scholarly journals De novo Whole-Genome Assembly of Moringa oleifera Helps Identify Genes Regulating Drought Stress Tolerance

2021 ◽  
Vol 12 ◽  
Author(s):  
P Sushree Shyamli ◽  
Seema Pradhan ◽  
Mitrabinda Panda ◽  
Ajay Parida
Keyword(s):  
Abiotic Stress ◽  
Drought Stress ◽  
Drought Tolerance ◽  
Moringa Oleifera ◽  
De Novo ◽  
Phylogenetic Analyses ◽  
Agroforestry System ◽  
Whole Genome ◽  
Duplication Events ◽  
Imminent Threat

Abiotic stresses, especially drought stress, are responsible for heavy losses in productivity, which in turn poses an imminent threat for future food security. Understanding plants’ response to abiotic stress at the molecular level is crucially important for mitigating the impacts of climate change. Moringa oleifera is an important multipurpose plant with medicinal and nutritional properties and with an ability to grow in low water conditions, which makes the species an ideal candidate to study the regulatory mechanisms that modulate drought tolerance and its possible use in agroforestry system. In the present communication, we report whole-genome sequencing (WGS) of this species and assemble about 90% of the genome of M. oleifera var. Bhagya into 915 contigs with a N50 value of 4.7 Mb and predicted 32,062 putative protein-coding genes. After annotating the genome, we have chosen to study the heat shock transcription factor (HSF) family of genes to analyze their role in drought tolerance in M. oleifera. We predicted a total of 21 HSFs in the M. oleifera genome and carried out phylogenetic analyses, motif identification, analysis of gene duplication events, and differential expression of the HSF-coding genes in M. oleifera. Our analysis reveals that members of the HSF family have an important role in the plant’s response to abiotic stress and are viable candidates for further characterization.

scholarly journals BrEXLB1, a Brassica rapa Expansin-Like B1 Gene Is Associated with Root Development, Drought Stress Response, and Seed Germination

Genes ◽  
2020 ◽  
Vol 11 (4) ◽  
pp. 404 ◽  
Author(s):  
Muthusamy Muthusamy ◽  
Joo Yeol Kim ◽  
Eun Kyung Yoon ◽  
Jin A. Kim ◽  
Soo In Lee
Keyword(s):  
Abiotic Stress ◽  
Drought Stress ◽  
Stress Response ◽  
Seed Germination ◽  
Drought Tolerance ◽  
Root Growth ◽  
Brassica Rapa ◽  
Root Development ◽  
Clubroot Disease ◽  
Qrt Pcr

Expansins are structural proteins prevalent in cell walls, participate in cell growth and stress responses by interacting with internal and external signals perceived by the genetic networks of plants. Herein, we investigated the Brassica rapa expansin-like B1 (BrEXLB1) interaction with phytohormones (IAA, ABA, Ethephon, CK, GA3, SA, and JA), genes (Bra001852, Bra001958, and Bra003006), biotic (Turnip mosaic Virus (TuMV), Pectobacterium carotovorum, clubroot disease), and abiotic stress (salt, oxidative, osmotic, and drought) conditions by either cDNA microarray or qRT-PCR assays. In addition, we also unraveled the potential role of BrEXLB1 in root growth, drought stress response, and seed germination in transgenic Arabidopsis and B. rapa lines. The qRT-PCR results displayed that BrEXLB1 expression was differentially influenced by hormones, and biotic and abiotic stress conditions; upregulated by IAA, ABA, SA, ethylene, drought, salt, osmotic, and oxidative conditions; and downregulated by clubroot disease, P. carotovorum, and TuMV infections. Among the tissues, prominent expression was observed in roots indicating the possible role in root growth. The root phenotyping followed by confocal imaging of root tips in Arabidopsis lines showed that BrEXLB1 overexpression increases the size of the root elongation zone and induce primary root growth. Conversely, it reduced the seed germination rate. Further analyses with transgenic B. rapa lines overexpressing BrEXLB1 sense (OX) and antisense transcripts (OX-AS) confirmed that BrEXLB1 overexpression is positively associated with drought tolerance and photosynthesis during vegetative growth phases of B. rapa plants. Moreover, the altered expression of BrEXLB1 in transgenic lines differentially influenced the expression of predicted BrEXLB1 interacting genes like Bra001852 and Bra003006. Collectively, this study revealed that BrEXLB1 is associated with root development, drought tolerance, photosynthesis, and seed germination.

scholarly journals Characterization of wheat homeodomain-leucine zipper family genes and functional analysis of TaHDZ5-6A in drought tolerance in transgenic Arabidopsis

2019 ◽  
Author(s):  
Shumin Li ◽  
Nan Chen ◽  
Fangfang Li ◽  
Fangming Mei ◽  
Zhongxue Wang ◽  
...  
Keyword(s):  
Functional Analysis ◽  
Abiotic Stress ◽  
Drought Stress ◽  
Drought Tolerance ◽  
Transgenic Arabidopsis ◽  
Expression Profiles ◽  
Wild Type ◽  
Protein Motifs ◽  
Zip Family ◽  
Zip Genes

Abstract Abstract Background: Many studies in Arabidopsis and rice have demonstrated that HD-Zip transcription factors play important roles in plant development and responses to abiotic stresses. Although common wheat (Triticum aestivum L.) is one of the most widely cultivated and consumed food crops in the world, the function of the HD-Zip proteins in wheat is still largely unknown. Results: To explore the potential biological functions of HD-Zip genes in wheat, we performed a bioinformatics and gene expression analysis of the HD-Zip family. We identified 113 HD-Zip members from wheat and classified them into four subfamilies (I-IV) based on phylogenic analysis against proteins from Arabidopsis, rice, and maize. Most HD-Zip genes are represented by two to three homeoalleles in wheat, which are named as TaHDZX_ZA, TaHDZX_ZB, or TaHDZX_ZD, where X denotes the gene number and Z the wheat chromosome on which it is located. TaHDZs in the same subfamily have similar protein motifs and intron/exon structures. The expression profiles of TaHDZ genes were analysed in different tissues, at different stages of vegetative growth, during seed development, and under drought stress. We found that most TaHDZ genes, especially those in subfamilies I and II, were induced by drought stress, suggesting the potential importance of subfamily I and II TaHDZ members in the responses to abiotic stress. Compared with wild-type (WT) plants, transgenic Arabidopsis plants overexpressing TaHDZ5-6A displayed enhanced drought tolerance, lower water loss rates, higher survival rates, and higher proline content under drought conditions. Additionally, the transcriptome analysis identified a number of differentially expressed genes between 35S::TaHDZ5-6A transgenic and wild-type plants, many of which are involved in stress response. Conclusions: Our results will facilitate further functional analysis of wheat HD-Zip genes, and also indicate that TaHDZ5-6A may participate in regulating the plant response to drought stress. Our experiments show that TaHDZ5-6A holds great potential for genetic improvement of abiotic stress tolerance in crops.

scholarly journals Characterization of wheat homeodomain-leucine zipper family genes and functional analysis of TaHDZ5-6A in drought tolerance in transgenic Arabidopsis

2020 ◽  
Author(s):  
Shumin Li ◽  
Nan Chen ◽  
Fangfang Li ◽  
Fangming Mei ◽  
Zhongxue Wang ◽  
...  
Keyword(s):  
Functional Analysis ◽  
Abiotic Stress ◽  
Drought Stress ◽  
Drought Tolerance ◽  
Transgenic Arabidopsis ◽  
Expression Profiles ◽  
Wild Type ◽  
Protein Motifs ◽  
Zip Family ◽  
Zip Genes

Abstract Background: Many studies in Arabidopsis and rice have demonstrated that HD-Zip transcription factors play important roles in plant development and responses to abiotic stresses. Although common wheat (Triticum aestivum L.) is one of the most widely cultivated and consumed food crops in the world, the function of the HD-Zip proteins in wheat is still largely unknown. Results: To explore the potential biological functions of HD-Zip genes in wheat, we performed a bioinformatics and gene expression analysis of the HD-Zip family. We identified 113 HD-Zip members from wheat and classified them into four subfamilies (I-IV) based on phylogenic analysis against proteins from Arabidopsis, rice, and maize. Most HD-Zip genes are represented by two to three homeoalleles in wheat, which are named as TaHDZX_ZA, TaHDZX_ZB, or TaHDZX_ZD, where X denotes the gene number and Z the wheat chromosome on which it is located. TaHDZs in the same subfamily have similar protein motifs and intron/exon structures. The expression profiles of TaHDZ genes were analysed in different tissues, at different stages of vegetative growth, during seed development, and under drought stress. We found that most TaHDZ genes, especially those in subfamilies I and II, were induced by drought stress, suggesting the potential importance of subfamily I and II TaHDZ members in the responses to abiotic stress. Compared with wild-type (WT) plants, transgenic Arabidopsis plants overexpressing TaHDZ5-6A displayed enhanced drought tolerance, lower water loss rates, higher survival rates, and higher proline content under drought conditions. Additionally, the transcriptome analysis identified a number of differentially expressed genes between 35S::TaHDZ5-6A transgenic and wild-type plants, many of which are involved in stress response. Conclusions: Our results will facilitate further functional analysis of wheat HD-Zip genes, and also indicate that TaHDZ5-6A may participate in regulating the plant response to drought stress. Our experiments show that TaHDZ5-6A holds great potential for genetic improvement of abiotic stress tolerance in crops.

scholarly journals Comparative Genomics of Clinical Isolates of the Emerging Tick-Borne Pathogen Neoehrlichia mikurensis

2021 ◽  
Vol 9 (7) ◽  
pp. 1488
Author(s):  
Anna Grankvist ◽  
Daniel Jaén-Luchoro ◽  
Linda Wass ◽  
Per Sikora ◽  
Christine Wennerås
Keyword(s):  
Vascular Endothelium ◽  
De Novo ◽  
Phylogenetic Analyses ◽  
Geographic Origin ◽  
Comparative Genomic ◽  
Whole Genome ◽  
Illumina Hiseq ◽  
Protein Coding ◽  
Ehrlichia Ruminantium ◽  
Protein Coding Genes

Tick-borne ‘Neoehrlichia (N.) mikurensis’ is the cause of neoehrlichiosis, an infectious vasculitis of humans. This strict intracellular pathogen is a member of the family Anaplasmataceae and has been unculturable until recently. The only available genetic data on this new pathogen are six partially sequenced housekeeping genes. The aim of this study was to advance the knowledge regarding ‘N. mikurensis’ genomic relatedness with other Anaplasmataceae members, intra-species genotypic variability and potential virulence factors explaining its tropism for vascular endothelium. Here, we present the de novo whole-genome sequences of three ‘N. mikurensis’ strains derived from Swedish patients diagnosed with neoehrlichiosis. The genomes were obtained by extraction of DNA from patient plasma, library preparation using 10x Chromium technology, and sequencing by Illumina Hiseq-4500. ‘N. mikurensis’ was found to have the next smallest genome of the Anaplasmataceae family (1.1 Mbp with 27% GC contents) consisting of 845 protein-coding genes, every third of which with unknown function. Comparative genomic analyses revealed that ‘N. mikurensis’ was more closely related to Ehrlichia chaffeensis than to Ehrlichia ruminantium, the opposite of what 16SrRNA sequence-based phylogenetic analyses determined. The genetic variability of the three whole-genome-sequenced ‘N. mikurensis’ strains was extremely low, between 0.14 and 0.22‰, a variation that was associated with geographic origin. No protein-coding genes exclusively shared by N. mikurensis and E. ruminantium were identified to explain their common tropism for vascular endothelium.

scholarly journals Selection of upland rice lines in advanced yield trials and response to abiotic stress

2021 ◽  
Vol 22 (10) ◽  
Author(s):  
Arif Tirtana ◽  
Bambang Sapta Purwoko ◽  
ISWARI SARASWATI DEWI ◽  
Trikoesoemaningtyas Trikoesoemaningtyas
Keyword(s):  
Abiotic Stress ◽  
Drought Stress ◽  
Drought Tolerance ◽  
Aluminum Toxicity ◽  
Upland Rice ◽  
Yield Potential ◽  
Research Station ◽  
High Productivity ◽  
Yield Trials ◽  
Selection Of

Abstract. Tirtana A, Purwoko BP, Dewi IS, Trikoesoemaningtyas. 2021. Selection of upland rice lines in advanced yield trials and response to abiotic stress. Biodiversitas 22: 4694-4703. Breeding programs to obtain superior upland rice varieties with high productivity and adaptive in dryland must be prioritized to maximize the potential of dryland. This research aimed to obtain information on the agronomic performance of upland rice lines in advanced yield trials and select the best lines with high productivity and tolerance to drought stress and aluminum toxicity. Advanced yield trials were conducted from November 2016 until March 2017 in Bogor and Sukabumi using a randomized complete block design, where three replications were nested in the environments. Aluminum and drought stress evaluations were conducted at Muara Research Station, Bogor, in May-June 2018 and September-October 2018. Based on the selection index, twelve lines were selected with superior agronomic characters and high yield potential. These lines had characteristics as follows: days to harvesting (110.2-116.0 days), number of filled grains (70.6-101.3 grains), number of unfilled grains (27.9-58.4 grains), and productivity (2.2-2.9 tons ha-1). Evaluation of drought tolerance showed four lines with better drought tolerance than the drought-sensitive check IR20. The aluminum tolerance evaluation obtained two tolerant lines and nine lines with moderate responses to aluminum toxicity. The selected lines need to be further evaluated in multilocation trials.

scholarly journals Diversification of Non-TIR Class NB-LRR Genes in Relation to Whole-Genome Duplication Events in Arabidopsis

2005 ◽  
Vol 18 (2) ◽  
pp. 103-109 ◽  
Author(s):  
Kan Nobuta ◽  
Tom Ashfield ◽  
Sun Kim ◽  
Roger W. Innes
Keyword(s):  
Segmental Duplication ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Phylogenetic Analyses ◽  
Synonymous Substitution ◽  
Duplication Event ◽  
Whole Genome ◽  
R Genes ◽  
Genome Duplication Event ◽  
Duplication Events

Arabidopsis thaliana is believed to have experienced at least two and possibly three whole-genome duplication events in its evolutionary history. In order to investigate the evolutionary relationships between these duplication events and diversification of disease resistance (R) genes, segmental-duplication events containing R genes belonging to the nucleotide binding-leucine rich repeat (NB-LRR) class were identified. Of 153 segmental-duplication events containing NB-LRR genes, only 22 contained NB-LRR genes in both members of the duplication pair, indicating a high frequency of NB-LRR gene loss after wholegenome duplication. The relative age of the duplication events was estimated based on the average synonymous substitution rate of the duplicated gene pairs in the segments. These data were combined with phylogenetic analyses. NB-LRR genes present in segment pairs derived from the most recent whole-genome duplication event, estimated to have occurred only 20 to 40 million years ago, occupy very distant branches of the NB-LRR phylogenetic tree. These data suggest that when NB-LRR clusters are duplicated as part of a whole-genome duplication, homoeologous NB-LRR genes are preferentially lost, either by eliminating one copy of the cluster or by eliminating individual genes such that only paralogous NB-LRR genes are maintained.

scholarly journals Overexpression of chalcone synthase gene improves flavonoid accumulation and drought tolerance in tobacco

2020 ◽  
Author(s):  
Ben Hu ◽  
Heng Yao ◽  
Yulong Gao ◽  
Ran Wang ◽  
Feng Li ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Drought Stress ◽  
Drought Tolerance ◽  
Transgenic Tobacco ◽  
Chalcone Synthase ◽  
Phylogenetic Analyses ◽  
Redox Balance ◽  
Transgenic Tobacco Plants ◽  
Flavonoid Pathway ◽  
Tobacco Plants

Abstract Flavonoids are important secondary metabolites in plants that play important roles in maintaining the cellular redox balance of cells. Chalcone synthase (CHS) is the key enzyme in the flavonoid biosynthesis pathway and has been found to monitor changes due to drought stress tolerance. In this study, a CHS gene in tobacco ( Nicotiana tabacum ) was overexpressed. Results revealed that transgenic tobacco plants were more tolerant than control plants to drought stress. Transcription levels of the key genes involved in the flavonoid pathway and the contents of seven flavonoids significantly increased in transgenic tobacco plants ( p < 0.01). Overexpression of the CHS gene led to lower concentrations of the oxidative stress product, malondialdehyde (MDA). Additionally, 11 CHS family genes were mined from the tobacco genome. Based on the phylogenetic tree, these genes split into two groups with eight genes clustered together with the bona fide Arabidopsis CHS gene, suggesting that those tobacco genes are CHS genes. Further phylogenetic analyses indicated that the tobacco CHS genes grouped further into three independent clades with the cloned tobacco CHS gene located within Clade iii. The tobacco CHS family genes exhibited a highly conserved CDS length, pI, and molecular weight of the encoded peptides. All CHS peptides contained two conserved domains, and the genes harbored two or three exons. Based on the results of this study, the NtCHS gene is considered a possible candidate gene for genetically engineering enhanced drought tolerance and improved responses to oxidative stress in plants.

scholarly journals Overexpression of chalcone synthase gene improves flavonoid accumulation and drought tolerance in tobacco

2019 ◽  
Author(s):  
Ben Hu ◽  
Heng Yao ◽  
Yulong Gao ◽  
Ran Wang ◽  
Feng Li ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Drought Stress ◽  
Drought Tolerance ◽  
Transgenic Tobacco ◽  
Chalcone Synthase ◽  
Phylogenetic Analyses ◽  
Redox Balance ◽  
Transgenic Tobacco Plants ◽  
Flavonoid Pathway ◽  
Tobacco Plants

Abstract Background: Flavonoids are important secondary metabolites in plants that play important roles in maintaining the cellular redox balance of cells. Chalcone synthase (CHS) is the key enzyme in the flavonoid biosynthesis pathway and has been found to monitor changes due to drought stress tolerance.Results: In this study, a CHS gene in tobacco (Nicotiana tabacum) was overexpressed. Results revealed that transgenic tobacco plants were more tolerant than control plants to drought stress. Transcription levels of the key genes involved in the flavonoid pathway and the contents of seven flavonoids significantly increased in transgenic tobacco plants (p < 0.01). Overexpression of the CHS gene led to lower concentrations of the oxidative stress product, malondialdehyde (MDA). Additionally, 11 CHS family genes were mined from the tobacco genome. Based on the phylogenetic tree, these genes split into two groups with eight genes clustered together with the bona fide Arabidopsis CHS gene, suggesting that those tobacco genes are CHS genes. Further phylogenetic analyses indicated that the tobacco CHS genes grouped further into three independent clades with the cloned tobacco CHS gene located within Clade iii. The tobacco CHS family genes exhibited a highly conserved CDS length, pI, and molecular weight of the encoded peptides. All CHS peptides contained two conserved domains, and the genes harbored two or three exons.Conclusions: Based on the results of this study, the NtCHS gene is considered a possible candidate gene for genetically engineering enhanced drought tolerance and improved responses to oxidative stress in plants.

scholarly journals Seed priming of plants aiding in drought stress tolerance and faster recovery: a review

2021 ◽  
Author(s):  
K. P. Raj Aswathi ◽  
Hazem M. Kalaji ◽  
Jos T. Puthur
Keyword(s):  
Drought Stress ◽  
Drought Tolerance ◽  
Stress Tolerance ◽  
De Novo ◽  
Low Cost ◽  
Seed Priming ◽  
Crop Productivity ◽  
Plant Performance ◽  
Beneficial Effects ◽  
Antioxidant Machinery

AbstractDrought stress exposure adversely affects plant growth and productivity. Various seed priming techniques are experimented to mitigate the adverse effect of drought stress on plant performance. It is a low-cost and sustainable technology that proved to be of immense potential to enhance drought tolerance and increase crop productivity. Drought episodes are followed by recovery through rain or irrigation and help the plants to recuperate from the damages caused by drought stress. The severity of drought-associated damages determines the recovery kinetics of plants. Under the recurrent cycle of drought events, recovery kinetics has immense importance in predicting the stress tolerance potential and survival status of a plant. Many processes like DNA damage repair, de-novo synthesis of nucleic acids and proteins, osmotic adjustment through the accumulation of osmolytes, the potential activity of antioxidant machinery occurring during seed priming play a significant role during recovery from drought stress. Alleviation of the severity of drought stress through the accumulation of osmolytes, the augmented activity of antioxidant machinery, improved photosynthetic performance, and the upregulated expression of stress-responsive genes attributed by seed priming will complement the recovery from drought stress. Although the beneficial effects of seed priming on drought tolerance are well explored, priming influenced recovery mechanism has not been well explored. There is a lacuna in the field of research related to the beneficial effects of seed priming for recovery from drought stress, and that is the focus of this paper.

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