scholarly journals Genome-Wide Identification, Expression Profile, and Alternative Splicing Analysis of the Brassinosteroid-Signaling Kinase (BSK) Family Genes in Arabidopsis

2019 ◽  
Vol 20 (5) ◽  
pp. 1138 ◽  
Author(s):  
Zhiyong Li ◽  
Jinyu Shen ◽  
Jiansheng Liang
Keyword(s):  
Alternative Splicing ◽  
Expression Profile ◽  
Profile Analysis ◽  
Expression Patterns ◽  
Expression Profile Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Brassinosteroid Signaling ◽  
Genome Wide Search ◽  
Functional Analyses

Brassinosteroids (BRs) are steroid hormones essential for different biological processes, ranging from growth to environmental adaptation in plants. The plant brassinosteroid-signaling kinase (BSK) proteins belong to a family of receptor-like cytoplasmic kinases, which have been reported to play an important role in BR signal transduction. However, the knowledge of BSK genes in plants is still quite limited. In the present study, a total of 143 BSK proteins were identified by a genome-wide search in 17 plant species. A phylogenetic analysis showed that the BSK gene originated in embryophytes, with no BSK found in green algae, and these BSK genes were divided into six groups by comparison with orthologs/paralogs. A further study using comparative analyses of gene structure, expression patterns and alternative splicing of BSK genes in Arabidopsis revealed that all BSK proteins shared similar protein structure with some exception and post-translation modifications including sumolyation and ubiquitination. An expression profile analysis showed that most Arabidopsis BSK genes were constitutively expressed in different tissues; of these, several BSK genes were significantly expressed in response to some hormones or abiotic stresses. Furthermore, reverse transcription-polymerase chain reaction (RT-PCR) assays showed that BSK5, BSK7, and BSK9 underwent alternative splicing in specific stress induced and tissue-dependent patterns. Collectively, these results lay the foundation for further functional analyses of these genes in plants.

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 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 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.

scholarly journals Genome-wide identification and evolution of HECT genes in wheat

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10457
Author(s):  
Xianwen Meng ◽  
Ting Yang ◽  
Jing Liu ◽  
Mingde Zhao ◽  
Jiuli Wang
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Segmental Duplication ◽  
Profile Analysis ◽  
Purifying Selection ◽  
Expression Profile Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Ubiquitin Proteasome ◽  
Proteasome Pathway

Background As an important class of E3 ubiquitin ligases in the ubiquitin proteasome pathway, proteins containing homologous E6-AP carboxyl terminus (HECT) domains are crucial for growth, development, metabolism, and abiotic and biotic stress responses in plants. However, little is known about HECT genes in wheat (Triticum aestivum L.), one of the most important global crops. Methods Using a genome-wide analysis of high-quality wheat genome sequences, we identified 25 HECT genes classified into six groups based on the phylogenetic relationship among wheat, rice, and Arabidopsis thaliana. Results The predicted HECT genes were distributed evenly in 17 of 21 chromosomes of the three wheat subgenomes. Twenty-one of these genes were hypothesized to be segmental duplication genes, indicating that segmental duplication was significantly associated with the expansion of the wheat HECT gene family. The Ka/Ks ratios of the segmental duplication of these genes were less than 1, suggesting purifying selection within the gene family. The expression profile analysis revealed that the 25 wheat HECT genes were differentially expressed in 15 tissues, and genes in Group II, IV, and VI (UPL8, UPL6, UPL3) were highly expressed in roots, stems, and spikes. This study contributes to further the functional analysis of the HECT gene family in wheat.

scholarly journals Genome-wide characterization, evolution and expression profiling of UDP-glycosyltransferase family in pomelo (Citrus grandis) fruit

2020 ◽  
Author(s):  
Boping Wu ◽  
Xiaohong Liu ◽  
Kai Xu ◽  
Bo Zhang
Keyword(s):  
Secondary Metabolites ◽  
Profile Analysis ◽  
Intron Insertion ◽  
Genome Database ◽  
Expression Profile Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Major Species ◽  
Screening And Identification ◽  
Available Information

Abstract Background: Pomelo is one of the three major species of citrus. The fruit accumulates a variety of abundant secondary metabolites that affect the flavor. UDP-glycosyltransferases (UGTs) are involved in the glycosylation of secondary metabolites. Results: In the present study, we performed a genome-wide analysis of pomelo UGT family, a total of 145 UGTs was identified based on the conserved plant secondary product glycosyltransferase (PSPG) motif. These UGT genes were clustered into 16 major groups through phylogenetic analysis of these genes with other plant UGTs (A-P). Pomelo UGTs were distributed unevenly among the chromosomes. At least 10 intron insertion events were observed in these UGT genome sequences, and I-5 was identified to be the highest conserved one. The expression profile analysis of pomelo UGT genes in different fruit tissues during development and ripening was carried out by RNA-seq. Conclusions: We identified 145 UGTs in pomelo fruit through transcriptome data and citrus genome database. Our research provides available information on UGTs studies in pomelo, and provides an important research foundation for screening and identification of functional UGT genes.

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