Transcriptional memory contributes to drought tolerance in coffee (Coffea canephora) plants

Guedes, Fernanda Alves de Freitas; Nobres, Priscilla; Ferreira, Daniela C.R.; Menezes‐Silva, Paulo Eduardo; Ribeiro-Alves, Marcelo; Corrêa, Régis L.; DaMatta, Fábio M.; Alves‐Ferreira, Márcio

doi:10.1016/j.envexpbot.2017.12.004

Cited by 61 publications

(47 citation statements)

References 104 publications

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“…Comparing our results with previously identified C. canephora miRNAs [18][19][20][21][22][23][24], we identified seven new precursors and 18 new mature miRNAs for C. canephora (Tables S12 and S13, Supplementary File S2, Supplementary File S3).…”

Section: Micrornas Predictionsupporting

confidence: 62%

“…Five studies have focused only on prediction [18][19][20][21][22]. Two studies have used small RNA sequencing to confirm the transcriptional activity of miRNAs [23,24]. There is only one study [22] that has focused on a comprehensive analysis of the C. canephora sequenced genome to annotate miRNAs, but this study has not taken account of recent changes in miRNA annotation rules in plants.…”

Section: Introductionmentioning

confidence: 99%

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Genome-Wide Screening and Characterization of Non-Coding RNAs in Coffea canephora

Lemos

Foncatti

Guyot

et al. 2020

ncRNA

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Coffea canephora grains are highly traded commodities worldwide. Non-coding RNAs (ncRNAs) are transcriptional products involved in genome regulation, environmental responses, and plant development. There is not an extensive genome-wide analysis that uncovers the ncRNA portion of the C. canephora genome. This study aimed to provide a curated characterization of six ncRNA classes in the Coffea canephora genome. For this purpose, we employed a combination of similarity-based and structural-based computational approaches with stringent curation. Candidate ncRNA loci had expression evidence analyzed using sRNA-seq libraries. We identified 7455 ncRNA loci (6976 with transcriptional evidence) in the C. canephora genome. This comprised of total 115 snRNAs, 1031 snoRNAs, 92 miRNA precursors, 602 tRNAs, 72 rRNAs, and 5064 lncRNAs. For miRNAs, we identified 159 putative high-confidence targets. This study was the most extensive genomic catalog of curated ncRNAs in the Coffea genus. This data might help elaborating more robust hypotheses in future comparative genomic studies as well as gene regulation and genome dynamics, helping to understand the molecular basis of domestication, environmental adaptation, resistance to pests and diseases, and coffee productivity.

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Section: Micrornas Predictionsupporting

confidence: 62%

Section: Introductionmentioning

confidence: 99%

Genome-Wide Screening and Characterization of Non-Coding RNAs in Coffea canephora

Lemos

Foncatti

Guyot

et al. 2020

ncRNA

View full text Add to dashboard Cite

show abstract

“…Some genes will have memory effect on stress in this process and will show higher expression level when drought occurs again. For example, response to dehydration 29B (RD29B) and response to ABA 18 (RAB18) in Arabidopsis [14], 120 genes in coffee including resistant protein RGA2, gibberellin dioxygenase 1 and gibberellin oxidase 1 [15], and also lncRNA, DNA methylation and endogenous phytohormones (especially abscisic acid) participate in rice short-term drought memory [13]. Potato can also adapt to drought through repeated and long-term drought [16,17].…”

Section: Introductionmentioning

confidence: 99%

Transcriptome Response to Drought, Rehydration and Re-Dehydration in Potato

Chen

et al. 2019

IJMS

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Potato is an important food crop and its production is susceptible to drought. Drought stress in crop growth is usually multiple- or long-term. In this study, the drought tolerant potato landrace Jancko Sisu Yari was treated with drought stress, rehydration and re-dehydration, and RNA-seq was applied to analyze the characteristics of gene regulation during these treatments. The results showed that drought-responsive genes mainly involved photosynthesis, signal transduction, lipid metabolism, sugar metabolism, wax synthesis, cell wall regulation, osmotic adjustment. Potato also can be recovered well in the re-emergence of water through gene regulation. The recovery of rehydration mainly related to patatin, lipid metabolism, sugar metabolism, flavonoids metabolism and detoxification besides the reverse expression of the most of drought-responsive genes. The previous drought stress can produce a positive responsive ability to the subsequent drought by drought hardening. Drought hardening was not only reflected in the drought-responsive genes related to the modified structure and cell components, but also in the hardening of gene expression or the “memory” of drought-responsive genes. Abundant genes involved photosynthesis, signal transduction, sugar metabolism, protease and protease inhibitors, flavonoids metabolism, transporters and transcription factors were subject to drought hardening or memorized drought in potato.

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“…Advanced studies that seek to understand the impacts of climate change in coffee plants-such as rising CO 2 concentration and average air temperature, reduction of soil water supply and even soil water deprivation-have pointed to effective metabolic and genetic adjustments as a way of mitigating the negative implications of climatic change [2] [4]- [9]; in particular to the water deficit, some results indicate that coffee plants acquire tolerance due to photosynthetic and metabolic acclimatization to repeated drought events [10] that can be strongly governed by transcriptional memory [11].…”

Section: Introductionmentioning

confidence: 99%

Adaptation to Long-Term Rainfall Variability for Robusta Coffee Cultivation in Brazilian Southeast

Martins¹,

Eugênio²,

Rodrigues³

et al. 2018

AJCC

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Coffee is one of the world most traded agricultural commodities. Currently, a lot of attention has been on Robusta coffee (Coffea canephora Pierre ex A. Froehner) because it seems to evidence a greater tolerance to extreme climatic events than Arabica coffee (C. arabica L.). Despite this, only a few works have been developed aimed at discriminating the climatic vulnerability in regions which prioritize robust coffee production. The aim of this work was to analyze historical climatic variables in space and time for the characterization of climatic vulnerability of micro-regions, in search of mitigation and adaptation, which might support the improvement of production systems of C. canephora coffee trees. The case study was carried out for one of the largest production regions of Robusta coffee of the world, in Brazil, geographically located between the 39˚38' and 41˚50' West longitude meridians and the 17˚52' and 21˚19' South latitude parallels. The vulnerability was characterized by the spatial and temporal variation of rainfall and rainfall seasonal pattern (based on 30 years of historical data), elements of climatic water balance, elevation and area planted with Robusta coffee. The choice of mitigation and adaptation were based on widely validated criteria. Overall, the results show that the vulnerability of Robusta coffee is related to low index of rainfall, the

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Transcriptional memory contributes to drought tolerance in coffee (Coffea canephora) plants

Cited by 61 publications

References 104 publications

Genome-Wide Screening and Characterization of Non-Coding RNAs in Coffea canephora

Genome-Wide Screening and Characterization of Non-Coding RNAs in Coffea canephora

Transcriptome Response to Drought, Rehydration and Re-Dehydration in Potato

Adaptation to Long-Term Rainfall Variability for Robusta Coffee Cultivation in Brazilian Southeast

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