scholarly journals Genome-wide sequence identification and expression analysis of ARF family in sugar beet (Beta vulgaris L.) under salinity stresses

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9131
Author(s):  
Jie Cui ◽  
Xinyan Li ◽  
Junliang Li ◽  
Congyu Wang ◽  
Dayou Cheng ◽  
...  
Keyword(s):  
Sugar Beet ◽  
Salinity Stress ◽  
Profile Analysis ◽  
Expression Profiles ◽  
Plant Growth And Development ◽  
Auxin Response ◽  
Expression Profile Analysis ◽  
Sequence Identification ◽  
Genome Wide ◽  
Intron Structure

Auxin response factor (ARF) proteins respond to biological and abiotic stresses and play important roles in regulating plant growth and development. In this study, based on the genome-wide database of sugar beet, 16 BvARF proteins were identified. A detailed investigation into the BvARF family is performed, including analysis of the conserved domains, chromosomal locations, phylogeny, exon-intron structure, conserved motifs, subcellular localization, gene ontology (GO) annotations and expression profiles of BvARF under salt-tolerant condition. The majority of BvARF proteins contain B3 domain, AUX_RESP domain and AUX/IAA domain and a few lacked of AUX/IAA domain. Phylogenetic analysis suggests that the 16 BvARF proteins are clustered into six groups. Expression profile analysis shows that most of these BvARF genes in sugar beet under salinity stress were up-regulated or down-regulated to varying degrees and nine of the BvARF genes changed significantly. They were thought to have a significant response to salinity stress. The current study provides basic information for the BvARF genes and will pave the way for further studies on the roles of BvARF genes in regulating sugar beet’s growth, development and responses to salinity stress.

Genome-Wide Identification and Expression Profile Analysis of WRKY Family Genes in Teak (Tectona Grandis)

2020 ◽  
Author(s):  
Xi-Yang Wang ◽  
Jie Song ◽  
Jia-Hui Xing ◽  
Jun-Feng Liang ◽  
Bi-ying Ke
Keyword(s):  
Profile Analysis ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Large Family ◽  
Tectona Grandis ◽  
Duplication Event ◽  
Whole Genome Sequence ◽  
Expression Profile Analysis ◽  
Genome Wide ◽  
A Genome

Abstract Background: WRKY proteins comprise a large family of transcription factors that play vital roles in many aspects of physiological processes and adaption to environment. However, little information was available about the WRKY genes in teak (Tectona grandis). The recent release of the whole-genome sequence of teak allowed us to perform a genome-wide investigation into the organization and expression profiling of teak WRKY genes. Results: In the present study, 102 teak WRKY (TgWRKY) genes were identified and renamed as per their positions on chromosome and scaffolds. According to their structural and phylogenetic analysis, the 102 TgWRKYs were further classified into three main groups with seceral subgroups. The segmental duplication event played a major role in the expansion of teak WRKY gene family and three WGD events were inferred. Expression profiles derived from transcriptome data exhibited distinct expression patterns of TgWRKY genes in various tissues and inresponse to different abiotic stress.Conclusions: 102 TgWRKY genes were identified in teak and the structure of their encoded proteins, their evolutionary characteristics and expression patterns were examined in this study. This study generated an important resource that will provide helpful information for further exploration of the TgWRKY genes role in the regulatory mechanism in response to abiotic stresses.

scholarly journals Genome-Wide Characterization, Evolution, and Expression Profile Analysis of GATA Transcription Factors in Brachypodium distachyon

2021 ◽  
Vol 22 (4) ◽  
pp. 2026
Author(s):  
Weiye Peng ◽  
Wei Li ◽  
Na Song ◽  
Zejun Tang ◽  
Jing Liu ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Expression Profile ◽  
Profile Analysis ◽  
Expression Profiles ◽  
Brachypodium Distachyon ◽  
Defense Responses ◽  
Regulatory Elements ◽  
Blast Disease ◽  
Expression Profile Analysis ◽  
Genome Wide

The GATA proteins, functioning as transcription factors (TFs), are involved in multiple plant physiological and biochemical processes. In this study, 28 GATA TFs of Brachypodium distachyon (BdGATA) were systematically characterized via whole-genome analysis. BdGATA genes unevenly distribute on five chromosomes of B. distachyon and undergo purifying selection during the evolution process. The putative cis-acting regulatory elements and gene interaction network of BdGATA were found to be associated with hormones and defense responses. Noticeably, the expression profiles measured by quantitative real-time PCR indicated that BdGATA genes were sensitive to methyl jasmonate (MeJA) and salicylic acid (SA) treatment, and 10 of them responded to invasion of the fungal pathogen Magnaporthe oryzae, which causes rice blast disease. Genome-wide characterization, evolution, and expression profile analysis of BdGATA genes can open new avenues for uncovering the functions of the GATA genes family in plants and further improve the knowledge of cellular signaling in plant defense.

scholarly journals Genome-wide identification and expression profiles of ERF subfamily transcription factors in Zea mays

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9551
Author(s):  
Lidong Hao ◽  
Shubing Shi ◽  
Haibin Guo ◽  
Ming Li ◽  
Pan Hu ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Plant Growth ◽  
Growth And Development ◽  
Expression Profiles ◽  
Vital Role ◽  
Ethylene Response Factor ◽  
Plant Growth And Development ◽  
Element Analysis ◽  
Genome Wide ◽  
Genes Expression

The Ethylene-Response Factor (ERF) subfamily transcription factors (TFs) belong to the APETALA2/Ethylene-Responsive Factor (AP2/ERF) superfamily and play a vital role in plant growth and development. However, identification and analysis of the ERF subfamily genes in maize have not yet been performed at genome-wide level. In this study, a total of 76 ERF subfamily TFs were identified and were found to be unevenly distributed on the maize chromosomes. These maize ERF (ZmERF) TFs were classified into six groups, namely groups B1 to B6, based on phylogenetic analysis. Synteny analysis showed that 50, 54, and 58 of the ZmERF genes were orthologous to those in rice, Brachypodium, and Sorghum, respectively. Cis-element analysis showed that elements related to plant growth and development, hormones, and abiotic stress were identified in the promoter region of ZmERF genes. Expression profiles suggested that ZmERF genes might participate in plant development and in response to salinity and drought stresses. Our findings lay a foundation and provide clues for understanding the biological functions of ERF TFs in maize.

scholarly journals Genome-Wide Identification of Barley ABC Genes and Their Expression in Response to Abiotic Stress Treatment

Plants ◽  
2020 ◽  
Vol 9 (10) ◽  
pp. 1281
Author(s):  
Ziling Zhang ◽  
Tao Tong ◽  
Yunxia Fang ◽  
Junjun Zheng ◽  
Xian Zhang ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Amino Acid ◽  
Stress Responses ◽  
Transmembrane Domain ◽  
Profile Analysis ◽  
Tissue Expression ◽  
Expression Profile Analysis ◽  
Genome Wide ◽  
Tissue Expression Profile ◽  
Amino Acid Length

Adenosine triphosphate-binding cassette transporters (ABC transporters) participate in various plant growth and abiotic stress responses. In the present study, 131 ABC genes in barley were systematically identified using bioinformatics. Based on the classification method of the family in rice, these members were classified into eight subfamilies (ABCA–ABCG, ABCI). The conserved domain, amino acid composition, physicochemical properties, chromosome distribution, and tissue expression of these genes were predicted and analyzed. The results showed that the characteristic motifs of the barley ABC genes were highly conserved and there were great diversities in the homology of the transmembrane domain, the number of exons, amino acid length, and the molecular weight, whereas the span of the isoelectric point was small. Tissue expression profile analysis suggested that ABC genes possess non-tissue specificity. Ultimately, 15 differentially expressed genes exhibited diverse expression responses to stress treatments including drought, cadmium, and salt stress, indicating that the ABCB and ABCG subfamilies function in the response to abiotic stress in barley.

scholarly journals Genome-wide identification and expression profile analysis of nuclear factor Y family genes in Sorghum bicolor L. (Moench)

PLoS ONE ◽  
2019 ◽  
Vol 14 (9) ◽  
pp. e0222203 ◽  
Author(s):  
P. Maheshwari ◽  
Divya Kummari ◽  
Sudhakar Reddy Palakolanu ◽  
U. Nagasai Tejaswi ◽  
M. Nagaraju ◽  
...  
Keyword(s):  
Sorghum Bicolor ◽  
Expression Profile ◽  
Profile Analysis ◽  
Nuclear Factor ◽  
Nuclear Factor Y ◽  
Expression Profile Analysis ◽  
Genome Wide ◽  
Y Family ◽  
Sorghum Bicolor L

scholarly journals tasiRNA-ARF Pathway Moderates Floral Architecture inArabidopsisPlants Subjected to Drought Stress

2014 ◽  
Vol 2014 ◽  
pp. 1-10 ◽  
Author(s):  
Akihiro Matsui ◽  
Kayoko Mizunashi ◽  
Maho Tanaka ◽  
Eli Kaminuma ◽  
Anh Hai Nguyen ◽  
...  
Keyword(s):  
Drought Stress ◽  
Salinity Stress ◽  
Floral Development ◽  
High Salinity ◽  
Expression Profiles ◽  
Fine Tuning ◽  
Wild Type ◽  
Auxin Response ◽  
Sequencing Technology ◽  
High Salinity Stress

In plants, miRNAs and siRNAs, such as transacting siRNAs (ta-siRNAs), affect their targets through distinct regulatory mechanisms. In this study, the expression profiles of small RNAs (smRNAs) inArabidopsisplants subjected to drought, cold, and high-salinity stress were analyzed using 454 DNA sequencing technology. Expression of three groups of ta-siRNAs (TAS1, TAS2, and TAS3) and their precursors was downregulated inArabidopsisplants subjected to drought and high-salinity stress. Analysis of ta-siRNA synthesis mutants and mutatedARF3-overexpressing plants that escape the tasiRNA-ARF target indicated that self-pollination was hampered by short stamens in plants under drought and high-salinity stress. Microarray analysis of flower buds ofrdr6and wild-type plants under drought stress and nonstressed conditions revealed that expression of floral development- and auxin response-related genes was affected by drought stress and by theRDR6mutation. The overall results of the present study indicated that tasiRNA-ARF is involved in maintaining the normal morphogenesis of flowers in plants under stress conditions through fine-tuning expression changes of floral development-related and auxin response-related genes.

scholarly journals Genome-Wide Expression Profile Analysis Reveals Coordinately Regulated Genes Associated with Stepwise Acquisition of Azole Resistance in Candida albicans Clinical Isolates

2003 ◽  
Vol 47 (4) ◽  
pp. 1220-1227 ◽  
Author(s):  
P. David Rogers ◽  
Katherine S. Barker
Keyword(s):  
Candida Albicans ◽  
Expression Profile ◽  
Profile Analysis ◽  
Clinical Isolates ◽  
Azole Resistance ◽  
Down Regulation ◽  
Human Fungal Pathogen ◽  
Expression Profile Analysis ◽  
Genome Wide ◽  
First Time

ABSTRACT Candida albicans is an opportunistic human fungal pathogen and a causative agent of oropharyngeal candidiasis (OPC), the most frequent opportunistic infection among patients with AIDS. Fluconazole and other azole antifungal agents have proven effective in the management of OPC; however, with increased use of these agents treatment failures have occurred. Such failures have been associated with the emergence of azole-resistant strains of C. albicans. In the present study we examined changes in the genome-wide gene expression profile of a series of C. albicans clinical isolates representing the stepwise acquisition of azole resistance. In addition to genes previously associated with azole resistance, we identified many genes whose differential expression was for the first time associated with this phenotype. Furthermore, the expression of these genes was correlated with that of the known resistance genes CDR1, CDR2, and CaMDR1. Genes coordinately regulated with the up-regulation of CDR1 and CDR2 included the up-regulation of GPX1 and RTA3 and the down-regulation of EBP1. Genes coordinately regulated with the up-regulation of CaMDR1 included the up-regulation of IFD1, IFD4, IFD5, IFD7, GRP2, DPP1, CRD2, and INO1 and the down-regulation of FET34, OPI3, and IPF1222. Several of these appeared to be coordinately regulated with both the CDR genes and CaMDR1. Many of these genes are involved in the oxidative stress response, suggesting that reduced susceptibility to oxidative damage may contribute to azole resistance. Further evaluation of the role these genes and their respective gene products play in azole antifungal resistance is warranted.

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