Hidden Compositional Heterogeneity of Fish Chromosomes in the Era of Polished Genome Assemblies

Fish chromosomes are considered homogeneous in their AT/GC nucleotide composition, and banding patterns enabling identification of homologs are largely missing. While cytogenomic approaches try to compensate for this issue by virtual karyotyping, they rely on the quality of genome assemblies available. Recently, soft-masked genome assemblies combining costly and arduous long- and short-read sequencing and new generation assemblers became available for two teleost fish species, climbing perch (Anabas testudineus) and channel bull blenny (Cottoperca gobio). Soft-masking turns repetitive sequences in a genome assembly into lower case letters, leaving unique sequences in upper case. This enables investigators to assess the proportion of guanine and cytosine nucleotides (GC%) of transposable elements as an indicator of AT/GC homogenisation in fish. We have developed a new version of our Python tool Evan, which utilises chromosome-level genome assemblies and combines the profiles of GC% and the proportion of repeats (rep%) along chromosomes. Our profiles of both of those fishes showed clear and abrupt but small-scale fluctuations in GC% along otherwise compositionally homogenised sequences. Our study also highlights the key role of the sliding window size in determining the resolution of GC% profiling. While the quality of the genome assemblies appeared to be sufficient for GC%/rep% profiling, more effective repeat masking is necessary to better distinguish to what extent repeats compositionally homogenize fish genomes.journal articl

Compared to conventional, ecological intensive management promotes beneficial proteolytic soil microbial communities for agro-ecosystem functioning under climate change-induced rain regimes

Projected climate change and rainfall variability will affect soil microbial communities, biogeochemical cycling and agriculture. Nitrogen (N) is the most limiting nutrient in agroecosystems and its cycling and availability is highly dependent on microbial driven processes. In agroecosystems, hydrolysis of organic nitrogen (N) is an important step in controlling soil N availability. We analyzed the effect of management (ecological intensive vs. conventional intensive) on N-cycling processes and involved microbial communities under climate change-induced rain regimes. Terrestrial model ecosystems originating from agroecosystems across Europe were subjected to four different rain regimes for 263 days. Using structural equation modelling we identified direct impacts of rain regimes on N-cycling processes, whereas N-related microbial communities were more resistant. In addition to rain regimes, management indirectly affected N-cycling processes via modifications of N-related microbial community composition. Ecological intensive management promoted a beneficial N-related microbial community composition involved in N-cycling processes under climate change-induced rain regimes. Exploratory analyses identified phosphorus-associated litter properties as possible drivers for the observed management effects on N-related microbial community composition. This work provides novel insights into mechanisms controlling agro-ecosystem functioning under climate change

Soil microclimate changes affect soil fungal communities in a Mediterranean pine forest

Soil microclimate is a potentially important regulator of the composition of plant‐associated fungal communities in climates with significant drought periods. Here, we investigated the spatio‐temporal dynamics of soil fungal communities in a Mediterranean Pinus pinaster forest in relation to soil moisture and temperature. Fungal communities in 336 soil samples collected monthly over 1 year from 28 long‐term experimental plots were assessed by PacBio sequencing of ITS2 amplicons. Total fungal biomass was estimated by analysing ergosterol. Community changes were analysed in the context of functional traits. Soil fungal biomass was lowest during summer and late winter and highest during autumn, concurrent with a greater relative abundance of mycorrhizal species. Intra‐annual spatio‐temporal changes in community composition correlated significantly with soil moisture and temperature. Mycorrhizal fungi were less affected by summer drought than free‐living fungi. In particular, mycorrhizal species of the short‐distance exploration type increased in relative abundance under dry conditions, whereas species of the long‐distance exploration type were more abundant under wetter conditions. Our observations demonstrate a potential for compositional and functional shifts in fungal communities in response to changing climatic conditions. Free‐living fungi and mycorrhizal species with extensive mycelia may be negatively affected by increasing drought periods in Mediterranean forest ecosystems.info:eu-repo/semantics/acceptedVersio

Large-scale genome sequencing of mycorrhizal fungi provides insights into the early evolution of symbiotic traits

Mycorrhizal fungi are mutualists that play crucial roles in nutrient acquisition in terrestrial ecosystems. Mycorrhizal symbioses arose repeatedly across multiple lineages of Mucoromycotina, Ascomycota, and Basidiomycota. Considerable variation exists in the capacity of mycorrhizal fungi to acquire carbon from soil organic matter. Here, we present a combined analysis of 135 fungal genomes from 73 saprotrophic, endophytic and pathogenic species, and 62 mycorrhizal species, including 29 new mycorrhizal genomes. This study samples ecologically dominant fungal guilds for which there were previously no symbiotic genomes available, including ectomycorrhizal Russulales, Thelephorales and Cantharellales. Our analyses show that transitions from saprotrophy to symbiosis involve (1) widespread losses of degrading enzymes acting on lignin and cellulose, (2) co-option of genes present in saprotrophic ancestors to fulfill new symbiotic functions, (3) diversification of novel, lineage-specific symbiosis-induced genes, (4) proliferation of transposable elements and (5) divergent genetic innovations underlying the convergent origins of the ectomycorrhizal guild. Mycorrhizal symbioses have evolved repeatedly in diverse fungal lineages. A large phylogenomic analysis sheds light on genomic changes associated with transitions from saprotrophy to symbiosis, including divergent genetic innovations underlying the convergent origins of the ectomycorrhizal guild.Peer reviewe

Molecular biology and ecology of microbial decomposition of plant-derived biopolymers in forest ecosystems

The abilities of fungi and bacteria to degrade simple and complex carbon compounds derived from different sources, such as root exudates, litter, soil organic matter or fungal mycelium were studied in this dissertation. Knowledge of functional traits, especially degradation abilities of fungi and bacteria, are important for deciphering the black box of microbial functioning in topsoil and thus aiding in modeling and predicting future directions of microbial communities development in face of global changes. Among fungal cultures form culture collection representing strains with different taxonomy and ecophysiology, the ecophysiology of fungi was more important in manifestation of functional traits than taxonomy. Among bacterial isolates from the litter and soil of spruce forest, Acidobacteria were confirmed to express multiple decomposition enzymes in high rates in vitro and were also abundant and active degraders in acidic spruce forest soil. The expression of degradation capacities of both bacteria and fungi were further studied in situ in spruce forest topsoil, that represents an important environment due to the ubiquity of coniferous forests on the Northern hemisphere. There is an obvious gap of knowledge, when comes to our understanding of seasonal effect on microbial functioning, and this is..

Single nucleotide polymorphism as a biomarker of colorectal cancer predispositon

Department of Cell BiologyKatedra buněčné biologieFaculty of SciencePřírodovědecká fakult

Single nucleotide polymorphism as a biomarker of colorectal cancer predispositon

Department of Cell BiologyKatedra buněčné biologieFaculty of SciencePřírodovědecká fakult

Data from: The rpb2 gene represents a viable alternative molecular marker for the analysis of environmental fungal communities

Although the commonly used internal transcribed spacer region of rDNA (ITS) is well suited for taxonomic identification of fungi, the information on the relative abundance of taxa and diversity is negatively affected by the multicopy nature of rDNA and the existence of ITS paralogues. Moreover, due to high variability, ITS sequences cannot be used for phylogenetic analyses of unrelated taxa. The part of single-copy gene encoding the second largest subunit of RNA polymerase II (rpb2) was thus compared with first spacer of ITS as an alternative marker for the analysis of fungal communities in spruce forest topsoil, and their applicability was tested on a comprehensive mock community. In soil, rpb2 exhibited broad taxonomic coverage of the entire fungal tree of life including basal fungal lineages. The gene exhibited sufficient variation for the use in phylogenetic analyses and taxonomic assignments, although it amplifies also paralogues. The fungal taxon spectra obtained with rbp2 region and ITS1 corresponded, but sequence abundance differed widely, especially in the basal lineages. The proportions of OTU counts and read counts of major fungal groups were close to the reality when rpb2 was used as a molecular marker while they were strongly biased towards the Basidiomycota when using the ITS primers ITS1/ITS4. Although the taxonomic placement of rbp2 sequences is currently more difficult than that of the ITS sequences, its discriminative power, quantitative representation of community composition and suitability for phylogenetic analyses represent significant advantages