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Genome size evolution of the extant lycophytes and ferns
No full textFerns and lycophytes have remarkably large genomes. However, little is known about how their genome size evolved in fern lineages. To explore the origins and evolution of chromosome numbers and genome size in ferns, we used flow cytometry to measure the genomes of 240 species (255 samples) of extant ferns and lycophytes comprising 27 families and 72 genera, of which 228 species (242 samples) represent new reports. We analyzed correlations among genome size, spore size, chromosomal features, phylogeny, and habitat type preference within a phylogenetic framework. We also applied ANOVA and multinomial logistic regression analysis to preference of habitat type and genome size. Using the phylogeny, we conducted ancestral character reconstruction for habitat types and tested whether genome size changes simultaneously with shifts in habitat preference. We found that 2C values had weak phylogenetic signal, whereas the base number of chromosomes (x) had a strong phylogenetic signal. Furthermore, our analyses revealed a positive correlation between genome size and chromosome traits, indicating that the base number of chromosomes (x), chromosome size, and polyploidization may be primary contributors to genome expansion in ferns and lycophytes. Genome sizes in different habitat types varied significantly and were significantly correlated with habitat types; specifically, multinomial logistic regression indicated that species with larger 2C values were more likely to be epiphytes. Terrestrial habitat is inferred to be ancestral for both extant ferns and lycophytes, whereas transitions to other habitat types occurred as the major clades emerged. Shifts in habitat types appear be followed by periods of genomic stability. Based on these results, we inferred that habitat type changes and multiple whole-genome duplications have contributed to the formation of large genomes of ferns and their allies during their evolutionary history. Copyright ?? 2022 Kunming Institute of Botany, Chinese Academy of Sciences. Publishing services by Elsevier B.V. on behalf of KeAi Communications Co. Ltd. This is an open access article under the CC BY NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/)
Dynamics of soil aggregate-associated carbon as influenced by simulated tillage and runoff
No full textTillage practices and water erosion are the most important anthropogenic and natural processes, respectively, driving soil organic C turnover in agricultural land. The aim of this study was to explore the responses of soil organic C (SOC) turnover to tillage and runoff by comparing the variation of soil aggregate-associated organic C (AOC) and intra-aggregate particulate organic C (iPOC) under simulated tillage and runoff conditions. Soil samples were collected from a native vegetation land with no cultivation history in the Mollisol region of Northeast China. After a series of simulated tillage (ST) and simulated runoff (SR) treatments, the samples were incubated for 30 d and then separated through 2-, 1-, 0.25-, and 0.053-mm sieves by wet-sieving to obtain different aggregate size fractions. Each aggregate fraction was subsequently shaken for 18 h in 0.5% hexametaphosphate to get different intra-aggregate particle size fractions. The proportion of the fractions and their AOC and iPOC were determined. The ST treatment promoted the reaggregation of macroaggregates (>2 mm) by accelerating the turnover of their coarse iPOC (0.25-2 mm), leading to a lower concentration of AOC. Runoff transformed larger aggregates (>0.25 mm) to smaller particles (1 mm) dynamics, especially associated with tillage operations. Our findings highlight the different influences of tillage and runoff, and the negative effect of tillage on SOC dynamics
Hydrothermal conditions determine soil potential net N mineralization rates in arid and semi-arid grasslands
No full textSoil net nitrogen (N) mineralization is a key biogeochemical process influencing plant available N and net primary productivity in terrestrial ecosystems. However, the spatial variations and controlling factors of soil net N mineralization (R-PNM) in arid and semi-arid grasslands are less studied and unclear. In this study, we investigated the soil R-PNM by performing a laboratory incubation experiment. Soil samples were collected from 30 sites in three east-west transects on the Inner Mongolia Plateau (MP), Loess Plateau (LP) and Tibetan Plateau (TP) along a 3200 km arid and semi-arid grassland gradient, with each transect containing three different grassland types (meadow steppe [MS], typical steppe [TS] and desert steppe [DS], respectively). Results showed that the average R-PNM values ranged from -0.37 to 1.29 mg N kg(-1) day(-1), with a significantly lower R-PNM found in the DS (0.08 +/- 0.01 mg N kg(-1) day(-1)) compared with those in the MS (0.30 +/- 0.03 mg N kg(-1) day(-1)) and in the TS (0.33 +/- 0.03 mg N kg(-1) day(-1)) in the MP and LP transects (p < 0.05). This difference could be explained by variations in climatic and soil factors, such as hydrothermal index (HT), the soil pH, soil organic matter (SOM) and precipitation. However, no significant differences in R-PNM were found among different grassland types in the TP transect, possibly due to the similarly low microbial activity, as indicated by the microbial biomass carbon values. Across all three grassland transects, HT, SOM and microbial variables were the major factors controlling R-PNM, which together explained 20.7% of the variation in R-PNM. Further structural equation model analysis indicated HT was an integral predictor of R-PNM, directly or indirectly via SOM, under different conditions of precipitation and temperature. Our findings provide field evidence and parameters for biogeochemical cycling to better predict future N transformation processes under changing precipitation and temperature regimes across a wide range of arid and semi-arid grassland ecosystems. Read the free Plain Language Summary for this article on the Journal blog
Genomes shed light on the evolution of Begonia, a mega-diverse genus
No full textClarifying the evolutionary processes underlying species diversification and adaptation is a key focus of evolutionary biology. Begonia (Begoniaceae) is one of the most species-rich angiosperm genera with c. 2000 species, most of which are shade-adapted. Here, we present chromosome-scale genome assemblies for four species of Begonia (B. loranthoides, B. masoniana, B. darthvaderiana and B. peltatifolia), and whole genome shotgun data for an additional 74 Begonia representatives to investigate lineage evolution and shade adaptation of the genus. The four genome assemblies range in size from 331.75 Mb (B. peltatifolia) to 799.83 Mb (B. masoniana), and harbor 22 059-23 444 protein-coding genes. Synteny analysis revealed a lineage-specific whole-genome duplication (WGD) that occurred just before the diversification of Begonia. Functional enrichment of gene families retained after WGD highlights the significance of modified carbohydrate metabolism and photosynthesis possibly linked to shade adaptation in the genus, which is further supported by expansions of gene families involved in light perception and harvesting. Phylogenomic reconstructions and genomics studies indicate that genomic introgression has also played a role in the evolution of Begonia. Overall, this study provides valuable genomic resources for Begonia and suggests potential drivers underlying the diversity and adaptive evolution of this mega-diverse clade
Plastome-based phylogeny improves community phylogenetics of subtropical forests in China
No full textPhylogenetic trees have been extensively used in community ecology. However, how the phylogeny construction affects ecological inferences is poorly understood. In this study, we constructed three different types of phylogenetic trees (a synthetic-tree generated using V.PhyloMaker, a barcode-tree generated using rbcL+matK+trnH-psbA, and a plastome-tree generated from plastid genomes) that represented an increasing level of phylogenetic resolution among 580 woody plant species from six forest dynamic plots in subtropical evergreen broadleaved forests of China. We then evaluated the performance of each phylogeny in estimations of community phylogenetic structure, turnover and phylogenetic signal in functional traits. As expected, the plastome-tree was most resolved and most supported for relationships among species. For local phylogenetic structure, the three trees showed consistent results with Faith's PD and MPD; however, only the synthetic-tree produced significant clustering patterns using MNTD for some plots. For phylogenetic turnover, contrasting results between the molecular trees and the synthetic-tree occurred only with nearest neighbor distance. The barcode-tree agreed more with the plastome-tree than the synthetic-tree for both phylogenetic structure and turnover. For functional traits, both the barcode-tree and plastome-tree detected phylogenetic signal in maximum height, but only the plastome-tree detected signal in leaf width. This is the first study that uses plastid genomes in large-scale community phylogenetics. Our results highlight the improvement of plastome-trees over barcode-trees and synthetic-trees for the analyses studied here. Our results also point to the possibility of type I and II errors in estimation of phylogenetic structure and turnover and detection of phylogenetic signal when using synthetic-trees
Genome-wide association study reveals a NAC transcription factor TaNAC074 linked to pre-harvest sprouting tolerance in wheat
No full textKey message Twelve QTL associated with pre-harvest sprouting tolerance were identified using association analysis in wheat. Two markers were validated and a candidate gene TaNAC074 for Qgpf.cas-3B.2 was verified using Agrobacterium-mediated transformation. Pre-harvest sprouting (PHS) is a considerable global threat to wheat yield and quality. Due to this threat, breeders must identify quantitative trait loci (QTL) and genes conferring PHS-tolerance (PHST) to reduce the negative effects of PHS caused by low seed dormancy. In this study, we evaluated a panel of 302 diverse wheat genotypes for PHST in four environments and genotyped the panel with a high-density wheat 660 K SNP array. By using a genome-wide association study (GWAS), we identified 12 stable loci significantly associated with PHST (P < 0.0001), explaining 3.34 - 9.88% of the phenotypic variances. Seven of these loci co-located with QTL and genes reported previously. Five loci (Qgpf.cas-3B.2, Qgpf.cas-3B.3, Qgpf.cas-3B.4, Qgpf.cas-7B.2, and Qgpf.cas-7B.3), located in genomic regions with no known PHST QTL or genes, are likely to be new QTL conferring PHST. Additionally, two molecular markers were developed for Qgpf.cas-3A and Qgpf.cas-7B.3, and validated using a different set of 233 wheat accessions. Finally, the PHST-related function of candidate gene TaNAC074 for Qgpf.cas-3B.2 was confirmed by CAPS (cleaved amplified polymorphic sequences) marker association analysis in 233 wheat accessions and by expression and phenotypic analysis of transgenic wheat. Overexpression of TaNAC074 significantly reduced seed dormancy in wheat. This study contributes to broaden the genetic basis and molecular marker-assisted breeding of PHST
Effects of grazing intensity on soil nematode community structure and function in different soil layers in a meadow steppe
No full textAims Grazing is a key driver of plant communities and soil functions in grassland ecosystems. Soil nematodes play a vital role in soil ecological functions. The aim of this study was to explore how grazing shapes soil nematode community in different soil layers. Methods We investigated the composition, abundance, diversity, metabolic footprint, and food web metrics of soil nematodes over a gradient of grazing in the 0-10 cm and 10-20 cm soil layers in a meadow steppe. The relationships between nematode community structure and biotic and abiotic factors were analyzed by principal component analysis and structural equation model analysis. Results Light grazing increased the abundance of total soil nematodes by 18.5%. Intensive grazing decreased the carbon used in production and metabolic footprints of plant parasites, fungivores, and total soil nematodes in 0-10 cm soils. There was no difference in the carbon used in production and metabolic footprints of soil nematodes among different grazing intensities in the 10-20 cm soil layer. Soil moisture, aboveground biomass, belowground biomass and Shannon diversity of grass contributed more to changes in soil nematode composition in both soil layers. In the 0-10 cm soil layer, grazing directly and indirectly affected soil nematode diversity via soil moisture and aboveground biomass, while grazing directly affected soil nematode diversity in 10-20 cm soil layer. Conclusions Our results indicate that increasing soil depth can weaken the effect of grazing intensities on soil nematode fauna. Grazing affected the soil nematode community structure via different paths in different soil layers
The RNA helicase UAP56 and the E3 ubiquitin ligase COP1 coordinately regulate alternative splicing to repress photomorphogenesis in Arabidopsis
No full textLight is a key environmental signal that regulates plant growth and development. While posttranscriptional regulatory mechanisms of gene expression include alternative splicing (AS) of pre-messenger RNA (mRNA) in both plants and animals, how light signaling affects AS in plants is largely unknown. Here, we identify DExD/H RNA helicase U2AF65-associated protein (UAP56) as a negative regulator of photomorphogenesis in Arabidopsis thaliana. UAP56 is encoded by the homologs UAP56a and UAP56b. Knockdown of UAP56 led to enhanced photomorphogenic responses and diverse developmental defects during vegetative and reproductive growth. UAP56 physically interacts with the central light signaling repressor constitutive photomorphogenic 1 (COP1) and U2AF65. Global transcriptome analysis revealed that UAP56 and COP1 co-regulate the transcription of a subset of genes. Furthermore, deep RNA-sequencing analysis showed that UAP56 and COP1 control pre-mRNA AS in both overlapping and distinct manners. Ribonucleic acid immunoprecipitation assays showed that UAP56 and COP1 bind to common small nuclear RNAs and mRNAs of downstream targets. Our study reveals that both UAP56 and COP1 function as splicing factors that coordinately regulate AS during light-regulated plant growth and development. The RNA helicase UAP56 and the E3 ubiquitin ligase COP1 function as splicing factors to coordinately regulate alternative splicing during light-regulated plant growth and development
Nitrogen input enhances microbial carbon use efficiency by altering plant-microbe-mineral interactions
No full textMicrobial growth and respiration are at the core of the soil carbon (C) cycle, as these microbial physiological performances ultimately determine the fate of soil C. Microbial C use efficiency (CUE), a critical metric to characterize the partitioning of C between microbial growth and respiration, thus controls the sign and magnitude of soil C-climate feedback. Despite its importance, the response of CUE to nitrogen (N) input and the relevant regulatory mechanisms remain poorly understood, leading to large uncertainties in predicting soil C dynamics under continuous N input. By combining a multi-level field N addition experiment with a substrate-independent O-18-H2O labelling approach as well as high-throughput sequencing and mineral analysis, here we elucidated how N-induced changes in plant-microbial-mineral interactions drove the responses of microbial CUE to N input. We found that microbial CUE increased significantly as a consequence of enhanced microbial growth after 6-year N addition. In contrast to the prevailing view, the elevated microbial growth and CUE were not mainly driven by the reduced stoichiometric imbalance, but strongly associated with the increased soil C accessibility from weakened mineral protection. Such attenuated organo-mineral association was further linked to the N-induced changes in the plant community and the increased oxalic acid in the soil. These findings provide empirical evidence for the tight linkage between mineral-associated C dynamics and microbial physiology, highlighting the need to disentangle the complex plant-microbe-mineral interactions to improve soil C prediction under anthropogenic N input
Phytoremediation of pollutants from wastewater: A concise review
No full textAs there is a global water crisis facing the whole world, it is important to find alternative solutions to treat wastewater for reuse. Hence, plants have an effective role in removing pollutants from wastewater, which has been emphasized in this review article. Biological treatment of wastewater can be considered an eco-friendly and cost-effective process that depends on in the future. Living organisms, including plants, can remediate pollutants in wastewater, especially in agricultural fields, such as dyes, heavy metals, hydrocarbons, pharmaceuticals, and pesticides. This review discusses the different activities of plants in pollutant elimination from wastewater and sheds light on the utilization of plants in this scope. This review focuses on the remediation of the most common contaminants present in wastewater, which are difficult to the removal with microorganisms, such as bacteria, fungi, and algae. Moreover, it covers the major role of plants in wastewater treatment and the potential of phytoremediation as a possible solution for the global water crisis