| 1. |
- Ma, Tao, et al.
(författare)
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Genomic insights into salt adaptation in a desert poplar
- 2013
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 4, s. 2797-
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Tidskriftsartikel (refereegranskat)abstract
- Despite the high economic and ecological importance of forests, our knowledge of the genomic evolution of trees under salt stress remains very limited. Here we report the genome sequence of the desert poplar, Populus euphratica, which exhibits high tolerance to salt stress. Its genome is very similar and collinear to that of the closely related mesophytic congener, P. trichocarpa. However, we find that several gene families likely to be involved in tolerance to salt stress contain significantly more gene copies within the P. euphratica lineage. Furthermore, genes showing evidence of positive selection are significantly enriched in functional categories related to salt stress. Some of these genes, and others within the same categories, are significantly upregulated under salt stress relative to their expression in another salt-sensitive poplar. Our results provide an important background for understanding tree adaptation to salt stress and facilitating the genetic improvement of cultivated poplars for saline soils.
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| 2. |
- Liu, Shuyu, et al.
(författare)
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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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Ingår i: Molecular biology and evolution. - : Oxford University Press. - 0737-4038 .- 1537-1719. ; 39:2
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Tidskriftsartikel (refereegranskat)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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| 3. |
- Miehe, Georg, et al.
(författare)
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The Kobresia pygmaea ecosystem of the Tibetan highlands – Origin, functioning and degradation of the world's largest pastoral alpine ecosystem: Kobresia pastures of Tibet
- 2019
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Ingår i: Science of the Total Environment. - : Elsevier BV. - 0048-9697. ; 648, s. 754-771
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Tidskriftsartikel (refereegranskat)abstract
- With 450,000 km2 Kobresia (syn. Carex) pygmaea dominated pastures in the eastern Tibetan highlands are the world's largest pastoral alpine ecosystem forming a durable turf cover at 3000–6000 m a.s.l. Kobresia's resilience and competitiveness is based on dwarf habit, predominantly below-ground allocation of photo assimilates, mixture of seed production and clonal growth, and high genetic diversity. Kobresia growth is co-limited by livestock-mediated nutrient withdrawal and, in the drier parts of the plateau, low rainfall during the short and cold growing season. Overstocking has caused pasture degradation and soil deterioration over most parts of the Tibetan highlands and is the basis for this man-made ecosystem. Natural autocyclic processes of turf destruction and soil erosion are initiated through polygonal turf cover cracking, and accelerated by soil-dwelling endemic small mammals in the absence of predators. The major consequences of vegetation cover deterioration include the release of large amounts of C, earlier diurnal formation of clouds, and decreased surface temperatures. These effects decrease the recovery potential of Kobresia pastures and make them more vulnerable to anthropogenic pressure and climate change. Traditional migratory rangeland management was sustainable over millennia, and possibly still offers the best strategy to conserve and possibly increase C stocks in the Kobresia turf.
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| 4. |
- Shi, Tingting, et al.
(författare)
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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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Ingår i: Molecular Plant. - : Elsevier. - 1674-2052 .- 1752-9867. ; 17:5, s. 725-746
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Tidskriftsartikel (refereegranskat)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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| 5. |
- Wang, Zhaofeng, et al.
(författare)
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Phylogeographical analyses of domestic and wild yaks based on mitochondrial DNA : new data and reappraisal
- 2010
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Ingår i: Journal of Biogeography. - : Wiley. - 0305-0270 .- 1365-2699. ; 37:12, s. 2332-2344
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Tidskriftsartikel (refereegranskat)abstract
- Aim We aimed to examine the phylogeographical structure and demographic history of domestic and wild yaks (Bos grunniens) based on a wide range of samples and complete mitochondrial genomic sequences. Location The Qinghai-Tibetan Plateau (QTP) of western China. Methods All available D-loop sequences for 405 domesticated yaks and 47 wild yaks were examined, including new sequences from 96 domestic and 34 wild yaks. We further sequenced the complete mitochondrial genomes of 48 domesticated and 21 wild yaks. Phylogeographical analyses were performed using the mitochondrial D-loop and the total genome datasets. Results We recovered a total of 123 haplotypes based on the D-loop sequences in wild and domestic yaks. Phylogenetic analyses of this dataset and the mitochondrial genome data suggested three well-supported and divergent lineages. Two lineages with six D-loop haplogroups were recovered for all morphological breeds of domestic yaks across their distributions in the QTP, while one more lineage and more endemic haplogroups or haplotypes were found for wild yaks. Based on the mitochondrial genome data, the divergences of the three lineages were estimated to have occurred around 420,000 and 580,000 years ago, consistent with the geological records of two large glaciation events experienced in the QTP. Main conclusions There are distinct phylogeographical differences between wild and domestic yaks. However, there is no apparent geographical correlation between identified haplogroups and distributions of domestic yaks. Three differentiated lineages of yaks probably evolved allopatrically in different regions during the Pleistocene glaciation events, then reunited into a single gene pool during post-glacial population expansion and migrations before the start of the domestication of yaks in the Holocene.
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| 6. |
- Xu, L., et al.
(författare)
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Silver-Catalyzed Controlled Intermolecular Cross-Coupling of Silyl Enol Ethers : Scalable Access to 1,4-Diketones
- 2022
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Ingår i: Organic Letters. - : American Chemical Society (ACS). - 1523-7060 .- 1523-7052. ; 24:25, s. 4513-4518
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Tidskriftsartikel (refereegranskat)abstract
- A protocol for silver-catalyzed controlled intermolecular cross-coupling of silyl enolates is disclosed. The protocol displays good functional group tolerance and allows efficient preparation of a series of synthetically useful 1,4-diketones. Preliminary mechanistic investigations suggest that the reaction proceeds through a one-electron process involving free radical species in which PhBr acts as the oxidant.
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| 7. |
- Chai, Gaoda, et al.
(författare)
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Deciphering the Role of Chalcogen-Containing Heterocycles in Nonfullerene Acceptors for Organic Solar Cells
- 2020
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Ingår i: ACS Energy Letters. - : AMER CHEMICAL SOC. - 2380-8195. ; 5:11, s. 3415-3425
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Tidskriftsartikel (refereegranskat)abstract
- The field of organic solar cells has experienced paradigm-shifting changes in recent years because of the emergence of nonfullerene acceptors (NFAs). It is critically important to gain more insight into the structure-property relationship of the emerging A-DAD-A-type NFAs. In this Letter, a family of NFAs named BPF-4F, BPT-4F, and BPS-4F incorporating various chalcogen-containing heterocycles, i.e., furan, thiophene, and selenophene, respectively, was designed and synthesized. These NFAs exhibited dramatic differences in their photovoltaic performances with device efficiencies of 16.8% achieved by the thiophene-based cells, which was much higher than the furan-based ones (12.6%). In addition, the selenophene-based NFA showed a red-shifted absorption relative to the furan- and thiophene-based ones and obtained a decent efficiency of 16.3% owing to an improved J(SC). The reasons why these NFAs performed differently are systematically studied by comparing their optoelectronic properties and film morphology, which provides new understandings of the molecular design of high-performance NFAs.
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| 8. |
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| 9. |
- Chen, Yan, et al.
(författare)
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Silver-Promoted (4+1) Annulation of Isocyanoacetates with Alkylpyridinium Salts : Divergent Regioselective Synthesis of 1,2-Disubstituted Indolizines
- 2021
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Ingår i: Organic Letters. - : American Chemical Society (ACS). - 1523-7060 .- 1523-7052. ; 23:19, s. 7555-7560
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Tidskriftsartikel (refereegranskat)abstract
- An unprecedented silver-promoted regioselective (4 + 1) annulation of isocyanoacetates with pyridinium salts is reported. The established protocol provides controlled, facile, and modular access to a range of synthetically useful N-fused heterocyclic scaffolds containing indolizines, pyrrolo[1,2-a]quinolines, pyrrolo[2,1-a]isoquinolines, and 1H-imidazo[4,5-a]indolizin-2(3H)-ones. A mechanistic pathway involving nucleophilic addition/protonation/elimination/cydoisomerization is proposed.
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| 10. |
- Chen, Zeyuan, et al.
(författare)
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Survival in the Tropics despite isolation, inbreeding and asexual reproduction : insights from the genome of the world's southernmost poplar (Populus ilicifolia)
- 2020
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Ingår i: The Plant Journal. - : Wiley. - 0960-7412 .- 1365-313X. ; 103:1, s. 430-442
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Tidskriftsartikel (refereegranskat)abstract
- Species are becoming extinct at unprecedented rates as a consequence of human activity. Hence it is important to understand the evolutionary dynamics of species with already small population sizes. Populus ilicifolia is a vulnerable poplar species that is isolated from other poplar species and is uniquely adapted to the Tropics. It has a very limited size, reproduces partly clonally and is therefore an excellent case study for conservation genomics. We present here the first annotated draft genome of P. ilicifolia, characterize genome-wide patterns of polymorphisms and compare those to other poplar species with larger natural ranges. P. ilicifolia experienced a more prolonged and severe decline of effective population size (Ne) and signs of genetic erosion than any other poplar species with which it was compared. At present, the species has the lowest genome-wide genetic diversity, the highest abundance of long runs of homozygosity, high inbreeding levels as well as a high overall accumulation of deleterious variants. However, more effective purging of severely deleterious variants and adaptation to the Tropics may have contributed to its survival. Hence, in spite of its limited genetic variation, it is certainly worth pursuing the conservation efforts of this unique species.
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