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The quantitative proteome atlas of a model cyanobacterium
No full textCyanobacteria are a group of oxygenic photosynthetic bacteria with great potentials in biotechnological applications and advantages as models for photosynthesis research. The subcellular localizations of the majority of proteins in any cyanobacteria remain undetermined, representing a major challenge in using cyanobacteria for both basic and industrial researches. Here, using label-free quantitative proteomics, we map 2027 proteins of Synechocystis sp. PCC6803, a model cyanobacterium, to different subcellular compartments and generate a proteome atlas with such information. The atlas leads to numerous unexpected but important findings, including the predominant localization of the histidine kinases Hik33 and Hik27 on the thylakoid but not the plasma membrane. Such information completely changes the concept regarding how the two kinases are activated. Together, the atlas provides subcellular localization information for nearly 60% proteome of a model cyanobacterium, and will serve as an important resource for the cyanobacterial research community. Copyright (C) 2021, The Authors. Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and Genetics Society of China. Published by Elsevier Limited and Science Press
Isolated Trees in Two Tibetan Plateau Treelines Reveal Growth Plasticity to Harsh Conditions of the Little Ice Age
No full textTrees greater than 150 years old growing in the current treelines were most likely isolated tree outposts above previous treelines of the Little Ice Age (LIA). An intuitive question is, how did these isolated trees grow at such a high elevation in the cold environment? Here, we tackle this question using tree-ring width data of the Northern Hemisphere's highest treelines at 4900 m a.s.l. (Basu) and 4680 m a.s.l. (Langkazi) on the Tibetan Plateau. The results showed that an age-related exponential growth trend did not exist in most of the ring-width sequences of the sampled trees. The values of ring widths in the isolated trees had a similar pattern of probability distribution during and after the LIA. The coefficients of variation in ring widths of the isolated trees were significantly greater than those of the non-isolated trees in their common growth period. Synchronicity of annual change in radial growth among trees varied in time. These results indicated that the isolated trees in the LIA developed an adaptive ability to slow down radial growth rate and modulate growth synchronicity among individuals in cold stressful environments. Our study highlights growth plasticity in isolated trees above treelines for coping with harsh conditions in the LIA
Applying a Portable Backpack Lidar to Measure and Locate Trees in a Nature Forest Plot: Accuracy and Error Analyses
No full textAccurate tree positioning and measurement of structural parameters are the basis of forest inventory and mapping, which are important for forest biomass calculation and community dynamics analyses. Portable backpack lidar that integrates the simultaneous localization and mapping (SLAM) technique with a global navigation satellite system receiver has greater flexibility for tree inventory than terrestrial laser scanning, but it has never been used to measure and map forest structure in a large area (>10(1) hectares) with high tree density. In the present study, we used the LiBackpack DG50 backpack lidar system to obtain the point cloud data of a 10 ha plot of subtropical evergreen broadleaved forest, and applied these data to quantify errors and related factors in the diameter at breast height (DBH) measurements and positioning for more than 1900 individual trees. We found an average error of 4.19 cm in the DBH measurements obtained by lidar, compared with manual field measurements. The incompleteness of the tree stem point clouds was the main factor that caused the DBH measurement errors, and the field DBH measurements and density of the point clouds also had significant impacts. The average tree positioning error was 4.64 m, and it was significantly affected by the distance and route length from the measured trees to the data acquisition start position, whereas it was affected little by the habitat complexity and characteristics of tree stems. The tree positioning measurement error led to increases in the mean value and variability of paired-tree distance error as the sample plot scale increased. We corrected the errors based on the estimates of predictive models. After correction, the DBH measurement error decreased by 31.3%, the tree positioning error decreased by 44.3%, and the paired-tree distance error decreased by 56.3%. As the sample plot scale increased, the accumulated paired-tree distance error stabilized gradually
Spatiotemporal Evolution of the Global Species Diversity of Rhododendron
No full textEvolutionary radiation is a widely recognized mode of species diversification, but its underlying mechanisms have not been unambiguously resolved for species-rich cosmopolitan plant genera. In particular, it remains largely unknown how biological and environmental factors have jointly driven its occurrence in specific regions. Here, we use Rhododendron, the largest genus of woody plants in the Northern Hemisphere, to investigate how geographic and climatic factors, as well as functional traits, worked together to trigger plant evolutionary radiations and shape the global patterns of species richness based on a solid species phylogeny. Using 3,437 orthologous nuclear genes, we reconstructed the first highly supported and dated backbone phylogeny of Rhododendron comprising 200 species that represent all subgenera, sections, and nearly all multispecies subsections, and found that most extant species originated by evolutionary radiations when the genus migrated southward from circumboreal areas to tropical/subtropical mountains, showing rapid increases of both net diversification rate and evolutionary rate of environmental factors in the Miocene. We also found that the geographically uneven diversification of Rhododendron led to a much higher diversity in Asia than in other continents, which was mainly driven by two environmental variables, that is, elevation range and annual precipitation, and were further strengthened by the adaptation of leaf functional traits. Our study provides a good example of integrating phylogenomic and ecological analyses in deciphering the mechanisms of plant evolutionary radiations, and sheds new light on how the intensification of the Asian monsoon has driven evolutionary radiations in large plant genera of the Himalaya-Hengduan Mountains
The SNF5-type protein BUSHY regulates seed germination via the gibberellin pathway and is dependent on HUB1 in Arabidopsis
No full textMain conclusion The SNF5-type protein BUSHY plays a role in the regulation of seed germination via the gibberellin pathway dependent on HUB1 in Arabidopsis thaliana. SWITCH/SUCROSE NONFERMENTING (SWI/SNF) complexes play diverse roles in plant development. Some components have roles in embryo development and seed maturation, however, whether the SNF5-type protein BUSHY (BSH), one of the components, plays a role in Arabidopsis seed related traits is presently unclear. In our study, we show that a loss-of-function mutation in BSH causes increased seed germination in Arabidopsis. BSH transcription was induced by the gibberellin (GA) inhibitor paclobutrazol (PAC) in the seed, and BSH regulates the expression of GA pathway genes, such as Gibberellin 3-Oxidase 1 (GA3OX1), Gibberellic Acid-Stimulated Arabidopsis 4 (GASA4), and GASA6 during seed germination. A genetic analysis showed that seed germination was distinctly improved in the bshga3ox1ga3ox2 triple mutant, indicating that BSH acts partially downstream of GA3OX1 and GA3OX2. Moreover, the regulation of seed germination by BSH in response to PAC is dependent on HUB1. These results provide new insights and clues to understand the mechanisms of phytohormones in the regulation of seed germination
The Shift from Energy to Water Limitation in Local Canopy Height from Temperate to Tropical Forests in China
No full textCanopy height greatly affects the biomass stock, carbon dynamics, and maintenance of biodiversity in forests. Previous research reported that the maximum forest canopy height (Hmax) at global and regional scales could be explained by variations in water or energy availability, that is, the water- or energy-related hypothesis. However, fundamental gaps remain in our understanding of how different drivers (i.e., water and energy) contribute to the Hmax at the local scale. In this study, we selected eight dynamic forest plots (20-30 ha) across a latitudinal gradient (from 21.6 degrees N to 48.1 degrees N) in China and measured the canopy structure using airborne light detection and ranging (LiDAR) data. Based on the LiDAR point cloud data, we extracted the maximum tree height (Hmax) in a 20 x 20 m quadrat as a proxy for canopy height, and the topographic wetness index (TWI) and digital terrain model-derived insolation (DTMI) were calculated as proxies for water and energy conditions. We used a linear mixed model and spatial simultaneous autoregressive error model to quantify how TWI and DTMI contributed to variations in Hmax at the local scale. We found that the positive effect of TWI was stronger in subtropical and tropical forests, highlighting that water was the main factor that drives the canopy height pattern in these regions. In contrast, although the effects of DTMI can be both positive and negative, its relative contribution was higher in temperate forest plots than in other forest types, supporting the idea that energy input is more critical for Hmax in temperate forests. Overall, our study revealed the directional change from energy to water limitation from temperate to subtropical and tropical forests. Our findings can offer important insights into forest management, especially under global climate change in the Anthropocene
Overexpression of grape ABA receptor gene VaPYL4 enhances tolerance to multiple abiotic stresses in Arabidopsis
No full textBackground Abscisic acid (ABA) plays a crucial role in abiotic stress responses. The pyrabactin resistance (PYR)/PYR-like (PYL)/regulatory component of ABA receptor (RCAR) proteins that have been characterized as ABA receptors function as the core components in ABA signaling pathway. However, the functions of grape PYL genes in response to different abiotic stresses, particularly cold stress, remain less studied. Results In this study, we investigated the expression profiles of grape PYL genes upon cold treatment and isolated the VaPYL4 gene from Vitis amurensis, a cold-hardy grape species. Overexpression of VaPYL4 gene in grape calli and Arabidopsis resulted in enhanced cold tolerance. Moreover, plant resistance to drought and salt stress was also improved by overexpressing VaPYL4 in Arabidopsis. More importantly, we evaluated the contribution of VaPYL4 to plant growth and development after the treatment with cold, salt and drought stress simultaneously. The transgenic plants showed higher survival rates, earlier flowering phenotype, and heavier fresh weight of seedlings and siliques when compared with wild-type plants. Physiological analyses showed that transgenic plants had much lower content of malondialdehyde (MDA) and higher peroxidase (POD) activity. Stress-responsive genes such as RD29A (Responsive to desiccation 29A), COR15A (Cold responsive 15A) and KIN2 (Kinase 2) were also significantly up-regulated in VaPYL4-overexpressing Arabidopsis plants. Conclusions Our results show that overexpression of VaPYL4 could improve plant performance upon different abiotic stresses, which therefore provides a useful strategy for engineering future crops to deal with adverse environments
New insights into the phylogeny and evolution of Podocarpaceae inferred from transcriptomic data
No full textPhylogenies of an increasing number of taxa have been resolved with the development of phylogenomics. However, the intergeneric relationships of Podocarpaceae, the second largest family of conifers comprising 19 genera and approximately 187 species mainly distributed in the Southern Hemisphere, have not been well disentangled in previous studies, even when genome-scale data sets were used. Here we used 993 nuclear orthologous groups (OGs) and 54 chloroplast OGs (genes), which were generated from 47 transcriptomes of Podocarpaceae and its sister group Araucariaceae, to reconstruct the phylogeny of Podocarpaceae. Our study completely resolved the intergeneric relationships of Podocarpaceae represented by all extant genera and revealed that topological conflicts among phylogenetic trees could be attributed to synonymous substitutions. Moreover, we found that two morphological traits, fleshy seed cones and flattened leaves, might be important for Podocarpaceae to adapt to angiosperm-dominated forests and thus could have promoted its species diversification. In addition, our results indicate that Podocarpaceae originated in Gondwana in the late Triassic and both vicariance and dispersal have contributed to its current biogeographic patterns. Our study provides the first robust transcriptome-based phylogeny of Podocarpaceae, an evolutionary framework important for future studies of this family
The genome of Dioscorea zingiberensis sheds light on the biosynthesis, origin and evolution of the medicinally important diosgenin saponins
No full textDiosgenin saponins isolated from Dioscorea species such as D. zingiberensis exhibit a broad spectrum of pharmacological activities. Diosgenin, the aglycone of diosgenin saponins, is an important starting material for the production of steroidal drugs. However, how plants produce diosgenin saponins and the origin and evolution of the diosgenin saponin biosynthetic pathway remain a mystery. Here we report a high-quality, 629-Mb genome of D. zingiberensis anchored on 10 chromosomes with 30322 protein-coding genes. We reveal that diosgenin is synthesized in leaves ('source'), then converted into diosgenin saponins, and finally transported to rhizomes ('sink') for storage in plants. By evaluating the distribution and evolutionary patterns of diosgenin saponins in Dioscorea species, we find that diosgenin saponin-containing may be an ancestral trait in Dioscorea and is selectively retained. The results of comparative genomic analysis indicate that tandem duplication coupled with a whole-genome duplication event provided key evolutionary resources for the diosgenin saponin biosynthetic pathway in the D. zingiberensis genome. Furthermore, comparative transcriptome and metabolite analysis among 13 Dioscorea species suggests that specific gene expression patterns of pathway genes promote the differential evolution of the diosgenin saponin biosynthetic pathway in Dioscorea species. Our study provides important insights and valuable resources for further understanding the biosynthesis, evolution, and utilization of plant specialized metabolites such as diosgenin saponins
PhUGT78A22, a novel glycosyltransferase in Paeonia 'He Xie', can catalyze the transfer of glucose to glucosylated anthocyanins during petal blotch formation
No full textBackground Flower color patterns play an important role in the evolution and subsequent diversification of flowers by attracting animal pollinators. This interaction can drive the diversity observed in angiosperms today in many plant families such as Liliaceae, Paeoniaceae, and Orchidaceae, and increased their ornamental values. However, the molecular mechanism underlying the differential distribution of anthocyanins within petals remains unclear in Paeonia. Results In this study, we used an intersectional hybrid between the section Moutan and Paeonia, hereafter named Paeonia 'He Xie', which has purple flowers with dark purple blotches. After Ultra-high performance liquid chromatography-diode array detector (UPLC-DAD) analysis of blotched and non-blotched parts of petals, we found the anthocyanin content in the blotched part was always higher than that in the non-blotched part. Four kinds of anthocyanins, namely cyanidin-3-O-glucoside (Cy3G), cyanidin-3,5-O-glucoside (Cy3G5G), peonidin-3-O-glucoside (Pn3G), and peonidin-3,5-O-glucoside (Pn3G5G) were detected in the blotched parts, while only Cy3G5G and Pn3G5G were detected in the non-blotched parts. This suggests that glucosyltransferases may play a vital role in the four kinds of glucosylated anthocyanins in the blotched parts. Moreover, 2433 differentially expressed genes (DEGs) were obtained from transcriptome analysis of blotched and non-blotched parts, and a key UDP-glycosyltransferase named PhUGT78A22 was identified, which could use Cy3G and Pn3G as substrates to produce Cy3G5G and Pn3G5G, respectively, in vitro. Furthermore, silencing of PhUGT78A22 reduced the content of anthocyanidin 3,5-O-diglucoside in P. 'He Xie'. Conclusions A UDP-glycosyltransferase, PhUGT78A22, was identified in P. 'He Xie', and the molecular mechanism underlying differential distribution of anthocyanins within petals was elucidated. This study provides new insights on the biosynthesis of different kinds of anthocyanins within colorful petals, and helps to explain petal blotch formation, which will facilitate the cultivar breeding with respect to increasing ornamental value. Additionally, it provides a reference for understanding the molecular mechanisms responsible for precise regulation of anthocyanin biosynthesis and distribution patterns