Pub Date : 2024-08-07DOI: 10.1101/2024.08.07.606640
Margalida Roig-Oliver, Jaume Flexas, María José Clemente-Moreno, Marc Carriquí
In the present study, we combine published and novel data on cell wall composition and photosynthesis limitations, including data for all the major land plant’s phylogenetic groups. We provide novel evidence on the importance of cell wall composition in determining mesophyll conductance to CO2 diffusion (gm) across land plants’ phylogeny. We address the hypothesis that the pectin fraction of total major cell wall compounds is positively related to gm and, consequently, to photosynthesis, when pooling species from across the entire phylogeny.
{"title":"Cell wall composition in relation to photosynthesis across land plants’ phylogeny: crops as outliers","authors":"Margalida Roig-Oliver, Jaume Flexas, María José Clemente-Moreno, Marc Carriquí","doi":"10.1101/2024.08.07.606640","DOIUrl":"https://doi.org/10.1101/2024.08.07.606640","url":null,"abstract":"In the present study, we combine published and novel data on cell wall composition and photosynthesis limitations, including data for all the major land plant’s phylogenetic groups. We provide novel evidence on the importance of cell wall composition in determining mesophyll conductance to CO<sub>2</sub> diffusion (<em>g</em><sub>m</sub>) across land plants’ phylogeny. We address the hypothesis that the pectin fraction of total major cell wall compounds is positively related to <em>g</em><sub>m</sub> and, consequently, to photosynthesis, when pooling species from across the entire phylogeny.","PeriodicalId":501341,"journal":{"name":"bioRxiv - Plant Biology","volume":"59 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141941348","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-07DOI: 10.1101/2024.08.05.606631
Luca Morelli, Payal Patwari, Florian Pruckner, Maxime Bastide, Michele Fabris
Microalgae, and among them, the diatom Phaeodactylum tricornutum stand out with their remarkable versatility and metabolic engineering potential. Diatoms exhibit substantial variability in metabolism, photosynthetic physiology and environmental adaptation, even across the same species. These factors can affect the design and outcome of metabolic engineering strategies. In this study, we profiled the diversity of biotechnologically relevant traits of three P. tricornutum strains (Pt1, Pt6, and Pt9) under different light regimes to identify the most suitable chassis to be employed as bio-factory to produce high-value terpenoids. We conducted detailed assessments of these strains, using pulse amplitude modulated (PAM) fluorometry to measure photosynthetic efficiency and we analyzed the composition of pigments and triterpenoids, as main terpenoid metabolic sinks. Parameters such as the maximum quantum yield of PSII (Fv/Fm), the efficiency of excitation energy capture (Fv’/Fm’), and OJIP kinetics were used to estimate photosynthetic performance in different light regimes. Additionally, we evaluated their transformation efficiency and their capacity to produce heterologous monoterpenoids, using geraniol as a model product. Our findings revealed that Pt1, widely used in laboratories, exhibits robust growth and photosynthetic performance under standard laboratory conditions. Pt6, adapted to intertidal environments, shows unique resilience in fluctuating conditions, while Pt9, with its high-temperature tolerance, excels under continuous high irradiance. Additionally, this variability across strains and light conditions influenced the metabolic output of each strain. We concluded that understanding the physiological responses of different P. tricornutum strains to light is crucial for optimizing their use in metabolic engineering. The insights gained from this research will facilitate the strategic selection and exploitation of these strains in algae biotechnology, enhancing the production of commercially valuable compounds such as high-value terpenoids and derivatives. This comprehensive characterization of strains under varying light conditions offers a pathway to more efficient and targeted metabolic engineering applications.
{"title":"Specific light-regime adaptations, terpenoid profiles and engineering potential in ecologically diverse Phaeodactylum tricornutum strains","authors":"Luca Morelli, Payal Patwari, Florian Pruckner, Maxime Bastide, Michele Fabris","doi":"10.1101/2024.08.05.606631","DOIUrl":"https://doi.org/10.1101/2024.08.05.606631","url":null,"abstract":"Microalgae, and among them, the diatom <em>Phaeodactylum tricornutum</em> stand out with their remarkable versatility and metabolic engineering potential. Diatoms exhibit substantial variability in metabolism, photosynthetic physiology and environmental adaptation, even across the same species. These factors can affect the design and outcome of metabolic engineering strategies. In this study, we profiled the diversity of biotechnologically relevant traits of three <em>P. tricornutum</em> strains (Pt1, Pt6, and Pt9) under different light regimes to identify the most suitable chassis to be employed as bio-factory to produce high-value terpenoids. We conducted detailed assessments of these strains, using pulse amplitude modulated (PAM) fluorometry to measure photosynthetic efficiency and we analyzed the composition of pigments and triterpenoids, as main terpenoid metabolic sinks. Parameters such as the maximum quantum yield of PSII (Fv/Fm), the efficiency of excitation energy capture (Fv’/Fm’), and OJIP kinetics were used to estimate photosynthetic performance in different light regimes. Additionally, we evaluated their transformation efficiency and their capacity to produce heterologous monoterpenoids, using geraniol as a model product. Our findings revealed that Pt1, widely used in laboratories, exhibits robust growth and photosynthetic performance under standard laboratory conditions. Pt6, adapted to intertidal environments, shows unique resilience in fluctuating conditions, while Pt9, with its high-temperature tolerance, excels under continuous high irradiance. Additionally, this variability across strains and light conditions influenced the metabolic output of each strain. We concluded that understanding the physiological responses of different <em>P. tricornutum</em> strains to light is crucial for optimizing their use in metabolic engineering. The insights gained from this research will facilitate the strategic selection and exploitation of these strains in algae biotechnology, enhancing the production of commercially valuable compounds such as high-value terpenoids and derivatives. This comprehensive characterization of strains under varying light conditions offers a pathway to more efficient and targeted metabolic engineering applications.","PeriodicalId":501341,"journal":{"name":"bioRxiv - Plant Biology","volume":"12 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141941351","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-07DOI: 10.1101/2024.08.05.606409
Kathryn Richardson, Amin Mirkouei, Kasia Duellman, Anthony Aylward, David Zirker, Eliezer Schwarz, Ying Sun
Environmentally-friendly and low emission extraction methods are needed to meet worldwide rare earth element (REE) demand. Within a greenhouse setting, we assessed the REE hyperaccumulation ability of four plant species (e.g., Phalaris arundinacea, Solanum nigrum, Phytolacca americana, and Brassica juncea) and the impact of amending REE-rich soil with biochar or fertilizer and watering with citric acid solution. Harvested samples were pyrolyzed, and the resulting bio-ores were acid-digested and underwent elemental analysis to determine REE content. Amending soil with fertilizer and biochar increased bio-ore production, while plant species explained most variation in bioaccumulation factor. Phalaris arundinacea achieved the highest average REE concentration of 27,940 ppm for targeted REEs (i.e., cerium, lanthanum, neodymium, praseodymium, and yttrium) and 37,844 ppm for total REEs. We successfully extracted REE-rich bio-ore from plant biomass and determined that soil amendment and plant species will be critical parameters in design and implementation of Idaho-based REE phytomining operations.
{"title":"Rare earth elements extraction from Idaho-sourced surface soil by phytomining","authors":"Kathryn Richardson, Amin Mirkouei, Kasia Duellman, Anthony Aylward, David Zirker, Eliezer Schwarz, Ying Sun","doi":"10.1101/2024.08.05.606409","DOIUrl":"https://doi.org/10.1101/2024.08.05.606409","url":null,"abstract":"Environmentally-friendly and low emission extraction methods are needed to meet worldwide rare earth element (REE) demand. Within a greenhouse setting, we assessed the REE hyperaccumulation ability of four plant species (e.g., <em>Phalaris arundinacea, Solanum nigrum, Phytolacca americana</em>, and <em>Brassica juncea</em>) and the impact of amending REE-rich soil with biochar or fertilizer and watering with citric acid solution. Harvested samples were pyrolyzed, and the resulting bio-ores were acid-digested and underwent elemental analysis to determine REE content. Amending soil with fertilizer and biochar increased bio-ore production, while plant species explained most variation in bioaccumulation factor. <em>Phalaris arundinacea</em> achieved the highest average REE concentration of 27,940 ppm for targeted REEs (i.e., cerium, lanthanum, neodymium, praseodymium, and yttrium) and 37,844 ppm for total REEs. We successfully extracted REE-rich bio-ore from plant biomass and determined that soil amendment and plant species will be critical parameters in design and implementation of Idaho-based REE phytomining operations.","PeriodicalId":501341,"journal":{"name":"bioRxiv - Plant Biology","volume":"23 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141941350","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Salinity threatens crop production worldwide, and salinized areas are steadily increasing. As most crops are sensitive to salt, there is a need to improve the salt tolerance of major crops and promote the cultivation of under-utilized salt-tolerant crops. Quinoa, a pseudocereal and leafy vegetable from the Andean region of South America, is highly salt-tolerant, thrives in marginal environments, and has excellent nutritional properties. Research has often focused on epidermal bladder cells, a feature of quinoa thought to contribute to salt tolerance; however recent evidence suggests that these cells are not directly involved. The salt tolerance mechanism in quinoa remains unclear. Here, we show genotype-dependent differences in Na+ and K+ accumulation mechanisms using representative 18 lines of three genotypes by focusing on young quinoa seedlings at a stage without epidermal bladder cells. High salinity (600 mM NaCl) did not affect the early growth of all three quinoa genotypes. Under high salinity, lowland quinoa lines accumulated the most Na+ in the aerial parts, whereas southern highland lines accumulated the least. By contrast, K+ accumulation was slightly reduced in the aerial parts but significantly decreased in roots of all the genotypes. Resequencing of 18 quinoa lines supports the notion that genotype determines aboveground Na+ uptake and gene expression in response to salt stress. Using virus-induced gene silencing, we further demonstrated that CqHKT1 and CqSOS1 mediate Na+ exclusion in quinoa. These findings provide insight into salt tolerance mechanisms, serving as a basis for improving crop production under salt stress.
{"title":"CqHKT1 and CqSOS1 mediate genotype-dependent Na+ exclusion under high salt stress in quinoa","authors":"Yasufumi Kobayashi, Ryohei Sugita, Miki Fujita, Yasuo Yasui, Yoshinori Murata, Takuya Ogata, Yukari Nagatoshi, Yasunari Fujita","doi":"10.1101/2024.08.05.606677","DOIUrl":"https://doi.org/10.1101/2024.08.05.606677","url":null,"abstract":"Salinity threatens crop production worldwide, and salinized areas are steadily increasing. As most crops are sensitive to salt, there is a need to improve the salt tolerance of major crops and promote the cultivation of under-utilized salt-tolerant crops. Quinoa, a pseudocereal and leafy vegetable from the Andean region of South America, is highly salt-tolerant, thrives in marginal environments, and has excellent nutritional properties. Research has often focused on epidermal bladder cells, a feature of quinoa thought to contribute to salt tolerance; however recent evidence suggests that these cells are not directly involved. The salt tolerance mechanism in quinoa remains unclear. Here, we show genotype-dependent differences in Na<sup>+</sup> and K<sup>+</sup> accumulation mechanisms using representative 18 lines of three genotypes by focusing on young quinoa seedlings at a stage without epidermal bladder cells. High salinity (600 mM NaCl) did not affect the early growth of all three quinoa genotypes. Under high salinity, lowland quinoa lines accumulated the most Na<sup>+</sup> in the aerial parts, whereas southern highland lines accumulated the least. By contrast, K<sup>+</sup> accumulation was slightly reduced in the aerial parts but significantly decreased in roots of all the genotypes. Resequencing of 18 quinoa lines supports the notion that genotype determines aboveground Na<sup>+</sup> uptake and gene expression in response to salt stress. Using virus-induced gene silencing, we further demonstrated that CqHKT1 and CqSOS1 mediate Na<sup>+</sup> exclusion in quinoa. These findings provide insight into salt tolerance mechanisms, serving as a basis for improving crop production under salt stress.","PeriodicalId":501341,"journal":{"name":"bioRxiv - Plant Biology","volume":"78 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141941347","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-07DOI: 10.1101/2024.08.04.606535
Marta Puchta-Jasińska, Jolanta Groszyk, Maja Boczkowska
Background One of the key elements in the analysis of gene expression and its post-translational regulation is miRNAs. Degradome-seq analyses are performed to analyze the cleavage of target RNAs in the transcriptome. In this work, an improved library preparation protocol for degradome sequencing is presented. The developed protocol improves the efficiency of library preparation in degradome-seq analysis used to identify microRNA targets, reduces the time of library preparation and lowers the cost of purchasing reagents..
{"title":"Improved Degradome Sequencing Protocol via Reagent Recycling from sRNAseq Library Preparations","authors":"Marta Puchta-Jasińska, Jolanta Groszyk, Maja Boczkowska","doi":"10.1101/2024.08.04.606535","DOIUrl":"https://doi.org/10.1101/2024.08.04.606535","url":null,"abstract":"<strong>Background</strong> One of the key elements in the analysis of gene expression and its post-translational regulation is miRNAs. Degradome-seq analyses are performed to analyze the cleavage of target RNAs in the transcriptome. In this work, an improved library preparation protocol for degradome sequencing is presented. The developed protocol improves the efficiency of library preparation in degradome-seq analysis used to identify microRNA targets, reduces the time of library preparation and lowers the cost of purchasing reagents..","PeriodicalId":501341,"journal":{"name":"bioRxiv - Plant Biology","volume":"33 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141941352","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-07DOI: 10.1101/2024.08.04.606531
Deying Zeng, Jiayu Peng, Lan Zhang, Mathew J. Hayden, Tina M. Rathjen, Bo Zhu, Zixian Zeng, Emmanuel Delhaize
We identified a mutant of hexaploid wheat (Triticum aestivum) with impaired responses to gravity. The mutant named Twisted Sister1 (TS1) had agravitropic roots that were often twisted along with altered shoot phenotypes. Roots of TS1 were insensitive of externally applied auxin with the genetics and physiology suggestive of a mutated AUX/IAA transcription factor gene. Hexaploid wheat possesses over eighty AUX/IAA genes and sequence information did not identify an obvious candidate. Bulked segregant analysis of an F2 population mapped the mutation to chromosome 5A and subsequent mapping located the mutation to a 41 Mbp region. RNA-seq identified the TraesCS5A03G0149800 gene encoding a TaAUX/IAA protein to be mutated in the highly conserved domain II motif. We confirmed TraesCS5A03G0149800 as underlying the mutant phenotype by generating transgenic Arabidopsis thaliana. Analysis of RNA-seq data suggested broad similarities between Arabidopsis and wheat for the role of AUX/IAA genes in gravity responses. Here we show that the sequenced wheat genome along with previous knowledge largely from the model species Arabidopsis, gene mapping, RNA-seq and expression in Arabidopsis have enabled cloning of a key wheat gene defining plant architecture.
{"title":"Twisted Sister1: an agravitropic mutant of bread wheat (Triticum aestivum) with altered root and shoot architectures","authors":"Deying Zeng, Jiayu Peng, Lan Zhang, Mathew J. Hayden, Tina M. Rathjen, Bo Zhu, Zixian Zeng, Emmanuel Delhaize","doi":"10.1101/2024.08.04.606531","DOIUrl":"https://doi.org/10.1101/2024.08.04.606531","url":null,"abstract":"We identified a mutant of hexaploid wheat (<em>Triticum aestivum</em>) with impaired responses to gravity. The mutant named <em>Twisted Sister1</em> (<em>TS1</em>) had agravitropic roots that were often twisted along with altered shoot phenotypes. Roots of <em>TS1</em> were insensitive of externally applied auxin with the genetics and physiology suggestive of a mutated <em>AUX/IAA</em> transcription factor gene. Hexaploid wheat possesses over eighty <em>AUX/IAA</em> genes and sequence information did not identify an obvious candidate. Bulked segregant analysis of an F<sub>2</sub> population mapped the mutation to chromosome 5A and subsequent mapping located the mutation to a 41 Mbp region. RNA-seq identified the <em>TraesCS5A03G0149800</em> gene encoding a TaAUX/IAA protein to be mutated in the highly conserved domain II motif. We confirmed <em>TraesCS5A03G0149800</em> as underlying the mutant phenotype by generating transgenic <em>Arabidopsis thaliana</em>. Analysis of RNA-seq data suggested broad similarities between Arabidopsis and wheat for the role of <em>AUX/IAA</em> genes in gravity responses. Here we show that the sequenced wheat genome along with previous knowledge largely from the model species Arabidopsis, gene mapping, RNA-seq and expression in Arabidopsis have enabled cloning of a key wheat gene defining plant architecture.","PeriodicalId":501341,"journal":{"name":"bioRxiv - Plant Biology","volume":"23 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141941353","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-07DOI: 10.1101/2024.08.05.606718
Chaozhong Zhang, Joshua Hegarty, Mariana Padilla, David M. Tricoli, Jorge Dubcovsky, Juan M. Debernardi
The REDUCED HEIGHT (RHT) dwarfing alleles Rht-B1b and Rht-D1b were essential in the “Green Revolution” to optimize wheat plant height and increase grain yield. However, those alleles reduce coleoptile length limiting sowing depth, which triggered the search for alternative dwarfing genes. In this study, we engineered the interaction between miR172 and AP2L2 genes to fine-tune wheat and triticale plant height without affecting coleoptile and first-leaf length.
{"title":"Manipulation of the microRNA172 - AP2L2 interaction provides precise control of wheat and triticale plant height","authors":"Chaozhong Zhang, Joshua Hegarty, Mariana Padilla, David M. Tricoli, Jorge Dubcovsky, Juan M. Debernardi","doi":"10.1101/2024.08.05.606718","DOIUrl":"https://doi.org/10.1101/2024.08.05.606718","url":null,"abstract":"The <em>REDUCED HEIGHT</em> (<em>RHT</em>) dwarfing alleles <em>Rht-B1b</em> and <em>Rht-D1b</em> were essential in the “Green Revolution” to optimize wheat plant height and increase grain yield. However, those alleles reduce coleoptile length limiting sowing depth, which triggered the search for alternative dwarfing genes. In this study, we engineered the interaction between miR172 and <em>AP2L2</em> genes to fine-tune wheat and triticale plant height without affecting coleoptile and first-leaf length.","PeriodicalId":501341,"journal":{"name":"bioRxiv - Plant Biology","volume":"62 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141941349","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-07DOI: 10.1101/2024.08.01.606180
Marek Glombik, Ramesh Arunkumar, Samuel Burrows, Sophie Louise Mogg, Xiaoming Wang, Philippa Borrill
Differences in the relative level of expression of homoeologs, known as homoeolog expression bias (HEB), are widely observed in allopolyploids. While the evolution of homoeolog expression bias through hybridisation has been characterised, on shorter timescales the extent to which homoeolog expression bias is preserved or altered between generations remains elusive.
{"title":"Rapid reprogramming and stabilisation of homoeolog expression bias in hexaploid wheat biparental populations","authors":"Marek Glombik, Ramesh Arunkumar, Samuel Burrows, Sophie Louise Mogg, Xiaoming Wang, Philippa Borrill","doi":"10.1101/2024.08.01.606180","DOIUrl":"https://doi.org/10.1101/2024.08.01.606180","url":null,"abstract":"Differences in the relative level of expression of homoeologs, known as homoeolog expression bias (HEB), are widely observed in allopolyploids. While the evolution of homoeolog expression bias through hybridisation has been characterised, on shorter timescales the extent to which homoeolog expression bias is preserved or altered between generations remains elusive.","PeriodicalId":501341,"journal":{"name":"bioRxiv - Plant Biology","volume":"593 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141941354","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-06DOI: 10.1101/2024.08.02.606319
Kelly L. Vomo-Donfack, Mariem Abaach, Ana M. Luna, Grégory Ginot, Verónica G. Doblas, Ian Morilla
Small signalling peptides (SSPs) play crucial roles in plant growth, development, and stress responses. However, accurately identifying and characterising SSPs remains challenging due to their structural diversity and the limitations of current prediction tools. Here, we introduce S2-PepAnalyst, a novel web tool designed to enhance the prediction of SSPs in plants. By integrating comprehensive plant-specific datasets into a machine learning model, S2-PepAnalyst offers versatility, improved accuracy of 99.5% on average, and reliability with a low rate of false negatives compared to existing tools. S2-PepAnalyst provides essential resources for plant biologists and facilitates new discoveries in plant peptide signalling.
{"title":"S2-PepAnalyst: A Web Tool for Predicting Plant Small Signalling Peptides","authors":"Kelly L. Vomo-Donfack, Mariem Abaach, Ana M. Luna, Grégory Ginot, Verónica G. Doblas, Ian Morilla","doi":"10.1101/2024.08.02.606319","DOIUrl":"https://doi.org/10.1101/2024.08.02.606319","url":null,"abstract":"Small signalling peptides (SSPs) play crucial roles in plant growth, development, and stress responses. However, accurately identifying and characterising SSPs remains challenging due to their structural diversity and the limitations of current prediction tools. Here, we introduce S<sup>2</sup>-PepAnalyst, a novel web tool designed to enhance the prediction of SSPs in plants. By integrating comprehensive plant-specific datasets into a machine learning model, S<sup>2</sup>-PepAnalyst offers versatility, improved accuracy of 99.5% on average, and reliability with a low rate of false negatives compared to existing tools. S<sup>2</sup>-PepAnalyst provides essential resources for plant biologists and facilitates new discoveries in plant peptide signalling.","PeriodicalId":501341,"journal":{"name":"bioRxiv - Plant Biology","volume":"23 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141941486","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-06DOI: 10.1101/2024.08.02.606357
Ravneet Kaur, Mary Durstock, Stephen A. Prior, G. Brett Runion, Elizabeth A. Ainsworth, Ivan Baxter, Alvaro Sanz-Sáez, Courtney P. Leisner
Rising atmospheric CO2 levels, projected to reach ∼650 ppm by 2050, threaten the nutritional value of food crops. This rise is expected to increase biomass yield in C3 plants through enhanced photosynthesis and water-use efficiency. However, elevated CO2 (eCO2) reduces protein, nitrogen, and essential minerals like zinc (Zn) and iron (Fe) in plant leaves and seeds, posing a global nutrition risk. We conducted an experiment using Open Top Chambers to examine the response of three soybean cultivars (Clark, Flyer, and Loda) to ambient (∼410 ppm) and eCO2 (∼610 ppm) conditions. These cultivars were selected due to their contrasting responses to eCO2. Measurements of physiological parameters (i.e., biomass, and nutrient concentration) were taken at different growth stages. Our results showed that eCO2 increased carbon assimilation, leading to higher aboveground biomass and seed yield (through increased seed number) while root biomass remained unchanged. eCO2 also reduced stomatal conductance and transpiration. There was a significant decrease in seed nutrient concentration at maturity, particularly iron (Fe), phosphorous (P), potassium (K), and magnesium (Mg), in plants grown in eCO2. These findings suggest that increased yield, reduced transpiration, and unchanged root biomass are key drivers of nutrient dilution in seeds under eCO2.
{"title":"Nutrient Challenges in a Changing Atmosphere: Investigating Biomass Growth and Mineral Concentration Changes in Soybean Plants under Elevated CO2","authors":"Ravneet Kaur, Mary Durstock, Stephen A. Prior, G. Brett Runion, Elizabeth A. Ainsworth, Ivan Baxter, Alvaro Sanz-Sáez, Courtney P. Leisner","doi":"10.1101/2024.08.02.606357","DOIUrl":"https://doi.org/10.1101/2024.08.02.606357","url":null,"abstract":"Rising atmospheric CO<sub>2</sub> levels, projected to reach ∼650 ppm by 2050, threaten the nutritional value of food crops. This rise is expected to increase biomass yield in C<sub>3</sub> plants through enhanced photosynthesis and water-use efficiency. However, elevated CO<sub>2</sub> (eCO2) reduces protein, nitrogen, and essential minerals like zinc (Zn) and iron (Fe) in plant leaves and seeds, posing a global nutrition risk. We conducted an experiment using Open Top Chambers to examine the response of three soybean cultivars (Clark, Flyer, and Loda) to ambient (∼410 ppm) and eCO<sub>2</sub> (∼610 ppm) conditions. These cultivars were selected due to their contrasting responses to eCO<sub>2</sub>. Measurements of physiological parameters (i.e., biomass, and nutrient concentration) were taken at different growth stages. Our results showed that eCO<sub>2</sub> increased carbon assimilation, leading to higher aboveground biomass and seed yield (through increased seed number) while root biomass remained unchanged. eCO<sub>2</sub> also reduced stomatal conductance and transpiration. There was a significant decrease in seed nutrient concentration at maturity, particularly iron (Fe), phosphorous (P), potassium (K), and magnesium (Mg), in plants grown in eCO<sub>2</sub>. These findings suggest that increased yield, reduced transpiration, and unchanged root biomass are key drivers of nutrient dilution in seeds under eCO<sub>2</sub>.","PeriodicalId":501341,"journal":{"name":"bioRxiv - Plant Biology","volume":"11 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141941358","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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