Genome-wide identification and expression profiling of glutathione S-transferase family under multiple abiotic and biotic stresses in Medicago truncatula L.

Glutathione transferases (GSTs) constitute an ancient, ubiquitous, multi-functional antioxidant enzyme superfamily that has great importance on cellular detoxification against abiotic and biotic stresses as well as plant development and growth. The present study aimed to a comprehensive genome-wide identification and functional characterization of GST family in one of the economically important legume plants—Medicago truncatula. Here, we have identified a total of ninety-two putative MtGST genes that code for 120 proteins. All these members were classified into twelve classes based on their phylogenetic relationship and the presence of structural conserved domain/motif. Among them, 7 MtGST gene pairs were identified to have segmental duplication. Expression profiling of MtGST transcripts revealed their high level of organ/tissue-specific expression in most of the developmental stages and anatomical tissues. The transcripts of MtGSTU5, MtGSTU8, MtGSTU17, MtGSTU46, and MtGSTU47 showed significant up-regulation in response to various abiotic and biotic stresses. Moreover, transcripts of MtGSTU8, MtGSTU14, MtGSTU28, MtGSTU30, MtGSTU34, MtGSTU46 and MtGSTF8 were found to be highly upregulated in response to drought treatment for 24h and 48h. Among the highly stress-responsive MtGST members, MtGSTU17 showed strong affinity towards its conventional substrates reduced glutathione (GSH) and 1‐chloro‐2,4‐dinitrobenzene (CDNB) with the lowest binding energy of—5.7 kcal/mol and -6.5 kcal/mol, respectively. Furthermore, the substrate-binding site residues of MtGSTU17 were found to be highly conserved. These findings will facilitate the further functional and evolutionary characterization of GST genes in Medicago.

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In Silico Prediction and Functional Characterization of Genes Related to Abiotic and Biotic Stresses in Chickpea (Cicer arietinum)

Current Research in Bioinformatics ◽

10.3844/ajbsp.2018.1.35 ◽

2018 ◽

Vol 7 (1) ◽

pp. 1-35

Author(s):

Sukhdeep Kaur ◽

Satendra Singh ◽

Gitanjali Tandon ◽

Sarika Jaiswal ◽

Mir Asif Iquebal ◽

...

Keyword(s):

Cicer Arietinum ◽

In Silico ◽

Functional Characterization ◽

In Silico Prediction ◽

Abiotic And Biotic Stresses ◽

Biotic Stresses

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Genome-Wide Identification, Expression Pattern Analysis and Evolution of the Ces/Csl Gene Superfamily in Pineapple (Ananas comosus)

Plants ◽

10.3390/plants8080275 ◽

2019 ◽

Vol 8 (8) ◽

pp. 275 ◽

Cited By ~ 1

Author(s):

Cao ◽

Cheng ◽

Zhang ◽

Aslam ◽

Yan ◽

...

Keyword(s):

Plant Cell Wall ◽

Developmental Stages ◽

Functional Characterization ◽

Gene Families ◽

Cellulose Synthase ◽

Ananas Comosus ◽

Tropical Fruit ◽

Genome Wide ◽

Gene Structures

The cellulose synthase (Ces) and cellulose synthase-like (Csl) gene families belonging to the cellulose synthase gene superfamily, are responsible for the biosynthesis of cellulose and hemicellulose of the plant cell wall, and play critical roles in plant development, growth and evolution. However, the Ces/Csl gene family remains to be characterized in pineapple, a highly valued and delicious tropical fruit. Here, we carried out genome-wide study and identified a total of seven Ces genes and 25 Csl genes in pineapple. Genomic features and phylogeny analysis of Ces/Csl genes were carried out, including phylogenetic tree, chromosomal locations, gene structures, and conserved motifs identification. In addition, we identified 32 pineapple AcoCes/Csl genes with 31 Arabidopsis AtCes/Csl genes as orthologs by the syntenic and phylogenetic approaches. Furthermore, a RNA-seq investigation exhibited the expression profile of several AcoCes/Csl genes in various tissues and multiple developmental stages. Collectively, we provided comprehensive information of the evolution and function of pineapple Ces/Csl gene superfamily, which would be useful for screening out and characterization of the putative genes responsible for tissue development in pineapple. The present study laid the foundation for future functional characterization of Ces/Csl genes in pineapple.

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Genome-wide identification and biochemical characterization of calcineurin B-like calcium sensor proteins in Chlamydomonas reinhardtii

Biochemical Journal ◽

10.1042/bcj20190960 ◽

2020 ◽

Vol 477 (10) ◽

pp. 1879-1892

Author(s):

Manoj Kumar ◽

Komal Sharma ◽

Akhilesh K. Yadav ◽

Kajal Kanchan ◽

Madhu Baghel ◽

...

Keyword(s):

Chlamydomonas Reinhardtii ◽

Biochemical Characterization ◽

Abiotic And Biotic Stresses ◽

Biotic Stresses ◽

Physiological Processes ◽

Calcineurin B ◽

Genome Wide ◽

Dependent Protein ◽

Sensor Proteins

Calcium (Ca2+) signaling is involved in the regulation of diverse biological functions through association with several proteins that enable them to respond to abiotic and biotic stresses. Though Ca2+-dependent signaling has been implicated in the regulation of several physiological processes in Chlamydomonas reinhardtii, Ca2+ sensor proteins are not characterized completely. C. reinhardtii has diverged from land plants lineage, but shares many common genes with animals, particularly those encoding proteins of the eukaryotic flagellum (or cilium) along with the basal body. Calcineurin, a Ca2+/calmodulin-dependent protein phosphatase, is an important effector of Ca2+ signaling in animals, while calcineurin B-like proteins (CBLs) play an important role in Ca2+ sensing and signaling in plants. The present study led to the identification of 13 novel CBL-like Ca2+ sensors in C. reinhardtii genome. One of the archetypical genes of the newly identified candidate, CrCBL-like1 was characterized. The ability of CrCBL-like1 protein to sense as well as bind Ca2+ were validated using two-step Ca2+-binding kinetics. The CrCBL-like1 protein localized around the plasma membrane, basal bodies and in flagella, and interacted with voltage-gated Ca2+ channel protein present abundantly in the flagella, indicating its involvement in the regulation of the Ca2+ concentration for flagellar movement. The CrCBL-like1 transcript and protein expression were also found to respond to abiotic stresses, suggesting its involvement in diverse physiological processes. Thus, the present study identifies novel Ca2+ sensors and sheds light on key players involved in Ca2+signaling in C. reinhardtii, which could further be extrapolated to understand the evolution of Ca2+ mediated signaling in other eukaryotes.

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Genome-wide analysis of gibberellin-dioxygenases gene family and their responses to GA applications in maize

PLoS ONE ◽

10.1371/journal.pone.0250349 ◽

2021 ◽

Vol 16 (5) ◽

pp. e0250349

Author(s):

Jiabin Ci ◽

Xingyang Wang ◽

Qi Wang ◽

Fuxing Zhao ◽

Wei Yang ◽

...

Keyword(s):

Gene Family ◽

Plant Development ◽

Functional Characterization ◽

Tissue Expression ◽

Leaf Sheath ◽

Solid Base ◽

Specific Expression ◽

Genome Wide ◽

Almost All

Gibberellin-dioxygenases genes plays important roles in the regulating plant development. However, Gibberellin-dioxygenases genes are rarely reported in maize, especially response to gibberellin (GA). In present study, 27 Gibberellin-dioxygenases genes were identified in the maize and they were classified into seven subfamilies (I-VII) based on phylogenetic analysis. This result was also further confirmed by their gene structure and conserved motif characteristics. And gibberellin-dioxygenases genes only occurred segmental duplication that occurs most frequently in plants. Furthermore, the gibberellin-dioxygenases genes showed different tissue expression pattern in different tissues and most of the gibberellin-dioxygenases genes showed tissue specific expression. Moreover, almost all the gibberellin-dioxygenases genes were significantly elevated in response to GA except for ZmGA2ox2 and ZmGA20ox10 of 15 gibberellin-dioxygenases genes normally expressed in leaves while 10 and 11 gibberellin-dioxygenases genes showed up and down regulated under GA treatment than that under normal condition in leaf sheath. In addition, we found that ZmGA2ox1, ZmGA2ox4, ZmGA20ox7, ZmGA3ox1 and ZmGA3ox3 might be potential genes for regulating balance of GAs which play essential roles in plant development. These findings will increase our understanding of Gibberellin-dioxygenases gene family in response to GA and will provide a solid base for further functional characterization of Gibberellin-dioxygenases genes in maize.

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Genome-Wide Identification and Expression Profiling of the Polygalacturonase (PG) and Pectin Methylesterase (PME) Genes in Grapevine (Vitis vinifera L.)

International Journal of Molecular Sciences ◽

10.3390/ijms20133180 ◽

2019 ◽

Vol 20 (13) ◽

pp. 3180 ◽

Cited By ~ 6

Author(s):

Nadeem Khan ◽

Fizza Fatima ◽

Muhammad Salman Haider ◽

Hamna Shazadee ◽

Zhongjie Liu ◽

...

Keyword(s):

Expression Profiling ◽

Developmental Stages ◽

Expression Patterns ◽

Functional Characterization ◽

Vitis Vinifera L ◽

Specific Response ◽

Gene Duplications ◽

Crop Species ◽

Specific Expression ◽

Tissue Specific

In pectin regulation, polygalacturonases (PGs) and pectin methylesterases (PMEs) are critical components in the transformation, disassembly network, and remodeling of plant primary cell walls. In the current study, we identified 36 PG and 47 PME genes using the available genomic resources of grapevine. Herein, we provide a comprehensive overview of PGs and PMEs, including phylogenetic and collinearity relationships, motif and gene structure compositions, gene duplications, principal component analysis, and expression profiling during developmental stages. Phylogenetic analysis of PGs and PMEs revealed similar domain composition patterns with Arabidopsis. The collinearity analysis showed high conservation and gene duplications with purifying selection. The type of duplications also varied in terms of gene numbers in PGs (10 dispersed, 1 proximal, 12 tandem, and 13 segmental, respectively) and PMEs (23 dispersed, 1 proximal, 16 tandem, and 7 segmental, respectively). The tissue-specific response of PG and PME genes based on the reported transcriptomic data exhibited diverged expression patterns in various organs during different developmental stages. Among PGs, VvPG8, VvPG10, VvPG13, VvPG17, VvPG18, VvPG19, VvPG20, VvPG22, and VvPG23 showed tissue- or organ-specific expression in majority of the tissues during development. Similarly, in PMEs, VvPME3, VvPME4, VvPME5, VvPME6, VvPME19, VvPME21, VvPME23, VvPME29, VvPME31, and VvPME32 suggested high tissue-specific response. The gene ontology (GO), Kyoto Encyclopedia of Genes and Genomics (KEGG) enrichment, and cis-elements prediction analysis also suggested the putative functions of PGs and PMEs in plant development, such as pectin and carbohydrate metabolism, and stress activities. Moreover, qRT-PCR validation of 32 PG and PME genes revealed their role in various organs of grapevines (i.e., root, stem, tendril, inflorescence, flesh, skins, and leaves). Therefore, these findings will lead to novel insights and encourage cutting-edge research on functional characterization of PGs and PMEs in fruit crop species.

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Genome-Wide Characterization of HSP90 Gene Family in Cucumber and Their Potential Roles in Response to Abiotic and Biotic Stresses

Frontiers in Genetics ◽

10.3389/fgene.2021.584886 ◽

2021 ◽

Vol 12 ◽

Author(s):

Kaijing Zhang ◽

Shuaishuai He ◽

Yihu Sui ◽

Qinghai Gao ◽

Shuangshuang Jia ◽

...

Keyword(s):

Gene Family ◽

Growth And Development ◽

Structural Characteristics ◽

Heat Shock Protein 90 ◽

The Other ◽

Specific Expression ◽

Abiotic And Biotic Stresses ◽

Biotic Stresses ◽

Genome Wide ◽

Cucumber Genome

Heat shock protein 90 (HSP90) possesses critical functions in plant developmental control and defense reactions. The HSP90 gene family has been studied in various plant species. However, the HSP90 gene family in cucumber has not been characterized in detail. In this study, a total of six HSP90 genes were identified from the cucumber genome, which were distributed to five chromosomes. Phylogenetic analysis divided the cucumber HSP90 genes into two groups. The structural characteristics of cucumber HSP90 members in the same group were similar but varied among different groups. Synteny analysis showed that only one cucumber HSP90 gene, Csa1G569290, was conservative, which was not collinear with any HSP90 gene in Arabidopsis and rice. The other five cucumber HSP90 genes were collinear with five Arabidopsis HSP90 genes and six rice HSP90 genes. Only one pair of paralogous genes in the cucumber HSP90 gene family, namely one pair of tandem duplication genes (Csa1G569270/Csa1G569290), was detected. The promoter analysis showed that the promoters of cucumber HSP90 genes contained hormone, stress, and development-related cis-elements. Tissue-specific expression analysis revealed that only one cucumber HSP90 gene Csa3G183950 was highly expressed in tendril but low or not expressed in other tissues, while the other five HSP90 genes were expressed in all tissues. Furthermore, the expression levels of cucumber HSP90 genes were differentially induced by temperature and photoperiod, gibberellin (GA), downy mildew, and powdery mildew stimuli. Two cucumber HSP90 genes, Csa1G569270 and Csa1G569290, were both differentially expressed in response to abiotic and biotic stresses, which means that these two HSP90 genes play important roles in the process of cucumber growth and development. These findings improve our understanding of cucumber HSP90 family genes and provide preliminary information for further studies of cucumber HSP90 gene functions in plant growth and development.

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Characterization of Germin-like Proteins (GLPs) and Their Expression in Response to Abiotic and Biotic Stresses in Cucumber

Horticulturae ◽

10.3390/horticulturae7100412 ◽

2021 ◽

Vol 7 (10) ◽

pp. 412

Author(s):

Liting Liao ◽

Zhaoyang Hu ◽

Shiqiang Liu ◽

Yingui Yang ◽

Yong Zhou

Keyword(s):

Stress Response ◽

Expression Profiles ◽

Tissue Expression ◽

Functional Identification ◽

Abiotic And Biotic Stresses ◽

Biotic Stresses ◽

Genome Wide ◽

Growth Development ◽

Tandem Duplications

Germins and germin-like proteins (GLPs) are glycoproteins closely associated with plant development and stress response in the plant kingdom. Here, we carried out genome-wide identification and expression analysis of the GLP gene family in cucumber to study their possible functions. A total of 38 GLP genes were identified in cucumber, which could be mapped to six out of the seven cucumber chromosomes. A phylogenetic analysis of the GLP members from cucumber, Arabidopsis and rice showed that these GLPs could be divided into six groups, and cucumber GLPs in the same group had highly similar conserved motif distribution and gene structure. Gene duplication analysis revealed that six cucumber GLP genes were located in the segmental duplication regions of cucumber chromosomes, while 14 genes were associated with tandem duplications. Tissue expression profiles of cucumber GLP genes showed that many genes were preferentially expressed in specific tissues. In addition, some cucumber GLP genes were differentially expressed under salt, drought and ABA treatments, as well as under DM inoculation. Our results provide important information for the functional identification of GLP genes in the growth, development and stress response of cucumber.

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Starch branching enzymes (SBEs) in banana: genome-wide identification and expression analysis reveal their involvement in fruit development, ripening and regulated responses to abiotic/biotic stresses

10.7287/peerj.preprints.27045v1 ◽

2018 ◽

Author(s):

Hongxia Miao ◽

Peiguang Sun ◽

Jiuhua Liu ◽

Zhiqiang Jin ◽

Biyu Xu

Keyword(s):

Fruit Development ◽

Response Patterns ◽

Abiotic And Biotic Stresses ◽

Biotic Stresses ◽

Genome Wide ◽

Fruit Development And Ripening ◽

Branching Enzymes ◽

Salt And Drought Stress ◽

Temporal And Spatial

Starch branching enzyme (SBE), which is one of the key enzymes associated with amylopectin biosynthesis, plays important roles in variable biological processes. Despite its importance, SBE is rarely studied in the banana (Musa acuminata L.) which is a typical starchy fruit. Here, a family of ten SBE proteins (MaSBE) was firstly identified through genome-wide characterization in M. acuminata, which could be clustered into three subfamilies. Systematic transcriptome analysis revealed temporal and spatial expression variations of MaSBE genes and differential response patterns under abiotic and biotic stresses in both banana genotypes, Fen Jiao (FJ) and BaXi Jiao (BX). Moreover, MaSBE2.4 was temporally regulated during fruit development and ripening as well as in response to various abiotic/biotic stresses in both genotypes. Specifically, MaSBE2.3 expression level was higher in FJ than in BX following cold, salt, and drought stress treatments, and it was specifically induced by fungal infection in BX. Characterization of hormone- and stress-related cis-acting elements in the promoters of MaSBE genes suggests their multiple biological functions. In conclusion, our study provides new insights into the complex transcriptional characteristics of the SBE genes, and demonstrates their crucial roles in improving amylopectin biosynthesis and strengthening stress resistance in banana.

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