In Silico Analyses of Autophagy-Related Genes in Rapeseed (Brassica napus L.) under Different Abiotic Stresses and in Various Tissues

Eshkiki, Elham Mehri; Hajiahmadi, Zahra; Abedi, Amin; Kordrostami, Mojtaba; Jacquard, Cédric

doi:10.3390/plants9101393

Cited by 7 publications

(3 citation statements)

References 95 publications

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“…The splicing phase and exon-intron structures play an important role in the evolution of gene families. 47 The two intron phases (0 and 1) in AsFAD were highly conserved, whereas intron phase 2 exhibited the lowest level of conservation. The same result for the splicing phase was observed in other plants, demonstrating that FAD genes have been highly conserved throughout evolution.…”

Section: Discussionmentioning

confidence: 93%

In Silico Identification and Characterization of Fatty Acid Desaturase (FAD) Genes in Argania spinosa L. Skeels: Implications for Oil Quality and Abiotic Stress

El Faqer,

Rabeh,

Alami

et al. 2024

Bioinform Biol Insights

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Fatty acid desaturase ( FAD) is the key enzyme that leads to the formation of unsaturated fatty acids by introducing double bonds into hydrocarbon chains, and it plays a critical role in plant lipid metabolism. However, no data are available on enzyme-associated genes in argan trees. In addition, a candidate gene approach was adopted to identify and characterize the gene sequences of interest that are potentially involved in oil quality and abiotic stress. Based on phylogenetic analyses, 18 putative FAD genes of Argania spinosa L. ( AsFAD) were identified and assigned to three subfamilies: stearoyl-ACP desaturase ( SAD), Δ-12 desaturase ( FAD2/ FAD6), and Δ-15 desaturase ( FAD3/ FAD7). Furthermore, gene structure and motif analyses revealed a conserved exon-intron organization among FAD members belonging to the various oil crops studied, and they exhibited conserved motifs within each subfamily. In addition, the gene structure shows a wide variation in intron numbers, ranging from 0 to 8, with two highly conserved intron phases (0 and 1). The AsFAD and AsSAD subfamilies consist of three (H(X)2-4H, H(X)2-3HH, and H/Q (X)2-3HH) and two (EEN(K)RHG and DEKRHE) conserved histidine boxes, respectively. A set of primer pairs were designed for each FAD gene, and tested on DNA extracted from argan leaves, in which all amplicons of the expected size were produced. These findings of candidate genes in A spinosa L. will provide valuable knowledge that further enhances our understanding of the potential roles of FAD genes in the quality of oil and abiotic stress in the argan tree.

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Section: Discussionmentioning

confidence: 93%

In Silico Identification and Characterization of Fatty Acid Desaturase (FAD) Genes in Argania spinosa L. Skeels: Implications for Oil Quality and Abiotic Stress

El Faqer,

Rabeh,

Alami

et al. 2024

Bioinform Biol Insights

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show abstract

“…Other gene families in rapeseed have also experienced a WGD/segmental duplication event, including 73.81% BnLBDs , 92.3% BnKCSs , 70.98% BnNPFs , 96.96% BnATGs , and 73.4% BnMATEs . Thus, WGD/segmental duplication is a main force for gene family expansion in rapeseed [ 66 , 91 , 92 , 93 , 94 ]. However, not all the duplicated genes were retained; some genes were quickly erased to maintain the genome stability [ 95 ].…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Analysis of the Type-B Authentic Response Regulator Gene Family in Brassica napus

Jiang

Chen

et al. 2022

Genes

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The type-B authentic response regulators (type-B ARRs) are positive regulators of cytokinin signaling and involved in plant growth and stress responses. In this study, we used bioinformatics, RNA-seq, and qPCR to study the phylogenetic and expression pattern of 35 type-B ARRs in Brassica napus. The BnARRs experienced gene expansion and loss during genome polyploidization and were classified into seven groups. Whole-genome duplication (WGD) and segmental duplication were the main forces driving type-B ARR expansion in B. napus. Several BnARRs with specific expression patterns during rapeseed development were identified, including BnARR12/14/18/23/33. Moreover, we found the type-B BnARRs were involved in rapeseed development and stress responses, through participating in cytokinin and ABA signaling pathways. This study revealed the origin, evolutionary history, and expression pattern of type-B ARRs in B. napus and will be helpful to the functional characterization of BnARRs.

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“…Subsequently, the outer membrane of the autophagosome fuses with the tonoplast, leading to the release of the internal vesicle as an autophagic body [ 3 ]. The autophagy pathway is regulated by a sophisticated mechanism for which over 40 ATG genes have been identified in plants [ 4 , 5 , 6 , 7 , 8 ]. In recent years, various studies have indicated that autophagy plays a crucial role in diverse biological processes in plants, including growth, development, degradation of starch, senescence, and control of lipid metabolism [ 9 ].…”

Section: Introductionmentioning

confidence: 99%

The Change in Whole-Genome Methylation and Transcriptome Profile under Autophagy Defect and Nitrogen Starvation

Shi,

Yu,

Cheng

et al. 2023

IJMS

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Through whole-genome bisulfite sequencing and RNA-seq, we determined the potential impact of autophagy in regulating DNA methylation in Arabidopsis, providing a solid foundation for further understanding the molecular mechanism of autophagy and how plants cope with nitrogen deficiency. A total of 335 notable differentially expressed genes (DEGs) were discovered in wild-type Arabidopsis (Col-0-N) and an autophagic mutant cultivated under nitrogen starvation (atg5-1-N). Among these, 142 DEGs were associated with hypomethylated regions (hypo-DMRs) and were upregulated. This suggests a correlation between DNA demethylation and the ability of Arabidopsis to cope with nitrogen deficiency. Examination of the hypo-DMR-linked upregulated DEGs indicated that the expression of MYB101, an ABA pathway regulator, may be regulated by DNA demethylation and the recruitment of transcription factors (TFs; ERF57, ERF105, ERF48, and ERF111), which may contribute to the growth arrest induced by abscisic acid (ABA). Additionally, we found that DNA methylation might impact the biosynthesis of salicylic acid (SA). The promoter region of ATGH3.12 (PBS3), a key enzyme in SA synthesis, was hypomethylated, combined with overexpression of PBS3 and its potential TF AT3G46070, suggesting that autophagy defects may lead to SA-activated senescence, depending on DNA demethylation. These findings suggest that DNA hypomethylation may impact the mechanism by which Arabidopsis autophagy mutants (atg5-1) respond to nitrogen deficiency, specifically in relation to ABA and SA regulation. Our evaluation of hormone levels verified that these two hormones are significantly enriched under nitrogen deficiency in atg5-1-N compared to Col-0-N.

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In Silico Analyses of Autophagy-Related Genes in Rapeseed (Brassica napus L.) under Different Abiotic Stresses and in Various Tissues

Cited by 7 publications

References 95 publications

In Silico Identification and Characterization of Fatty Acid Desaturase (FAD) Genes in Argania spinosa L. Skeels: Implications for Oil Quality and Abiotic Stress

In Silico Identification and Characterization of Fatty Acid Desaturase (FAD) Genes in Argania spinosa L. Skeels: Implications for Oil Quality and Abiotic Stress

Genome-Wide Analysis of the Type-B Authentic Response Regulator Gene Family in Brassica napus

The Change in Whole-Genome Methylation and Transcriptome Profile under Autophagy Defect and Nitrogen Starvation

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