| 1. |
- Abarenkov, Kessy, et al.
(författare)
-
Protax-fungi: A web-based tool for probabilistic taxonomic placement of fungal internal transcribed spacer sequences
- 2018
-
Ingår i: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; 220:2, s. 517-525
-
Tidskriftsartikel (refereegranskat)abstract
- © 2018 New Phytologist Trust. Incompleteness of reference sequence databases and unresolved taxonomic relationships complicates taxonomic placement of fungal sequences. We developed Protax-fungi, a general tool for taxonomic placement of fungal internal transcribed spacer (ITS) sequences, and implemented it into the PlutoF platform of the UNITE database for molecular identification of fungi. With empirical data on root- and wood-associated fungi, Protax-fungi reliably identified (with at least 90% identification probability) the majority of sequences to the order level but only around one-fifth of them to the species level, reflecting the current limited coverage of the databases. Protax-fungi outperformed the Sintax and Rdb classifiers in terms of increased accuracy and decreased calibration error when applied to data on mock communities representing species groups with poor sequence database coverage. We applied Protax-fungi to examine the internal consistencies of the Index Fungorum and UNITE databases. This revealed inconsistencies in the taxonomy database as well as mislabelling and sequence quality problems in the reference database. The according improvements were implemented in both databases. Protax-fungi provides a robust tool for performing statistically reliable identifications of fungi in spite of the incompleteness of extant reference sequence databases and unresolved taxonomic relationships.
|
|
| 2. |
- Alvarez, José M, et al.
(författare)
-
The WUSCHEL-RELATED HOMEOBOX 3 gene PaWOX3 regulates lateral organ formation in Norway spruce
- 2015
-
Ingår i: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; 208:4, s. 1078-1088
-
Tidskriftsartikel (refereegranskat)abstract
- In angiosperms, WUSCHEL-RELATED HOMEOBOX 3 (WOX3) genes are required for the recruitment of founder cells from the lateral domains of shoot meristems that form lateral regions of leaves. However, the regulation of the formation of lateral organs in gymnosperms remains unknown. By using somatic embryos of Norway spruce ( Picea abies) we have studied the expression and function of PaWOX3 during embryo development. The mRNA abundance of PaWOX3 was determined by quantitative real-time PCR, and the spatial expression of PaWOX3 was analysed by histochemical beta-glucuronidase (GUS) assays and in situ mRNA hybridization. To investigate the function of PaWOX3, we analysed how downregulation of PaWOX3 in RNA interference lines affected embryo development and morphology. PaWOX3 was highly expressed in mature embryos at the base of each cotyledon close to the junction between the cotyledons, and in the lateral margins of cotyledons and needles, separating them into an adaxial and an abaxial side. Downregulation of the expression of PaWOX3 caused defects in lateral margin outgrowth in cotyledons and needles, and reduced root elongation. Our data suggest that the WOX3 function in margin outgrowth in lateral organs is conserved among the seed plants, whereas its function in root elongation may be unique to gymnosperms.
|
|
| 3. |
- Bachmann, Jörg A., et al.
(författare)
-
Genetic basis and timing of a major mating system shift in Capsella
- 2019
-
Ingår i: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; 224:1, s. 505-517
-
Tidskriftsartikel (refereegranskat)abstract
- A crucial step in the transition from outcrossing to self-fertilization is the loss of genetic self-incompatibility (SI). In the Brassicaceae, SI involves the interaction of female and male specificity components, encoded by the genes SRK and SCR at the self-incompatibility locus (S-locus). Theory predicts that S-linked mutations, and especially dominant mutations in SCR, are likely to contribute to loss of SI. However, few studies have investigated the contribution of dominant mutations to loss of SI in wild plant species. Here, we investigate the genetic basis of loss of SI in the self-fertilizing crucifer species Capsella orientalis, by combining genetic mapping, long-read sequencing of complete S-haplotypes, gene expression analyses and controlled crosses. We show that loss of SI in C. orientalis occurred S-locus. We identify a fixed frameshift deletion in the male specificity gene SCR and confirm loss of male SI specificity. We further identify an S-linked small RNA that is predicted to cause dominance of self-compatibility. Our results agree with predictions on the contribution of dominant S-linked mutations to loss of SI, and thus provide new insights into the molecular basis of mating system transitions.
|
|
| 4. |
- Bai, Bing, et al.
(författare)
-
Combined transcriptome and translatome analyses reveal a role for tryptophan-dependent auxin biosynthesis in the control of DOG1-dependent seed dormancy
- 2018
-
Ingår i: New Phytologist. - : WILEY. - 0028-646X .- 1469-8137. ; 217:3, s. 1077-1085
-
Tidskriftsartikel (refereegranskat)abstract
- The importance of translational regulation during Arabidopsis seed germination has been shown previously. Here the role of transcriptional and translational regulation during seed imbibition of the very dormant DELAY OF GERMINATION 1 (DOG1) near-isogenic line was investigated. Polysome profiling was performed on dormant and after-ripened seeds imbibed for 6 and 24 h in water and in the transcription inhibitor cordycepin. Transcriptome and translatome changes were investigated. Ribosomal profiles of after-ripened seeds imbibed in cordycepin mimic those of dormant seeds. The polysome occupancy of mRNA species is not affected by germination inhibition, either as a result of seed dormancy or as a result of cordycepin treatment, indicating the importance of the regulation of transcript abundance. The expression of auxin metabolism genes is discriminative during the imbibition of after-ripened and dormant seeds, which is confirmed by altered concentrations of indole-3-acetic acid conjugates and precursors.
|
|
| 5. |
- Bai, Bing, et al.
(författare)
-
Extensive translational regulation during seed germination revealed by polysomal profiling
- 2017
-
Ingår i: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; 214:1, s. 233-244
-
Tidskriftsartikel (refereegranskat)abstract
- This work investigates the extent of translational regulation during seed germination. The polysome occupancy of each gene is determined by genome-wide profiling of total mRNA and polysome-associated mRNA. This reveals extensive translational regulation during Arabidopsis thaliana seed germination. The polysome occupancy of thousands of individual mRNAs changes to a large extent during the germination process. Intriguingly, these changes are restricted to two temporal phases (shifts) during germination, seed hydration and germination. Sequence features, such as upstream open reading frame number, transcript length, mRNA stability, secondary structures, and the presence and location of specific motifs correlated with this translational regulation. These features differed significantly between the two shifts, indicating that independent mechanisms regulate translation during seed germination. This study reveals substantial translational dynamics during seed germination and identifies development-dependent sequence features and cis elements that correlate with the translation control, uncovering a novel and important layer of gene regulation during seed germination.
|
|
| 6. |
- Barraclough, Timothy G., et al.
(författare)
-
The evolutionary reality of species and higher taxa in plants : a survey of post-modern opinion and evidence
- 2015
-
Ingår i: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; 207:2, s. 291-296
-
Forskningsöversikt (refereegranskat)abstract
- Species are normally considered to be the fundamental unit for understanding the evolution of biodiversity. Yet, in a survey of botanists in 1940, twice as many felt that plant genera were more natural units than plant species. Revisiting the survey, we found more people now regarded species as a more evolutionarily real unit, but a sizeable number still felt that genera were more evolutionarily real than species. Definitions of evolutionarily real' split into those based on shared evolutionary history and those based on shared evolutionary fate via ongoing evolutionary processes. We discuss recent work testing for shared evolutionary fate at the species and higher levels and present preliminary evidence for evolutionarily significant higher taxa in plants.
|
|
| 7. |
- Baskaran, Preetisri, et al.
(författare)
-
Modelling the influence of ectomycorrhizal decomposition on plant nutrition and soil carbon sequestration in boreal forest ecosystems
- 2017
-
Ingår i: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; 213:3, s. 1452-1465
-
Tidskriftsartikel (refereegranskat)abstract
- Tree growth in boreal forests is limited by nitrogen (N) availability. Most boreal forest trees form symbiotic associations with ectomycorrhizal (ECM) fungi, which improve the uptake of inorganic N and also have the capacity to decompose soil organic matter (SOM) and to mobilize organic N (ECM decomposition'). To study the effects of ECM decomposition' on ecosystem carbon (C) and N balances, we performed a sensitivity analysis on a model of C and N flows between plants, SOM, saprotrophs, ECM fungi, and inorganic N stores. The analysis indicates that C and N balances were sensitive to model parameters regulating ECM biomass and decomposition. Under low N availability, the optimal C allocation to ECM fungi, above which the symbiosis switches from mutualism to parasitism, increases with increasing relative involvement of ECM fungi in SOM decomposition. Under low N conditions, increased ECM organic N mining promotes tree growth but decreases soil C storage, leading to a negative correlation between C stores above- and below-ground. The interplay between plant production and soil C storage is sensitive to the partitioning of decomposition between ECM fungi and saprotrophs. Better understanding of interactions between functional guilds of soil fungi may significantly improve predictions of ecosystem responses to environmental change.
|
|
| 8. |
- Berghuijs, Herman
(författare)
-
Using a reaction-diffusion model to estimate day respiration and reassimilation of (photo)respired CO2 in leaves
- 2019
-
Ingår i: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; 223, s. 619-631
-
Tidskriftsartikel (refereegranskat)abstract
- Methods using gas exchange measurements to estimate respiration in the light (day respiration Rd) make implicit assumptions about reassimilation of (photo)respired CO2; however, this reassimilation depends on the positions of mitochondria. We used a reaction-diffusion model without making these assumptions to analyse datasets on gas exchange, chlorophyll fluorescence and anatomy for tomato leaves. We investigated how Rd values obtained by the Kok and the Yin methods are affected by these assumptions and how those by the Laisk method are affected by the positions of mitochondria. The Kok method always underestimated Rd. Estimates of Rd by the Yin method and by the reaction-diffusion model agreed only for nonphotorespiratory conditions. Both the Yin and Kok methods ignore reassimilation of (photo)respired CO2, and thus underestimated Rd for photorespiratory conditions, but this was less so in the Yin than in the Kok method. Estimates by the Laisk method were affected by assumed positions of mitochondria. It did not work if mitochondria were in the cytosol between the plasmamembrane and the chloroplast envelope. However, mitochondria were found to be most likely between the tonoplast and chloroplasts. Our reaction-diffusion model effectively estimates Rd, enlightens the dependence of Rd estimates on reassimilation and clarifies (dis)advantages of existing methods.
|
|
| 9. |
- Binkley, Dan
(författare)
-
Ecosystem in four dimensions
- 2015
-
Ingår i: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; 206, s. 883-885
-
Annan publikation (refereegranskat)
|
|
| 10. |
- Bjorklund, J., et al.
(författare)
-
Cell size and wall dimensions drive distinct variability of earlywood and latewood density in Northern Hemisphere conifers
- 2017
-
Ingår i: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; 216:3, s. 728-740
-
Tidskriftsartikel (refereegranskat)abstract
- Interannual variability of wood density - an important plant functional trait and environmental proxy - in conifers is poorly understood. We therefore explored the anatomical basis of density. We hypothesized that earlywood density is determined by tracheid size and latewood density by wall dimensions, reflecting their different functional tasks. To determine general patterns of variability, density parameters from 27 species and 349 sites across the Northern Hemisphere were correlated to tree-ring width parameters and local climate. We performed the same analyses with density and width derived from anatomical data comprising two species and eight sites. The contributions of tracheid size and wall dimensions to density were disentangled with sensitivity analyses. Notably, correlations between density and width shifted from negative to positive moving from earlywood to latewood. Temperature responses of density varied intraseasonally in strength and sign. The sensitivity analyses revealed tracheid size as the main determinant of earlywood density, while wall dimensions become more influential for latewood density. Our novel approach of integrating detailed anatomical data with large-scale tree-ring data allowed us to contribute to an improved understanding of interannual variations of conifer growth and to illustrate how conifers balance investments in the competing xylem functions of hydraulics and mechanical support.
|
|
