Browsing by Subject "11831 Plant biology"

Sort by: Order: Results:

Now showing items 1-20 of 184
  • Kjaerbolling, Inge; Vesth, Tammi; Frisvad, Jens C.; Nybo, Jane L.; Theobald, Sebastian; Kildgaard, Sara; Petersen, Thomas Isbrandt; Kuo, Alan; Sato, Atsushi; Lyhne, Ellen K.; Kogle, Martin E.; Wiebenga, Ad; Kun, Roland S.; Lubbers, Ronnie J. M.; Makela, Miia R.; Barry, Kerrie; Chovatia, Mansi; Clum, Alicia; Daum, Chris; Haridas, Sajeet; He, Guifen; LaButti, Kurt; Lipzen, Anna; Mondo, Stephen; Pangilinan, Jasmyn; Riley, Robert; Salamov, Asaf; Simmons, Blake A.; Magnuson, Jon K.; Henrissat, Bernard; Mortensen, Uffe H.; Larsen, Thomas O.; de Vries, Ronald P.; Grigoriev, Igor V.; Machida, Masayuki; Baker, Scott E.; Andersen, Mikael R. (2020)
    Section Flavi encompasses both harmful and beneficial Aspergillus species, such as Aspergillus oryzae, used in food fermentation and enzyme production, and Aspergillus flavus, food spoiler and mycotoxin producer. Here, we sequence 19 genomes spanning section Flavi and compare 31 fungal genomes including 23 Flavi species. We reassess their phylogenetic relationships and show that the closest relative of A. oryzae is not A. flavus, but A. minisclerotigenes or A. aflatoxiformans and identify high genome diversity, especially in sub-telomeric regions. We predict abundant CAZymes (598 per species) and prolific secondary metabolite gene clusters (73 per species) in section Flavi. However, the observed phenotypes (growth characteristics, polysaccharide degradation) do not necessarily correlate with inferences made from the predicted CAZyme content. Our work, including genomic analyses, phenotypic assays, and identification of secondary metabolites, highlights the genetic and metabolic diversity within section Flavi.
  • Haapalainen, Minna; Latvala, Satu; Wickstrom, Annika; Wang, Jinhui; Pirhonen, Minna; Nissinen, Anne I. (2020)
    A previously unknown haplotype of the plant pathogen 'Candidatus Liberibacter solanacearum' (Lso) was found in cultivated carrots and parsnips in eastern Finland. That same haplotype was found in western Finland, over 300 km away, in the family Polygonaceae, the species Fallopia convolvulus (wild buckwheat) and Persicaria lapathifolia (pale persicaria) growing as weeds within carrot and parsnip fields. The infected plants, both apiaceous and polygonaceous, showed symptoms of foliar discolouration. This is the first report of Lso bacteria in plants of the family Polygonaceae. The finding that the polygonaceous plants infected with a previously unknown haplotype of Lso were growing among the apiaceous plants infected with Lso haplotype C suggests that these two haplotypes might be transmitted by different vectors. Phylogenetic analyses showed that the new haplotype, called haplotype H, is distinct from the previously characterized haplotypes and appears to have diverged early from their common ancestor. Multi-locus sequence analysis revealed four different sequence types (strains) within the haplotype H. These findings suggest that the haplotype H is likely to be endemic in northern Europe and that the genetic diversity within the Lso species is higher than previously assumed.
  • Iida, Hiroyuki; Takada, Shinobu (2021)
    The cloning of the ATML1 gene, encoding an HD-ZIP class IV transcription factor, was first reported in 1996. Because ATML1 mRNA was preferentially detected in the shoot epidermis, cis-regulatory sequences of ATML1 have been used to drive gene expression in the outermost cells of the shoot apical meristem and leaves, even before the function of ATML1 was understood. Later studies revealed that ATML1 is required for developmental processes related to shoot epidermal specification and differentiation. Consistent with its central role in epidermal development, ATML1 activity has been revealed to be restricted to the outermost cells via several regulatory mechanisms. In this review, we look back on the history of ATML1 research and provide a perspective for future studies.
  • Wang, Kai; Liu, Mengxia; Cui, Fuqiang; Asiegbu, Fred (2021)
  • Lim, Kean-Jin; Paasela, Tanja; Harju, Anni; Venalainen, Martti; Paulin, Lars; Auvinen, Petri; Karkkainen, Katri; Teeri, Teemu H. (2021)
    We studied the stress response of five-year-old Scots pine xylem to mechanical wounding using RNA sequencing. In general, we observed a bimodal response in pine xylem after wounding. Transcripts associated with water deficit stress, defence, and cell wall modification were induced at the earliest time point of three hours; at the same time, growth-related processes were down-regulated. A second temporal wave was triggered either at the middle and/or at the late time points (one and four days). Secondary metabolism, such as stilbene and lignan biosynthesis started one day after wounding. Scots pine synthesises the stilbenes pinosylvin and its monomethyl ether both as constitutive and induced defence compounds. Stilbene biosynthesis is induced by wounding, pathogens and UV stress, but is also developmentally regulated when heartwood is formed. Comparison of wounding responses to heartwood formation shows that many induced processes (in addition to stilbene biosynthesis) are similar and relate to defence or desiccation stress, but often specific transcripts are up-regulated in the developmental and wounding induced contexts. Pine resin biosynthesis was not induced in response to wounding, at least not during the first four days.
  • Aphalo, Pedro J. (2020)
    Most photobiologists sooner or later have to measure light absorption, reflection and/or transmission by objects such as plant leaves, optical filters or solutes in a liquid medium. The physical quantities we measure may vary: absorbance, optical density, absorptance, transmittance and reflectance. In addition to these extensive properties of objects we use intensive properties such as the molar extinction coefficient and refractive index. This article disusses the defintions of these quantities and exemplifies some of their uses in research in the field plant photobiology including the study and application of UV radiation. It also touches on some less frequently discussed alspects such as the effect of the angle of incidence on the reflectance at the surface of windows and optical filters.
  • Kamarainen, A.; Jokinen, K.; Linden, L. (2020)
    The addition of Sphagnum to peat-based growing media ('Sphagnum replacement') influences plant performance. The primary physical effect of Sphagnum addition appears to be enhanced water retention. Good performance of plants cultivated in Sphagnum seems partly explainable in terms of its water retention properties. The large body of nutrient solution retained in Sphagnum can delay disadvantageous changes in its concentration during cultivation. The physical quantity of Sphagnum per unit volume, i.e. its bulk density, governs the volume of retained water and thus determines the strength of effects contributing to plant performance. When subjected to severe drought, plants cultivated in Sphagnum did not show clear signs of water deficit up to at least 1,572 hPa of matric suction, which is the estimated wilting point for plants grown in light peat. Using Sphagnum to replace peat in the growing medium appears advantageous to plants not only during drought but also during ordinary greenhouse cultivation.
  • Susi, Hanna; Laine, Anna-Liisa (2021)
    Human alteration of natural habitats may change the processes governing species interactions in wild communities. Wild populations are increasingly impacted by agricultural intensification, yet it is unknown whether this alters biodiversity mediation of disease dynamics. We investigated the association between plant diversity (species richness, diversity) and infection risk (virus richness, prevalence) in populations of Plantago lanceolata in natural landscapes as well as those occurring at the edges of cultivated fields. Altogether, 27 P. lanceolata populations were surveyed for population characteristics and sampled for PCR detection of five recently characterized viruses. We find that plant species richness and diversity correlated negatively with virus infection prevalence. Virus species richness declined with increasing plant diversity and richness in natural populations while in agricultural edge populations species richness was moderately higher, and not associated with plant richness. This difference was not explained by changes in host richness between these two habitats, suggesting potential pathogen spill-over and increased transmission of viruses across the agro-ecological interface. Host population connectivity significantly decreased virus infection prevalence. We conclude that human use of landscapes may change the ecological laws by which natural communities are formed with far reaching implications for ecosystem functioning and disease.
  • Castillejo, Cristina; Waurich, Veronika; Wagner, Henning; Ramos, Ruben; Oiza, Nicolas; Munoz, Pilar; Trivino, Juan C.; Caruana, Julie; Liu, Zhongchi; Cobo, Nicolas; Hardigan, Michael A.; Knapp, Steven J.; Vallarino, Jose G.; Osorio, Sonia; Martin-Pizarro, Carmen; Pose, David; Toivainen, Tuomas; Hytonen, Timo; Oh, Youngjae; Barbey, Christopher R.; Whitaker, Vance M.; Lee, Seonghee; Olbricht, Klaus; Sanchez-Sevilla, Jose F.; Amaya, Iraida (2020)
    Independent mutations in the transcription factor MYB10 cause most of the anthocyanin variation observed in diploid woodland strawberry (Fragaria vesca) and octoploid cultivated strawberry (Fragaria x ananassa). The fruits of diploid and octoploid strawberry (Fragaria spp) show substantial natural variation in color due to distinct anthocyanin accumulation and distribution patterns. Anthocyanin biosynthesis is controlled by a clade of R2R3 MYB transcription factors, among which MYB10 is the main activator in strawberry fruit. Here, we show that mutations in MYB10 cause most of the variation in anthocyanin accumulation and distribution observed in diploid woodland strawberry (F. vesca) and octoploid cultivated strawberry (F. xananassa). Using a mapping-by-sequencing approach, we identified a gypsy-transposon in MYB10 that truncates the protein and knocks out anthocyanin biosynthesis in a white-fruited F. vesca ecotype. Two additional loss-of-function mutations in MYB10 were identified among geographically diverse white-fruited F. vesca ecotypes. Genetic and transcriptomic analyses of octoploid Fragaria spp revealed that FaMYB10-2, one of three MYB10 homoeologs identified, regulates anthocyanin biosynthesis in developing fruit. Furthermore, independent mutations in MYB10-2 are the underlying cause of natural variation in fruit skin and flesh color in octoploid strawberry. We identified a CACTA-like transposon (FaEnSpm-2) insertion in the MYB10-2 promoter of red-fleshed accessions that was associated with enhanced expression. Our findings suggest that cis-regulatory elements in FaEnSpm-2 are responsible for enhanced MYB10-2 expression and anthocyanin biosynthesis in strawberry fruit flesh.
  • Wang, Xin; Ye, Lingling; Lyu, Munan; Ursache, Robertas; Löytynoja, Ari; Mähönen, Ari Pekka (2020)
    Conditional manipulation of gene expression is a key approach to investigating the primary function of a gene in a biological process. While conditional and cell-type-specific overexpression systems exist for plants, there are currently no systems available to disable a gene completely and conditionally. Here, we present a new tool with which target genes can efficiently and conditionally be knocked out by genome editing at any developmental stage. Target genes can also be knocked out in a cell-type-specific manner. Our tool is easy to construct and will be particularly useful for studying genes having null alleles that are non-viable or show pleiotropic developmental defects.
  • Haliloglu, Kamil; Hosseinpour, Arash; Cinisli, Kağan Tolga; Ozturk, Halil Ibrahim; Ozkan, Guller; Pour-Aboughadareh, Alireza; Poczai, Péter (2020)
    Salinity is an edaphic stress that dramatically restricts worldwide crop production. Nanomaterials and plant growth-promoting bacteria (PGPB) are currently used to alleviate the negative effects of various stresses on plant growth and development. This study investigates the protective effects of different levels of zinc oxide nanoparticles (ZnO-NPs) (0, 20, and 40 mg L-1) and PGPBs (no bacteria, Bacillus subtilis, Lactobacillus casei, Bacillus pumilus) on DNA damage and cytosine methylation changes in the tomato (Solanum lycopersicum L. 'Linda') seedlings under salinity stress (250 mM NaCl). Coupled Restriction Enzyme Digestion-Random Amplification (CRED-RA) and Randomly Amplified Polymorphic DNA (RAPD) approaches were used to analyze changes in cytosine methylation and to determine how genotoxic effects influence genomic stability. Salinity stress increased the polymorphism rate assessed by RAPD, while PGPB and ZnO-NPs reduced the adverse effects of salinity stress. Genomic template stability was increased by the PGPBs and ZnO-NPs application; this increase was significant when Lactobacillus casei and 40 mg L-1 of ZnO-NPs were used.A decreased level of DNA methylation was observed in all treatments. Taken together, the use of PGPB and ZnO-NPs had a general positive effect under salinity stress reducing genetic impairment in tomato seedlings.
  • Liu, Miao; Liu, Xingxing; Kang, Jieyu; Korpelainen, Helena; Li, Chunyang (2020)
    This study clarifies the mechanisms of Cd uptake, translocation and detoxification in Populus cathayana Rehder females and males, and reveals a novel strategy for dioecious plants to cope with Cd contamination. Females exhibited a high degree of Cd uptake and root-to-shoot translocation, while males showed extensive Cd accumulation in roots, elevated antioxidative capacity, and effective cellular and bark Cd sequestration. Our study also found that Cd is largely located in epidermal and cortical tissues of male roots and leaves, while in females, more Cd was present in vascular tissues of roots and leaves, as well as in leaf mesophyll. In addition, the distributions of sulphur (S) and phosphorus (P) were very similar as that of Cd in males, but the associations were weak in females. Scanning electron microscopy and energy spectroscopy analyses suggested that the amounts of tissue Cd were positively correlated with P and S amounts in males, but not in females (a weak correlation between S and Cd). Transcriptional data suggested that Cd stress promoted the upregulation of genes related to Cd uptake and translocation in females, and that of genes related to cell wall biosynthesis, metal tolerance and secondary metabolism in males. Our results indicated that coordinated physiological, microstructural and transcriptional responses to Cd stress endowed superior Cd tolerance in males compared with females, and provided new insights into mechanisms underlying sexually differential responses to Cd stress.
  • Korpelainen, Helena; Elshibli, Sakina (2021)
    We conducted genomic characterization based on SNP and SilicoDArT markers on the invasive Himalayan balsam (Impatiens glandulifera) plants originating from native and non-native regions of their distribution. When genetic relationships were explored by PCoA using SNP and SilicoDArT marker data, the first, second, and third principal coordinates explained altogether 37.4% and 31.0% of the variability, respectively. Samples from the UK, Canada, and Pakistan were grouped together, while Indian plants were clearly distinct based on SNP markers but relatively close to the UK-Canada-Pakistan group based on SilicoDArT markers. Constructed trees differentiated individuals into clusters resembling the PCoA patterns. The Bayesian BAPS analysis performed for the SNP data revealed that the individuals were distributed in seven clusters, representing samples from each of the four Finnish populations, India, Pakistan, and the combination of the UK and Canada. Similar clustering was visible in the UPGMA tree. The Indian cluster did not display any ancestral gene flow with the others, while the Pakistani cluster showed ancestral gene flow only with the combined UK and Canada cluster. Furthermore, the latter cluster displayed ancestral gene flow with the Finnish populations varying from 0% to 3.1%. The BAPS analyses conducted for the SilicoDArT data differ slightly: The individuals were distributed in nine clusters, and the Indian cluster exhibited ancestral gene flow with the mixed cluster including Canadian, Pakistani, and UK samples, and one Finnish sample. The AMOVA showed that 45% and 26% of variation was present among the I. glandulifera groups/populations and the rest within them based on SNP and SilicoDArT markers, respectively. The Bayesian BAPS analyses and the gene flow networks were the most informative tools for resolving relationships among native and introduced plants. It is notable that the small sample sizes for non-Finnish plant materials may affect the accuracy of the gene flow and other estimates.
  • Cervantes, Sandra; Vuosku, Jaana; Pyhajarvi, Tanja (2021)
    Despite their ecological and economical importance, conifers genomic resources are limited, mainly due to the large size and complexity of their genomes. Additionally, the available genomic resources lack complete structural and functional annotation. Transcriptomic resources have been commonly used to compensate for these deficiencies, though for most conifer species they are limited to a small number of tissues, or capture only a fraction of the genes present in the genome. Here we provide an atlas of gene expression patterns for conifer Pinus sylvestris across five tissues: embryo, megagametophyte, needle, phloem and vegetative bud. We used a wide range of tissues and focused our analyses on the expression profiles of genes at tissue level. We provide comprehensive information of the per-tissue normalized expression level, indication of tissue preferential upregulation and tissue-specificity of expression. We identified a total of 48,001 tissue preferentially upregulated and tissue specifically expressed genes, of which 28% have annotation in the Swiss-Prot database. Even though most of the putative genes identified do not have functional information in current biological databases, the tissue-specific patterns discovered provide valuable information about their potential functions for further studies, as for example in the areas of plant physiology, population genetics and genomics in general. As we provide information on tissue specificity at both diploid and haploid life stages, our data will also contribute to the understanding of evolutionary rates of different tissue types and ploidy levels.
  • Ma, Yang; Qu, Zhao-Lei; Liu, Bing; Tan, Jia-Jin; Asiegbu, Fred O.; Sun, Hui (2020)
    Pine wilt disease (PWD) caused by the nematode Bursaphelenchus xylophilus is a devastating disease in conifer forests in Eurasia. However, information on the effect of PWD on the host microbial community is limited. In this study, the bacterial community structure and potential function in the needles, roots, and soil of diseased pine were studied under field conditions using Illumina MiSeq coupled with Phylogenetic Investigation of Communities by Reconstruction of Unobserved states (PICRUSt) software. The results showed that the community and functional structure of healthy and diseased trees differed only in the roots and needles, respectively (p <0.05). The needles, roots, and soil formed unique bacterial community and functional structures. The abundant phyla across all samples were Proteobacteria (41.9% of total sequence), Actinobacteria (29.0%), Acidobacteria (12.2%), Bacteroidetes (4.8%), and Planctomycetes (2.1%). The bacterial community in the healthy roots was dominated by Acidobacteria, Planctomycetes, and Rhizobiales, whereas in the diseased roots, Proteobacteria, Firmicutes, and Burkholderiales were dominant. Functionally, groups involved in the cell process and genetic information processing had a higher abundance in the diseased needles, which contributed to the difference in functional structure. The results indicate that PWD can only affect the host bacteria community structure and function in certain anatomical regions of the host tree.
  • Lundell, Robin; Hänninen, Heikki; Saarinen, Timo; Åström, Helena; Zhang, Rui (2020)
    Bud dormancy of plants has traditionally been explained either by physiological growth arresting conditions in the bud or by unfavourable environmental conditions, such as non-growth-promoting low air temperatures. This conceptual dichotomy has provided the framework also for developing process-based plant phenology models. Here, we propose a novel model that in addition to covering the classical dichotomy as a special case also allows the quantification of an interaction of physiological and environmental factors. According to this plant-environment interaction suggested conceptually decades ago, rather than being unambiguous, the concept of "non-growth-promoting low air temperature" depends on the dormancy status of the plant. We parameterized the model with experimental results of growth onset for seven boreal plant species and found that based on the strength of the interaction, the species can be classified into three dormancy types, only one of which represents the traditional dichotomy. We also tested the model with four species in an independent experiment. Our study suggests that interaction of environmental and physiological factors may be involved in many such phenomena that have until now been considered simply as plant traits without any considerations of effects of the environmental factors.
  • Vaario, Lu-Min; Asamizu, Shumpei; Sarjala, Tytti; Matsushita, Norihisa; Onaka, Hiroyasu; Xia, Yan; Kurokochi, Hiroyuki; Morinaga, Shin-Ichi; Huang, Jian; Zhang, Shijie; Lian, Chunlan (2020)
    Tricholoma matsutake is known to be the dominant fungal species in matsutake fruitbody neighboring (shiro) soil. To understand the mechanisms behind matsutake dominance, we studied the bacterial communities in matsutake dominant shiro soil and non-shiro soil, isolated the strains of Streptomyces from matsutake mycorrhizal root tips both from shiro soil and from the Pinus densiflora seedlings cultivated in shiro soil. Further, we investigated three Streptomyces spp. for their ability to inhibit fungal growth and Pinus densiflora seedling root elongation as well as two strains for their antifungal and antioxidative properties. Our results showed that Actinobacteria was the most abundant phylum in shiro soil. However, the differences in the Actinobacterial community composition (phylum or order level) between shiro and non-shiro soils were not significant, as indicated by PERMANOVA analyses. A genus belonging to Actinobacteria, Streptomyces, was present on the matsutake mycorrhizas, although in minority. The two antifungal assays revealed that the broths of three Streptomyces spp. had either inhibitory, neutral or promoting effects on the growth of different forest soil fungi as well as on the root elongation of the seedlings. The extracts of two strains, including one isolated from the P. densiflora seedlings, inhibited the growth of either pathogenic or ectomycorrhizal fungi. The effect depended on the medium used to cultivate the strains, but not the solvent used for the extraction. Two Streptomyces spp. showed antioxidant activity in one out of three assays used, in a ferric reducing antioxidant power assay. The observed properties seem to have several functions in matsutake shiro soil and they may contribute to the protection of the shiro area for T. matsutake dominance.
  • Paterlini, Andrea; Dorussen, Delfi; Fichtner, Franziska; van Rongen, Martin; Delacruz, Ruth; Vojnovic, Ana; Helariutta, Yrjö; Leyser, Ottoline (2021)
  • Lizarazo, Clara; Lampi, Anna-Maija; Mäkelä, Pirjo (2021)
    Caraway seeds contain between 0.5-7% essential oil, rich in monoterpenes that have a characteristic aroma and chemical properties. Caraway oil has several bioactive compounds that are of industrial importance, particularly for pharmaceutical and health care products. Carvone and limonene are the main terpenes present in caraway oil, which along with some unique fatty acids (i.e. petroselinic acid) determine caraway (Carum carvi L.) oil quality. Both terpenes are important raw materials for industrial applications and their concentration influences the price of caraway seed and oil, hence there is need for identifying management practices that may increase the concentration of these and other bioactive compounds to improve caraway seed oil quality. A field experiment with five treatments: a control and a series of foliar-applied micronutrients (either Cu, Mg, Mn or Zn was done to identify their potential to enhance caraway oil quality. Solid-phase microextraction and gas chromatography with a flame ionization detector were used to characterize oil quality. Our results indicate that while the micronutrient treatments have a significant effect on essential oil composition, both in carvone and limonene, such an effect was not found on all fatty acids but only in two of them-palmitoleic and vaccenic acid-, which were highest after the Mn treatment. Overall, the carvone content of the seeds decreased the least between years following Mn treatment. Mn treatment also caused an increase in limonene in the second year in contrast to the trend for all other treatments. The Mn foliar spray needs to be studied further to elucidate whether it could have a consistent positive effect on caraway oil seed quality upon adjusting dosage and spraying time.
  • Väre, Henry (2021)
    Mårten Magnus Wilhelm Brenner (1843–1930) was a non-professional Finnish botanist who published 220 articles or notes. Brenner worked on East Fennoscandian vascular plants (the territory of present-day Finland and adjacent Russia). He validly published ca. 833 new taxa, especially in genus Hieracium (including Pilosella), and introduced 56 names as nomina nuda. Brenner had no concept of type specimens and therefore all his plant taxa need typification, and 151 of those are lectotypified here. In this paper, nomina nuda and the taxa whose type material was not found are also listed, except those of the apomictic genera Hieracium and Taraxacum. Many of Brenner’s new taxa are forms and varieties, generally not recognised nowadays. Many of his taxa were based on single or few specimens and therefore were characterised by local distributions, whereas some include ample original material. Finnish botanists generally ignored Brenner’s contributions to taxonomy. However, 11 species of Hieracium, 20 of Taraxacum and Euphrasia stricta var. tenuis (Brenner) Jalas are currently recognised, and recently also E. wettsteinii var. botniensium (Brenner) Piirainen. Together Brenner’s type collection treated here consists of 254 sheets (Hieracium and Taraxacum excluded), deposited at the Botanical Museum (H), Finnish Museum of Natural History, University of Helsinki, Finland.