Transcriptome differences between 20- and 3,000-year-old Platycladus orientalis reveal that ROS are involved in senescence regulation

Background: Platycladus orientalis has an extremely long life span of several thousands of years, attracting great interests in the mechanisms involved in such successful senescence regulation and resistance at physiological and molecular levels. Results: The levels of reactive oxygen species (ROS) were higher in 3,000-year-old than in 20-year-old P. orientalis, and the activities of GR and GSH demonstrated the same trend. We produced and analyzed massive sequence information from pooled samples of P. orientalis through transcriptome sequencing, which generated 51,664 unigenes with an average length of 475 bp. We then used RNA-seq analysis to obtain a high-resolution age\u2013course profile of gene expression in 20- and 3,000-year-old P. orientalis individuals. Totally, 106 differentially expressed genes were obtained, of which 47 genes were downregulated and 59 upregulated in the old tree. These genes were involved in transcription factors, hormone-related responses, ROS scavengers, senescence-related responses, stress response, and defense and possibly play crucial roles in tackling various stresses in the 3,000-year-old P. orientalis during its life time. The expression patterns of genes related to ROS homeostasis further indicated that the high ability of ROS scavenging could be helpful for the 3,000-year-old P. orientalis to resist senescence. Conclusions: This study provides a foundation for the elucidation of senescence resistance through molecular studies and the discovery of useful genes in P. orientalis

Significance of Photosynthetic Characters in the Evolution of Asian Gnetum (Gnetales)

Gnetum is a genus in the Gnetales that has a unique but ambiguous placement within seed plant phylogeny. Previous studies have shown that Gnetum has lower values of photosynthetic characters than those of other seed plants, but few Gnetum species have been studied, and those that have been studied are restricted to narrow taxonomic and geographic ranges. In addition, the mechanism underlying the lower values of photosynthetic characters in Gnetum remains poorly understood. Here, we investigated the photosynthetic characters of a Chinese lianoid species, i.e., Gnetum parvifolium, and co-occurring woody angiosperms growing in the wild, as well as seedlings of five Chinese Gnetum species cultivated in a greenhouse. The five Gnetum species had considerably lower values for photosynthesis parameters (net photosynthetic rate, transpiration rate, intercellular CO2 concentration, and stomatal conductance) than those of other seed plant representatives. Interrelated analyses revealed that the low photosynthetic capacity may be an intrinsic property of Gnetum, and may be associated with its evolutionary history. Comparison of the chloroplast genomes (cpDNAs) of Gnetum with those of other seed plant representatives revealed that 17 coding genes are absent from the cpDNAs of all species of Gnetum. This lack of multiple functional genes from the cpDNAs probably leads to the low photosynthetic rates of Gnetum. Our results provide a new perspective on the evolutionary history of the Gnetales, and on the ecophysiological and genomic attributes of tropical biomes in general. These results could also be useful for the breeding and cultivation of Gnetum

Genomic Analyses Reveal Mutational Signatures and Frequently Altered Genes in Esophageal Squamous Cell Carcinoma

Esophageal squamous cell carcinoma (ESCC) is one of the most common cancers worldwide and the fourth most lethal cancer in China. However, although genomic studies have identified some mutations associated with ESCC, we know little of the mutational processes responsible. To identify genome-wide mutational signatures, we performed either whole-genome sequencing (WGS) or whole-exome sequencing (WES) on 104 ESCC individuals and combined our data with those of 88 previously reported samples. An APOBEC-mediated mutational signature in 47% of 192 tumors suggests that APOBEC-catalyzed deamination provides a source of DNA damage in ESCC. Moreover, PIK3CA hotspot mutations (c.1624G>A [p.Glu542Lys] and c.1633G>A [p.Glu545Lys]) were enriched in APOBEC-signature tumors, and no smoking-associated signature was observed in ESCC. In the samples analyzed by WGS, we identified focal (<100 kb) amplifications of CBX4 and CBX8. In our combined cohort, we identified frequent inactivating mutations in AJUBA, ZNF750, and PTCH1 and the chromatin-remodeling genes CREBBP and BAP1, in addition to known mutations. Functional analyses suggest roles for several genes (CBX4, CBX8, AJUBA, and ZNF750) in ESCC. Notably, high activity of hedgehog signaling and the PI3K pathway in approximately 60% of 104 ESCC tumors indicates that therapies targeting these pathways might be particularly promising strategies for ESCC. Collectively, our data provide comprehensive insights into the mutational signatures of ESCC and identify markers for early diagnosis and potential therapeutic targets

Acclimation Strategy of Masson Pine (<i>Pinus massoniana</i>) by Limiting Flavonoid and Terpenoid Production under Low Light and Drought

Low light and drought often limit the growth and performance of Masson pines (Pinus massoniana) in the subtropical forest ecosystem of China. We speculated that stress-induced defensive secondary metabolites, such as flavonoids and terpenoids, might influence the growth of Masson pines, considering the existence of tradeoffs between growth and defense. However, the mechanisms of Masson pines responsive to low light and drought at the levels of these two metabolites remain unclear. In the present work, the compositions of flavonoids and terpenoids, as well as their biosynthetic pathways, were revealed through metabolome and transcriptome analyses, respectively, coupled with a study on carbon allocation using a 13CO2-pulse-labeling experiment in two-year-old seedlings under low light (LL), drought (DR), and their combined stress (DL) compared to a control (CK). A total of 35 flavonoids and derivatives (LL vs. CK: 18; DR vs. CK: 20; and DL vs. CK: 18), as well as 29 terpenoids and derivatives (LL vs. CK: 23; DR vs. CK: 13; and DL vs. CK: 7), were differentially identified in the leaves. Surprisingly, most of them were decreased under all three stress regimes. At the transcriptomic level, most or all of the detected DEGs (differentially expressed genes) involved in the biosynthetic pathways of flavonoids and terpenoids were downregulated in phloem and xylem under stress treatments. This indicated that stress treatments limited the production of flavonoids and terpenoids. The reduction in the 13C allocation to stems might suggest that it is necessary for maintaining the growth of Masson pine seedlings at the whole-plant level by attenuating energetic resources to the biosynthetic pathways of flavonoids and terpenoids when facing the occurrence of adverse environments. Our results provide new insight into understanding the acclimation strategy of Masson pines or other conifers in adverse environments

Isolation of high-quality RNA from Platycladus orientalis and other Cupressaceae plants

Platycladus orientalis has a lifespan of several thousand years in China, making it a good plant in which to study aging at the molecular level, but this requires sufficient quantities of high-quality P. orientalis RNA. However, no appropriate methods have been reported for total RNA isolation from P. orientalis leaves. The TRIzol method did not extract RNA, while cetyltrimethylammonium bromide, sodium dodecyl sulfate-phenol, and plant RNAout kit (Tianz, Inc., China) protocols resulted in low yields of poor quality RNA. Isolating total RNA using the Spectrum™ Plant Total RNA Kit (Sigma-Aldrich, St. Louis, MO, USA) resulted in a high-quality product but a low yield. However, the two-step removal of polyphenols and polysaccharides in the improved plant RNAout kit protocol resulted in the isolation of RNA with a 28S:18S rRNA ratio of band intensities that was ~2:1, the A260/A280 absorbance ratio was 2.03, and the total RNA yield from P. orientalis leaves was high. This protocol was tested on different P. orientalis tissues of different ages and on leaves of five other Cupressaceae plants. The total RNAs were successfully used in complementary DNA synthesis for transcriptome sequencing and would be suitable to use in additional experiments. The results of this study will benefit future studies in Cupressaceae plants

The Role of &gamma;-Aminobutyric Acid (GABA) in the Occurrence of Adventitious Roots and Somatic Embryos in Woody Plants

The occurrence of adventitious roots and somatic embryos is a crucial step in micropropagation that frequently limits the application of this technique in woody plants. Recent studies demonstrated that they can be negatively or positively regulated with &gamma;-aminobutyric acid (GABA), which is a four-carbon non-proteinous amino acid that not only acts as a main inhibitory neurotransmitter in mammals. It has been reported that GABA affects plant growth and their response to stress although its mode of action is still unclear. This review dealt with the effects of GABA on adventitious root formation and growth as well as on somatic embryogenesis. Furthermore, we focused on discussing the interaction of GABA with phytohormones, such as auxin, ethylene, abscisic acid, and gibberellin, as well as with the carbon and nitrogen metabolism during adventitious root development. We suggested that research on GABA will contribute to the application of micropropagation in the recalcitrant fruit and forest species

Harmonizing atmospheric ozone column concentrations over the Tibetan Plateau from 2005 to 2022 using OMI and Sentinel-5P TROPOMI: A deep learning approach

Atmospheric ozone plays a pivotal role in Earth's climate system, influencing solar radiation absorption in the stratosphere and regulating ultraviolet light reaching the surface. Accurate monitoring of ozone concentration is crucial for environmental assessments, air quality monitoring, and climate change studies. The Ozone Monitoring Instrument (OMI) and Sentinel-5 Precursor TROPOspheric Monitoring Instrument (TROPOMI) provide valuable data for such monitoring. While OMI offers a long data record since 2004, but its effectiveness is hindered by its limitations in spatial resolution and signal-to-noise ratio, stemming from satellite hardware and retrieval algorithms. Sentinel-5P TROPOMI provides higher spatial resolution and improved signal-to-noise ratio, nevertheless, data record from it is rather short. Harmonizing these two datasets by taking the best use of their specific advantages is essential for creating a comprehensive and accurate atmospheric ozone concentration dataset. To maximize the advantages of these multi-source data products, our method utilizes a neural network to learn the mapping relationship between OMI and Sentinel-5P TROPOMI ozone column concentration products, constructing a harmonized model that optimizes the spatial and temporal sequence of historical OMI ozone column concentrations while considering topographic factors. The reconstructed ozone column concentration product is a long time series with the high spatial resolution and accuracy characteristics of Sentinel-5P TROPOMI. This research leverages powerful nonlinear modeling and spatial feature mapping capabilities based on deep learning networks to create a harmonized dataset of atmospheric ozone column concentrations, offering a comprehensive understanding of ozone distribution across the Tibetan Plateau. This dataset not only improves accuracy and precision in ozone concentration measurements but also facilitates in-depth analysis of local ozone variations, providing reliable dataset for scientific investigations into the atmospheric environment. The complete dataset is openly accessible at https://doi.org/10.5281/zenodo.10430751

Variations in Acorn Traits in Two Oak Species: <i>Quercus mongolica</i> Fisch. ex Ledeb. and <i>Quercus variabilis</i> Blume

Quercus mongolica Fisch. ex Ledeb. and Q. variabilis Blume are two main oak species in China, producing large amounts of acorns every year. However, the trait variations in acorns, as a promising energy crop material, are not fully understood, hence we compared the traits of acorns from the different populations with the altered geographic distribution in this study. Thirteen acorn traits, including phenotype, proximate compositions and functional compounds, were analyzed in both Quercus L. species collected from 44 populations across China. The results showed that, except large differences found among accessions in acorn sizes, the starch varied from 140.96–297.09 mg/g in Q. mongolica and 130.99–306.28 mg/g in Q. variabilis, indicating its substantial differences among populations. The total polyphenols, total flavonoids and soluble tannins varied from 41.76–158.92, 23.43–91.94, and 15.11–17.81 mg/g, respectively, in Q. mongolica, 89.36–188.37, 50.59–116.07, 15.24–17.33 mg/g, respectively, in Q. variabilis, demonstrating their large variations in the levels of polyphenols among populations. Moreover, the acorns of Q. mongolica in North China and Q. variabilis in Southwest China had higher levels of starch and polyphenols. As the geographical location approached in the distribution of two Quercus species, the difference in acorn sizes gradually increased, while that in polyphenols were opposite. Principal component analysis and cluster analysis further revealed that the acorn sizes became larger and polyphenols became less with the increasing latitudes in both species. In North China, the acorns of Q. mongolica had small sizes and high polyphenols, which was contrary to those in Q. variabilis. These findings indicated that acorn traits were closely associated with the geographical distribution. Thus, our results will provide references for the selection breeding of acorn with the high starch, high or low polyphenols in the different regions