scholarly journals Genome-wide comprehensive analysis of transcriptomes and small RNAs offers insights into the molecular mechanism of alkaline stress tolerance in a citrus rootstock

2019 ◽  
Vol 6 (1) ◽  
Author(s):  
Juxun Wu ◽  
Junying Cao ◽  
Mei Su ◽  
Guizhi Feng ◽  
Yanhui Xu ◽  
...  
Keyword(s):  
Stress Tolerance ◽  
Molecular Mechanism ◽  
Small Rnas ◽  
Comprehensive Analysis ◽  
Alkaline Stress ◽  
Genome Wide ◽  
Citrus Rootstock

scholarly journals Genome-Wide Identification and Expression Profiling of the PDI Gene Family Reveals Their Probable Involvement in Abiotic Stress Tolerance in Tomato (Solanum lycopersicum L.)

Genes ◽  
2020 ◽  
Vol 12 (1) ◽  
pp. 23
Author(s):  
Antt Htet Wai ◽  
Muhammad Waseem ◽  
A B M Mahbub Morshed Khan ◽  
Ujjal Kumar Nath ◽  
Do Jin Lee ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Gene Family ◽  
Stress Tolerance ◽  
Solanum Lycopersicum ◽  
Expression Profiling ◽  
Abiotic Stress Tolerance ◽  
Dependent Manner ◽  
Solanum Lycopersicum L ◽  
Genome Wide ◽  
Protein Disulfide

Protein disulfide isomerases (PDI) and PDI-like proteins catalyze the formation and isomerization of protein disulfide bonds in the endoplasmic reticulum and prevent the buildup of misfolded proteins under abiotic stress conditions. In the present study, we conducted the first comprehensive genome-wide exploration of the PDI gene family in tomato (Solanum lycopersicum L.). We identified 19 tomato PDI genes that were unevenly distributed on 8 of the 12 tomato chromosomes, with segmental duplications detected for 3 paralogous gene pairs. Expression profiling of the PDI genes revealed that most of them were differentially expressed across different organs and developmental stages of the fruit. Furthermore, most of the PDI genes were highly induced by heat, salt, and abscisic acid (ABA) treatments, while relatively few of the genes were induced by cold and nutrient and water deficit (NWD) stresses. The predominant expression of SlPDI1-1, SlPDI1-3, SlPDI1-4, SlPDI2-1, SlPDI4-1, and SlPDI5-1 in response to abiotic stress and ABA treatment suggested they play regulatory roles in abiotic stress tolerance in tomato in an ABA-dependent manner. Our results provide new insight into the structure and function of PDI genes and will be helpful for the selection of candidate genes involved in fruit development and abiotic stress tolerance in tomato.

Comprehensive analysis of CCCH-type zinc finger gene family in citrus (Clementine mandarin) by genome-wide characterization

2014 ◽  
Vol 289 (5) ◽  
pp. 855-872 ◽  
Author(s):  
Shengrui Liu ◽  
Muhammad Rehman Gul Khan ◽  
Yongping Li ◽  
Jinzhi Zhang ◽  
Chungen Hu
Keyword(s):  
Gene Family ◽  
Zinc Finger ◽  
Comprehensive Analysis ◽  
Zinc Finger Gene ◽  
Genome Wide

scholarly journals PGC7 suppresses TET3 for protecting DNA methylation

2013 ◽  
Vol 42 (5) ◽  
pp. 2893-2905 ◽  
Author(s):  
Chunjing Bian ◽  
Xiaochun Yu
Keyword(s):  
Dna Methylation ◽  
Molecular Mechanism ◽  
Biological Process ◽  
Cpg Islands ◽  
Binding Motifs ◽  
Genome Wide Analysis ◽  
Dna Motif ◽  
Genome Wide

Abstract Ten-eleven translocation (TET) family enzymes convert 5-methylcytosine to 5-hydroxylmethylcytosine. However, the molecular mechanism that regulates this biological process is not clear. Here, we show the evidence that PGC7 (also known as Dppa3 or Stella) interacts with TET2 and TET3 both in vitro and in vivo to suppress the enzymatic activity of TET2 and TET3. Moreover, lacking PGC7 induces the loss of DNA methylation at imprinting loci. Genome-wide analysis of PGC7 reveals a consensus DNA motif that is recognized by PGC7. The CpG islands surrounding the PGC7-binding motifs are hypermethylated. Taken together, our study demonstrates a molecular mechanism by which PGC7 protects DNA methylation from TET family enzyme-dependent oxidation.

Proline Accumulation Is Not Correlated with Saline-Alkaline Stress Tolerance in Rice Seedlings

2015 ◽  
Vol 107 (1) ◽  
pp. 51-60 ◽  
Author(s):  
Bing-Sheng Lv ◽  
Hong-Yuan Ma ◽  
Xiao-Wei Li ◽  
Li-Xing Wei ◽  
Hai-Yan Lv ◽  
...  
Keyword(s):  
Stress Tolerance ◽  
Proline Accumulation ◽  
Alkaline Stress ◽  
Rice Seedlings

Genome-wide identification of AP2/ERF transcription factors in mungbean (Vigna radiata) and expression profiling of the VrDREB subfamily under drought stress

2018 ◽  
Vol 69 (10) ◽  
pp. 1009 ◽  
Author(s):  
Abdullahi Muhammad Labbo ◽  
Maryam Mehmood ◽  
Malik Nadeem Akhtar ◽  
Muhammad Jawad Khan ◽  
Aamira Tariq ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Drought Stress ◽  
Stress Tolerance ◽  
Vigna Radiata ◽  
Critical Role ◽  
Drought Stress Tolerance ◽  
Legume Crop ◽  
Genome Wide ◽  
Responsive Element ◽  
Major Factors

Mungbean (Vigna radiata L.) is a valuable legume crop grown in tropical and subtropical areas of Asia. Drought is one of the major factors hindering its growth globally. APETALA2/ethylene-responsive element factor binding proteins (AP2/ERF) are an important family of plant-specific transcription factors (TFs) involved in drought-stress tolerance. We identified 71 AP2/ERF TFs in the mungbean genome by using bioinformatics tools and classified them into subfamilies: AP2 (16 members), ERF (22), RAV (2), DREB (30) and soloist (other proteins with no domain, 1). Members of DREB play a critical role in drought-stress tolerance. Ten-day-old mungbean plants cv. AZRI-06 were exposed to drought stress by complete withholding of water for 7 days. Root samples were collected from control and drought-stressed plants, and the expression pattern of 30 identified VrDREB genes was determined by qPCR. Most VrDREB genes exhibited differential expression in response to drought. Five genes (VrDREB5, VrDREB12, VrDREB13, VrDREB22, VrDREB30) were highly expressed under drought stress and might be considered excellent candidates for further functional analysis and for improvement of mungbean drought tolerance.

scholarly journals EXCESSO DE FERRO SOBRE O DESENVOLVIMENTO DE PORTA-ENXERTOS CÍTRICOS

Nativa ◽  
2019 ◽  
Vol 7 (1) ◽  
pp. 50
Author(s):  
Kassio Ewerton Santos Sombra ◽  
Andreza Cristina Chagas de Oliveira ◽  
Ronyce Do Nascimento Ferreira ◽  
Alexandre Caique Costa e Silva ◽  
Cleilson Do Nascimento Uchôa ◽  
...  
Keyword(s):  
Stress Tolerance ◽  
San Diego ◽  
Block Design ◽  
Dry Mass ◽  
Stem Diameter ◽  
Santa Cruz ◽  
Initial Development ◽  
Citrus Rootstock ◽  
Randomized Complete Block Design

O trabalho objetivou avaliar os efeitos do excesso de ferro sobre a emergência e desenvolvimento inicial de genótipos de porta-enxertos cítricos. Adotou-se delineamento em blocos casualizados (DBC), em fatorial 5x2, com cinco porta-enxertos e dois substratos, repetidos quatro vezes, com parcela útil de 15 recipientes. Os genótipos consistiram do limoeiro ‘Cravo Santa Cruz’; citrandarins ‘Riverside’, ‘San Diego’ e ‘Índio’, além de, tangerineira ‘Sunki Tropical’, cultivados com ou sem óxido de ferro no substrato. Analisaram-se as porcentagens de emergência (PE) e calculou-se o índice de velocidade de emergência (IVE). Realizaram-se biometrias aos 30, 60 e 90 dias após a semeadura (DAS), mensurando-se a altura (H) e diâmetro de caule (D) das plântulas, determinando-se massa fresca (MV) e seca (MS). O excesso de ferro induziu subdesenvolvimento, e até mortalidade de plântulas já emergidas, o que refletiu diretamente nos resultados, porém, todos os genótipos apresentaram emergência superior a 75%, destacando-se o citrandarin ‘San Diego’, com maior altura e caule mais espesso, e o citrandarin ‘Riverside’ com maior sensibilidade ao estresse, registrando os menores valores. O citrandarin ’San Diego’ demonstrou tolerância o estresse e desenvolveu-se satisfatoriamente, necessitando estudos que avaliem a manutenção das características inferidas em combinação com a cultivar copa.Palavras-chave: ambiente protegido, citricultura, enxertia, estresse, mudas. EXCESS OF IRON ON THE DEVELOPMENT OF CITRUS ROOTSTOCKS ABSTRACT: The objective of this work was evaluated the effects of iron excess on the emergence and initial development of citrus rootstock genotypes. A randomized complete block design (DBC), factorial 5x2, with five rootstocks and two substrates, repeated four times, with useful plot of 15 containers was adopted. Genotypes consisted of the 'Santa Cruz' Rangpur lemon; 'Riverside', 'San Diego' and 'Indio' citrandarins, as well as 'Sunki Tropical' tangerine, grown with or without iron excess in substrate. The percentages of emergency (PE) were analyzed and the rate of emergency (IVE) was calculated. Biometry was performed at 30, 60 and 90 days after sowing (DAS), by measuring the height (H) and stem diameter (D) of the seedlings, determining fresh (MV) and dry mass (DM). The excess of iron induced underdevelopment, and even mortality of already emerged seedlings, which reflected directly in the results, however, all genotypes presented an emergency higher to 75%, standing out ’San Diego’ citrandarin, with greater height and more stem thick, and the ‘Riverside’ citrandarin with greater sensitivity to stress, registering the lowest values. 'San Diego’ citrandarin demonstrated stress tolerance and developed satisfactorily, requiring studies that evaluate maintenance of inferred characteristics in combination with cultivar canopy.Keywords: protected environment, citriculture, grafting, stress, seedlings.

scholarly journals Genome-Wide Essentiality Analysis of Mycobacterium abscessus by Saturated Transposon Mutagenesis and Deep Sequencing

mBio ◽  
2021 ◽  
Author(s):  
Dalin Rifat ◽  
Liang Chen ◽  
Barry N. Kreiswirth ◽  
Eric L. Nuermberger
Keyword(s):  
Deep Sequencing ◽  
Mycobacterium Abscessus ◽  
Transposon Mutagenesis ◽  
Comprehensive Analysis ◽  
Data Sets ◽  
Similar Data ◽  
Intrinsic Resistance ◽  
Effective Strategies ◽  
Genome Wide

Limited knowledge regarding Mycobacterium abscessus pathogenesis and intrinsic resistance to most classes of antibiotics is a major obstacle to developing more effective strategies to prevent and mitigate disease. Using optimized procedures for Himar1 transposon mutagenesis and deep sequencing, we performed a comprehensive analysis to identify M. abscessus genetic elements essential for in vitro growth and compare them to similar data sets for M. tuberculosis and M. avium subsp. hominissuis .

scholarly journals Functional genomic approaches to improve crop plant heat stress tolerance

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 1721 ◽  
Author(s):  
Baljeet Singh ◽  
Neha Salaria ◽  
Kajal Thakur ◽  
Sarvjeet Kukreja ◽  
Shristy Gautam ◽  
...  
Keyword(s):  
Heat Stress ◽  
Stress Tolerance ◽  
Association Studies ◽  
Subtractive Hybridization ◽  
Molecular Networks ◽  
Genome Wide Association Studies ◽  
Functional Genomic ◽  
Genome Wide ◽  
Signalling Network ◽  
Heat Stress Tolerance

Heat stress as a yield limiting issue has become a major threat for food security as global warming progresses. Being sessile, plants cannot avoid heat stress. They respond to heat stress by activating complex molecular networks, such as signal transduction, metabolite production and expressions of heat stress-associated genes. Some plants have developed an intricate signalling network to respond and adapt it. Heat stress tolerance is a polygenic trait, which is regulated by various genes, transcriptional factors, proteins and hormones. Therefore, to improve heat stress tolerance, a sound knowledge of various mechanisms involved in the response to heat stress is required. The classical breeding methods employed to enhance heat stress tolerance has had limited success. In this era of genomics, next generation sequencing techniques, availability of genome sequences and advanced biotechnological tools open several windows of opportunities to improve heat stress tolerance in crop plants. This review discusses the potential of various functional genomic approaches, such as genome wide association studies, microarray, and suppression subtractive hybridization, in the process of discovering novel genes related to heat stress, and their functional validation using both reverse and forward genetic approaches. This review also discusses how these functionally validated genes can be used to improve heat stress tolerance through plant breeding, transgenics and genome editing approaches.

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