Comparative transcriptome analysis reveals differential gene expression in resistant and susceptible tobacco cultivars in response to infection by cucumber mosaic virus

Liú, Dan; Cheng, Yazeng; Gong, Min; Zhao, Qiang; Jiang, Caihong; Cheng, Lei; Ren, Min; Wang, Yuanying; Yang, Aiguo

doi:10.1016/j.cj.2018.11.008

Cited by 17 publications

(14 citation statements)

References 42 publications

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“…Similar results were reported in Dowling (Rag1) when compared with Williams 82 (susceptible) after aphid treatment: 104 DEGs were detected in Dowling and 51 DEGs in Williams 82 at 6 HAI, but the number of DEGs in the two genotypes became comparable at 24 HAI [20]. Likewise, resistant tobacco cultivars had more DEGs than did the susceptible cultivar one day after the infection with cucumber mosaic virus [29]. The faster response in antibiotic resistant plants indicated that the plant defense to aphid and other biotic stresses is initiated at early stage of aphid attack and lasts during infestation.…”

Section: Discussionsupporting

confidence: 82%

A Genome-Wide View of Transcriptional Responses during Aphis glycines Infestation in Soybean

Yao

Yang

et al. 2020

IJMS

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Soybean aphid (Aphis glycines Matsumura) is one of the major limiting factors in soybean production. The mechanism of aphid resistance in soybean remains enigmatic as little information is available about the different mechanisms of antibiosis and antixenosis. Here, we used genome-wide gene expression profiling of aphid susceptible, antibiotic, and antixenotic genotypes to investigate the underlying aphid–plant interaction mechanisms. The high expression correlation between infested and non-infested genotypes indicated that the response to aphid was controlled by a small subset of genes. Plant response to aphid infestation was faster in antibiotic genotype and the interaction in antixenotic genotype was moderation. The expression patterns of transcription factor genes in susceptible and antixenotic genotypes clustered together and were distant from those of antibiotic genotypes. Among them APETALA 2/ethylene response factors (AP2/ERF), v-myb avian myeloblastosis viral oncogene homolog (MYB), and the transcription factor contained conserved WRKYGQK domain (WRKY) were proposed to play dominant roles. The jasmonic acid-responsive pathway was dominant in aphid–soybean interaction, and salicylic acid pathway played an important role in antibiotic genotype. Callose deposition was more rapid and efficient in antibiotic genotype, while reactive oxygen species were not involved in the response to aphid attack in resistant genotypes. Our study helps to uncover important genes associated with aphid-attack response in soybean genotypes expressing antibiosis and antixenosis.

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Section: Discussionsupporting

confidence: 82%

A Genome-Wide View of Transcriptional Responses during Aphis glycines Infestation in Soybean

Yao

Yang

et al. 2020

IJMS

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“…Raw sequence data of different tissues were obtained from PLncDB ( http://plncdb.tobaccodb.org/ ) ( Jin et al, 2021 ) and our unpublished data. Raw RNA-seq datasets, including cold ( Jin et al, 2017 ), drought ( Yang H et al, 2017 ), cadmium (Cd) ( He et al, 2016 ), topping ( Chen et al, 2019 ), NaCl, abscisic acid (ABA) ( Wu et al, 2021 ), cucumber mosaic virus (CMV) ( Liu et al, 2019 ), and Phytophthora nicotianae ( Yang J. K et al, 2017 ) were obtained from the SRA database ( Leinonen et al, 2010 ). All clean reads were mapped to the tobacco reference genome using Hisat2 (2.2.1) ( Kim et al, 2019 ).…”

Section: Methodsmentioning

confidence: 99%

Genome-Wide Identification and Analysis of the Class III Peroxidase Gene Family in Tobacco (Nicotiana tabacum)

Cheng

Meng

et al. 2022

Front. Genet.

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Class III peroxidases (PODs) are plant-specific enzymes that play significant roles in plant physiological processes and stress responses. However, a comprehensive analysis of the POD gene family in tobacco has not yet been conducted. In this study, 210 non-redundant POD gene members (NtPODs) were identified in tobacco (Nicotiana tabacum) and distributed unevenly throughout 24 tobacco chromosomes. Phylogenetic analysis clustered these genes into six subgroups (I-VI). Gene structure and motif analyses showed the structural and functional diversity among the subgroups. Segmental duplication and purifying selection were the main factors affecting NtPOD gene evolution. Our analyses also suggested that NtPODs might be regulated by miRNAs and cis-acting regulatory elements of transcription factors that are involved in various biological processes. In addition, the expression patterns in different tissues and under various stress treatments were investigated. The results showed that the majority of NtPODs had tissue-specific expression patterns and may be involved in many biotic and abiotic responses. qRT-PCR analyses of different tissues and stress treatments were performed to verify transcriptome patterns. Expression of a green fluorescent protein-NtPOD fusion confirmed the plasma membrane localization of NtPOD121 and NtPOD4. Furthermore, 3D structures provided evidences of membrane-bound peroxidase. These findings provide useful information to better understand the evolution of the NtPOD gene family and lay the foundation for further studies on POD gene function in tobacco.

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“…RNA-Seq analysis can provide information regarding the transcriptional regulation of gene expression; this is an effective approach for data mining in species (e.g., persimmon) where genomic data are unavailable ( Utsumi et al, 2019 ; Li Y. S. et al, 2020 ; Wang L. et al, 2020 ). Integrative analysis from biological-omics data (i.e., metabolomics combined with transcriptomics) reveals differential metabolites that are related to phenotypic changes, as well as genes that cause changes in such metabolites ( Shi et al, 2017 ; Liu D. et al, 2019 ; Qiao et al, 2021 ). In the present study, we investigated the roles of ethrel and ZT in regulating the morphological, cellular, physiological, and molecular characteristics of persimmon flowers.…”

Section: Discussionmentioning

confidence: 99%

Effects of Different Chemicals on Sexual Regulation in Persimmon (Diospyros kaki Thunb.) Flowers

Wang

Suo

et al. 2022

Front. Plant Sci.

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Research on crop sexuality is important for establishing systems for germplasm innovation and cultivating improved varieties. In this study, androecious persimmon trees were treated with various concentrations of ethrel (100, 500, and 1,000 mg/L) and zeatin (1, 5, and 10 mg/L) to investigate the morphological, physiological, and molecular characteristics of persimmon. Ethrel at 1,000 mg/L and zeatin at 10 mg/L both significantly reduced the stamen length and pollen grain diameter in androecious trees. Ethrel treatment also led to reduced stamen development with degenerated cellular contents; zeatin treatment promoted the development of arrested pistils via maintaining relatively normal mitochondrial morphology. Both treatments altered carbohydrate, amino acid, and endogenous phytohormone contents, as well as genes associated with hormone production and floral organ development. Thereafter, we explored the combined effects of four chemicals, including ethrel and zeatin, as well as zebularine and 5-azacytidine, both of which are DNA methylation inhibitors, on androecious persimmon flower development. Morphological comparisons showed that stamen length, pollen viability, and pollen grain diameter were significantly inhibited after combined treatment. Large numbers of genes involving in carbohydrate metabolic, mitogen-activated protein kinase (MAPK) signaling, and ribosome pathways, and metabolites including uridine monophosphate (UMP) and cyclamic acid were identified in response to the treatment, indicating complex regulatory mechanisms. An association analysis of transcriptomic and metabolomic data indicated that ribosomal genes have distinct effects on UMP and cyclamic acid metabolites, explaining how male floral buds of androecious persimmon trees respond to these exogenous chemicals. These findings extend the knowledge concerning sexual differentiation in persimmon; they also provide a theoretical basis for molecular breeding, high-yield cultivation, and quality improvement in persimmon.

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Comparative transcriptome analysis reveals differential gene expression in resistant and susceptible tobacco cultivars in response to infection by cucumber mosaic virus

Cited by 17 publications

References 42 publications

A Genome-Wide View of Transcriptional Responses during Aphis glycines Infestation in Soybean

A Genome-Wide View of Transcriptional Responses during Aphis glycines Infestation in Soybean

Genome-Wide Identification and Analysis of the Class III Peroxidase Gene Family in Tobacco (Nicotiana tabacum)

Effects of Different Chemicals on Sexual Regulation in Persimmon (Diospyros kaki Thunb.) Flowers

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