Comparative Analysis of Drought-Responsive Transcriptome in Different Genotype Saccharum spontaneum L.

Wang, Tianju; Wang, Xianhong; Yang, Qinghui

doi:10.1007/s12355-019-00774-1

Cited by 11 publications

(9 citation statements)

References 64 publications

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“…Importantly, in addition to being overexpressed in Sbi, the members of the CMGC_GSK subfamily also contain many functional domains, which might reflect their high expression. Another overexpressed subfamily in the Sbi kinome (but not in Ssp) was CMGC_MAPK, which has previously been associated with stress signaling in Ssp and Sbi ( Zhang et al, 2015 ; Li et al, 2016b ; Paungfoo-Lonhienne et al, 2016 ; Srivastava and Kumar, 2020 ; Tuleski et al, 2020 ; Wang et al, 2020 ). Although their expression values were significantly increased, these subfamilies did not contain the highest numbers of kinases.…”

Section: Resultsmentioning

confidence: 98%

The Wild Sugarcane and Sorghum Kinomes: Insights Into Expansion, Diversification, and Expression Patterns

et al. 2021

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The protein kinase (PK) superfamily is one of the largest superfamilies in plants and the core regulator of cellular signaling. Despite this substantial importance, the kinomes of sugarcane and sorghum have not been profiled. Here, we identified and profiled the complete kinomes of the polyploid Saccharum spontaneum (Ssp) and Sorghum bicolor (Sbi), a close diploid relative. The Sbi kinome was composed of 1,210 PKs; for Ssp, we identified 2,919 PKs when disregarding duplications and allelic copies, and these were related to 1,345 representative gene models. The Ssp and Sbi PKs were grouped into 20 groups and 120 subfamilies and exhibited high compositional similarities and evolutionary divergences. By utilizing the collinearity between the species, this study offers insights into Sbi and Ssp speciation, PK differentiation and selection. We assessed the PK subfamily expression profiles via RNA-Seq and identified significant similarities between Sbi and Ssp. Moreover, coexpression networks allowed inference of a core structure of kinase interactions with specific key elements. This study provides the first categorization of the allelic specificity of a kinome and offers a wide reservoir of molecular and genetic information, thereby enhancing the understanding of Sbi and Ssp PK evolutionary history.

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Section: Resultsmentioning

confidence: 98%

The Wild Sugarcane and Sorghum Kinomes: Insights Into Expansion, Diversification, and Expression Patterns

et al. 2021

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“…Interestingly, "ribosome" pathway was enriched with 118 genes in susceptible genotype and 129 genes in tolerant genotype and "spliceosome" pathway with 78 genes in susceptible and 84 genes in tolerant genotypes in the present study. The results emphasise the importance of translational machinery under the control of ribosomes and the role of spliceosomal complex in alternate splicing of mRNAs, thereby resulting in proteins with altered structures, functions and localizations for effective stress tolerance (Wang et al 2020;Liu et al 2018;Xu et al 2018).…”

Section: Discussionmentioning

confidence: 96%

Comparative analysis of drought-responsive transcriptomes of sugarcane genotypes with differential tolerance to drought

et al. 2020

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Water stress causes considerable yield losses in sugarcane. To investigate differentially expressed genes under water stress, two sugarcane genotypes were subjected to three water-deficit levels (mild, moderate, and severe) and subsequent recovery and leaf transcriptome was generated using Illumina NextSeq sequencing. Among the differentially expressed genes, the tolerant genotype Co 06022 generated 2970 unigenes (p ≤ 0.05, functionally known, non-redundant DEGs) at 2-day stress, and there was a progressive decrease in the expressed genes as the stress period increased with 2109 unigenes at 6-day stress and 2307 unigenes at 10-day stress. There was considerable reduction at recovery with 1334 unigenes expressed at 10 days after recovery. However, in the susceptible genotype Co 8021, the number of unigenes expressed at 2 days was lower (2025) than the tolerant genotype and a further reduction was seen at 6-day stress (1552). During recovery, more differentially expressed genes were observed in the susceptible cultivar indicating that the cultivar has to activate more functions/processes to recover from the damage caused by stress. Comparison of DEGs between all stages of stress and recovery in both genotypes revealed that, the commonly up-and down-regulated genes across different stages were approximately double in the tolerant genotype. The most enriched gene ontology classes were heme binding, peroxidase activity and metal ion binding in the biological process and response to oxidative stress, hydrogen peroxide catabolic process and response to stress in the molecular function category. The cellular component was enriched with DEGs involved in extracellular region followed by integral component of membrane. The KEGG pathway analysis revealed important metabolic activities and functionally important genes involved in mitigating water-deficit stress in both the varieties. In addition, several unannotated genes in important pathways were detected and together may provide novel insights into water-deficit tolerance mechanisms in sugarcane. The reliability of the observed expression patterns was confirmed by qRT-PCR. The results of this study will help to identify useful genes for improving drought tolerance in sugarcane.

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“…This finding suggested that drought stimulated S. spontaneum sterols to protect cells and maintain normal photosynthesis. Similarly, transcriptome analysis by Wang et al 27 revealed that the phosphoesterase gene was up-regulated and played an active role in sugarcane drought response.…”

Section: Discussionmentioning

confidence: 96%

“…It has been used to study smut infection response 19 , 20 , vital genes involved in cellulose and lignin biosynthesis 21 , plant growth-promoting rhizobacteria inoculation response 22 , and water, salt, and cold stress response 23 – 25 in cultivated sugarcane. Transcriptome sequencing has also been extensively applied to study gene expression changes in S. spontaneum in response to drought stress 26 , 27 , cold damage 28 – 31 , and identification of transcription factors 32 .…”

Section: Introductionmentioning

confidence: 99%

Physiological changes and transcriptome profiling in Saccharum spontaneum L. leaf under water stress and re-watering conditions

Wang

Qian

et al. 2021

Sci Rep

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As the polyploidy progenitor of modern sugarcane, Saccharum spontaneum is considered to be a valuable resistance source to various biotic and abiotic stresses. However, little has been reported on the mechanism of drought tolerance in S. spontaneum. Herein, the physiological changes of S. spontaneum GXS87-16 at three water-deficit levels (mild, moderate, and severe) and after re-watering during the elongation stage were investigated. RNA sequencing was utilized for global transcriptome profiling of GXS87-16 under severe drought and re-watered conditions. There were significant alterations in the physiological parameters of GXS87-16 in response to drought stress and then recovered differently after re-watering. A total of 1569 differentially expressed genes (DEGs) associated with water stress and re-watering were identified. Notably, the majority of the DEGs were induced by stress. GO functional annotations and KEGG pathway analysis assigned the DEGs to 47 GO categories and 93 pathway categories. The pathway categories were involved in various processes, such as RNA transport, mRNA surveillance, plant hormone signal transduction, and plant-pathogen interaction. The reliability of the RNA-seq results was confirmed by qRT-PCR. This study shed light on the regulatory processes of drought tolerance in S. spontaneum and identifies useful genes for genetic improvement of drought tolerance in sugarcane.

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Comparative Analysis of Drought-Responsive Transcriptome in Different Genotype Saccharum spontaneum L.

Cited by 11 publications

References 64 publications

The Wild Sugarcane and Sorghum Kinomes: Insights Into Expansion, Diversification, and Expression Patterns

The Wild Sugarcane and Sorghum Kinomes: Insights Into Expansion, Diversification, and Expression Patterns

Comparative analysis of drought-responsive transcriptomes of sugarcane genotypes with differential tolerance to drought

Physiological changes and transcriptome profiling in Saccharum spontaneum L. leaf under water stress and re-watering conditions

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