| 11. |
- Shi, Tian-Le, et al.
(författare)
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High-quality genome assembly enables prediction of allele-specific gene expression in hybrid poplar
- 2024
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Ingår i: Plant Physiology. - : Oxford University Press. - 0032-0889 .- 1532-2548. ; 195:1, s. 652-670
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Tidskriftsartikel (refereegranskat)abstract
- Poplar (Populus) is a well-established model system for tree genomics and molecular breeding, and hybrid poplar is widely used in forest plantations. However, distinguishing its diploid homologous chromosomes is difficult, complicating advanced functional studies on specific alleles. In this study, we applied a trio-binning design and PacBio high-fidelity long-read sequencing to obtain haplotype-phased telomere-to-telomere genome assemblies for the 2 parents of the well-studied F1 hybrid “84K” (Populus alba × Populus tremula var. glandulosa). Almost all chromosomes, including the telomeres and centromeres, were completely assembled for each haplotype subgenome apart from 2 small gaps on one chromosome. By incorporating information from these haplotype assemblies and extensive RNA-seq data, we analyzed gene expression patterns between the 2 subgenomes and alleles. Transcription bias at the subgenome level was not uncovered, but extensive-expression differences were detected between alleles. We developed machine-learning (ML) models to predict allele-specific expression (ASE) with high accuracy and identified underlying genome features most highly influencing ASE. One of our models with 15 predictor variables achieved 77% accuracy on the training set and 74% accuracy on the testing set. ML models identified gene body CHG methylation, sequence divergence, and transposon occupancy both upstream and downstream of alleles as important factors for ASE. Our haplotype-phased genome assemblies and ML strategy highlight an avenue for functional studies in Populus and provide additional tools for studying ASE and heterosis in hybrids.
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| 12. |
- Teng, Chao, et al.
(författare)
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Influence of Triple Bonds as pi-Spacer Units in Metal-Free Organic Dyes for Dye-Sensitized Solar Cells
- 2010
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Ingår i: The Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 114:25, s. 11305-11313
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Tidskriftsartikel (refereegranskat)abstract
- Four metal-free organic sensitizers (TC101-TC104) with triple bonds in pi-spacers and five reference dyes (TC, TC105, TPC1, D5, and TH208) without triple bonds were applied in dye-sensitized solar cells to study the influence of triple bonds as pi-spacer units on their photoelectrochemical properties and dye-sensitized solar cells (DSCs) performance. Results show that the introduction of triple bond could red-shift the dye's absorption spectrum due to the enhancement of the pi-spacer. However, the spectrum red-shift is much less than that of the introduction of double bond because of more electronegativity of triple bond. The incident photon-to-current conversion efficiency reveals that the electron transfer yield (Phi(nu)(ET)) of DSCs becomes larger with the introduction of triple bond. Electrochemical impedance spectroscopy analysis reveals that the introduction of triple bond almost does not change the electron lifetimes in TiO2 films but decreases the effective diffusion lengths.
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| 13. |
- Tian, Xue-Chan, et al.
(författare)
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Plant-LncPipe: a computational pipeline providing significant improvement in plant lncRNA identification
- 2024
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Ingår i: Horticulture Research. - 2662-6810 .- 2052-7276. ; 11:4
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Tidskriftsartikel (refereegranskat)abstract
- Long non-coding RNAs (lncRNAs) play essential roles in various biological processes, such as chromatin remodeling, post-transcriptional regulation, and epigenetic modifications. Despite their critical functions in regulating plant growth, root development, and seed dormancy, the identification of plant lncRNAs remains a challenge due to the scarcity of specific and extensively tested identification methods. Most mainstream machine learning-based methods used for plant lncRNA identification were initially developed using human or other animal datasets, and their accuracy and effectiveness in predicting plant lncRNAs have not been fully evaluated or exploited. To overcome this limitation, we retrained several models, including CPAT, PLEK, and LncFinder, using plant datasets and compared their performance with mainstream lncRNA prediction tools such as CPC2, CNCI, RNAplonc, and LncADeep. Retraining these models significantly improved their performance, and two of the retrained models, LncFinder-plant and CPAT-plant, alongside their ensemble, emerged as the most suitable tools for plant lncRNA identification. This underscores the importance of model retraining in tackling the challenges associated with plant lncRNA identification. Finally, we developed a pipeline (Plant-LncPipe) that incorporates an ensemble of the two best-performing models and covers the entire data analysis process, including reads mapping, transcript assembly, lncRNA identification, classification, and origin, for the efficient identification of lncRNAs in plants. The pipeline, Plant-LncPipe, is available at: https://github.com/xuechantian/Plant-LncRNA-pipline.
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| 14. |
- Tian, Xue-Chan, et al.
(författare)
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Unique gene duplications and conserved microsynteny potentially associated with resistance to wood decay in the Lauraceae
- 2023
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Ingår i: Frontiers in Plant Science. - : Frontiers Media S.A.. - 1664-462X. ; 14
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Tidskriftsartikel (refereegranskat)abstract
- Wood decay resistance (WDR) is marking the value of wood utilization. Many trees of the Lauraceae have exceptional WDR, as evidenced by their use in ancient royal palace buildings in China. However, the genetics of WDR remain elusive. Here, through comparative genomics, we revealed the unique characteristics related to the high WDR in Lauraceae trees. We present a 1.27-Gb chromosome-level assembly for Lindera megaphylla (Lauraceae). Comparative genomics integrating major groups of angiosperm revealed Lauraceae species have extensively shared gene microsynteny associated with the biosynthesis of specialized metabolites such as isoquinoline alkaloids, flavonoid, lignins and terpenoid, which play significant roles in WDR. In Lauraceae genomes, tandem and proximal duplications (TD/PD) significantly expanded the coding space of key enzymes of biosynthesis pathways related to WDR, which may enhance the decay resistance of wood by increasing the accumulation of these compounds. Among Lauraceae species, genes of WDR-related biosynthesis pathways showed remarkable expansion by TD/PD and conveyed unique and conserved motifs in their promoter and protein sequences, suggesting conserved gene collinearity, gene expansion and gene regulation supporting the high WDR. Our study thus reveals genomic profiles related to biochemical transitions among major plant groups and the genomic basis of WDR in the Lauraceae.
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| 15. |
- Yan, Xue-Mei, et al.
(författare)
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Unraveling the evolutionary dynamics of the TPS gene family in land plants
- 2023
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Ingår i: Frontiers in Plant Science. - : Frontiers Media S.A.. - 1664-462X. ; 14
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Tidskriftsartikel (refereegranskat)abstract
- Terpenes and terpenoids are key natural compounds for plant defense, development, and composition of plant oil. The synthesis and accumulation of a myriad of volatile terpenoid compounds in these plants may dramatically alter the quality and flavor of the oils, which provide great commercial utilization value for oil-producing plants. Terpene synthases (TPSs) are important enzymes responsible for terpenic diversity. Investigating the differentiation of the TPS gene family could provide valuable theoretical support for the genetic improvement of oil-producing plants. While the origin and function of TPS genes have been extensively studied, the exact origin of the initial gene fusion event - it occurred in plants or microbes - remains uncertain. Furthermore, a comprehensive exploration of the TPS gene differentiation is still pending. Here, phylogenetic analysis revealed that the fusion of the TPS gene likely occurred in the ancestor of land plants, following the acquisition of individual C- and N- terminal domains. Potential mutual transfer of TPS genes was observed among microbes and plants. Gene synteny analysis disclosed a differential divergence pattern between TPS-c and TPS-e/f subfamilies involved in primary metabolism and those (TPS-a/b/d/g/h subfamilies) crucial for secondary metabolites. Biosynthetic gene clusters (BGCs) analysis suggested a correlation between lineage divergence and potential natural selection in structuring terpene diversities. This study provides fresh perspectives on the origin and evolution of the TPS gene family.
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| 16. |
- Zhao, Shi-Wei, et al.
(författare)
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Haplotype-resolved genome assembly of Coriaria nepalensis a non-legume nitrogen-fixing shrub
- 2023
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Ingår i: Scientific Data. - : Springer Nature. - 2052-4463. ; 10:1
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Tidskriftsartikel (refereegranskat)abstract
- Coriaria nepalensis Wall. (Coriariaceae) is a nitrogen-fixing shrub which forms root nodules with the actinomycete Frankia. Oils and extracts of C. nepalensis have been reported to be bacteriostatic and insecticidal, and C. nepalensis bark provides a valuable tannin resource. Here, by combining PacBio HiFi sequencing and Hi-C scaffolding techniques, we generated a haplotype-resolved chromosome-scale genome assembly for C. nepalensis. This genome assembly is approximately 620 Mb in size with a contig N50 of 11 Mb, with 99.9% of the total assembled sequences anchored to 40 pseudochromosomes. We predicted 60,862 protein-coding genes of which 99.5% were annotated from databases. We further identified 939 tRNAs, 7,297 rRNAs, and 982 ncRNAs. The chromosome-scale genome of C. nepalensis is expected to be a significant resource for understanding the genetic basis of root nodulation with Frankia, toxicity, and tannin biosynthesis.
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| 17. |
- Becker, Joel, et al.
(författare)
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Resource profile and user guide of the Polygenic Index Repository
- 2021
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Ingår i: Nature Human Behaviour. - : Nature Research (part of Springer Nature). - 2397-3374. ; 51:6, s. 694-695
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Tidskriftsartikel (refereegranskat)abstract
- Polygenic indexes (PGIs) are DNA-based predictors. Their value for research in many scientific disciplines is growing rapidly. As a resource for researchers, we used a consistent methodology to construct PGIs for 47 phenotypes in 11 datasets. To maximize the PGIs’ prediction accuracies, we constructed them using genome-wide association studies—some not previously published—from multiple data sources, including 23andMe and UK Biobank. We present a theoretical framework to help interpret analyses involving PGIs. A key insight is that a PGI can be understood as an unbiased but noisy measure of a latent variable we call the ‘additive SNP factor’. Regressions in which the true regressor is this factor but the PGI is used as its proxy therefore suffer from errors-in-variables bias. We derive an estimator that corrects for the bias, illustrate the correction, and make a Python tool for implementing it publicly available. © 2021, The Author(s), under exclusive licence to Springer Nature Limited.
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| 18. |
- Chen, Ruilin, et al.
(författare)
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Experimental demonstration of real-time optical DFT-S DMT signal transmission for a blue-LED-based UWOC system using spatial diversity reception
- 2023
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Ingår i: Applied Optics. - : Optica Publishing Group. - 1559-128X .- 2155-3165. ; 62:3, s. 541-551
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Tidskriftsartikel (refereegranskat)abstract
- Underwater wireless optical communication (UWOC) has broad prospects in underwater real-time applications. We design and experimentally demonstrate a real-time discrete Fourier transform spread discrete multi-tone (DFT-S DMT) signal transmission based on a field programmable gate array for a blue-LED-based UWOC system with a data rate of up to 30 Mbps over a 15-m underwater channel. The architecture and usage of an on-chip resource as well as power consumption are analyzed and discussed. To reduce the impacts of multipath fading and received intensity fluctuation, spatial diversity reception is also introduced. Furthermore, the receiver sensitivity at a speci-fied bit error rate (BER) threshold and the quality of the images are evaluated using three types of Reed-Solomon (RS) codes. At the BER threshold of 10-4, over 2.8-dB receiver sensitivity improvement is obtained by the DFT-S DMT scheme with the RS (64, 56) code as compared to the uncoded one at the data rate of 30 Mbps. The perform-ance of BER, color difference, and structural similarity in the image transmission of DFT-S DMT is superior to that of the conventional hard clipping quadrature amplitude modulation DMT in a high-data-rate region because of the low peak-to-average-power ratio and ability to mitigate high-frequency fading in a band-limited UWOC system. With schemes of the RS code, DFT-S, and diversity reception, error-free transmission of images is achieved over a 15-m water channel. The proposed UWOC system has the advantages of low power consumption and porta-bility, which foresees a bright future in underwater applications over short to moderate distances.
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| 19. |
- Cheng, Huailei, et al.
(författare)
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Truck platooning reshapes greenhouse gas emissions of the integrated vehicle-road infrastructure system
- 2023
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Ingår i: Nature Communications. - 2041-1723 .- 2041-1723. ; 14:1
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Tidskriftsartikel (refereegranskat)abstract
- Reducing greenhouse gas emissions has turned into a pillar of climate change mitigation. Truck platooning is proposed as a strategy to lower emissions from vehicles on roads. However, the potential interactive impacts of this technology on road infrastructure emissions remain unclear. Here, we evaluate the decarbonization effects of truck platooning on the integrated vehicle-road system at a large-scale road network level, spanning 1457 road sections across North America. We show that truck platooning decreases emissions induced by truck operations, but it degrades faster the durability of road infrastructure and leads to a 27.9% rise in road emissions due to more frequent maintenance work. Overall, truck platooning results in a 5.1% emission reduction of the integrated vehicle-road system. In contrast to the benefits of emission reduction, truck platooning leads to additional financial burdens on car users and transportation agencies, calling for the consideration of tradeoffs between emissions and costs and between agencies and users. Our research provides insights into the potential applications of truck platooning to mitigate climate change.
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| 20. |
- Chung, Sharon A, et al.
(författare)
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European population substructure is associated with mucocutaneous manifestations and autoantibody production in systemic lupus erythematosus
- 2009
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Ingår i: Arthritis and Rheumatism. - : Wiley. - 0004-3591 .- 1529-0131. ; 60:8, s. 2448-2456
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Tidskriftsartikel (refereegranskat)abstract
- OBJECTIVE: To determine whether genetic substructure in European-derived populations is associated with specific manifestations of systemic lupus erythematosus (SLE), including mucocutaneous phenotypes, autoantibody production, and renal disease. METHODS: SLE patients of European descent (n=1,754) from 8 case collections were genotyped for >1,400 ancestry informative markers that define a north-south gradient of European substructure. Using the Structure program, each SLE patient was characterized in terms of percent Northern (versus percent Southern) European ancestry based on these genetic markers. Nonparametric methods, including tests for trend, were used to identify associations between Northern European ancestry and specific SLE manifestations. RESULTS: In multivariate analyses, increasing levels of Northern European ancestry were significantly associated with photosensitivity (Ptrend=0.0021, odds ratio for highest quartile of Northern European ancestry versus lowest quartile [ORhigh-low] 1.64, 95% confidence interval [95% CI] 1.13-2.35) and discoid rash (Ptrend=0.014, ORhigh-low 1.93, 95% CI 0.98-3.83). In contrast, increasing levels of Northern European ancestry had a protective effect against the production of anticardiolipin autoantibodies (Ptrend=1.6x10(-4), ORhigh-low 0.46, 95% CI 0.30-0.69) and anti-double-stranded DNA autoantibodies (Ptrend=0.017, ORhigh-low 0.67, 95% CI 0.46-0.96). CONCLUSION: This study demonstrates that specific SLE manifestations vary according to Northern versus Southern European ancestry. Thus, genetic ancestry may contribute to the clinical heterogeneity and variation in disease outcomes among SLE patients of European descent. Moreover, these results suggest that genetic studies of SLE subphenotypes will need to carefully address issues of population substructure based on genetic ancestry.
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