scholarly journals Genome-wide Characterization and Expression Analysis of YABBY Gene Family in Three Cultivars of Cucurbita Linn. And Their Response of Salt Stress in Cucurbita Moschata

2020 ◽  
Author(s):  
Jingping Yuan ◽  
Changwei Shen ◽  
Jingjing Xin ◽  
Zhenxia Li ◽  
Xinzheng Li ◽  
...  
Keyword(s):  
Salt Stress ◽  
Abiotic Stress ◽  
Plant Growth ◽  
Gene Family ◽  
Expression Analysis ◽  
Expression Patterns ◽  
Pcr Analysis ◽  
Abiotic Stress Response ◽  
Element Analysis ◽  
Qrt Pcr

Abstract BackgroundPlant specific YABBY transcription factors have important biological roles in plant growth and abiotic stress. However, the identification of Cucurbita Linn. YABBY and their response to salt stress have not yet been reported. The gene number, gene distribution on chromosome, gene structure, protein conserved structure, protein motif and the cis-acting element of YABBY in three cultivars of Cucurbita Linn. were analyzed by bioinformatics tools, and their tissue expression patterns and expression profile under salt stress were analyzed.ResultsIn this study, 34 YABBY genes (11 CmoYABBYs in Cucurbita moschata, 12 CmaYABBYs in Cucurbita maxima, and 11 CpeYABBYs in Cucurbita pepo) were identified and they were divided into five subfamilies (YAB1/YAB3, YAB2, INO, CRC and YAB5). YABBYs in the same subfamily usually have similar gene structures (intron-exon distribution) and conserved domains. Chromosomal localization analysis showed that these CmoYABBYs, CmaYABBYs, and CpeYABBYs were unevenly distributed in 8, 9, and 9 chromosomes of 21 chromosomes, respectively. Total of 6 duplicated gene pairs, and they all experienced segmental duplication events. Cis-acting element analysis showed that some Cucurbita Linn. YABBYs were associated with at least one of plant hormone response, plant growth, and abiotic stress response. Transcriptional profiles of CmoYABBYs and CmaYABBYs in roots, stems, leaves, and fruits, and CpeYABBYs in seed and fruit mesocarp showed that YABBYs of Cucurbita Linn. had tissue specificity. Finally, the transcriptional profile of 11 CmoYABBYs in leaf and qRT-PCR analysis of CmoYABBYs in root under salt stress indicated that some genes may play an important role in salt stress.ConclusionsGenome-wide identification and expression analysis of YABBYs revealed the characteristics of YABBY gene family in three cultivars of Cucurbita Linn.. Transcriptome and qRT-PCR analysis revealed the response of the CmoYABBYs to salt stress.This provides a theoretical basis for the functional research and utilization of YABBY genes in Cucurbita Linn..

scholarly journals Identification, Characterization and Expression Analysis Reveal the Potential Function of Annexin Genes in Response to Abiotic stress, Calcium and Hormones in Cassava (Manihot esculeta Crantz)

2019 ◽  
Author(s):  
Ruimei Li ◽  
Yuqing Wang ◽  
Yangjiao Zhou ◽  
Tingting Qiu ◽  
Yu Song ◽  
...  
Keyword(s):  
Salt Stress ◽  
Abiotic Stress ◽  
Expression Patterns ◽  
Membrane Lipid ◽  
Pcr Analysis ◽  
Abiotic Stress Response ◽  
Promoter Regions ◽  
Manihot Esculenta Crantz ◽  
Diverse Range ◽  
Drought And Salt Stress

Abstract Background The calcium (Ca2+)-dependent phospholipid binding protein annexin gene family, which is known to be related to membrane lipid and cytoskeletal components, is involved in a diverse range of biological functions. However, in cassava (Manihot esculenta Crantz), no studies focusing on the roles of annexin genes in response to abiotic stresses, calcium, and hormones have been informed. Results 12 annexin genes were found and assigned to eight chromosomes in the cassava genome. All of the MeAnns contain a typical annexin domain with four 70-amino acid repeats. The MeAnns are classified into six groups in the phylogenetic tree. In their promoter regions, MeAnns possess at least 3 hormone response-related cis-elements and 1 abiotic stress response-related cis-acting element. MeAnn1, MeAnn2 and MeAnn5 exhibit very high levels of expression in each tested organs or tissues. By contrast, MeAnn12 exhibits very low levels in all the tested organs or tissues. qRT-PCR analysis indicates that both MeAnn5 and MeAnn9 have significantly high expression in leaves after cold, drought, and salt treatments and are highly responsive to CaCl2, GA and JA treatments. MeAnn2 and MeAnn10 are significantly downregulated in leaves by cold, drought and salt stress and negatively respond to CaCl2, GA and JA. The expression patterns of MeAnns under cold, drought, and salt stress are irregular in shoots. In roots, MeAnn1 and MeAnn9 are downregulated by cold, CaCl2 and JA treatments, while their other gene expression patterns are irregular. Conclutions In this study, we identified annexin genes in cassava and our expression profiling analysis demonstrated that cassava annexin genes responded to multiple stresses. Our results laid the foundation for further study of the function of cassava anesxin genes and provided an entry point for understanding the response mechanism of cassava to abiotic stress.

scholarly journals Identification of the Golden-2-like transcription factors gene family in Gossypium hirsutum

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12484
Author(s):  
Zilin Zhao ◽  
Jiaran Shuang ◽  
Zhaoguo Li ◽  
Huimin Xiao ◽  
Yuling Liu ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Transcription Factors ◽  
Abiotic Stress ◽  
Stress Response ◽  
Gossypium Hirsutum ◽  
Gene Family ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Abiotic Stress Response ◽  
Qrt Pcr

Background Golden2-Like (GLK) transcription factors are a type of transcriptional regulator in plants. They play a pivotal role in the plant physiological activity process and abiotic stress response. Methods In this study, the potential function of GLK family genes in Gossypium hirsutum was studied based on genomic identification, phylogenetic analysis, chromosome mapping and cis-regulatory elements prediction. Gene expression of nine key genes were analyzed by qRT-PCR experiments. Results Herein, we identified a total of 146 GhGLK genes in Gossypium hirsutum, which were unevenly distributed on each of the chromosomes. There were significant differences in the number and location of genes between the At sub-genome and the Dt sub-genome. According to the phylogenetic analysis, they were divided into ten subgroups, each of which had very similar number and structure of exons and introns. Some cis-regulatory elements were identified through promoter analysis, including five types of elements related to abiotic stress response, five types of elements related to phytohormone and five types of elements involved in growth and development. Based on public transcriptome data analysis, we identified nine key GhGLKs involved in salt, cold, and drought stress. The qRT-PCR results showed that these genes had different expression patterns under these stress conditions, suggesting that GhGLK genes played an important role in abiotic stress response. This study laid a theoretical foundation for the screening and functional verification of genes related to stress resistance of GLK gene family in cotton.

scholarly journals Molecular Characterization, Gene Evolution and Expression Analysis of the F-Box Gene Family in Tomato (Solanum lycopersicum)

Genes ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 417
Author(s):  
Fulei Mo ◽  
Nian Zhang ◽  
Youwen Qiu ◽  
Lingjun Meng ◽  
Mozhen Cheng ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Cold Stress ◽  
Gene Family ◽  
Solanum Lycopersicum ◽  
Expression Analysis ◽  
Gene Evolution ◽  
Expression Patterns ◽  
Pcr Analysis ◽  
Whole Genome ◽  
Cis Elements

F-box genes play an important role in the growth and development of plants, but there are few studies on its role in a plant’s response to abiotic stresses. In order to further study the functions of F-box genes in tomato (Solanum lycopersicum, Sl), a total of 139 F-box genes were identified in the whole genome of tomato using bioinformatics methods, and the basic information, transcript structure, conserved motif, cis-elements, chromosomal location, gene evolution, phylogenetic relationship, expression patterns and the expression under cold stress, drought stress, jasmonic acid (JA) treatment and salicylic acid (SA) treatment were analyzed. The results showed that SlFBX genes were distributed on 12 chromosomes of tomato and were prone to TD (tandem duplication) at the ends of chromosomes. WGD (whole genome duplication), TD, PD (proximal duplication) and TRD (transposed duplication) modes seem play an important role in the expansion and evolution of tomato SlFBX genes. The most recent divergence occurred 1.3042 million years ago, between SlFBX89 and SlFBX103. The cis-elements in SlFBX genes’ promoter regions were mainly responded to phytohormone and abiotic stress. Expression analysis based on transcriptome data and qRT-PCR (Real-time quantitative PCR) analysis of SlFBX genes showed that most SlFBX genes were differentially expressed under abiotic stress. SlFBX24 was significantly up-regulated at 12 h under cold stress. This study reported the SlFBX gene family of tomato for the first time, providing a theoretical basis for the detailed study of SlFBX genes in the future, especially the function of SlFBX genes under abiotic stress.

scholarly journals The maize hexokinase gene ZmHXK7 confers salt resistance in transgenic Arabidopsis plants

2021 ◽  
Author(s):  
Qianqian Liu ◽  
Zengyuan Tian ◽  
Yuqi Guo
Keyword(s):  
Salt Stress ◽  
Abiotic Stress ◽  
Gene Family ◽  
Transgenic Arabidopsis ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Salt Resistance ◽  
Pcr Analysis ◽  
Plant Expression Vector ◽  
Localization Analysis

AbstractThe hexokinase (HXK) gene family, whose members play vital roles in sugar induction signals and glycolysis in organisms, is widely found in plants. Although some hexokinase genes have been studied in maize, a systematic report of the gene family and its role in plant resistance is lacking. In this study, 10 hexokinase genes were systematically identified in maize based on the maize genome-wide database. Phylogenetic analysis divides the maize HXK protein family into four clusters. Prediction of cis-regulatory elements showed that a number of elements responding to abiotic stress exist in the promoter of hexokinase genes. The expression profile of these genes, originated from B73, showed that different members of hexokinase genes are highly expressed in roots and leaves of maize under salt or drought stress, which is similar to that of Mo17.The coding sequence of ZmHXK7 gene, isolated from maize B73, was constructed into plant expression vector pMDC45 and then transformed into athxk3 (Salk_022188C). By hyg resistance detection, PCR analysis, and western blot confirmation, the homozygous progenies of transgenic Arabidopsis lines were identified. Subcellular localization analysis showed that the ZmHXK7 gene was located in cytosol. Seedling growth and salt stress inhibition in complementary mutant plants of ZmHXK7 gene were significantly improved, and enhanced salt tolerance was displayed. Our study provides insights into the evolution and expression patterns of the hexokinase gene and show that maize ZmHXK7 proteins play an important role in resisting salt stress, which will be useful in plant breeding for abiotic stress resistance.

scholarly journals Comprehensive Analysis of the TIFY Gene Family and Its Expression Profiles under Phytohormone Treatment and Abiotic Stresses in Roots of Populus trichocarpa

Forests ◽  
2020 ◽  
Vol 11 (3) ◽  
pp. 315
Author(s):  
Hanzeng Wang ◽  
Xue Leng ◽  
Xuemei Xu ◽  
Chenghao Li
Keyword(s):  
Gene Family ◽  
Abiotic Stresses ◽  
Expression Profiles ◽  
Populus Trichocarpa ◽  
Expression Patterns ◽  
Interaction Network ◽  
Pcr Analysis ◽  
Phylogenetic Tree Analysis ◽  
Element Analysis ◽  
Cis Element

The TIFY gene family is specific to land plants, exerting immense influence on plant growth and development as well as responses to biotic and abiotic stresses. Here, we identify 25 TIFY genes in the poplar (Populus trichocarpa) genome. Phylogenetic tree analysis revealed these PtrTIFY genes were divided into four subfamilies within two groups. Promoter cis-element analysis indicated most PtrTIFY genes possess stress- and phytohormone-related cis-elements. Quantitative real-time reverse transcription polymerase chain reaction (qRT–PCR) analysis showed that PtrTIFY genes displayed different expression patterns in roots under abscisic acid, methyl jasmonate, and salicylic acid treatments, and drought, heat, and cold stresses. The protein interaction network indicated that members of the PtrTIFY family may interact with COI1, MYC2/3, and NINJA. Our results provide important information and new insights into the evolution and functions of TIFY genes in P. trichocarpa.

Genome-wide identification, phylogeny and expression analysis of HSF gene family in barley during abiotic stress response and reproductive development

Plant Gene ◽  
2020 ◽  
Vol 23 ◽  
pp. 100231
Author(s):  
Sumit Kumar Mishra ◽  
Anuj Kumar Poonia ◽  
Reeku Chaudhary ◽  
Vinay K. Baranwal ◽  
Deepanksha Arora ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Stress Response ◽  
Gene Family ◽  
Expression Analysis ◽  
Reproductive Development ◽  
Abiotic Stress Response ◽  
Genome Wide

scholarly journals Genome-Wide Analysis of the IQM Gene Family in Rice (Oryza sativa L.)

Plants ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 1949
Author(s):  
Tian Fan ◽  
Tianxiao Lv ◽  
Chuping Xie ◽  
Yuping Zhou ◽  
Changen Tian
Keyword(s):  
Abiotic Stress ◽  
Stress Response ◽  
Gene Family ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Abiotic Stress Response ◽  
Biotic And Abiotic Stress ◽  
Yeast Two Hybrid ◽  
Iq Motif ◽  
Two Hybrid

Members of the IQM (IQ-Motif Containing) gene family are involved in plant growth and developmental processes, biotic and abiotic stress response. To systematically analyze the IQM gene family and their expression profiles under diverse biotic and abiotic stresses, we identified 8 IQM genes in the rice genome. In the current study, the whole genome identification and characterization of OsIQMs, including the gene and protein structure, genome localization, phylogenetic relationship, gene expression and yeast two-hybrid were performed. Eight IQM genes were classified into three subfamilies (I–III) according to the phylogenetic analysis. Gene structure and protein motif analyses showed that these IQM genes are relatively conserved within each subfamily of rice. The 8 OsIQM genes are distributed on seven out of the twelve chromosomes, with three IQM gene pairs involved in segmental duplication events. The evolutionary patterns analysis revealed that the IQM genes underwent a large-scale event within the last 20 to 9 million years. In addition, quantitative real-time PCR analysis of eight OsIQMs genes displayed different expression patterns at different developmental stages and in different tissues as well as showed that most IQM genes were responsive to PEG, NaCl, jasmonic acid (JA), abscisic acid (ABA) treatment, suggesting their crucial roles in biotic, and abiotic stress response. Additionally, a yeast two-hybrid assay showed that OsIQMs can interact with OsCaMs, and the IQ motif of OsIQMs is required for OsIQMs to combine with OsCaMs. Our results will be valuable to further characterize the important biological functions of rice IQM genes.

scholarly journals Genome-Wide Analysis of the WOX Gene Family and Function Exploration of GmWOX18 in Soybean

Plants ◽  
2019 ◽  
Vol 8 (7) ◽  
pp. 215 ◽  
Author(s):  
Qingnan Hao ◽  
Ling Zhang ◽  
Yanyan Yang ◽  
Zhihui Shan ◽  
Xin-an Zhou
Keyword(s):  
Abiotic Stress ◽  
Gene Family ◽  
Function Analysis ◽  
Expression Patterns ◽  
Protein Structures ◽  
Pcr Analysis ◽  
Regeneration Ability ◽  
Functional Identification ◽  
Phylogenetic Tree Analysis ◽  
Wox Genes

WUSCHEL-related homeobox (WOX) is a family of transcription factors that are unique to plants and is characterized by the presence of a homeodomain. The WOX transcription factor plays an important role in regulating plant growth and development and the response to abiotic stress. Soybean is one of the most important oil crops worldwide. In this study, based on the available genome data of soybean, the WOX gene family was identified by bioinformatics analysis. The chromosome distribution, gene and protein structures, phylogenetic relationship and gene expression patterns of this family were comprehensively compared. The results showed that a total of 33 putative WOX genes in the soybean genome were found and then designated as GmWOX1- GmWOX33, which were distributed across 19 chromosomes except chromosome 16. Multiple sequence analysis of the GmWOX gene family revealed a highly conserved homeodomain. Phylogenetic tree analysis showed that 33 WOX genes could be divided into three major clades (modern/WUS, intermediate and ancient) in soybean. Of these 33 WOX genes, some showed differential expression patterns in the tested tissues (leaves, pods, unopen and open flowers, nodules, seed, roots, root hairs, stems, shoot apical meristems and shoot tips). In addition, the expression profile and qRT-PCR analysis showed that most of the GmWOX genes responded to different abiotic stress treatments (cold and drought). According to the expression pattern of GmWOX genes in the high regeneration capacity soybean material P3, overexpression of GmWOX18 was selected for function analysis. The overexpression of GmWOX18 increased the regeneration ability of clustered buds. The results will provide valuable information for further studies on the roles of WOX genes in regulating soybean growth, development and responses to abiotic stress, as well as a basis for the functional identification and analysis of WOX genes in soybean.

scholarly journals Genome-wide analysis of the WRKY gene family and its response to abiotic stress in buckwheat (Fagopyrum tataricum)

2019 ◽  
Vol 14 (1) ◽  
pp. 80-96 ◽  
Author(s):  
Xia He ◽  
Jing-jian Li ◽  
Yuan Chen ◽  
Jia-qi Yang ◽  
Xiao-yang Chen
Keyword(s):  
Abiotic Stress ◽  
Plant Growth ◽  
Gene Family ◽  
Stress Responses ◽  
Growth Regulation ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Tartary Buckwheat ◽  
Wrky Gene ◽  
Fagopyrum Tataricum

AbstractThe WRKY gene family is an ancient plant transcription factor (TF) family with a vital role in plant growth and development, especially in response to biotic and abiotic stresses. Although many researchers have studied WRKY TFs in numerous plant species, little is known of them in Tartary buckwheat (Fagopyrum tataricum). Based on the recently reported genome sequence of Tartary buckwheat, we identified 78 FtWRKY proteins that could be classified into three major groups. All 77 WRKY genes were distributed unevenly across all eight chromosomes. Exon–intron analysis and motif composition prediction revealed the complexity and diversity of FtWRKYs, indicating that WRKY TFs may be of significance in plant growth regulation and stress response. Two separate pairs of tandem duplication genes were found, but no segmental duplications were identified. Overall, most orthologous gene-pairs between Tartary and common buckwheat evolved under strong purifying selection. qRT-PCR was used to analyze differences in expression among four FtWRKYs (FtWRKY6, 74, 31, and 7) under salt, drought, cold, and heat treatments. The results revealed that all four proteins are related to abiotic stress responses, although they exhibited various expression patterns. In particular, the relative expression levels of FtWRKY6, 74, and 31 were significantly upregulated under salt stress, while the highest expression of FtWRKY7 was observed from heat treatment. This study provides comprehensive insights into the WRKY gene family in Tartary buckwheat, and can support the screening of additional candidate genes for further functional characterization of WRKYs under various stresses.

scholarly journals Genome-wide Identification and Abiotic Stress Response Pattern Analysis of NF-Y Gene Family in Peanut (Arachis Hypogaea L.)

2021 ◽  
Author(s):  
Qian Wan ◽  
Lu Luo ◽  
Xiurong Zhang ◽  
Yuying Lv ◽  
Suqing Zhu ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Stress Response ◽  
Gene Family ◽  
Developmental Stages ◽  
Expression Patterns ◽  
Regulatory Region ◽  
Amino Acid Sequences ◽  
Start Codon ◽  
Abiotic Stress Response ◽  
Specific Expression

AbstractThe nuclear factor Y (NF-Y) transcription factor (TF) family consists of three subfamilies NF-YA, NF-YB and NF-YC. Many studies have proven that NF-Y complex plays multiple essential roles in stress response in Arabidopsis and other plant species. However, little attention has been given to these genes in peanut. In this study, thirty-three AhNF-Y genes were identified in cultivated peanut and they were distributed on 16 chromosomes. A phylogenetic analysis of the NF-Y amino acid sequences indicated that the peanut NF-Y proteins were clustered in pairs at the end of the branches and showed high conservation with previous reported plant NF-Ys. Evolutionary history analysis showed that only segmental duplication contributed to expansion of this gene family. Analysis of the 1500-bp regulatory regions upstream the start codon showed that, except for AhNF-YB6, peanut NF-Ys contained at least one abiotic stress response element in their regulatory region. Expression patterns of peanut NF-Ys in 22 tissues and developmental stages were analyzed. A few NF-Ys showed universal expression patterns, while most NF-Ys showed specific expression patterns. Through RNA-seq and qRT-PCR analyses, expression of six AhNF-Y genes was induced under salt stress in leaves or roots. In addition, AhNF-YA4/8/11, NF-YB4 and NF-YC2/8 also responded to osmotic stress, ABA (abscisic acid) and salicylic acid (SA) treatment.

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