Stress responses of plants through transcriptome plasticity by mRNA alternative polyadenylation

Climate change affects the suitability of Chinese cherry (Prunus pseudocerasus Lindl.) in China

The rapid development of Prunus pseudocerasus related industry has increasingly contributed to rural vitalization in China. This study employed a biomod2 ensemble model, utilizing environmental and species occurrence data from 151 P. pseudocerasus germplasm wild/local samples, to predict potential geographical distribution, suitability changes, climate dependence, and ecological niche dynamics. The optimized maximum entropy (MaxEnt) model yielded the most accurate predictions. The climate variables with the greatest impact on suitability were precipitation of warmest quarter and mean diurnal temperature range. The total potential suitable area for P. pseudocerasus was approximately 2.78 × 106 km2, increasing with CO2 concentration. The highly suitable area was primarily concentrated in basin terrains, plateaus, and plains of Sichuan Province. The current centroid in Lichuan exhibited gradual latitudinal and longitudinal movement. The predicted (2090s) ecological niche trends of P. pseudocerasus varied under different pathways and periods, with higher CO2 concentration associated with lower niche overlap. The CO2 emission concentration in the SSP246 scenario emerged as the most suitable climate model. Climate change is driving both the expansion of geographical distribution and the contraction of overlapping geographical distribution areas of P. pseudocerasus. These findings provide a theoretical basis for wild resource conservation, site selection for production, and introduction of allopatry for P. pseudocerasus.

Revisiting CPSF30-mediated alternative polyadenylation in Arabidopsis thaliana

Alternative polyadenylation (APA) is an important contributor to the regulation of gene expression in plants. One subunit of the complex that cleaves and polyadenylates mRNAs in the nucleus, CPSF30 (for the 30 kD subunit of the mammalian Cleavage and Polyadenylation Specificity Factor), has been implicated in a wide-ranging network of regulatory events. CPSF30 plays roles in root development, flowering time, and response to biotic and abiotic stresses. CPSF30 also is a conduit that links cellular signaling and RNA modification with alternative RNA processing events and transcriptional dynamics. While much is known about CPSF30 and its roles in plants, questions remain regarding the connections between CPSF30-mediated APA and the downstream events that lead to specific phenotypic outcomes. To address these, we conducted a detailed analysis of poly(A) site usage in the CPSF30 mutant. Our results corroborate earlier reports that link CPSF30 with a distinctive cis element (AAUAAA) that is present 10-30 nts upstream of some, but not all, plant pre-mRNAs. Interestingly, our results reveal a distinctive shift in poly(A) site in mutants deficient in CPSF30, resulting in cleavage and polyadenylation at the location of motifs similar to AAUAAA. Importantly, CPSF30-associated APA had at best a small impact on mRNA functionality. These results necessitate the formulation of new hypotheses for mechanisms by which CPSF30-mediated APA influences physiological processes.

Full-length transcriptome sequencing provides insights into alternative splicing under cold stress in peanut

Introduction

Peanut (Arachis hypogaea L.), also called groundnut is an important oil and cash crop grown widely in the world. The annual global production of groundnuts has increased to approximately 50 million tons, which provides a rich source of vegetable oils and proteins for humans. Low temperature (non-freezing) is one of the major factors restricting peanut growth, yield, and geographic distribution. Since the complexity of cold-resistance trait, the molecular mechanism of cold tolerance and related gene networks were largely unknown in peanut.

Methods

In this study, comparative transcriptomic analysis of two peanut cultivars (SLH vs. ZH12) with differential cold tolerance under low temperature (10°C) was performed using Oxford Nanopore Technology (ONT) platform.

Results and discussion

As a result, we identified 8,949 novel gene loci and 95,291 new/novel isoforms compared with the reference database. More differentially expressed genes (DEGs) were discovered in cold-sensitive cultivar (ZH12) than cold-tolerant cultivar (SLH), while more alternative splicing events were found in SLH compared to ZH12. Gene Ontology (GO) analyses of the common DEGs showed that the "response to stress", "chloroplast part", and "transcription factor activity" were the most enriched GO terms, indicating that photosynthesis process and transcription factors play crucial roles in cold stress response in peanut. We also detected a total of 708 differential alternative splicing genes (DASGs) under cold stress compared to normal condition. Intron retention (IR) and exon skipping (ES) were the most prevalent alternative splicing (AS) events. In total, 4,993 transcription factors and 292 splicing factors were detected, many of them had differential expression levels and/or underwent AS events in response to cold stress. Overexpression of two candidate genes (encoding trehalose-6-phosphatephosphatases, AhTPPs) in yeast improves cold tolerance. This study not only provides valuable resources for the study of cold resistance in peanut but also lay a foundation for genetic modification of cold regulators to enhance stress tolerance in crops.