Periodic Reporting for period 1 - RESIST (Resurrection plants reveal secrets of vegetative desiccation tolerance)
Período documentado: 2019-03-01 hasta 2021-02-28
A major challenge faced by modern agriculture is plant stress caused by the unfavourable environmental conditions. Global warming is predicted to further intensify these problems, including increasing the frequency and severity of drought stress, which seriously affect both crop quality and yield. Therefore, timely action is needed to find solutions to mitigate the consequences of water deprivation in plants. A small number of species called resurrection plants can tolerate desiccation of their vegetative organs and are a natural resource that can be tapped to solve this problem. They can withstand transition to air-dried state and completely restore physiological activities upon rehydration. Moreover, some of these resurrection species are shown to tolerate other stresses, including low temperature/freezing, severe oxidative stress, and long-term darkness. Therefore, research on resurrection plants has not only significant fundamental scientific importance, it has also immediate practical application, especially in the context of growing population and the ever-increasing demand for higher quality and sustainably produced foods. The interest in these unique plants is additionally fueled by the identification of compounds from resurrection species with medicinal (anticancer and antiviral) activities. However, still little is known about the organization of their genomes and the genetic mechanisms that determine their exotic physiology.
The characterization of the genomes of resurrection species, and the identification and functional characterization of important desiccation gene networks, could bring valuable information about the molecular mechanisms of abiotic stress tolerance and identify new strategies that can be used for crop improvement. Therefore, the major goal of this project is to unravel the genetic determinants of desiccation tolerance in resurrection plants and to identify similarities and differences with model and crop species. The newly acquired fundamental knowledge on resurrection plants will be translated to economically important species. A secondary objective will be to explore the possibility of integrating seaweed based stress mitigation technology to improve crop tolerance to drought.
The characterization of the genomes of resurrection species, and the identification and functional characterization of important desiccation gene networks, could bring valuable information about the molecular mechanisms of abiotic stress tolerance and identify new strategies that can be used for crop improvement. Therefore, the major goal of this project is to unravel the genetic determinants of desiccation tolerance in resurrection plants and to identify similarities and differences with model and crop species. The newly acquired fundamental knowledge on resurrection plants will be translated to economically important species. A secondary objective will be to explore the possibility of integrating seaweed based stress mitigation technology to improve crop tolerance to drought.
- High quality genomic DNA from H. rhodopensis was prepared and used to generate PacBio and Dovetail HiC libraries subjected to sequencing. The obtained assemblies were processed, analyzed and evaluated by a number of bioinformatic tools. Statistical analyses revealed a near complete assembly - 90.1% of the genome.
In parallel, a total of 87.8 million paired-end reads were generated from a dataset of 30 transcriptome sequencing samples. As a result, a non-redundant set of 44,388 gene models was predicted and most of them are supported by RNA-seq alignments.
- Two comparative genomics analysis of different scale, dedicated to the ROS-related gene families across species, were performed. The first study was focused not only on the distribution, but also the expression of a smaller subset of specific ROS genes: ascorbate peroxidase, glutathione peroxidase, catalase and superoxide dismutase in the resurrection species Boea hygrometrica, Selaginella lepidophylla, Xerophyta viscosa, and Oropetium thomaeum, we well as the mesophile Selaginella moellendorffii. The second comparative genomics study was much larger and involved a total of 65 species, of which 37 plants (including 8 extremophiles) and 28 non-plant organisms (of which 8 were extremophiles).
- A combined transcriptomics, metabolomics and lipidomics experiment was performed with H. rhodopensis subjected to desiccation, cold stress, freezing stress and all their combinations.
- Metabomomics analyses were performed on several sets of samples. For example in order to characterize and compare the metabolic responses of a homoiochlorophyllous and a poikilochlorophyllous resurrection plant, samples from X. elegans and X. humilis were taken during a desiccation curve – from full turgor to ~5% relative water content (RWC). Moreover, X. schlechteri leaves were analyzed under drought stress. In turn, a metabolome dataset was generated for Haberlea rhodopensis subjected to desiccation, darkness, as well the combination of desiccation and darkness.
- Тhe effect of biostimulants on the fruit size of two varieties of tomato - Heinz 1706 and MicroTom, was assessed under normal and drought stress conditions – moderate and severe, as well as 4 days after rewatering.
In an independent experiment with sweet pepper, plants treated with a biostimulant twice before application of cold stress (2X priming) or once before the stress and once during the stress recovery period, showed better growth and mitigation of the stress symptoms.
The effects of biostimulant priming on tomato plants was evaluated also in response to elevated temperatures during fruit-set and development. Initial results indicated that the biostimulant alleviates the stress and is beneficial to fruit-set, fruit size and mass. A much larger experiment was conducted thereafter, which included also investigation of the molecular responses by transcriptomics and metabolomics.
In parallel, a total of 87.8 million paired-end reads were generated from a dataset of 30 transcriptome sequencing samples. As a result, a non-redundant set of 44,388 gene models was predicted and most of them are supported by RNA-seq alignments.
- Two comparative genomics analysis of different scale, dedicated to the ROS-related gene families across species, were performed. The first study was focused not only on the distribution, but also the expression of a smaller subset of specific ROS genes: ascorbate peroxidase, glutathione peroxidase, catalase and superoxide dismutase in the resurrection species Boea hygrometrica, Selaginella lepidophylla, Xerophyta viscosa, and Oropetium thomaeum, we well as the mesophile Selaginella moellendorffii. The second comparative genomics study was much larger and involved a total of 65 species, of which 37 plants (including 8 extremophiles) and 28 non-plant organisms (of which 8 were extremophiles).
- A combined transcriptomics, metabolomics and lipidomics experiment was performed with H. rhodopensis subjected to desiccation, cold stress, freezing stress and all their combinations.
- Metabomomics analyses were performed on several sets of samples. For example in order to characterize and compare the metabolic responses of a homoiochlorophyllous and a poikilochlorophyllous resurrection plant, samples from X. elegans and X. humilis were taken during a desiccation curve – from full turgor to ~5% relative water content (RWC). Moreover, X. schlechteri leaves were analyzed under drought stress. In turn, a metabolome dataset was generated for Haberlea rhodopensis subjected to desiccation, darkness, as well the combination of desiccation and darkness.
- Тhe effect of biostimulants on the fruit size of two varieties of tomato - Heinz 1706 and MicroTom, was assessed under normal and drought stress conditions – moderate and severe, as well as 4 days after rewatering.
In an independent experiment with sweet pepper, plants treated with a biostimulant twice before application of cold stress (2X priming) or once before the stress and once during the stress recovery period, showed better growth and mitigation of the stress symptoms.
The effects of biostimulant priming on tomato plants was evaluated also in response to elevated temperatures during fruit-set and development. Initial results indicated that the biostimulant alleviates the stress and is beneficial to fruit-set, fruit size and mass. A much larger experiment was conducted thereafter, which included also investigation of the molecular responses by transcriptomics and metabolomics.
Progress:
- 40 putative APX, 28 GPX, 16 CAT, and 41 SOD genes were identified from genomes of the resurrection species Boea hygrometrica, Selaginella lepidophylla, Xerophyta viscosa, and Oropetium thomaeum, and the mesophile Selaginella moellendorffii. Using co-expression network analysis, various regulatory modules were discovered, mainly involving glutathione, that likely work together to maintain ROS homeostasis upon desiccation stress in resurrection species. These regulatory modules also support the existence of species-specific ROS detoxification systems.
- The genome of Haberlea rhodopensis was sequenced, assembled, annotated and thoroughly analyzed.
- An Ascophyllum nodosum-based biostimulant successfully induces mitigation of long-term heat stress effects in tomatoes and improves multipal economically important traits.
Expected results:
- A sequenced genome of another resurrection species - Xerophyta elegans will be assembled, annotated and thoroughly analyzed.
- Comparative genomics of extremophiles, which will help define novel genes and expanding gene families that contribute to the adaptation to stresses.
- The genomics data will be further integrated with analysis of corresponding transcriptomes, metabolomes and lipidomes to reveal common and specific footprints related to drought tolerance.
- The roles of selected Haberlea rhodopensis and Xerophyta sp. genes and metabolites related to desiccation responses will be verified by functional analyses. This knowledge will be subsequently translated to economically important plants by studying the behaviour of confirmed drought tolerance markers or their homologues in crop models like tomato (dicot) and wheat (monocot).
- The outputs generated from all –omics experiments will be integrated and used for computational modelling of desiccation tolerance in resurrection species.
- The in-depth characterization of the responses of stressed and control plants to supplementation with sea-weed biostimulants will reveal more aspects of the mechanism of their positive effect on yield and quality parameters, as well as whether and how they may be applied to a wider variety of crops.
- The transfer of knowledge task will enhance the quality of science and improve the human capacity in all partner institutions.
- 40 putative APX, 28 GPX, 16 CAT, and 41 SOD genes were identified from genomes of the resurrection species Boea hygrometrica, Selaginella lepidophylla, Xerophyta viscosa, and Oropetium thomaeum, and the mesophile Selaginella moellendorffii. Using co-expression network analysis, various regulatory modules were discovered, mainly involving glutathione, that likely work together to maintain ROS homeostasis upon desiccation stress in resurrection species. These regulatory modules also support the existence of species-specific ROS detoxification systems.
- The genome of Haberlea rhodopensis was sequenced, assembled, annotated and thoroughly analyzed.
- An Ascophyllum nodosum-based biostimulant successfully induces mitigation of long-term heat stress effects in tomatoes and improves multipal economically important traits.
Expected results:
- A sequenced genome of another resurrection species - Xerophyta elegans will be assembled, annotated and thoroughly analyzed.
- Comparative genomics of extremophiles, which will help define novel genes and expanding gene families that contribute to the adaptation to stresses.
- The genomics data will be further integrated with analysis of corresponding transcriptomes, metabolomes and lipidomes to reveal common and specific footprints related to drought tolerance.
- The roles of selected Haberlea rhodopensis and Xerophyta sp. genes and metabolites related to desiccation responses will be verified by functional analyses. This knowledge will be subsequently translated to economically important plants by studying the behaviour of confirmed drought tolerance markers or their homologues in crop models like tomato (dicot) and wheat (monocot).
- The outputs generated from all –omics experiments will be integrated and used for computational modelling of desiccation tolerance in resurrection species.
- The in-depth characterization of the responses of stressed and control plants to supplementation with sea-weed biostimulants will reveal more aspects of the mechanism of their positive effect on yield and quality parameters, as well as whether and how they may be applied to a wider variety of crops.
- The transfer of knowledge task will enhance the quality of science and improve the human capacity in all partner institutions.