The full-length transcriptome of <i>Spartina alterniflora</i> reveals the complexity of high salt tolerance in monocotyledonous halophyte

Fraser, Michael; Wang, Taotao; Wei, Wei; Lou, Shuaitong; Lan, Faxiu; Sheng, Zhaoxue; Li, Qinzhen; Ji, Guoli; Wu, Xiaohui; Ma, Liuyin

doi:10.1101/680819

Cited by 9 publications

(11 citation statements)

References 88 publications

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“…Halophytes can survive better under ambient salinity than glycophytes, which might be attributable to proper modulation of genes that play crucial roles in triggering their salt tolerance mechanisms [ 76 , 144 ]. High-throughput transcriptome sequencing is increasingly being used to understand the responses of plants to abiotic stresses at gene expression level [ 145 ]. Recently, Guo et al [ 146 ] conducted a comparative transcriptome analysis of the model halophyte Puccinellia tenuiflora and several glycophytic Gramineae plants to uncover their underlying molecular responses to excessive salt stress.…”

Section: Potential Of Halophytes As Genetic Resources For the Engineering Of Crops With Improved Salt Tolerancementioning

confidence: 99%

Adaptive Mechanisms of Halophytes and Their Potential in Improving Salinity Tolerance in Plants

Rahman

Mostofa

Keya

et al. 2021

IJMS

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Soil salinization, which is aggravated by climate change and inappropriate anthropogenic activities, has emerged as a serious environmental problem, threatening sustainable agriculture and future food security. Although there has been considerable progress in developing crop varieties by introducing salt tolerance-associated traits, most crop cultivars grown in saline soils still exhibit a decline in yield, necessitating the search for alternatives. Halophytes, with their intrinsic salt tolerance characteristics, are known to have great potential in rehabilitating salt-contaminated soils to support plant growth in saline soils by employing various strategies, including phytoremediation. In addition, the recent identification and characterization of salt tolerance-related genes encoding signaling components from halophytes, which are naturally grown under high salinity, have paved the way for the development of transgenic crops with improved salt tolerance. In this review, we aim to provide a comprehensive update on salinity-induced negative effects on soils and plants, including alterations of physicochemical properties in soils, and changes in physiological and biochemical processes and ion disparities in plants. We also review the physiological and biochemical adaptation strategies that help halophytes grow and survive in salinity-affected areas. Furthermore, we illustrate the halophyte-mediated phytoremediation process in salinity-affected areas, as well as their potential impacts on soil properties. Importantly, based on the recent findings on salt tolerance mechanisms in halophytes, we also comprehensively discuss the potential of improving salt tolerance in crop plants by introducing candidate genes related to antiporters, ion transporters, antioxidants, and defense proteins from halophytes for conserving sustainable agriculture in salinity-prone areas.

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Section: Potential Of Halophytes As Genetic Resources For the Engineering Of Crops With Improved Salt Tolerancementioning

confidence: 99%

Adaptive Mechanisms of Halophytes and Their Potential in Improving Salinity Tolerance in Plants

Rahman

Mostofa

Keya

et al. 2021

IJMS

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“…In this study, transcriptome-wide analysis indicated that APA involves in response to high salt stress (Figures 3-4). High salt stress induces a higher number of differential used APA sites along salt stress gradients (Figure 3a), and ∼42% of APA sites are associated with high salt stress, which is much higher than the prevalence of AS events (∼10%) (Ye et al, 2020). In addition, we found that pathways that are related to ion transport, response to osmotic stress, and respond to salt stress are significantly enriched in high salt stress-associated APA (Figure 3c-d).…”

Section: Discussionmentioning

confidence: 99%

“…The invasive monocotyledonous halophyte - Spartina alterniflora ( Spartina ) is a good model to study high salt tolerance mechanism, as it could tolerant to harsh salinity environment in salt marsh (Bedre et al, 2016; Ye et al, 2020). In this study, we used PacBio SMRT sequencing and poly(A) tag sequencing (PAT-seq) to get insight into how APA responds to high salt stress in Spartina .…”

Section: Introductionmentioning

confidence: 99%

Alternative 3′ UTRs contributes to post-transcriptional gene expression regulation under high salt stress

Wang

Fraser

Zhang

et al. 2022

Preprint

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High salt stress continually challenges growth and survival of many plants, but the underlying molecular basis is not fully explored. Alternative polyadenylation (APA) produces mRNAs with different 3′UTRs (alternative 3′UTRs) to regulate gene expression at post-transcriptional level. However, the roles of such process in response to salt stress remain elusive. Here, we reported that alternative 3′UTRs responded to high salt stress in the halophyte-Spartina alterniflora, which tolerant to hash salt environment. High salt stress induced the global APA and increased the prevalence of APA events. Strikingly, high salt stress significantly led to 3′ UTR lengthening of 207 transcripts through increasing the usage of distal poly(A) sites. Transcripts with alternative 3′ UTRs were mainly enriched in salt stress related ion transporters. Alternative 3′ UTRs of SaHKT1 increased RNA stability and protein synthesis in vivo. Regulatory AU-rich elements were identified in the alternative 3′ UTRs and alternative 3′ UTRs increased protein level of SaHKT1 in an AU-rich element dependent manner. Finally, 3′ UTR lengthening might result from variations in poly(A) signals and poly(A) factors. Overall, these results suggest that APA is a potential novel high salt stress responsive mechanism by modulating mRNA 3′ UTR length. These results also reveal complex regulator roles of alternative 3′ UTRs coupling alternative polyadenylation and regulatory elements at post-transcriptional level in plants.One sentence summaryAlternative 3′ UTRs acts as a potential novel mechanism in gene expression regulation of high salt tolerant genes

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“…Spartina alterniflora maintained a higher K + accumulation under high salt stress via the active gene expression dynamics of SaAKT2, SaKAT2, SaSKOR, and SaNHX2. Moreover, the SaNHX2 showed significant upregulation under high salt stress, further indicating the involvement of SaNHX2 in the K + reservoir of Spartina (Ye et al 2019). In S. virginicus, exclusion of ions from roots and secretion of ions from salt glands helped in the achievement of salt balance (Yamamoto et al 2015).…”

Section: Transcriptomic Analysis Revealed Salt Stress-responsive Genesmentioning

confidence: 91%

Recent Advances on Cellular Signaling Paradigm and Salt Stress Responsive Genes in Halophytes

Saddhe

Jamdade

Gairola

2020

Handbook of Halophytes

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The full-length transcriptome of Spartina alterniflora reveals the complexity of high salt tolerance in monocotyledonous halophyte

Cited by 9 publications

References 88 publications

Adaptive Mechanisms of Halophytes and Their Potential in Improving Salinity Tolerance in Plants

Adaptive Mechanisms of Halophytes and Their Potential in Improving Salinity Tolerance in Plants

Alternative 3′ UTRs contributes to post-transcriptional gene expression regulation under high salt stress

Recent Advances on Cellular Signaling Paradigm and Salt Stress Responsive Genes in Halophytes

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