Background: Elevated temperature as a result of global climate warming, either in form of sudden heatwave (heat shock) or prolonged warming, has profound effects on the growth and development of plants. However, how plants differentially respond to these two forms of elevated temperatures is largely unknown. Here we have therefore performed a comprehensive comparison of multi-level responses of Arabidopsis leaves to heat shock and prolonged warming. Results: The plant responded to prolonged warming through decreased stomatal conductance, and to heat shock by increased transpiration. In carbon metabolism, the glycolysis pathway was enhanced while the tricarboxylic acid (TCA) cycle was inhibited under prolonged warming, and heat shock significantly limited the conversion of pyruvate into acetyl coenzyme A. The cellular concentration of hydrogen peroxide (H 2 O 2) and the activities of antioxidant enzymes were increased under both conditions but exhibited a higher induction under heat shock. Interestingly, the transcription factors, class A1 heat shock factors (HSFA1s) and dehydration responsive elementbinding proteins (DREBs), were up-regulated under heat shock, whereas with prolonged warming, other abiotic stress response pathways, especially basic leucine zipper factors (bZIPs) were up-regulated instead. Conclusions: Our findings reveal that Arabidopsis exhibits different response patterns under heat shock versus prolonged warming, and plants employ distinctly different response strategies to combat these two types of thermal stress.

Background: The number of studies using third-generation sequencing utilising Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) is rapidly increasing in many different research areas. Among them, plant full-length single-molecule transcriptome studies have mostly used PacBio sequencing, whereas ONT is rarely used. Therefore, in this study, we examined ONT RNA sequencing methods in plants. We performed a detailed evaluation of reads from PacBio, Nanopore direct cDNA (ONT Dc), and Nanopore PCR cDNA (ONT Pc) sequencing including characteristics of raw data and identification of transcripts. In addition, matched Illumina data were generated for comparison. Results: ONT Pc showed overall better raw data quality, whereas PacBio generated longer read lengths. In the transcriptome analysis, PacBio and ONT Pc performed similarly in transcript identification, simple sequence repeat analysis, and long non-coding RNA prediction. PacBio was superior in identifying alternative splicing events, whereas ONT Pc could estimate transcript expression levels. Conclusions: This paper made a comprehensive comparison of PacBio and nanopore-based RNA sequencing of the Arabidopsis transcriptome, the results indicate that ONT Pc is more cost-effective for generating extremely long reads and can characterise the transcriptome as well as quantify transcript expression. Therefore, ONT Pc is a new cost-effective and worthwhile method for full-length single-molecule transcriptome analysis in plants.

Aging is a universal property of multicellular organisms. Although some tree species can live for centuries or millennia, the molecular and metabolic mechanisms underlying their longevity are unclear. To address this, we investigated age-related changes in the vascular cambium from 15- to 667-y-old Ginkgo biloba trees. The ring width decreased sharply during the first 100 to 200 y, with only a slight change after 200 y of age, accompanied by decreasing numbers of cambial cell layers. In contrast, average basal area increment (BAI) continuously increased with aging, showing that the lateral meristem can retain indeterminacy in old trees. The indole-3-acetic acid (IAA) concentration in cambial cells decreased with age, whereas the content of abscisic acid (ABA) increased significantly. In addition, cell division-, cell expansion-, and differentiation-related genes exhibited significantly lower expression in old trees, especially miR166 and HD-ZIP III interaction networks involved in cambial activity. Disease resistance-associated genes retained high expression in old trees, along with genes associated with synthesis of preformed protective secondary metabolites. Comprehensive evaluation of the expression of genes related to autophagy, senescence, and age-related miRNAs, together with analysis of leaf photosynthetic efficiencies and seed germination rates, demonstrated that the old trees are still in a healthy, mature state, and senescence is not manifested at the whole-plant level. Taken together, our results reveal that long-lived trees have evolved compensatory mechanisms to maintain a balance between growth and aging processes. This involves continued cambial divisions, high expression of resistance-associated genes, and continued synthetic capacity of preformed protective secondary metabolites.

Background Elevated temperatures can cause physiological, biochemical, and molecular responses in plants that can greatly affect their growth and development. Mutations are the most fundamental force driving biological evolution. However, how long-term elevations in temperature influence the accumulation of mutations in plants remains unknown. Results Multigenerational exposure of Arabidopsis MA (mutation accumulation) lines and MA populations to extreme heat and moderate warming results in significantly increased mutation rates in single-nucleotide variants (SNVs) and small indels. We observe distinctive mutational spectra under extreme and moderately elevated temperatures, with significant increases in transition and transversion frequencies. Mutation occurs more frequently in intergenic regions, coding regions, and transposable elements in plants grown under elevated temperatures. At elevated temperatures, more mutations accumulate in genes associated with defense responses, DNA repair, and signaling. Notably, the distribution patterns of mutations among all progeny differ between MA populations and MA lines, suggesting that stronger selection effects occurred in populations. Methylation is observed more frequently at mutation sites, indicating its contribution to the mutation process at elevated temperatures. Mutations occurring within the same genome under elevated temperatures are significantly biased toward low gene density regions, special trinucleotides, tandem repeats, and adjacent simple repeats. Additionally, mutations found in all progeny overlap significantly with genetic variations reported in 1001 Genomes, suggesting non-uniform distribution of de novo mutations through the genome. Conclusion Collectively, our results suggest that elevated temperatures can accelerate the accumulation, and alter the molecular profiles, of DNA mutations in plants, thus providing significant insight into how environmental temperatures fuel plant evolution.

Circular RNAs (circRNAs) are a family of transcripts with covalently closed circular structures and still largely unknown functions. Large numbers of circRNAs have been found in various biological processes in humans and animals, but fewer circRNAs have been identified in plants. We performed a genome-wide analysis of circRNAs in Arabidopsis thaliana via deep sequencing. We constructed 14 strand-specific libraries from 13 samples of plants from four developmental stages, four stress treatments, and five organs and a mixed sample across the lifespan. In total, we identified 5861 circRNAs, including 1275 novel ones, using the strict threshold of at least two unique back-spliced supporting reads. The circRNAs were non-randomly distributed in all chromosomes; most were exonic. Sequence similarity analysis of circRNAs between A. thaliana and four other species showed that some circRNAs are conserved in plants. Functional annotation indicated that many parent genes of circRNAs are involved in many fundamental processes including plant development, reproduction, and response to stimulus. In addition, a small proportion of circRNAs was shown to be potential targets of miRNAs, indicating that the circRNAs could interact with miRNAs to regulate gene expression. qRT-PCR analysis revealed that circRNAs displayed diverse expression patterns at different growth stages. Our results provide an important resource for continuing circRNA research in A. thaliana, and should enhance our understanding of circRNAs in plants.