| 1. |
- Shi, Tingting, et al.
(author)
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The super-pangenome of Populus unveils genomic facets for its adaptation and diversification in widespread forest trees
- 2024
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In: Molecular Plant. - : Elsevier. - 1674-2052 .- 1752-9867. ; 17:5, s. 725-746
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Journal article (peer-reviewed)abstract
- Understanding the underlying mechanisms and links between genome evolution and adaptive innovations stands as a key goal in evolutionary studies. Poplars, among the world's most widely distributed and cultivated trees, exhibit extensive phenotypic diversity and environmental adaptability. In this study, we present a genus-level super-pangenome comprising 19 Populus genomes, revealing the likely pivotal role of private genes in facilitating local environmental and climate adaptation. Through the integration of pangenomes with transcriptomes, methylomes, and chromatin accessibility mapping, we unveil that the evolutionary trajectories of pangenes and duplicated genes are closely linked to local genomic landscapes of regulatory and epigenetic architectures, notably CG methylation in gene-body regions. Further comparative genomic analyses have enabled the identification of 142 202 structural variants across species that intersect with a significant number of genes and contribute substantially to both phenotypic and adaptive divergence. We have experimentally validated a ∼180-bp presence/absence variant affecting the expression of the CUC2 gene, crucial for leaf serration formation. Finally, we developed a user-friendly web-based tool encompassing the multi-omics resources associated with the Populus super-pangenome (http://www.populus-superpangenome.com). Together, the present pioneering super-pangenome resource in forest trees not only aids in the advancement of breeding efforts of this globally important tree genus but also offers valuable insights into potential avenues for comprehending tree biology.
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| 2. |
- Zhang, Fan, et al.
(author)
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Proliferative and Survival Effects of PUMA Promote Angiogenesis
- 2012
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In: Cell Reports. - : Elsevier (Cell Press). - 2211-1247. ; 2:5, s. 1272-1285
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Journal article (peer-reviewed)abstract
- The p53 upregulated modulator of apoptosis (PUMA) is known as an essential apoptosis inducer. Here, we report the seemingly paradoxical finding that PUMA is a proangiogenic factor critically required for the proliferation and survival of vascular and microglia cells. Strikingly, Puma deficiency by genetic deletion or small hairpin RNA knockdown inhibited developmental and pathological angiogenesis and reduced microglia numbers in vivo, whereas Puma gene delivery increased angiogenesis and cell survival. Mechanistically, we revealed that PUMA plays a critical role in regulating autophagy by modulating Erk activation and intracellular calcium level. Our findings revealed an unexpected function of PUMA in promoting angiogenesis and warrant more careful investigations into the therapeutic potential of PUMA in treating cancer and degenerative diseases.
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| 3. |
- Liu, Shuyu, et al.
(author)
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Demographic History and Natural Selection Shape Patterns of Deleterious Mutation Load and Barriers to Introgression across Populus Genome
- 2022
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In: Molecular biology and evolution. - : Oxford University Press. - 0737-4038 .- 1537-1719. ; 39:2
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Journal article (peer-reviewed)abstract
- Hybridization and resulting introgression are important processes shaping the tree of life and appear to be far more common than previously thought. However, how the genome evolution was shaped by various genetic and evolutionary forces after hybridization remains unresolved. Here we used whole-genome resequencing data of 227 individuals from multiple widespread Populus species to characterize their contemporary patterns of hybridization and to quantify genomic signatures of past introgression. We observe a high frequency of contemporary hybridization and confirm that multiple previously ambiguous species are in fact F1 hybrids. Seven species were identified, which experienced different demographic histories that resulted in strikingly varied efficacy of selection and burdens of deleterious mutations. Frequent past introgression has been found to be a pervasive feature throughout the speciation of these Populus species. The retained introgressed regions, more generally, tend to contain reduced genetic load and to be located in regions of high recombination. We also find that in pairs of species with substantial differences in effective population size, introgressed regions are inferred to have undergone selective sweeps at greater than expected frequencies in the species with lower effective population size, suggesting that introgression likely have higher potential to provide beneficial variation for species with small populations. Our results, therefore, illustrate that demography and recombination have interplayed with both positive and negative selection in determining the genomic evolution after hybridization.
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| 4. |
- He, Haoran, et al.
(author)
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Linking soil depth to aridity effects on soil microbial community composition, diversity and resource limitation
- 2023
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In: Catena. - 0341-8162. ; 232
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Journal article (peer-reviewed)abstract
- With ongoing climate change, aridity is increasing worldwide, affecting biodiversity and ecosystem function in drylands. However, how the depth-profile microbial community structure and metabolic limitations change along aridity gradients are still poorly explored. Here, 16S rRNA and ITS amplicon sequencing and ecoenzymatic stoichiometry analysis were used to investigate both bacterial and fungal diversities and resource limitations in 1 m depth profiles across a wide aridity gradient (0.51–0.78) in a semiarid region. Results showed a sharp decrease in microbial diversity with soil depth, accompanied by an increase in microbial phosphorus (P) vs. N (nitrogen) limitation and a decrease in microbial carbon (C) vs. nutrient limitation. Aridity led to a strong shift in microbial community composition, but aridity has a threshold effect on microbial resource limitation through impacts on soil pH and C/P or N/P. When the aridity threshold (1-precipitation/evapotranspiration) exceeds 0.65, relationship between aridity and microbial resource demand was decoupled; but at aridity threshold = 0.65, microbial relative C limitation and C-acquiring enzyme activity dropped. These results suggest that aridity might have a stronger influence on microbial community composition, than on diversity, shaped by inherent soil biotic factors (i.e., MBC:MBP or MBN:MBP). These findings suggest that soil microbial diversity or enzymatic stoichiometry may be not necessary to mirror changes in water availability in the drylands, while aridity would be well explained by microbial community composition.
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