Comparative omics analysis for novel target discovery in plant pathogens: A case study for Magnaporthe oryzae

Comparative omics analysis for novel target discovery in plant pathogens: A case study for Magnaporthe oryzae

A novel strategy, integrating omics and bioinformatics, identifies distinct fungal pathways, revealing a promising target for precision fungicides against Magnaporthe oryzae, causing rice blast disease.


Abstract

The central concern surrounding chemical pesticide application is its potential adverse effects on non-target organisms. For fungal pathogens, the search for specific targets has been complicated by the similarities in pathways shared between these pathogens and humans. We present a comprehensive strategy, integrating comparative omics and bioinformatics, to pinpoint precise targets for fungicides effective against the fungal pathogen Magnaporthe oryzae, responsible for rice blast disease. Our approach involves subtractive metabolic pathways, homology screening and target prioritization. Through subtractive metabolic analysis, we identified three unique M. oryzae pathways, distinct from human and rice. Nonredundant protein sequences were subsequently subjected to BLASTP screening against human and rice, as well as other databases from diverse organisms. Target subcellular localization was predicted using eight tools, including artificial intelligence and a deep-learning method. A comprehensive examination of biological processes was conducted, including gene expression, protein–protein interactions, network enrichment, broad-spectrum activity and physicochemical analysis. Glutamate 5-kinase emerged as the prime candidate for targeted fungicide development, promising progress in precision-oriented solutions.

Plant spectral diversity from high‐resolution multispectral imagery detects functional diversity patterns in coastal dune communities

Plant spectral diversity from high-resolution multispectral imagery detects functional diversity patterns in coastal dune communities

In this study, we estimated spectral and functional diversity in a common framework encompassing all their multivariate components. Our findings indicate that spectral diversity accurately captures the functional structure of plant communities and approximates species patterns in the functional space. Furthermore, we showed the efficient approximation of functional diversity patterns by spectral diversity across spatial scales and along ecological gradients.


Abstract

Question

Remote sensing is a fundamental tool to monitor biodiversity and spectral diversity may represent a proxy for different biodiversity facets such as taxonomic (TD) and functional diversity (FD). We used fine-resolution multispectral imagery to explore spectral diversity (SD) patterns across spatial scales (i.e., plot, transect, area), and assess SD relationships with TD and FD along an environmental gradient.

Location

Coastal sand dune, Viareggio, Italy (“Migliarino–San Rossore–Massaciuccoli” Regional Park, 43°83′ N, 10°25′ E).

Methods

We measured TD as species richness, while SD and FD were computed using probability density functions based on pixel and species position in multivariate spaces. We compared SD and FD patterns in space occupation, and we tested whether these patterns are coordinated along the sea–inland gradient. We also assessed univariate relationships between SD and biodiversity facets, and we tested how these facets were partitioned across scales.

Results

We found a strong correspondence between functional and spectral patterns in space occupation and along the environmental gradient, with a lack of significance when considering TD. However, TD and SD showed higher variation at broader scale while most FD variation occurred at plot level.

Conclusion

By measuring FD and SD with a common methodological framework, we demonstrate that SD approximates functional patterns in plant communities. Moreover, we show that SD retrieved using high-resolution images can capture different aspects of FD, and that the occupation of the spectral space is analogous to the occupation of the functional space.

A chromosome‐level genome of mango exclusively from long‐read sequence data

Abstract

Improvements in long-read sequencing techniques have greatly accelerated plant genome sequencing. Current de novo assemblies are routinely achieved by assembling long-read sequence data into contigs that are assembled to chromosome level by chromatin conformation capture. We report here a chromosome-level mango genome using only PacBio high-fidelity (HiFi) long reads. HiFi reads at high coverage (204x) resulted in the assembly of 17 chromosomes, each as a single contig with telomeres at both ends. The remaining three chromosomes were represented each by two contigs, with telomeres at one end and ribosomal repeats at the other end. Analyzing contig ends allowed them to be paired and linked to generate the remaining three complete chromosomes, telomere-to-telomere but with ribosomal repeats of uncertain length. The assembled genome was 365 Mb with 100% completeness as assessed by Benchmarking Universal Single-Copy Orthologs analysis. The haplotypes assembled demonstrated extensive structural differences. This approach using very high genome coverage may be useful for assembling high-quality genomes for many other plants.

Cloning and functional analysis of Gb4CL1 and Gb4CL2 from Ginkgo biloba

Abstract

4-Coumarate-CoA ligase (4CL) gene plays vital roles in plant growth and development, especially the regulation of lignin metabolism and flavonoid synthesis. To investigate the potential function of 4CL in the lignin biosynthesis of Ginkgo biloba, this study identified two 4CL genes, Gb4CL1 and Gb4CL2, from G. biloba genome. Based on the phylogenetic tree analysis, Gb4CL1 and Gb4CL2 protein were classified into Class I, which has been confirmed to be involved in lignin biosynthesis. Therefore, it can be inferred that these two genes may also participate in lignin metabolism. The tissue-specific expression patterns of these two genes revealed that Gb4CL1 was highly expressed in microstrobilus, whereas Gb4CL2 was abundant in immature leaves. The onion transient expression assay indicated that Gb4CL1 was predominantly localized in the nucleus, indicating its potential involvement in nuclear functions, while Gb4CL2 was observed in the cell wall, suggesting its role in cell wall-related processes. Phytohormone response analysis revealed that the expression of both genes was upregulated in response to indole acetic acid, while methyl jasmonate suppressed it, gibberellin exhibited opposite effects on these genes. Furthermore, Gb4CL1 and Gb4CL2 expressed in all tissues containing lignin that showed a positive correlation with lignin content. Thus, these findings suggest that Gb4CL1 and Gb4CL2 are likely involved in lignin biosynthesis. Gb4CL1 and Gb4CL2 target proteins were successfully induced in Escherichia coli BL21 with molecular weights of 85.5 and 89.2 kDa, proving the integrity of target proteins. Our findings provided a basis for revealing that Gb4CL participated in lignin synthesis in G. biloba.

Structure, floristic composition, and distribution of swamp forests across a white‐water flood‐plain in the Colombian Amazon

Structure, floristic composition, and distribution of swamp forests across a white-water flood-plain in the Colombian Amazon

We identified three types of swamp forests across the flood-plains of the Caquetá River: permanent várzea, oxandrales and cananguchales. These forests showed successional patterns dissociated from their position relative to the main river channel. Still, they seemed more influenced by the interaction of floodings, sediment and nutrients input from white-water and/or black-water rivers, and peat accumulation.


Abstract

Questions

The fluvial dynamics of meandering white-water rivers of Amazonia drive vegetation primary succession. Directional successional processes have been recorded for the seasonal várzea forests that occupy well-drained soils on levees and point bars across the spatial gradient of the flood-plains. However, the types of forests occupying the swampy depressions interspersed between the point bars and their distribution along the flood-plain's spatial gradient are poorly understood. Here, we aimed to unravel the spatial patterns of swamp forests along the sequence defined by an axis perpendicular to the river and the relationship with edaphic and spatial factors.

Location

The flood-plains of the middle Caquetá River basin, Colombian Amazonia.

Methods

Forest types were identified by cluster analysis performed on 42 square plots (33 m × 33 m) set in poorly drained depressions of the flood-plain. Floristic composition and vegetation structure as response data, and edaphic and spatial variables as predictors, were analyzed through partial redundancy analysis (pRDA). The effect of geographic position was included by using the first two axes of a principal coordinates of neighbor matrix analysis as conditional factors in the pRDA.

Results

The three identified swamp forest types were not arranged along a directional spatial pattern. Permanent várzea forests, closest to the river, showed the greatest diversity and alluvial sediment input. Oxandrales, furthest from the river, dominated by Oxandra polyantha, showed the greatest tree density, basal area and soil sand content, and received additional flooding from black-water streams. Cananguchales, dominated by Mauritia flexuosa, exhibited the highest dominance and soil organic matter layer thickness. Distribution of the permanent várzea and oxandrales was relatively constrained by the distance to the river, whereas that of the cananguchales was not.

Conclusions

Flooding dynamics delay vegetation development of the swamp forests in permanent várzea and oxandrales. Cananguchales keep accumulating organic matter, becoming ombrotrophic peats after isolation from the river flooding influence. The swamp forests across these flood-plains are far from being arranged along a linear sequence.

Leaf trait variation in grassland plant species in response to soil phosphorus

Leaf trait variation in grassland plant species in response to soil phosphorus

This experimental study examines the changes in leaf functional traits in grassland species with different resource-use strategies along a soil phosphorus gradient. Findings indicate that within species there was a more acquisitive trait expression with increased phosphorus and more conservative with increased community biomass. Interestingly, the trait responses were generally consistent for species representing very different resource-use strategies and growth forms. The pictures show four species mixtures before trait measurements and harvest (May 2020).


Abstract

Questions

Increased soil phosphorus (P) availability in fertilized grasslands can drive both community degradation and delayed community recovery upon agricultural abandonment. Beyond describing grassland community patterns along gradients in P availability, it remains unclear how individual species with different strategies respond to increasing phosphorus. Here we studied intraspecific variability of leaf functional traits in response to soil phosphorus, for species with contrasting resource-use strategies.

Methods

We set up a pot experiment with communities containing four species, assembled from a pool of 20 mesotrophic grassland species growing along a soil P gradient. Species selection included various growth forms (grasses vs forbs) and resource-use strategies (acquisitive vs conservative resource use). We measured three variables characterizing the (a)biotic environmental context: bioavailable soil P concentration, total community biomass as a proxy for the intensity of competition, and the proportional biomass of a species in the community as a proxy for its competitive dominance. We investigated the effect of this environmental context on the expression of two leaf traits, specific leaf area (SLA) and leaf dry matter content (LDMC).

Results

We found an acquisitive trait expression within species (increase in SLA and decrease in LDMC) in response to increased soil P supply and a conservative trait expression (decrease in SLA and increase in LDMC) in response to an increase in total community biomass. Importantly, the trait responses to the environmental context were generally consistent for species representing very different resource-use strategies and growth forms.

Conclusions

Species responded with a shift from an acquisitive to a conservative trait expression in response to limited resources; i.e., driven by a decrease in soil phosphorus concentration or an increase in total community biomass. Unexpectedly, the intraspecific variability in response to the changing environmental conditions was not clearly mediated by the species’ strategy. These findings show that plant ecological strategies are probably not the main driver for intraspecific trait variability in an experimental grassland community.

Climbing aroids in a Panamanian lowland forest: We should reconsider our categories

Climbing aroids in a Panamanian lowland forest: We should reconsider our categories

Because of a lack of field data, ontogenetic patterns of herbaceous climbers like germination site and changes in root/shoot connection with the soil remain unclear. We provide rare quantitative data regarding this aspect and species richness and abundance in a tropical lowland forest. Few species fall neatly in the so far applied categories of vines, nomadic vines and hemiepiphytes.


Abstract

Background

In contrast to woody climbers, information on community composition or vertical extension within the forest is scarce for herbaceous climbers, even in well-studied field sites like Barro Colorado Island. Moreover, questions regarding ontogenetic patterns (site of germination, changes in root/shoot connection with the soil) are unresolved because of a lack of field data.

Location

Barro Colorado Island, Panama.

Methods

In 17 plots of 400 m2 each, which were distributed all over the island, we recorded all potential hosts (trees, palms, lianas) with a diameter at breast height larger than 1 cm, and all climbing aroids attached to them. For aroids, we recorded species identity, number of shoots, root connections to the ground, and vertical shoot extension. By distinguishing three size classes for each species in our analyses we deduced the site of germination and ontogenetic changes in the root/shoot connection with the soil.

Results

Only 16% of all potential hosts were occupied by climbing aroids. We recorded 1196 individuals of 17 species. Aroids preferred larger trees and old-growth forest. Species differed strongly in vertical distribution. Hemiepiphytic species germinate epiphytically, often high up in tree crowns and later establish root contact with the soil, while the majority of species establish on or close to the ground and reach moderate heights of 5–15 m (forest height ca. 35 m). In all of these species, we observed dieback of the proximal portion of the shoot to a varying extent but contact with the soil was invariably retained via adventitious roots.

Conclusions

We provide rare quantitative data on species richness and abundance of herbaceous climbers in a tropical lowland forest. Few species fall neatly into the categories of vines, nomadic vines and hemiepiphytes. This highlights the need for longitudinal observational and experimental studies to resolve the current debate on the appropriate grouping of these climbers.

Spatiotemporal patterns of microclimatic buffering in relict alpine communities

Spatiotemporal patterns of microclimatic buffering in relict alpine communities

We investigated the variation of soil microclimate in time and space in a relict alpine system of northern Spain. Spatial microclimatic variation in one year was higher than in 10 years of microclimate monitoring in permanent plots, supporting the buffer effect of topography in alpine landscapes. Protected sites with relatively longer snow cover are key microclimatic refugia for preventing local extinctions.


Abstract

Questions

In alpine landscapes, topography creates a mosaic of microclimatic niches that might prevent local extinctions, but the influence of this spatial heterogeneity on plant communities is largely unknown. Here we ask (1) how soil microclimatic variation is comparable at temporal and spatial scales, and (2) how such variation influences species composition and local extinctions in relict alpine communities.

Location

Picos de Europa National Park, northern Spain.

Methods

We resurveyed permanent plots in four alpine sites following the recording of soil temperatures (temporal survey) for 10 years. We then sampled the spatial variation in species composition and microclimatic temperatures in 80 plots around the permanent plots (spatial survey). We evaluated the variation of six microclimatic indices between the temporal and the spatial surveys, and calculated the temporal trends observed in species cover. We finally predicted local extinction rates under microclimatic scenarios based on the observed microclimate–community relations.

Results

Despite high interannual variation, we found a 10-year trend of temperature warming on (microridge) fellfields and (microvalley) snowbeds. Microclimatic variation was larger in space than in time, with little temperature variation in snowbeds and extreme low temperatures recorded in fellfields. Species composition was mainly influenced by growing degree days (GDD) and freezing degree days (FDD), which were both related to snow cover duration. Plant cover of 16 species (out of 36 frequent species) showed significant responses to microclimatic variation. Local extinctions were mainly predicted under relatively hotter and more freezing conditions.

Conclusions

Our results support the idea that microclimatic spatial heterogeneity can reduce the negative influence of climate change on alpine plant communities. However, a continuous reduction of snow cover will result in a tipping point beyond which the buffer effect of this spatial heterogeneity will not be effective in protected microsites, leading to community homogenization. This process may have started in relict alpine communities where species from snowy microclimates are being outcompeted by species adapted to below-zero winter temperatures.