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| 1 | Phased,chromosome-scale genome assemblies of tetraploid potato reveal a complex genome,transcriptome,and predicted proteome landscape underpinning genetic diversity显示文摘Cultivated potato is a clonally propagated autotetraploid species with a highly heterogeneous genome.Phased assemblies of six cultivars including two chromosome-scale phased genome assemblies revealed extensive allelic diversity,including altered coding and transcript sequences,preferential allele expression,and structural variation that collectively result in a highly complex transcriptome and predicted proteome,which are distributed across the homologous chromosomes.Wild species contribute to the extensive allelic diversity in tetraploid cultivars,demonstrating ancestral introgressions predating modern breeding efforts.As a clonally propagated autotetraploid that undergoes limited meiosis,dysfunctional and deleterious alleles are not purged in tetraploid potato.Nearly a quarter of the loci bore mutations are predicted to have a high negative impact on protein function,complicating breeder’s efforts to reduce genetic load.The StCDF1 locus controls maturity,and analysis of six tetraploid genomes revealed that 12 allelic variants of StCDF1 are correlated with maturity in a dosage-dependent manner.Knowledge of the complexity of the tetraploid potato genome with its rampant structural variation and embedded deleterious and dysfunctional alleles will be key not only to implementing precision breeding of tetraploid cultivars but also to the construction of homozygous,diploid potato germplasm containing favorable alleles to capitalize on heterosis in F1 hybrids. | Genevieve Hoopes Xiaoxi Meng John P.Hamilton Sai Reddy Achakkagari Fernanda de Alves Freitas Guesdes Marie E.Bolger Joseph J.Coombs Danny Esselink Natalie R.Kaiser Linda Kodde Maria Kyriakidou Brian Lavrijssen Natascha van Lieshout Rachel Shereda Heather K.Tuttle Brieanne Vaillancourt Joshua C.Wood Jan Mde Boer Nolan Bornowski Peter Bourke David Douches Herman Jvan Eck Dave Ellis Max J.Feldman Kyle M.Gardner Johannes C.P.Hopman Jiming Jiang Walter S.De Jong Joseph C.Kuhl Richard G.Novy Stan Oome Vidyasagar Sathuvalli Ek Han Tan Remco A.Ursum M.Isabel Vales Kelly Vining Richard G.F.Visser Jack Vossen G.Craig Yencho Noelle L.Anglin Christian W.B.Bachem Jeffrey B.Endelman Laura M.Shannon Martina V.Stromvik Helen H.Tai Bjorn Usadel C.Robin Buell Richard Finkers | 2022 | Molecular Plant2022，15，3： | 4 |
| 2 | Exploiting Natural Variation in Tomato to Define Pathway Structure and Metabolic Regulation of Fruit Polyphenolics in the Lycopersicum Complex显示文摘While the structures of plant primary metabolic pathways are generally well defined and highly conserved across species,those defining specialized metabolism are less well characterized and more highly variable across species.In this study,we investigated polyphenolic metabolism in the lycopersicum complex by characterizing the underlying biosynthetic and decorative reactions that constitute the metabolic network of polyphenols across eight different species of tomato.For this purpose,GC-MS-and LC-MS-based metabolomics of different tissues of Solatium lycopersicum and wild tomato species were carried out,in concert with the evaluation of cross-hybridized microarray data for MapMan-based transcriptomic analysis,and publicly available RNA-sequencing data for annotation of biosynthetic genes.The combined data were used to compile species-specific metabolic networks of polyphenolic metabolism,allowing the establishment of an entire pan-species biosynthetic framework as well as annotation of the functions of decoration enzymes involved in the formation of metabolic diversity of the flavonoid pathway.The combined results are discussed in the context of the current understanding of tomato flavonol biosynthesis as well as a global view of metabolic shifts during fruit ripening.Our results provide an example as to how large-scale biology approaches can be used for the definition and refinement of large specialized metabolism pathways. | Takayuki Tohge Federico Scossa Regina Wendenburg Pierre Frasse llse Balbo Mutsumi Watanabe Saleh Alseekh Sagar Sudam Jadhav Jay C.Delfin Marc Lohse Patrick Giavalisco Bjoern Usadel Youjun Zhang Jie Luo Mondher Bouzayen Alisdair R.Fernie | 2020 | Molecular Plant2020，13，7： | 3 |
| 3 | Transcriptional Wiring of Cell Wall-Related Genes in Arabidopsis显示文摘Transcriptional 协作,或合作表示,可以基因意味着相应蛋白质的功能的相关。例如,涉及第二等的房间墙纤维素生合成的几基因被共同表示,基因从事了木聚糖的合成,它是第二等的房间墙的一个主要部件。扩大分析的这些类型,我们调查了所有糖类活跃的酶(CAZy ) 的合作表示关系为 Arabidopsis thaliana 的相关基因。因此,意愿是 transcriptionally 连接不同房间墙相关的进程到互相,并且也到另外的生物函数。便于容易的用手的检查,我们作为网络和矩阵显示了这些相互作用,并且创造了为所有 transcriptional 协会包含可下载的文件的一个基于万维网的接口(http://gffzzd07dfdf4eb194e87hx5ufn96wcnck6uon.ffgz.tsg.suse.edu.cn/corecarb ) 。 | Marek Mutwil Colin Ruprecht Federico M. Giorgi Martin Bringmann Bjorn Usadel Staffan Persson | 2009 | Molecular Plant2009，2，5： | 2 |
| 4 | MapMan4: A Refined Protein Classification and Annotation Framework Applicable to Multi-Omics Data Analysis显示文摘Genome sequences from over 200 plant species have already been published, with this number expected to increase rapidly due to advances in sequencing technologies. Once a new genome has been assembled and the genes identified, the functional annotation of their putative translational products, proteins, using ontologies is of key importance as it places the sequencing data in a biological context. Furthermore, to keep pace with rapid production of genome sequences, this functional annotation process must be fully automated. Here we present a redesigned and significantly enhanced MapMan4 framework, together with a revised version of the associated online Mercator annotation tool. Compared with the original MapMan, the new ontology has been expanded almost threefold and enforces stricter assignment rules. This framework was then incorporated into Mercator4, which has been upgraded to reflect current knowledge across the land plant group, providing protein annotations for all embryophytes with a comparably high quality. The annotation process has been optimized to allow a plant genome to be annotated in a matter of minutes. The output results continue to be compatible with the established MapMan desktop application. | Rainer Schwacke Gabriel Y.Ponce-Soto Kirsten Krause Anthony M.Bolger Borjana Arsova Asis Hallab Kristina Gruden Mark Stitt Marie E.Bolger Bjorn Usadel | 2019 | Molecular Plant2019，12，6： | 2 |
| 5 | Nateglinide improves glycaemic control when added to metformin monotherapy:results of a randomized trial with type 2 diabetes patients显示文摘 | Marre M Van Gaal L Usadel KH | | Diabetes0，，： | 1 |
| 6 | One-year prophylactic treatment of euthyroid Hashimoto' s thyroiditis patients with levothyroxine: is there a benefit显示文摘 | Padberg S Heller K Usadel KH | 2001 | Thyroid2001，11，： | 1 |
| 7 | Regulatory features underlying pollination-dependent and-independent tomato fruit set revealed by transcript and primary metabolite profiling 显示文摘 | Wang H Schauer N Usadel B | 2009 | Plant Cell2009，21，： | 1 |
| 8 | Facile detection of mitochondrial DNA mutations in tumors and bodily fluids显示文摘 | Fliss MS Usadel H Caballero OL | 2000 | Science2000，287，： | 1 |
| 9 | The effect of alpha-lipoic acid on the neurovascular reflex arc in patients with diabetic neuropathy assessed by capillary microscopy显示文摘 | Haak ES Usadel KH Kohleisen M | 1999 | Microvaso Res1999，58，1： | 1 |
| 10 | The possible etiological role of psychologicaldisturbances in Graves' disease 显示文摘 | Harsch I Paschke R Usadel KH | 1992 | Acta Med Austriaea1992，19，1： | 1 |
| 11 | Integrated analysis ofmetabolite and transcript levels reveals the metabolic shifts thatunderlie tomato fruit development and highlight regulatory aspectsof metabolic network behavior 显示文摘 | Carrari F Baxter C Usadel B | 2006 | Plant Physiology2006，142，： | 1 |
| 12 | Facile detection of mitochondrial DNA mutations in tumor and bodily fluids 显示文摘 | Usadel H Otavia L | 2000 | Science2000，287，： | 1 |
| 13 | Quantitative O6-methylguanine-DNA methyltransferase methylation analysis in curatively resected non-small cell lung cancer: associations with clinical outcome显示文摘 | Brabender J Usadel H Metzger R | 2003 | Clin Cancer Res2003，9，1： | 1 |
| 14 | Facile detection of mitochondriat DNA mutations in tumors and bodily fluids 显示文摘 | Fliss MS Usadel H Caballero OL | 2000 | Science2000，287，5460： | 1 |
| 15 | Facile detection of mitochondrial DNA mutations in tumors and bodily fluids显示文摘 | Fliss MS Usadel H Caballero OL | 2000 | Science2000，287，5460： | 1 |
| 16 | Barley grain matura- tion and germination: metabolic pathway and regulatory network commonalities and differences highlighted by new MapMan/PageMan profiling tools显示文摘 | Sreenivasulu N Usadel B Winter A | 2008 | Plant Physiol2008，1，46： | 1 |
| 17 | Facile detection of mitochondrial DNA mutations in tumors and bodily flu- ids 显示文摘 | Fliss MS Usadel H Caballero OL | 2000 | Science2000，287，5460： | 1 |
| 18 | Fenofibrate improves microcirculation in patients with hyperlipidemia显示文摘 | Haak T Haak E Kusterer K Weber A Kohleisen M Usadel KH | 1998 | Eur J Med Res1998，213，12： | 1 |
| 19 | Facile detection of mitochondrial DNA mutations in tumors and bodily fluids显示文摘 | Fliss M S Usadel H Caballero O L | 2000 | Science2000，287，5460： | 1 |
| 20 | Effects of alpha-lipoic acid on microcirculation in patients with peripheral diabetic ncuropathy 显示文摘 | Hank E Usadel KH Kusterer K | 2000 | Exp Clin Endocrinol Diabetes2000，108，： | 1 |
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