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| 2. |
- Liu, Hui, et al.
(författare)
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Centromere-Specific Retrotransposons and Very-Long-Chain Fatty Acid Biosynthesis in the Genome of Yellowhorn (Xanthoceras sorbifolium, Sapindaceae), an Oil-Producing Tree With Significant Drought Resistance
- 2021
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Ingår i: Frontiers in Plant Science. - : Frontiers Media S.A.. - 1664-462X. ; 12
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Tidskriftsartikel (refereegranskat)abstract
- In-depth genome characterization is still lacking for most of biofuel crops, especially for centromeres, which play a fundamental role during nuclear division and in the maintenance of genome stability. This study applied long-read sequencing technologies to assemble a highly contiguous genome for yellowhorn (Xanthoceras sorbifolium), an oil-producing tree, and conducted extensive comparative analyses to understand centromere structure and evolution, and fatty acid biosynthesis. We produced a reference-level genome of yellowhorn, ∼470 Mb in length with ∼95% of contigs anchored onto 15 chromosomes. Genome annotation identified 22,049 protein-coding genes and 65.7% of the genome sequence as repetitive elements. Long terminal repeat retrotransposons (LTR-RTs) account for ∼30% of the yellowhorn genome, which is maintained by a moderate birth rate and a low removal rate. We identified the centromeric regions on each chromosome and found enrichment of centromere-specific retrotransposons of LINE1 and Gypsy in these regions, which have evolved recently (∼0.7 MYA). We compared the genomes of three cultivars and found frequent inversions. We analyzed the transcriptomes from different tissues and identified the candidate genes involved in very-long-chain fatty acid biosynthesis and their expression profiles. Collinear block analysis showed that yellowhorn shared the gamma (γ) hexaploidy event with Vitis vinifera but did not undergo any further whole-genome duplication. This study provides excellent genomic resources for understanding centromere structure and evolution and for functional studies in this important oil-producing plant.
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| 3. |
- Pecunia, Vincenzo, et al.
(författare)
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Roadmap on energy harvesting materials
- 2023
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Ingår i: Journal of Physics. - : IOP Publishing. - 2515-7639. ; 6:4
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Tidskriftsartikel (refereegranskat)abstract
- Ambient energy harvesting has great potential to contribute to sustainable development and address growing environmental challenges. Converting waste energy from energy-intensive processes and systems (e.g. combustion engines and furnaces) is crucial to reducing their environmental impact and achieving net-zero emissions. Compact energy harvesters will also be key to powering the exponentially growing smart devices ecosystem that is part of the Internet of Things, thus enabling futuristic applications that can improve our quality of life (e.g. smart homes, smart cities, smart manufacturing, and smart healthcare). To achieve these goals, innovative materials are needed to efficiently convert ambient energy into electricity through various physical mechanisms, such as the photovoltaic effect, thermoelectricity, piezoelectricity, triboelectricity, and radiofrequency wireless power transfer. By bringing together the perspectives of experts in various types of energy harvesting materials, this Roadmap provides extensive insights into recent advances and present challenges in the field. Additionally, the Roadmap analyses the key performance metrics of these technologies in relation to their ultimate energy conversion limits. Building on these insights, the Roadmap outlines promising directions for future research to fully harness the potential of energy harvesting materials for green energy anytime, anywhere.
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| 4. |
- Xu, Chao-Qun, et al.
(författare)
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Genome sequence of Malania oleifera, a tree with great value for nervonic acid production
- 2019
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Ingår i: GigaScience. - : Oxford University Press. - 2047-217X. ; 8:2
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Tidskriftsartikel (refereegranskat)abstract
- Background Malania oleifera, a member of the Olacaceae family, is an IUCN red listed tree, endemic and restricted to the Karst region of southwest China. This tree's seed is valued for its high content of precious fatty acids (especially nervonic acid). However, studies on its genetic makeup and fatty acid biogenesis are severely hampered by a lack of molecular and genetic tools. Findings We generated 51 Gb and 135Gb of raw DNA sequences, using Pacific Biosciences (PacBio) single-molecule real-time and 10x Genomics sequencing, respectively. A final genome assembly, with a scaffold N50 size of 4.65 Mb and a total length of 1.51Gb, was obtained by primary assembly based on PacBio long reads plus scaffolding with 10x Genomics reads. Identified repeats constituted approximate to 82% of the genome, and 24,064 protein-coding genes were predicted with high support. The genome has low heterozygosity and shows no evidence for recent whole genome duplication. Metabolic pathway genes relating to the accumulation of long-chain fatty acid were identified and studied in detail. Conclusions Here, we provide the first genome assembly and gene annotation for M. oleifera. The availability of these resources will be of great importance for conservation biology and for the functional genomics of nervonic acid biosynthesis.
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| 5. |
- Zheng, Shao Fei, et al.
(författare)
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An inverse optimization of turbulent flow and heat transfer for a cooling passage with hierarchically arranged ribs in turbine blades
- 2024
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Ingår i: International Journal of Heat and Mass Transfer. - 0017-9310. ; 220
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Tidskriftsartikel (refereegranskat)abstract
- Owing to the limited cold-air amount and pressure in supply systems, high-efficient heat transfer with low-level friction loss is highly desired for cooling units of a turbine blade. To exploit the potential improvement of hierarchically arranged ribs in cooling passages proposed previously, multi-parameter optimizations for rib arrangements are implemented by integrating the simplified conjugate-gradient algorithm with the turbulent flow and heat transfer model. Rib heights as design variables are optimized with various performance indices as objective functions at a fixed Re. The optimizations confirm that using the wall temperature difference and Nu as the objective function, respectively, a limited heat transfer improvement is achieved with a greatly increased friction loss. Taking the overall performance factor as the objective function, different optimal designs at different constraint conditions possess hierarchical characteristics. A significant friction loss reduction of 52.1%, 54.7%, and 54.8%, is achieved with a moderate heat transfer loss of 10.9%, 7.0%, and 2.3%. Despite different thermal and friction performances, their overall performances are consistent with a remarkable increase of 13.9%, 21.2%, and 27.3%. Finally, the optimization strategy coupling the multi-parameter optimization and hierarchical scheme is confirmed as effective for enhancing the thermohydraulic performance of convective heat transfer systems with perturbation elements.
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| 6. |
- Zheng, Shao Fei, et al.
(författare)
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Performance evaluation with turbulent flow and heat transfer characteristics in rectangular cooling channels with various novel hierarchical rib schemes
- 2023
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Ingår i: International Journal of Heat and Mass Transfer. - 0017-9310. ; 214
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Tidskriftsartikel (refereegranskat)abstract
- Turbulators, such as ribs, dimples, and pin-fins, play a vital role in the internal cooling efficiency of turbine blades. As a typical turbulator, various rib configurations using a uniform arrangement scheme have indicated high heat transfer enhancement but the friction loss is simultaneously subject to a great increase. In this work, a novel hierarchical arrangement scheme of ribs is developed aiming to improve the cooling efficiency. Adopting the uniform scheme as a baseline, the hierarchical scheme is implemented for six representative rib configurations (including transverse ribs, angled ribs, V-shaped ribs, inverted V-shaped ribs, M-shaped ribs, and inverted M-shaped ribs) and evaluated for its feasibility and generality. For different cooling designs, turbulent flow and heat transfer of the ribbed cooling channel are studied by three-dimensional numerical simulations based on the finite volume method with a constructed turbulence model. It is found that for all rib configurations, the hierarchical scheme can remarkably reduce the friction loss as desired, especially for the inverted V-shaped rib with a reduction of up to 50%. Due to the occurrence of flow separation, secondary flows offered by transverse ribs are characterized by a two-dimensional recirculation vortex behind the rib. For other rib configurations, secondary flows present a typical three-dimensional characteristic including the downwash flows along the inclined rib leg and the longitudinal vortices. The usage of the hierarchical scheme with small ribs strongly suppresses these secondary flows, which contributes to the significant decrease in form drag loss. Meanwhile, using the hierarchical scheme produces a slight heat transfer deterioration commonly, which is because the constrained secondary vortices weaken the turbulent mixing and convection heat transfer. Significantly, for the two W-shaped ribs, the limited secondary vortices but fully developed under the hierarchical scheme achieve a higher heat transfer enhancement. Finally, for all considered ribs, the hierarchical scheme can improve the overall performance factor of (Nu/Nu0)/(f/f0)1/3 by more than 10%, and up to 21.15% for the V-shaped rib. Adjusting design variables, including the decreasing ratio of the rib size and the initial rib size, the hierarchical scheme still provides even higher performance enhancement.
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| 7. |
- Cheng, Shi-Ping, et al.
(författare)
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Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger
- 2021
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Ingår i: Horticulture Research. - : Springer Nature. - 2052-7276. ; 8:1
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Tidskriftsartikel (refereegranskat)abstract
- Ginger (Zingiber officinale) is one of the most valued spice plants worldwide; it is prized for its culinary and folk medicinal applications and is therefore of high economic and cultural importance. Here, we present a haplotype-resolved, chromosome-scale assembly for diploid ginger anchored to 11 pseudochromosome pairs with a total length of 3.1 Gb. Remarkable structural variation was identified between haplotypes, and two inversions larger than 15 Mb on chromosome 4 may be associated with ginger infertility. We performed a comprehensive, spatiotemporal, genome-wide analysis of allelic expression patterns, revealing that most alleles are coordinately expressed. The alleles that exhibited the largest differences in expression showed closer proximity to transposable elements, greater coding sequence divergence, more relaxed selection pressure, and more transcription factor binding site differences. We also predicted the transcription factors potentially regulating 6-gingerol biosynthesis. Our allele-aware assembly provides a powerful platform for future functional genomics, molecular breeding, and genome editing in ginger.
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| 8. |
- Gao, Jie, et al.
(författare)
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Demography and speciation history of the homoploid hybrid pine Pinus densata on the Tibetan Plateau
- 2012
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Ingår i: Molecular Ecology. - : John Wiley & Sons. - 0962-1083 .- 1365-294X. ; 21:19, s. 4811-4827
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Tidskriftsartikel (refereegranskat)abstract
- Pinus densata is an ecologically successful homoploid hybrid that inhabits vast areas of heterogeneous terrain on the south-eastern Tibetan Plateau as a result of multiple waves of colonization. Its region of origin, route of colonization onto the plateau and the directions of introgression with its parental species have previously been defined, but little is known about the isolation and divergence history of its populations. In this study, we surveyed nucleotide polymorphism over eight nuclear loci in 19 representative populations of P. densata and its parental species. Using this information and coalescence simulations, we assessed the historical changes in its population size, gene flow and divergence in time and space. The results indicate a late Miocene origin for P. densata associated with the recent uplift of south-eastern Tibet. The subsequent differentiation between geographical regions of this species began in the late Pliocene and was induced by regional topographical changes and Pleistocene glaciations. The ancestral P. densata population had a large effective population size but the central and western populations were established by limited founders, suggesting that there were severe bottlenecks during the westward migration out of the ancestral hybrid zone. After separating from their ancestral populations, population expansion occurred in all geographical regions especially in the western range. Gene flow in P. densata was restricted to geographically neighbouring populations, resulting in significant differentiation between regional groups. The new information on the divergence and demographic history of P. densata reported herein enhances our understanding of its speciation process on the Tibetan Plateau.
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| 9. |
- Gao, Jie, et al.
(författare)
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Phylogeography and introgression between Pinus kesiya and Pinus yunnanensis in Southeast Asia
- 2023
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Ingår i: Journal of Systematics and Evolution. - : John Wiley & Sons. - 1674-4918 .- 1759-6831.
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Tidskriftsartikel (refereegranskat)abstract
- Southeast Asia (SEA) has seen strong climatic oscillations and fluctuations in sea levels during the Quaternary. The impact of past climate changes on the evolution and distribution of local flora in SEA is still poorly understood. Here we aim to infer how the Quaternary climate change affects the evolutionary process and range shifts in two pine species. We investigated the population genetic structure and diversity using cytoplasmic DNA markers, and performed ecological niche modeling to reconstruct the species past distribution and to project range shift under future climates. We found substantial gene flow across the continuous distribution of the subtropical Pinus yunnanensis. In contrast, the tropical Pinus kesiya showed a strong population structure in accordance with its disjunct distribution across montane islands in Indochina and the Philippines. A broad hybrid zone of the two species occurs in southern Yunnan. Asymmetric introgression from the two species was detected in this zone with dominant mitochondrial gene flow from P. yunnanensis and chloroplast gene flow from P. kesiya. The observed population structure suggests a typical postglaciation expansion in P. yunnanensis, and a glacial expansion and interglacial contraction in P. kesiya. Ecological niche modeling supports the inferred demographic history and predicts a decrease in range size for P. kesiya under future climates. Our results suggest that tropical pine species in SEA have undergone evolutionary trajectories different from high latitude species related to their Quaternary climate histories. We also illustrate the need for urgent conservation actions in this fragmented landscape.
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| 10. |
- Guo, Jing-Fang, et al.
(författare)
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Low genetic diversity and population connectivity fuel vulnerability to climate change for the Tertiary relict pine Pinus bungeana
- 2023
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Ingår i: Journal of Systematics and Evolution. - : John Wiley & Sons. - 1674-4918 .- 1759-6831. ; 61:1, s. 143-156
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Tidskriftsartikel (refereegranskat)abstract
- Endemic species are important components of regional biodiversity and hold the key to understanding local adaptation and evolutionary processes that shape species distributions. This study investigated the biogeographic history of a relict conifer Pinus bungeana Zucc. ex Endl. confined to central China. We examined genetic diversity in P. bungeana using genotyping-by-sequencing and chloroplast and mitochondrial DNA markers. We performed spatial and temporal inference of recent genetic and demographic changes, and dissected the impacts of geography and environmental gradients on population differentiation. We then projected P. bungeana's risk of decline under future climates. We found extremely low nucleotide diversity (average π 0.0014), and strong population structure (global FST 0.234) even at regional scales, reflecting long-term isolation in small populations. The species experienced severe bottlenecks in the early Pliocene and continued to decline in the Pleistocene in the western distribution, whereas the east expanded recently. Local adaptation played a small (8%) but significant role in population diversity. Low genetic diversity in fragmented populations makes the species highly vulnerable to climate change, particularly in marginal and relict populations. We suggest that conservation efforts should focus on enhancing gene pool and population growth through assisted migration within each genetic cluster to reduce the risk of further genetic drift and extinction.
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