scholarly journals Genome-Wide Identification and Analysis of CC-NBS-LRR Family in Response to Downy Mildew and Black Rot in Chinese Cabbage

2021 ◽  
Vol 22 (8) ◽  
pp. 4266
Author(s):  
Yan Liu ◽  
Dalong Li ◽  
Na Yang ◽  
Xiaolong Zhu ◽  
Kexin Han ◽  
...  
Keyword(s):  
Downy Mildew ◽  
Chinese Cabbage ◽  
Plant Disease Resistance ◽  
Expression Profiles ◽  
Black Rot ◽  
Genome Wide ◽  
Pathogenesis Related ◽  
Effector Triggered Immunity ◽  
Gene Structures ◽  
Bacteria And Fungi

The nucleotide-binding site–leucine-rich repeat (NBS–LRR) gene family is the largest group of plant disease resistance (R) genes widespread in response to viruses, bacteria, and fungi usually involved in effector triggered immunity (ETI). Forty members of the Chinese cabbage CC type NBS–LRR family were investigated in this study. Gene and protein characteristics, such as distributed locations on chromosomes and gene structures, were explored through comprehensive analysis. CC–NBS–LRR proteins were classified according to their conserved domains, and the phylogenetic relationships of CC–NBS–LRR proteins in Brassica rapa, Arabidopsis thaliana, and Oryza sativa were compared. Moreover, the roles of BrCC–NBS–LRR genes involved in pathogenesis-related defense were studied and analyzed. First, the expression profiles of BrCC–NBS–LRR genes were detected by inoculating with downy mildew and black rot pathogens. Second, sensitive and resistant Chinese cabbage inbred lines were screened by downy mildew and black rot. Finally, the differential expression levels of BrCC–NBS–LRR genes were monitored at 0, 1, 3, 6, 12 and 24 h for short and 0, 3, 5, 7, 10 and 14 days for long inoculation time. Our study provides information on BrCC–NBS–LRR genes for the investigation of the functions and mechanisms of CC-NBS-LRR genes in Chinese cabbage.

Genome-wide expression profiles of contrasting inbred lines of Chinese cabbage, Chiifu and Kenshin, under temperature stress

2013 ◽  
Vol 35 (3) ◽  
pp. 273-288 ◽  
Author(s):  
Jeongyeo Lee ◽  
Yong-Pyo Lim ◽  
Ching-Tack Han ◽  
Ill-Sup Nou ◽  
Yoonkang Hur
Keyword(s):  
Temperature Stress ◽  
Chinese Cabbage ◽  
Expression Profiles ◽  
Inbred Lines ◽  
Genome Wide ◽  
Genome Wide Expression

scholarly journals Genome-Wide Analysis of the β-Amylase Gene Family in Brassica L. Crops and Expression Profiles of BnaBAM Genes in Response to Abiotic Stresses

Agronomy ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. 1855
Author(s):  
Dan Luo ◽  
Ziqi Jia ◽  
Yong Cheng ◽  
Xiling Zou ◽  
Yan Lv
Keyword(s):  
Gene Family ◽  
Abiotic Stresses ◽  
Sequence Similarity ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Chromosomal Distribution ◽  
Brassica Napus L ◽  
Oil Crops ◽  
Genome Wide ◽  
Gene Structures

The β-amylase (BAM) gene family, known for their property of catalytic ability to hydrolyze starch to maltose units, has been recognized to play critical roles in metabolism and gene regulation. To date, BAM genes have not been characterized in oil crops. In this study, the genome-wide survey revealed the identification of 30 BnaBAM genes in Brassica napus L. (B. napus L.), 11 BraBAM genes in Brassica rapa L. (B. rapa L.), and 20 BoBAM genes in Brassica oleracea L. (B. oleracea L.), which were divided into four subfamilies according to the sequence similarity and phylogenetic relationships. All the BAM genes identified in the allotetraploid genome of B. napus, as well as two parental-related species (B. rapa and B. oleracea), were analyzed for the gene structures, chromosomal distribution and collinearity. The sequence alignment of the core glucosyl-hydrolase domains was further applied, demonstrating six candidate β-amylase (BnaBAM1, BnaBAM3.1-3.4 and BnaBAM5) and 25 β-amylase-like proteins. The current results also showed that 30 BnaBAMs, 11 BraBAMs and 17 BoBAMs exhibited uneven distribution on chromosomes of Brassica L. crops. The similar structural compositions of BAM genes in the same subfamily suggested that they were relatively conserved. Abiotic stresses pose one of the significant constraints to plant growth and productivity worldwide. Thus, the responsiveness of BnaBAM genes under abiotic stresses was analyzed in B. napus. The expression patterns revealed a stress-responsive behaviour of all members, of which BnaBAM3s were more prominent. These differential expression patterns suggested an intricate regulation of BnaBAMs elicited by environmental stimuli. Altogether, the present study provides first insights into the BAM gene family of Brassica crops, which lays the foundation for investigating the roles of stress-responsive BnaBAM candidates in B. napus.

scholarly journals Genome-Wide Identification and Expression Analysis of MYB Transcription Factor Superfamily in Dendrobium catenatum

2021 ◽  
Vol 12 ◽  
Author(s):  
Tingting Zhang ◽  
Zheng Cui ◽  
Yuxin Li ◽  
Yuqian Kang ◽  
Xiqiang Song ◽  
...  
Keyword(s):  
Abiotic Stresses ◽  
Molecular Breeding ◽  
Theoretical Foundation ◽  
Expression Profiles ◽  
Myb Transcription Factor ◽  
Rna Seq ◽  
Genome Wide ◽  
Gene Structures ◽  
Myb Proteins ◽  
R2r3 Myb

Dendrobium catenatum is an important traditional Chinese medicine and naturally grows on tree trunks and cliffs, where it can encounter diverse environmental stimuli. MYB transcription factors are widely involved in response to abiotic stresses. However, the MYB gene family has not yet been systematically cataloged in D. catenatum. In this study, a total of 133 MYB proteins were identified in D. catenatum, including 32 MYB-related, 99 R2R3-MYB, 1 3R-MYB, and 1 4R-MYB proteins. Phylogenetic relationships, conserved motifs, gene structures, and expression profiles in response to abiotic stresses were then analyzed. Phylogenetic analysis revealed MYB proteins in D. catenatum could be divided into 14 subgroups, which was supported by the conserved motif compositions and gene structures. Differential DcMYB gene expression and specific responses were analyzed under drought, heat, cold, and salt stresses using RNA-seq and validated by qRT-PCR. Forty-two MYB genes were differentially screened following exposure to abiotic stresses. Five, 12, 11, and 14 genes were specifically expressed in response to drought, heat, cold, and salt stress, respectively. This study identified candidate MYB genes with possible roles in abiotic tolerance and established a theoretical foundation for molecular breeding of D. catenatum.

scholarly journals Genome-Wide Identification and Characterization of HSP70 Gene Family in Aquilaria sinensis (Lour.) Gilg

Genes ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 8
Author(s):  
Cuicui Yu ◽  
Mei Rong ◽  
Yang Liu ◽  
Peiwen Sun ◽  
Yanhong Xu ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Profiles ◽  
Pcr Analysis ◽  
Hsp70 Gene ◽  
Aquilaria Sinensis ◽  
Genome Wide ◽  
Gene Structures ◽  
Systematic Identification ◽  
Identification And Characterization

The heat shock protein 70 (HSP70) gene family perform a fundamental role in protecting plants against biotic and abiotic stresses. Aquilaria sinensis is a classic stress-induced medicinal plant, producing a valuable dark resin in a wood matrix, known as agarwood, in response to environmental stresses. The HSP70 gene family has been systematic identified in many plants, but there is no comprehensive analysis at the genomic level in A. sinensis. In this study, 15 putative HSP70 genes were identified in A. sinensis through genome-wide bioinformatics analysis. Based on their phylogenetic relationships, the 15 AsHSP70 were grouped into six sub-families that with the conserved motifs and gene structures, and the genes were mapped onto six separate linkage groups. A qRT-PCR analysis showed that the relative expression levels of all the AsHSP70 genes were up-regulated by heat stress. Subcellular localization of all HSP70s was predicted, and three were verified by transiently expressed in Arabidopsis protoplasts. Based on the expression profiles in different tissues and different layers treated with Agar-Wit, we predict AsHSP70 genes are involved in different stages of agarwood formation. The systematic identification and expression analysis of HSP70s gene family imply some of them may play important roles in the formation of agarwood. Our findings not only provide a foundation for further study their biological function in the later research in A. sinensis, but also provides a reference for the analysis of HSPs in other species.

scholarly journals Mungbean DIRIGENT Gene Subfamilies and Their Expression Profiles Under Salt and Drought Stresses

2021 ◽  
Vol 12 ◽  
Author(s):  
Wenying Xu ◽  
Tong Liu ◽  
Huiying Zhang ◽  
Hong Zhu
Keyword(s):  
Stress Responses ◽  
Expression Profiles ◽  
Pfam Domain ◽  
Vascular Plant ◽  
Expression Patterns ◽  
Promoter Regions ◽  
Genome Wide ◽  
A Genome ◽  
Salt And Drought Stress ◽  
Gene Structures

DIRIGENT (DIR) genes are key players in environmental stress responses that have been identified in many vascular plant species. However, few studies have examined the VrDIR genes in mungbean. In this study, we characterized 37 VrDIR genes in mungbean using a genome-wide identification method. VrDIRs were distributed on seven of the 11 mungbean chromosomes, and chromosome three contained the most VrDIR genes, with seven members. Thirty-two of the 37 VrDIRs contained a typical DIR gene structure, with one exon; the conserved DIR domain (i.e., Pfam domain) occupied most of the protein in 33 of the 37 VrDIRs. The gene structures of VrDIR genes were analyzed, and a total of 19 distinct motifs were detected. VrDIR genes were classified into five groups based on their phylogenetic relationships, and 13 duplicated gene pairs were identified. In addition, a total of 92 cis-acting elements were detected in all 37 VrDIR promoter regions, and VrDIR genes contained different numbers and types of cis-acting elements. As a result, VrDIR genes showed distinct expression patterns in different tissues and in response to salt and drought stress.

scholarly journals Genome-wide identification and expression profile of YABBY genes in Averrhoa carambola

PeerJ ◽  
2022 ◽  
Vol 9 ◽  
pp. e12558
Author(s):  
Chengru Li ◽  
Na Dong ◽  
Liming Shen ◽  
Meng Lu ◽  
Junwen Zhai ◽  
...  
Keyword(s):  
Fruit Development ◽  
Developmental Stages ◽  
Expression Profiles ◽  
Fruit Size ◽  
Fleshy Fruit ◽  
Averrhoa Carambola ◽  
Star Fruit ◽  
Genome Wide ◽  
Yabby Gene ◽  
Gene Structures

Background Members of the plant-specific YABBY gene family are thought to play an important role in the development of leaf, flower, and fruit. The YABBY genes have been characterized and regarded as vital contributors to fruit development in Arabidopsis thaliana and tomato, in contrast to that in the important tropical economic fruit star fruit (Averrhoa carambola), even though its genome is available. Methods In the present study, a total of eight YABBY family genes (named from AcYABBY1 to AcYABBY8) were identified from the genome of star fruit, and their phylogenetic relationships, functional domains and motif compositions, physicochemical properties, chromosome locations, gene structures, protomer elements, collinear analysis, selective pressure, and expression profiles were further analyzed. Results Eight AcYABBY genes (AcYABBYs) were clustered into five clades and were distributed on five chromosomes, and all of them had undergone negative selection. Tandem and fragment duplications rather than WGD contributed to YABBY gene number in the star fruit. Expression profiles of AcYABBYs from different organs and developmental stages of fleshy fruit indicated that AcYABBY4 may play a specific role in regulating fruit size. These results emphasize the need for further studies on the functions of AcYABBYs in fruit development.

scholarly journals Genome-wide identification, characterization, and expression patterns analysis of the SBP-box gene family in wheat (Triticum aestivum L.)

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Ying Li ◽  
Qilu Song ◽  
Yamin Zhang ◽  
Zheng Li ◽  
Jialin Guo ◽  
...  
Keyword(s):  
Triticum Aestivum ◽  
Abiotic Stress ◽  
Stress Responses ◽  
Tandem Duplication ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Triticum Aestivum L ◽  
Genome Wide ◽  
Related Development ◽  
Gene Structures

Abstract SQUAMOSA promoter-binding protein (SBP)-box genes encode a family of plant-specific transcription factors that play roles in plant growth and development. The characteristics of SBP-box genes in rice (Oryza sativa) and Arabidopsis have been reported, but their potential roles in wheat (Triticum aestivum) are not fully understood. In this study, 48 SBP-box genes (TaSBPs) were identified; they were located in all wheat chromosomes except for 4B and 4D. Six TaSBPs were identified as tandem duplication genes that formed three tandem duplication pairs, while 22 were segmentally duplicated genes that formed 16 segmental duplication pairs. Subcellular localization prediction showed TaSBPs were located in nucleus. Among the 48 TaSBPs, 24 were predicted to be putative targets of TamiR156. Phylogenetic analysis showed that TaSBPs, AtSBPs, and OsSBPs that shared similar functions were clustered into the same subgroups. The phylogenetic relationships between the TaSBPs were supported by the identification of highly conserved motifs and gene structures. Four types of cis-elements––transcription-related, development-related, hormone-related, and abiotic stress-related elements––were found in the TaSBP promoters. Expression profiles indicated most TaSBPs participate in flower development and abiotic stress responses. This study establishes a foundation for further investigation of TaSBP genes and provides novel insights into their biological functions.

scholarly journals Genome-Wide Identification, Gene Structure and Expression Analysis of the MADS-Box Gene Family Indicate Their Function in the Development of Tobacco (Nicotiana tabacum L.)

2019 ◽  
Vol 20 (20) ◽  
pp. 5043 ◽  
Author(s):  
Bai ◽  
Yang ◽  
Cao ◽  
Yao ◽  
Zhang ◽  
...  
Keyword(s):  
Nicotiana Tabacum ◽  
Expression Profiles ◽  
Mads Box ◽  
In Planta ◽  
Genome Wide ◽  
Nicotiana Tabacum L ◽  
Tobacco Genome ◽  
Mads Box Gene ◽  
Gene Structures ◽  
Gene Structure And Expression

MADS-box genes play a pivotal role in various processes, including floral and seed development, controlling flowering time, regulation of fruits ripening, and respond to abiotic and biotic stressors in planta. Tobacco (Nicotiana tabacum) has been widely used as a model plant for analyzing the gene function, however, there has been less information on the regulation of flowering, and the associated genes. In the present study, a total of 168 NtMADS-box genes were identified from tobacco, and their phylogenetic relationship, chromosome locations, and gene structures were further analyzed. NtMADS-box genes can be clustered into four sub-families of Mα, Mγ, MIKC*, and MIKCC. A total of 111 NtMADS-box genes were distributed on 20 chromosomes, and 57 NtMADS-box genes were located on the unanchored scaffolds due to the complex and incomplete assembly of the tobacco genome. Expression profiles of NtMADS-box genes by microarray from 23 different tissues indicated that members in different NtMADS-box gene subfamilies might play specific roles in the growth and flower development, and the transcript levels of 24 NtMADS-box genes were confirmed by quantitative real-time PCR. Importantly, overexpressed NtSOC1/NtMADS133 could promote early flowering and dwarfism in transgenic tobacco plants. Therefore, our findings provide insights on the characterization of NtMADS-box genes to further study their functions in plant development.

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