The adaptive value of transgenerational effects (the ancestor environmental effects on offspring) in changing environments has received much attention in recent years, but the related empirical ...evidence remains equivocal. Here, we conducted a meta‐analysis summarising 139 experimental studies in plants and animals with 1170 effect sizes to investigate the generality of transgenerational effects across taxa, traits, and environmental contexts. It was found that transgenerational effects generally enhanced offspring performance in response to both stressful and benign conditions. The strongest effects are in annual plants and invertebrates, whereas vertebrates appear to benefit mostly under benign conditions, and perennial plants show hardly any transgenerational responses at all. These differences among taxonomic/life‐history groups possibly reflect that vertebrates can avoid stressful conditions through their mobility, and longer‐lived plants have alternative strategies. In addition to environmental contexts and taxonomic/life‐history groups, transgenerational effects also varied among traits and developmental stages of ancestors and offspring, but the effects were similarly strong across three generations of offspring. By way of a more comprehensive data set and a different effect size, our results differ from those of a recent meta‐analysis, suggesting that transgenerational effects are widespread, strong and persistent and can substantially impact the responses of plants and animals to changing environments.
The Avicennia marina is a mangrove species widely distributed throughout the tropical and subtropical intertidal wetlands. To adapt to adverse tidal waves and hypoxia environments, A. marina has ...evolved a sophisticated root system to better secure itself on the muddy soil with downward-grown anchor roots and upward-grown aerial roots, called pneumatophores. However, the process behind the development of a negative-gravitropic pneumatophore is not understood. Paraffin sections reveal anatomical differences among the shoots, anchor roots, and gas exchanging pneumatophores, clearly reflecting their functional diversions. The pneumatophore, in particular, contains abundant aerenchyma tissues and a thin cap structure at the tip. Transcriptomic analyses of both anchor roots and pneumatophores were performed to elucidate gene expression dynamics during the formation of pneumatophores. The results show that the plant hormone auxin regulates multiple different root initiations. The auxin related gene IAA19 plays a key role in pneumatophore development while the interaction of ethylene and abscisic acid is important for aerenchyma formation. Moreover, the molecular mechanisms behind pneumatophore anti-gravitropic growth may be regulated by the reduced strength of the statolith formation signaling pathway. These results shed light on the mechanistic understanding of pneumatophore formation in mangrove plants.
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•The actions of plant hormone auxin regulate pneumatophore and anchor root initiations.•Pneumatophore negative gravitropism may be due to less statolith contents.•Ethylene and ABA play key roles in the formation of aerenchyma of the A. marina root system.
Silver nanoparticles (AgNPs) are widely used in medical and commercial products for their unique antibacterial functions. However, the impact of AgNPs on human neural development is not well ...understood. To investigate the effect of AgNPs on human neural development, various doses of 20 nm citrate-coated AgNP (AgSC) were administered to human embryonic stem cell derived neural progenitors during the neuronal differentiation. Immunofluorescence staining with neuronal progenitor markers SOX2 (sex determining region Y-box 2) and Nestin (VI intermediate filament protein) showed that AgSC inhibited rosette formation, neuronal progenitor proliferation, and neurite outgrowth. Furthermore, AgSC promoted astrocyte activation and neuronal apoptosis. These adverse effects can be partially recovered with ascorbic acid. A genome-wide transcriptome analysis of both AgSC treated and untreated samples indicated that the most up-graduated genes were a group of Metallothionein (1F, 1E, 2A) proteins, a metal-binding protein that plays an essential role in metal homeostasis, heavy metal detoxification, and cellular anti-oxidative defence. The most significantly down-regulated genes were neuronal differentiation 6 (NEUROD6) and fork head box G1 (FOXG1). GO analyse indicated that the regulation of cholesterol biosynthetic process, neuron differentiation, synapse organization and pattern specification, oliogenesis, and neuronal apoptosis were the most impacted biological processes. KEGG pathway analyse showed that the most significantly impacted pathways were C5 isoprenoid, axon guidance, Notch, WNT, RAS-MAPK signalling pathways, lysosome, and apoptosis. Our data suggests that AgSCs interfered with metal homeostasis and cholesterol biosynthesis which induced oxidative stress, inhibited neurogenesis, axon guidance, and promoted apoptosis. Supplementation with ascorbic acid could act as an antioxidant to prevent AgSC-mediated neurotoxicity.
Genetic admixture, the intraspecific hybridization among divergent introduced sources, can immediately facilitate colonization via hybrid vigor and profoundly enhance invasion via contributing novel ...genetic variation to adaption. As hybrid vigor is short‐lived, provisioning adaptation is anticipated to be the dominant and long‐term profit of genetic admixture, but the evidence for this is rare. We employed the 30 years' geographic‐scale invasion of the salt marsh grass, Spartina alterniflora, as an evolutionary experiment and evaluated the consequences of genetic admixture by combining the reciprocal transplant experiment with quantitative and population genetic surveys. Consistent with the documentation, we found that the invasive populations in China had multiple origins from the southern Atlantic coast and the Gulf of Mexico in the US. Interbreeding among these multiple sources generated a “hybrid swarm” that spread throughout the coast of China. In the northern and mid‐latitude China, natural selection greatly enhanced fecundity, plant height and shoot regeneration compared to the native populations. Furthermore, genetic admixture appeared to have broken the negative correlation between plant height and shoot regeneration, which was genetically‐based in the native range, and have facilitated the evolution of super competitive genotypes in the invasive range. In contrast to the evolved northern and mid‐latitude populations, the southern invasive populations showed slight increase of plant height and shoot regeneration compared to the native populations, possibly reflecting the heterotic effect of the intraspecific hybridization. Therefore, our study suggests a critical role of genetic admixture in accelerating the geographic invasion via provisioning rapid adaptive evolution.
Alternative polyadenylation (APA) has been shown to play an important role in gene expression regulation in animals and plants. However, the extent of sense and antisense APA at the genome level is ...not known. We developed a deep-sequencing protocol that queries the junctions of 3′UTR and poly(A) tails and confidently maps the poly(A) tags to the annotated genome. The results of this mapping show that 70% of Arabidopsis genes use more than one poly(A) site, excluding microheterogeneity. Analysis of the poly(A) tags reveal extensive APA in introns and coding sequences, results of which can significantly alter transcript sequences and their encoding proteins. Although the interplay of intron splicing and polyadenylation potentially defines poly(A) site uses in introns, the polyadenylation signals leading to the use of CDS protein-coding region poly(A) sites are distinct from the rest of the genome. Interestingly, a large number of poly(A) sites correspond to putative antisense transcripts that overlap with the promoter of the associated sense transcript, a mode previously demonstrated to regulate sense gene expression. Our results suggest that APA plays a far greater role in gene expression in plants than previously expected.
The architecture of inflorescence in crops is a key agronomic feature determining grain yield and thus has been a major target trait of cereal domestication.
In this study, we show that a simple ...spreading panicle change in rice panicle shape, controlled by the Spreading Panicle 9 (SPR9) locus, also has a significant impact on the resistance to rice false smut (RFS). Meanwhile, we mapped a novel spr9 mutant gene between markers Indel5-18 and Indel5-22 encompassing a genomic region of 43-kb with six candidate genes. Through gene prediction and cDNA sequencing, we confirmed that LOC_Os05g38520 is the target gene in the spr9 mutant, which encodes 60 S ribosomal protein L36-2. Further analysis showed that the spr9 mutant is caused by a 1 bp deletion in the first exon that resulted in premature termination. Knockout experiments showed that the SPR9 gene is responsible for the spreading panicle phenotype of the spr9 mutant. Interestingly, the spr9 mutant was found to improve resistance to RFS without affecting major agronomic traits. Taken together, our results revealed that the spr9 allele has good application prospects in rice breeding for disease resistance and panicle improvement.
We report the map-based cloning and functional characterization of SPR9, which encodes a 60 S ribosomal protein that regulates spreading panicles and affects the resistance to false smut in rice.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
SUMMARY
Because allohexaploid wheat genome contains ABD subgenomes, how the expression of homoeologous genes is coordinated remains largely unknown, particularly at the co‐transcriptional level. ...Alternative polyadenylation (APA) is an important part of co‐transcriptional regulation, which is crucial in developmental processes and stress responses. Drought stress is a major threat to the stable yield of wheat. Focusing on APA, we used poly(A) tag sequencing to track poly(A) site dynamics in wheat under drought stress. The results showed that drought stress led to extensive APA involving 37–47% of differentially expressed genes in wheat. Significant poly(A) site switching was found in stress‐responsive genes. Interestingly, homoeologous genes exhibit unequal numbers of poly(A) sites, divergent APA patterns with tissue specificity and time‐course dynamics, and distinct 3′‐UTR length changes. Moreover, differentially expressed transcripts in leaves and roots used different poly(A) signals, the up‐ and downregulated isoforms had distinct preferences for non‐canonical poly(A) sites. Genes that encode key polyadenylation factors showed differential expression patterns under drought stress. In summary, poly(A) signals and the changes in core poly(A) factors may widely affect the selection of poly(A) sites and gene expression levels during the response to drought stress, and divergent APA patterns among homoeologous genes add extensive plasticity to this responsive network. These results not only reveal the significant role of APA in drought stress response, but also provide a fresh perspective on how homoeologous genes contribute to adaptability through transcriptome diversity. In addition, this work provides information about the ends of transcripts for a better annotation of the wheat genome.
Significance Statement
The functional conservation and divergence in a polyploidy genome across the subgenomes of wheat have always been intriguing. From the angle of APA, this work not only reveals the widespread occurrence of APA in the allohexaploid wheat and the important role it plays, but also broadens the knowledge of how homoeologous genes contribute to the adaptability and transcriptional plasticity in a polyploidy genome through RNA processing.
Parental or ancestral environments can induce heritable phenotypic changes, but whether such environment-induced heritable changes are a common phenomenon remains unexplored. Here, we subject 14 ...genotypes of Arabidopsis thaliana to 10 different environmental treatments and observe phenotypic and genome-wide gene expression changes over four successive generations. We find that all treatments caused heritable phenotypic and gene expression changes, with a substantial proportion stably transmitted over all observed generations. Intriguingly, the susceptibility of a genotype to environmental inductions could be predicted based on the transposon abundance in the genome. Our study thus challenges the classic view that the environment only participates in the selection of heritable variation and suggests that the environment can play a significant role in generating of heritable variations.
Eukaryotic histone deacetylation, critical for maintaining nucleosome structure and regulating gene expression, is mediated by histone deacetylases (HDACs). Although nucleosomes have been reported to ...regulate mRNA polyadenylation in humans, the role of HDACs in regulating polyadenylation has not been uncovered. Taking advantage of phenotypic studies on
, HDA6 (one of HDACs) was found to be a critical part of many biological processes. Here, we report that HDA6 affects mRNA polyadenylation in
Poly(A) sites of up-regulated transcripts are closer to the histone acetylation peaks in
compared to the wild-type Col-0. HDA6 is required for the deacetylation of histones around DNA on nucleosomes, which solely coincides with up-regulated or uniquely presented poly(A) sites in
Furthermore, defective HDA6 results in an overrepresentation of the canonical poly(A) signal (AAUAAA) usage. Chromatin loci for generating AAUAAA-type transcripts have a comparatively low H3K9K14ac around poly(A) sites when compared to other noncanonical poly(A) signal-containing transcripts. These results indicate that HDA6 regulates polyadenylation in a histone deacetylation-dependent manner in
.
Summary
Auxin is widely involved in plant growth and development. However, the molecular mechanism on how auxin carries out this work is unclear. In particular, the effect of auxin on pre‐mRNA ...post‐transcriptional regulation is mostly unknown. By using a poly(A) tag (PAT) sequencing approach, mRNA alternative polyadenylation (APA) profiles after auxin treatment were revealed. We showed that hundreds of poly(A) site clusters (PACs) are affected by auxin at the transcriptome level, where auxin reduces PAC distribution in 5′‐untranslated region (UTR), but increases in the 3′UTR. APA site usage frequencies of 42 genes were switched by auxin, suggesting that auxin affects the choice of poly(A) sites. Furthermore, poly(A) signal selection was altered after auxin treatment. For example, a mutant of poly(A) signal binding protein CPSF30 showed altered sensitivity to auxin treatment, indicating interactions between auxin and the poly(A) signal recognition machinery. We also found that auxin activity on lateral root development is likely mediated by altered expression of ARF7, ARF19 and IAA14 through poly(A) site switches. Our results shed light on the molecular mechanisms of auxin responses relative to its interactions with mRNA polyadenylation.
Significance Statement
Although auxin and polyadenylation are both widely involved in plant growth and development, studies reporting the function of auxin in this post‐transcriptional process are few. Our findings uncover the role of auxin on plant growth and development through affecting mRNA post‐transcriptional polyadenylation process.
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