups including a species-specific WKKY group. Besides, HaWRKY genes within the same group or subgroup generally showed similar exon-intron structures and motif compositions. The gene duplication analysis showed that five pairs of HaWRKY genes (HaWRKY8/9, HaWRKY53/54, HaWRKY65/66, HaWRKY66/67 and HaWRKY71/72) are tandem duplicated and four HaWRKY gene pairs (HaWRKY15/82, HaWRKY25/65, HaWRKY28/55 and HaWRKY50/53) are also identified as segmental duplication events, indicating that these duplication genes were contribute to the diversity and expansion of HaWRKY gene families. The dN/dS ratio of these duplicated gene pairs were also calculated to understand the evolutionary constraints. In addition, synteny analyses of sunflower WRKY genes provided deep insight to the evolution of HaWRKY genes. Transcriptomic and qRT-PCR analyses of HaWRKY genes displayed distinct expression patterns in different plant tissues, as well as under various abiotic and biotic stresses, which provide a foundation for further functional analyses of these genes. Those functional genes related to stress tolerance and quality improvement could be applied in marker assisted breeding of the crop.

scholarly journals Genome-Wide Identification of the Q-type C2H2 Transcription Factor Family in Alfalfa (Medicago sativa) and Expression Analysis under Different Abiotic Stresses

Genes ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 1906
Author(s):  
Jun Pu ◽  
Mingyu Li ◽  
Pei Mao ◽  
Qiang Zhou ◽  
Wenxian Liu ◽  
...  
Keyword(s):  
Gene Family ◽  
Medicago Sativa ◽  
Stress Responses ◽  
Abiotic Stresses ◽  
Zinc Finger Protein ◽  
Expression Profiles ◽  
Regulatory Elements ◽  
Vital Role ◽  
Chromosomal Mapping ◽  
Duplication Events

Q-type C2H2 zinc-finger protein (C2H2-ZFP) transcription factors are associated with many plant growth development and environmental stress responses. To date, there have been few analyses of the Q-type C2H2-ZFP gene family in alfalfa (Medicago sativa subsp. sativa). In this study, we identified 58 Q-type C2H2-ZFPs across the entire alfalfa genome, and the gene structure, motif composition, chromosomal mapping, and cis-regulatory elements were explored, as well as the expression profiles of specific tissues and the response under different abiotic stresses. According to their phylogenetic features, these 58 MsZFPs were divided into 12 subgroups. Synteny analysis showed that duplication events play a vital role in the expansion of the MsZFP gene family. The collinearity results showed that a total of 26 and 42 of the 58 MsZFP genes were homologous with Arabidopsis and M. truncatula, respectively. The expression profiles showed that C2H2-ZFP genes played various roles in different tissues and abiotic stresses. The results of subsequent quantitative real-time polymerase chain reaction (qRT-PCR) showed that the nine selected MsZFP genes were rapidly induced under different abiotic stresses, indicating that C2H2-ZFP genes are closely related to abiotic stress. This study provides results on MsZFP genes, their response to various abiotic stresses, and new information on the C2H2 family in alfalfa.

scholarly journals The Craterostigma plantagineum protein kinase CpWAK1 interacts with pectin and integrates different environmental signals in the cell wall

Planta ◽  
2021 ◽  
Vol 253 (5) ◽  
Author(s):  
Peilei Chen ◽  
Valentino Giarola ◽  
Dorothea Bartels
Keyword(s):  
Cell Wall ◽  
Stress Responses ◽  
Expression Profiles ◽  
Phylogenetic Analyses ◽  
Cell Wall Protein ◽  
Biological Processes ◽  
Environmental Signals ◽  
High Affinity ◽  
Craterostigma Plantagineum ◽  
Receptor Kinases

Abstract Main conclusion The cell wall protein CpWAK1 interacts with pectin, participates in decoding cell wall signals, and induces different downstream responses. Abstract Cell wall-associated protein kinases (WAKs) are transmembrane receptor kinases. In the desiccation-tolerant resurrection plant Craterostigma plantagineum, CpWAK1 has been shown to be involved in stress responses and cell expansion by forming a complex with the C. plantagineum glycine-rich protein1 (CpGRP1). This prompted us to extend the studies of WAK genes in C. plantagineum. The phylogenetic analyses of WAKs from C. plantagineum and from other species suggest that these genes have been duplicated after species divergence. Expression profiles indicate that CpWAKs are involved in various biological processes, including dehydration-induced responses and SA- and JA-related reactions to pathogens and wounding. CpWAK1 shows a high affinity for “egg-box” pectin structures. ELISA assays revealed that the binding of CpWAKs to pectins is modulated by CpGRP1 and it depends on the apoplastic pH. The formation of CpWAK multimers is the prerequisite for the CpWAK–pectin binding. Different pectin extracts lead to opposite trends of CpWAK–pectin binding in the presence of Ca2+ at pH 8. These observations demonstrate that CpWAKs can potentially discriminate and integrate cell wall signals generated by diverse stimuli, in concert with other elements, such as CpGRP1, pHapo, Ca2+[apo], and via the formation of CpWAK multimers.

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