cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.30111722
title: Short-term transcriptional memory and association-forming ability of tomato plants in response to ultrasound and drought stress stimuli

description: Plant memory is an adaptive mechanism that plants can use to increase their fitness and cope with adverse environmental stresses. In this study, mRNA-sequencing (mRNA-seq), whole-genome bisulfite sequencing (WGBS) and real-time quantitative PCR (RT-qPCR) methods were applied for evaluating formation and maintenance of somatic transcriptional memory after treatment with ultrasound and drought stimuli in tomatoes. In addition, the effects of repeated stimuli, as well as the association-forming ability of plants were studied when they were trained previously with combined stimuli. Two days after exposure to the two stimuli applied alone or in combination, significantly altered gene transcription and DNA methylation were revealed. Using four selected target genes, we demonstrated that plants memorized stimuli for 5–10 d, in a gene- and stimulus-dependent way. The repeated application of the stimuli caused various alterations in gene transcription behavior, such as habituation, sustained induction or modified reinduction. Plants were able to use one conditioned stimulus as a predictor of the other, unconditioned one, after conditioning in the case of 3 out of 4 target genes, and used their transcriptional memory associatively. The exploitation of plant memory and associative learning may contribute to the development of new strategies to increase plant stress resilience.
DOI: 10.6084/m9.figshare.30111722.v1
title: Short-term transcriptional memory and association-forming ability of tomato plants in response to ultrasound and drought stress stimuli

description: Plant memory is an adaptive mechanism that plants can use to increase their fitness and cope with adverse environmental stresses. In this study, mRNA-sequencing (mRNA-seq), whole-genome bisulfite sequencing (WGBS) and real-time quantitative PCR (RT-qPCR) methods were applied for evaluating formation and maintenance of somatic transcriptional memory after treatment with ultrasound and drought stimuli in tomatoes. In addition, the effects of repeated stimuli, as well as the association-forming ability of plants were studied when they were trained previously with combined stimuli. Two days after exposure to the two stimuli applied alone or in combination, significantly altered gene transcription and DNA methylation were revealed. Using four selected target genes, we demonstrated that plants memorized stimuli for 5–10 d, in a gene- and stimulus-dependent way. The repeated application of the stimuli caused various alterations in gene transcription behavior, such as habituation, sustained induction or modified reinduction. Plants were able to use one conditioned stimulus as a predictor of the other, unconditioned one, after conditioning in the case of 3 out of 4 target genes, and used their transcriptional memory associatively. The exploitation of plant memory and associative learning may contribute to the development of new strategies to increase plant stress resilience.
DOI: 10.3535/45y-97z-aty
title: Athetis (Hydrillula) Tams, 1938

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/xda-nqn-b9b
title: Caradrina (Platyperigea) montana Bremer, 1864

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.6084/m9.figshare.30759294
title: <i><b>Arabidopsis thaliana</b></i><b>Fibrillin 3a binds saturated fatty acids of chloroplast membranes</b>

description: Fibrillins (FBNs) are conserved plastid lipid–associated proteins involved in lipid storage, stress adaptation and plastid ultrastructure. While several <i>Arabidopsis thaliana</i> FBNs have been functionally characterized, the biochemical properties of the thylakoid-associated FBN3a remain poorly understood. AlphaFold modeling revealed that AtFBN3a adopts an eight-stranded <i>β</i>-barrel fold typical of the lipocalin family, with high-confidence predictions for the core <i>β</i>-strands and conservation of the structurally conserved region 1 (SCR1) motif that stabilizes the barrel and defines the ligand-binding cavity. This structural topology is also shared with AlphaFold models of the other members of the family in <i>A. thaliana</i>. Consistent with the lipocalin-like structural and sequence features, protein–lipid overlay assays showed that AtFBN3a bound the anionic plastid lipids phosphatidic acid and sulfoquinovosyl diacylglycerol, but not phosphatidylcholine. Additional assays revealed a clear preference for saturated fatty acids, with stronger binding to long-chain saturated species. Together, these findings identify AtFBN3a as a lipocalin-like domain–containing protein with selective affinity for saturated fatty acids, suggesting a conserved role for FBNs in plastid lipid metabolism and stress adaptation.
DOI: 10.3535/0me-fq4-lqv
title: Phengaris Doherty, 1891

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.6084/m9.figshare.30759294.v1
title: <i><b>Arabidopsis thaliana</b></i><b>Fibrillin 3a binds saturated fatty acids of chloroplast membranes</b>

description: Fibrillins (FBNs) are conserved plastid lipid–associated proteins involved in lipid storage, stress adaptation and plastid ultrastructure. While several <i>Arabidopsis thaliana</i> FBNs have been functionally characterized, the biochemical properties of the thylakoid-associated FBN3a remain poorly understood. AlphaFold modeling revealed that AtFBN3a adopts an eight-stranded <i>β</i>-barrel fold typical of the lipocalin family, with high-confidence predictions for the core <i>β</i>-strands and conservation of the structurally conserved region 1 (SCR1) motif that stabilizes the barrel and defines the ligand-binding cavity. This structural topology is also shared with AlphaFold models of the other members of the family in <i>A. thaliana</i>. Consistent with the lipocalin-like structural and sequence features, protein–lipid overlay assays showed that AtFBN3a bound the anionic plastid lipids phosphatidic acid and sulfoquinovosyl diacylglycerol, but not phosphatidylcholine. Additional assays revealed a clear preference for saturated fatty acids, with stronger binding to long-chain saturated species. Together, these findings identify AtFBN3a as a lipocalin-like domain–containing protein with selective affinity for saturated fatty acids, suggesting a conserved role for FBNs in plastid lipid metabolism and stress adaptation.
DOI: 10.3535/0gw-4lp-ff6
title: Diachrysia chrysitis (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/1rs-gw4-ckw
title: Agriphila selasella Hübner

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/jq8-h4y-kay
title: Aglais urticae (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/53w-77w-n5e
title: Xestia lyngei subsp. Xestia lyngei lankialai (Rebel, 1923)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ns3-9k2-n84
title: Xestia (Pachnobia) laetabilis Zetterstedt, 1839

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.6084/m9.figshare.28113552
title: Genome-wide characterization and expression pattern analysis of <i>Xanthoceras sorbifolium FAD</i> at different growth stages

description: <i>Xanthoceras sorbifolium</i> is a crucial oil tree species in northern China. Additionally, fatty acid constituents in its fruits possess remarkable medicinal value. Hence, probing the regulatory role of <i>FAD</i> family members in fatty acid components accumulation in <i>X. sorbifolium</i> fruits is crucial. Drawing on <i>X. sorbifolium</i> genome data, 22 <i>XsFAD</i> members distributed across 10 chromosomes were identified. The physicochemical properties and subcellular localization predictions thereof were analyzed. Phylogenetic and conserved domain analyses demonstrated that same subfamily members are highly conserved in both gene structure and conserved domains. Cis-acting element analysis indicated that <i>XsFAD</i> members are highly susceptible to light. Furthermore, transcriptome data and qRT-PCR findings corroborated that <i>XsFAD</i> members play an active regulatory role in <i>X. sorbifolium</i> fruit ripening and fatty acid metabolism. The bioinformatic analysis and preliminary verification of regulatory functions of <i>XsFAD</i> members establish conditions for in-depth research on the functions of key <i>XsFAD</i> in the future. The study findings will be conducive to determine the accumulation of fatty acids substances in <i>X. sorbifolium</i> and screening of germplasm resources with superior traits.
DOI: 10.3535/ja0-yw5-h95
title: Dypterygia scabriuscula (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.6084/m9.figshare.28113552.v1
title: Genome-wide characterization and expression pattern analysis of <i>Xanthoceras sorbifolium FAD</i> at different growth stages

description: <i>Xanthoceras sorbifolium</i> is a crucial oil tree species in northern China. Additionally, fatty acid constituents in its fruits possess remarkable medicinal value. Hence, probing the regulatory role of <i>FAD</i> family members in fatty acid components accumulation in <i>X. sorbifolium</i> fruits is crucial. Drawing on <i>X. sorbifolium</i> genome data, 22 <i>XsFAD</i> members distributed across 10 chromosomes were identified. The physicochemical properties and subcellular localization predictions thereof were analyzed. Phylogenetic and conserved domain analyses demonstrated that same subfamily members are highly conserved in both gene structure and conserved domains. Cis-acting element analysis indicated that <i>XsFAD</i> members are highly susceptible to light. Furthermore, transcriptome data and qRT-PCR findings corroborated that <i>XsFAD</i> members play an active regulatory role in <i>X. sorbifolium</i> fruit ripening and fatty acid metabolism. The bioinformatic analysis and preliminary verification of regulatory functions of <i>XsFAD</i> members establish conditions for in-depth research on the functions of key <i>XsFAD</i> in the future. The study findings will be conducive to determine the accumulation of fatty acids substances in <i>X. sorbifolium</i> and screening of germplasm resources with superior traits.
DOI: 10.6084/m9.figshare.28614854
title: Advances in deciphering the mechanisms of salt tolerance in Maize

description: Maize (<i>Zea mays</i> L.) is a vital crop worldwide, serving as a cornerstone for food security, livestock feed, and biofuel production. However, its cultivation is increasingly jeopardized by environmental challenges, notably soil salinization, which severely constrains growth, yield, and quality. To combat salinity stress, maize employs an array of adaptive mechanisms, including enhanced antioxidant enzyme activity and modulated plant hormone levels, which work synergistically to maintain reactive oxygen species (ROS) balance and ion homeostasis. This review explores the intricate interactions among ROS, antioxidant systems, plant hormones, and ion regulation in maize under salt stress, providing a comprehensive understanding of the physiological and molecular basis of its tolerance. By elucidating these mechanisms, this study contributes to the development of salt-tolerant maize varieties and informs innovative strategies to sustain agricultural productivity under adverse environmental conditions, offering significant theoretical insights into plant stress biology and practical solutions for achieving sustainable agriculture amidst global climate challenges.
DOI: 10.3535/db4-nzr-gre
title: Phengaris Doherty, 1891

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/nzm-q3r-zex
title: Scopariinae

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.6084/m9.figshare.28614854.v1
title: Advances in deciphering the mechanisms of salt tolerance in Maize

description: Maize (<i>Zea mays</i> L.) is a vital crop worldwide, serving as a cornerstone for food security, livestock feed, and biofuel production. However, its cultivation is increasingly jeopardized by environmental challenges, notably soil salinization, which severely constrains growth, yield, and quality. To combat salinity stress, maize employs an array of adaptive mechanisms, including enhanced antioxidant enzyme activity and modulated plant hormone levels, which work synergistically to maintain reactive oxygen species (ROS) balance and ion homeostasis. This review explores the intricate interactions among ROS, antioxidant systems, plant hormones, and ion regulation in maize under salt stress, providing a comprehensive understanding of the physiological and molecular basis of its tolerance. By elucidating these mechanisms, this study contributes to the development of salt-tolerant maize varieties and informs innovative strategies to sustain agricultural productivity under adverse environmental conditions, offering significant theoretical insights into plant stress biology and practical solutions for achieving sustainable agriculture amidst global climate challenges.
DOI: 10.6084/m9.figshare.28733087
title: Contrasting gene expression patterns during floral induction in two <i>Chenopodium ficifolium</i> genotypes reveal putative flowering regulators

description: <i>Chenopodium ficifolium</i> is a close diploid relative of the tetraploid crop <i>Chenopodium quinoa</i>. Owing to its reproducible germination and seedling development, it becomes a promising model for studying floral induction, providing a basis for the comparison with <i>C. quinoa</i>. Two <i>C. ficifolium</i> genotypes differ in photoperiodic requirement: <i>C. ficifolium</i> 283 accelerates flowering under long days, whereas <i>C. ficifolium</i> 459 flowers earlier under short days. This study conducted a comprehensive transcriptomic and hormonomic analysis of floral induction in the long-day <i>C. ficifolium</i> 283 and compared the findings to previous experiments with the short-day <i>C. ficifolium</i>. Phytohormone concentrations and gene expression profiles during floral induction were largely similar between the two genotypes. However, a subset of genes exhibited contrasting expression patterns, aligning with the genotypes’ differing photoperiodic requirements. These genes, predominantly homologs of flowering-related genes in <i>Arabidopsis thaliana</i>, were activated under long days in <i>C. ficifolium</i> 283 and under short days in <i>C. ficifolium</i> 459. Notably, the contrasting expression of the <i>FLOWERING LOCUS T-LIKE 2–1</i> gene, which was previously shown to induce precocious flowering in <i>A. thaliana</i>, confirmed its role as a floral activator, despite its low expression levels.
DOI: 10.3535/x8w-hgq-z0y
title: Autographa Hübner, 1821

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.6084/m9.figshare.28588977
title: When two become one: perceptual completion in pea plants

description: Pea plants depend on external structures to reach the strongest light source. To do this, they need to perceive a potential support and to flexibly adapt the movement of their motile organs (e.g. tendrils). In natural environments, there are several above- and belowground elements that could impede the complete perception of potential supports. In such instances, plants may be required to perform a sort of perceptual “completion” to establish a unified percept. We tested whether pea plants are capable of performing perceptual completion by investigating their ascent and attachment behavior using three-dimensional (3D) kinematic analysis. Pea plants were tested in the presence of a support divided into two parts positioned at opposite locations. One part was grounded and perceived only by the root system. The remaining portion was elevated from the ground so that it was only accessible by the aerial part. Control conditions were also included. We hypothesized that if pea plants are able to perceptually integrate the two parts of the support, then they would perform a successful clasping movement. Alternatively, if such integration does not occur, plants may exhibit disoriented exploratory behavior that does not lead to clasping the support. The results demonstrated that pea plants are capable of perceptual completion, allowing for the integration of information coming from the root system and the aerial part. We contend that perceptual completion may be achieved through a continuous crosstalk between a plant’s modules determined by a complex signaling network. By integrating these findings with ecological observations, it may be possible to identify specific factors related to support detection and coding in climbing plants.
DOI: 10.6084/m9.figshare.28733087.v1
title: Contrasting gene expression patterns during floral induction in two <i>Chenopodium ficifolium</i> genotypes reveal putative flowering regulators

description: <i>Chenopodium ficifolium</i> is a close diploid relative of the tetraploid crop <i>Chenopodium quinoa</i>. Owing to its reproducible germination and seedling development, it becomes a promising model for studying floral induction, providing a basis for the comparison with <i>C. quinoa</i>. Two <i>C. ficifolium</i> genotypes differ in photoperiodic requirement: <i>C. ficifolium</i> 283 accelerates flowering under long days, whereas <i>C. ficifolium</i> 459 flowers earlier under short days. This study conducted a comprehensive transcriptomic and hormonomic analysis of floral induction in the long-day <i>C. ficifolium</i> 283 and compared the findings to previous experiments with the short-day <i>C. ficifolium</i>. Phytohormone concentrations and gene expression profiles during floral induction were largely similar between the two genotypes. However, a subset of genes exhibited contrasting expression patterns, aligning with the genotypes’ differing photoperiodic requirements. These genes, predominantly homologs of flowering-related genes in <i>Arabidopsis thaliana</i>, were activated under long days in <i>C. ficifolium</i> 283 and under short days in <i>C. ficifolium</i> 459. Notably, the contrasting expression of the <i>FLOWERING LOCUS T-LIKE 2–1</i> gene, which was previously shown to induce precocious flowering in <i>A. thaliana</i>, confirmed its role as a floral activator, despite its low expression levels.
DOI: 10.3535/1tt-n09-dsj
title: Hydraecia micacea Esper, 1789

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/4ea-aq4-7xb
title: Orthosia (Monima) cruda [Denis & Schiffermüller], 1775

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.6084/m9.figshare.28588977.v1
title: When two become one: perceptual completion in pea plants

description: Pea plants depend on external structures to reach the strongest light source. To do this, they need to perceive a potential support and to flexibly adapt the movement of their motile organs (e.g. tendrils). In natural environments, there are several above- and belowground elements that could impede the complete perception of potential supports. In such instances, plants may be required to perform a sort of perceptual “completion” to establish a unified percept. We tested whether pea plants are capable of performing perceptual completion by investigating their ascent and attachment behavior using three-dimensional (3D) kinematic analysis. Pea plants were tested in the presence of a support divided into two parts positioned at opposite locations. One part was grounded and perceived only by the root system. The remaining portion was elevated from the ground so that it was only accessible by the aerial part. Control conditions were also included. We hypothesized that if pea plants are able to perceptually integrate the two parts of the support, then they would perform a successful clasping movement. Alternatively, if such integration does not occur, plants may exhibit disoriented exploratory behavior that does not lead to clasping the support. The results demonstrated that pea plants are capable of perceptual completion, allowing for the integration of information coming from the root system and the aerial part. We contend that perceptual completion may be achieved through a continuous crosstalk between a plant’s modules determined by a complex signaling network. By integrating these findings with ecological observations, it may be possible to identify specific factors related to support detection and coding in climbing plants.
DOI: 10.6084/m9.figshare.29041375
title: Phylogenetic relationship of WRKY transcription factors in <i>Solanum</i> and potato genes in response to hormonal and biotic stresses

description: WRKY transcription factors are important regulators of plant responses to environmental stresses and hormone signaling. This study analyzes the WRKY gene family in <i>Solanum tuberosum</i> by examining the phylogenetic relationships, expression profiles, and their roles in abiotic stress and hormone responses. Phylogenetic tree was constructed using 322 WRKY genes from four <i>Solanum</i> species: <i>S. tuberosum, S. pennellii, S. pimpinellifolium</i>, and <i>S. lycopersicum</i>. The results revealed conserved and expanded WRKY genes across these species. We then studied the expression of 75 SotuWRKY genes in response to salt, drought, heat stresses, and hormone treatments (IAA, ABA, BABA, GA3, and BAP). Results showed that 19, 25, and 29 genes were regulated under salt, drought, and heat stresses, respectively. Several WRKY genes (e.g. SotuWRKY03 and SotuWRKY24) were also regulated by biotic stresses like <i>Phytophthora infestans</i> infection and hormone treatments, indicating their involvement in plant defense mechanisms. A gene co-expression network was constructed based on gene-to-gene correlations, where <i>SotuWRKY52</i> was identified as a hub gene, positively regulating six WRKY genes and negatively regulating four. These findings suggest that potato WRKY genes play key roles in regulating stress responses and hormone signaling, potentially enhancing potato resistance to stresses and diseases. This study provides new insights into WRKY transcription factors in <i>S. tuberosum</i> and other <i>Solanum</i> species.