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From manual curation to visualization of gene families and networks across Solanaceae plant species

Anuradha Pujar, Naama Menda, Aureliano Bombarely, Jeremy D. Edwards, Susan R. Strickler, Lukas A. Mueller
2013 Database: The Journal of Biological Databases and Curation  
Conflict of interest. None declared.  ...  Gene family and gene network curation depend on highquality structural annotations, which often have to be manually curated.  ...  Visualizing networks of genes and multigene families annotated to drought stress Here, we use drought response as an example of how gene family and gene networks are annotated.  ... 
doi:10.1093/database/bat028 pmid:23681907 pmcid:PMC3655285 fatcat:2xq6ka3agngzrjeoqihb6rszfq

SolCyc: a database hub at the Sol Genomics Network (SGN) for the manual curation of metabolic networks in Solanum and Nicotiana specific databases

Hartmut Foerster, Aureliano Bombarely, James N D Battey, Nicolas Sierro, Nikolai V Ivanov, Lukas A Mueller
2018 Database: The Journal of Biological Databases and Curation  
Abstract SolCyc is the entry portal to pathway/genome databases (PGDBs) for major species of the Solanaceae family hosted at the Sol Genomics Network.  ...  SolCyc has been recently extended by taxon-specific databases, i.e. the family-specific SolanaCyc database, containing only curated data pertinent to species of the nightshade family, and NicotianaCyc,  ...  Except for new compounds that were created in MetaCyc to stay compatible with MetaCyc's compound identifier system and curation standard, new pathways, genes and enzymes from Solanaceae species were curated  ... 
doi:10.1093/database/bay035 pmid:29762652 pmcid:PMC5946812 fatcat:s3r3n6tqyrbjvm3iakvag5gjs4

Metabolic networks of the Nicotiana genus in the spotlight: content, progress and outlook

Hartmut Foerster, James N D Battey, Nicolas Sierro, Nikolai V Ivanov, Lukas A Mueller
2020 Briefings in Bioinformatics  
Manually curated metabolic databases residing at the Sol Genomics Network comprise two taxon-specific databases for the Solanaceae family, i.e. SolanaCyc and the genus Nicotiana, i.e.  ...  Solanaceae family and Nicotiana genus, respectively.  ...  Although MetaCyc includes curated metabolic data from 2980 species across all kingdoms and PlantCyc covers the same for more than 350 plant species, SolanaCyc and NicotianaCyc contain the metabolic content  ... 
doi:10.1093/bib/bbaa136 pmid:32662816 pmcid:PMC8138835 fatcat:qgybfnay2rhvdh5w6ff7z2pufm

DES-TOMATO: A Knowledge Exploration System Focused On Tomato Species

Adil Salhi, Sónia Negrão, Magbubah Essack, Mitchell J. L. Morton, Salim Bougouffa, Rozaimi Razali, Aleksandar Radovanovic, Benoit Marchand, Maxat Kulmanov, Robert Hoehndorf, Mark Tester, Vladimir B. Bajic
2017 Scientific Reports  
Knowledge obtained from tomato research initiated improvements in tomato and, being transferrable to other such economically important crops, has led to a surge of tomato-related research and published  ...  We developed DES-TOMATO knowledgebase (KB) for exploration of information related to tomato. Information exploration is enabled through terms from 26 dictionaries and combination of these terms.  ...  Acknowledgements The computational analysis for this study was performed on Dragon and Snapdragon compute clusters of the  ... 
doi:10.1038/s41598-017-05448-0 pmid:28729549 pmcid:PMC5519719 fatcat:2xl3s62blvhplmvvrbgbhlggwm

Genome-Wide Comparative Analyses Reveal the Dynamic Evolution of Nucleotide-Binding Leucine-Rich Repeat Gene Family among Solanaceae Plants

Eunyoung Seo, Seungill Kim, Seon-In Yeom, Doil Choi
2016 Frontiers in Plant Science  
Comparative analysis of duplications showed distinct duplication patterns within pepper and among Solanaceae plants suggesting subgroup-or species-specific gene duplication events after speciation, resulting  ...  Phylogenetic analysis and classification of Solanaceae NLRs revealed that the majority of NLR super family members fell into 14 subgroups, including a TIR-NLR (TNL) subgroup and 13 non-TNL subgroups.  ...  ., 2014) , but the number of NLRs in the pepper genome increased due to manual curation and improvements of pipeline.  ... 
doi:10.3389/fpls.2016.01205 pmid:27559340 pmcid:PMC4978739 fatcat:h6khh24utzah3inmckyqgpbcse

Gramene 2013: comparative plant genomics resources

Marcela K. Monaco, Joshua Stein, Sushma Naithani, Sharon Wei, Palitha Dharmawardhana, Sunita Kumari, Vindhya Amarasinghe, Ken Youens-Clark, James Thomason, Justin Preece, Shiran Pasternak, Andrew Olson (+14 others)
2013 Nucleic Acids Research  
Its strength derives from the application of a phylogenetic framework for genome comparison and the use of ontologies to integrate structural and functional annotation data.  ...  Recently, we released a Plant Reactome portal featuring 133 curated rice pathways. This portal will be expanded for Arabidopsis, maize and other plant species.  ...  curation.  ... 
doi:10.1093/nar/gkt1110 pmid:24217918 pmcid:PMC3964986 fatcat:lcgbm3znjnaptk4vprqeoowt34

The Evolutionary History of Small RNAs in the Solanaceae [article]

Patricia Baldrich, Sébastien Bélanger, Shuyao Kong, Suresh Pokhrel, Saleh Tamim, Chong Teng, Courtney Schiebout, Sai Guna Ranjan Gurazada, Pallavi Gupta, Parth Patel, Mayumi Nakano, Ayush Dusia (+2 others)
2021 bioRxiv   pre-print
We applied a suite of computational tools to predict and annotate two major small RNA classes: (1) microRNAs (miRNAs), typically 20-22 nt RNAs generated from a hairpin precursor and functioning in gene  ...  The birth, death, expansion, and contraction of these small RNA loci are dynamic evolutionary processes that characterize the Solanaceae family.  ...  652 genera in the nightshade family (Xia et al., 2013). 653 To investigate whether PHAS loci are generated from orthologous genes across 654 species, we constructed gene orthogroups and searched for conserved  ... 
doi:10.1101/2021.05.26.445884 fatcat:kd2wvby7vfg3rabydg5jf3kzue

Wild tobacco genomes reveal the evolution of nicotine biosynthesis

Shuqing Xu, Thomas Brockmöller, Aura Navarro-Quezada, Heiner Kuhl, Klaus Gase, Zhihao Ling, Wenwu Zhou, Christoph Kreitzer, Mario Stanke, Haibao Tang, Eric Lyons, Priyanka Pandey (+4 others)
2017 Proceedings of the National Academy of Sciences of the United States of America  
Together, these results provide evidence that TEs and gene duplications facilitated the emergence of a key metabolic innovation relevant to plant fitness.  ...  Transcription factor binding motifs derived from TEs may have contributed to the coexpression of nicotine biosynthetic pathway genes and coordinated the metabolic flux.  ...  We thank members of the Department of Molecular Ecology for assistance with the manual curation of gene models and for scientific discussions; Dr. Sang-Gyu Kim  ... 
doi:10.1073/pnas.1700073114 pmid:28536194 pmcid:PMC5468653 fatcat:ftdrcwbm6nci7icm7cxpe2gfd4

GoMapMan: integration, consolidation and visualization of plant gene annotations within the MapMan ontology

Živa Ramšak, Špela Baebler, Ana Rotter, Matej Korbar, Igor Mozetič, Björn Usadel, Kristina Gruden
2013 Nucleic Acids Research  
It was developed to facilitate improvement, consolidation and visualization of gene annotations across several plant species.  ...  The main features of GoMapMan are (i) dynamic and interactive gene product annotation through various curation options; (ii) consolidation of gene annotations for different plant species through the integration  ...  The authors would also like to thank Vid Podpecˇan and Marko Petek for their assistance concerning the implementation and consequent testing of the export files, and Henrik Krnec for his assistance with  ... 
doi:10.1093/nar/gkt1056 pmid:24194592 pmcid:PMC3965006 fatcat:tfwfmnboxveyrpvuzkgwvqnpvi

solQTL: a tool for QTL analysis, visualization and linking to genomes at SGN database

Isaak Y Tecle, Naama Menda, Robert M Buels, Esther van der Knaap, Lukas A Mueller
2010 BMC Bioinformatics  
Description: The Sol Genomics Network (SGN, http://solgenomics.net) is a primary repository for phenotypic, genetic, genomic, expression and metabolic data for the Solanaceae family and other related Asterids  ...  species and houses a variety of bioinformatics tools.  ...  For part of the duration of this project the first author of this manuscript has been a visiting scientist at Wageningen University, Plant Breeding and Genetics Department, The Netherlands.  ... 
doi:10.1186/1471-2105-11-525 pmid:20964836 pmcid:PMC2984588 fatcat:76jqq2e56bgxzjhj56keb55hgu

Advances in Omics and Bioinformatics Tools for Systems Analyses of Plant Functions

K. Mochida, K. Shinozaki
2011 Plant and Cell Physiology  
Furthermore, in several plant species, the development of omics resources has progressed to address particular biological properties of individual species.  ...  From these perspectives, we provide this review of the emerging aspects of plant systems research based on omics and bioinformatics analyses together with their associated resources and technological advances  ...  Acknowledgments The authors thank Tetsuya Sakurai, Takuhiro Yoshida, Lam-Son Phan Tran and Yuji Sawada of the RIKEN Plant Science Center, and Kei Iida of RIKEN BASE for their valuable suggestions and comments  ... 
doi:10.1093/pcp/pcr153 pmid:22156726 pmcid:PMC3233218 fatcat:5p4m7xlrknflrfbjfb4pwdug4u

LeafMachine: Using machine learning to automate leaf trait extraction from digitized herbarium specimens

William N. Weaver, Julienne Ng, Robert G. Laport
2020 Applications in Plant Sciences  
Obtaining phenotypic data from herbarium specimens can provide important insights into plant evolution and ecology but requires significant manual effort and time.  ...  Of the unmeasured specimens, only 0.9% and 2.1% of high- and low-resolution images, respectively, were visually judged to have measurable leaves.  ...  This work was supported by a Microsoft AI for Earth grant to all authors and a National Science Foundation grant to J.N. and R.G.L. (NSF-EF 1550813).  ... 
doi:10.1002/aps3.11367 pmid:32626609 pmcid:PMC7328653 fatcat:qrdhu6pcjjbmhiqzdov6aoxvdy

Evolution and applications of plant pathway resources and databases

Y. Sucaet, T. Deva
2011 Briefings in Bioinformatics  
We lay out trends and challenges in the ongoing efforts to integrate plant pathway databases and the applications of database integration.  ...  Plants are important sources of food and plant products are essential for modern human life.  ...  Eve Syrkin Wurtele and Dr Julie Dickerson at Iowa State University, who supported us in a number of ways with encouragement, sound advice, guidance and lots of good ideas.  ... 
doi:10.1093/bib/bbq083 pmid:21949268 fatcat:v4w7i5b47zhj7idwb7k5wrpdgi

TomExpress, a unified tomato RNA-Seq platform for visualization of expression data, clustering and correlation networks

Mohamed Zouine, Elie Maza, Anis Djari, Mattieu Lauvernier, Pierre Frasse, Abdelaziz Smouni, Julien Pirrello, Mondher Bouzayen
2017 The Plant Journal  
In addition, it allows for the identification of co-expressed genes and for the visualization of correlation networks of co-regulated gene groups.  ...  Sample details were manually curated to be easily understandable by biologists.  ...  The authors are grateful to Christophe Klopp from GenoToul bioinformatics for his help. The authors declare no conflict of interest. Short Supporting Information Legends  ... 
doi:10.1111/tpj.13711 pmid:28873253 fatcat:zxpcuowtzncrpe55uy7md47zbq

Evolutionary routes to biochemical innovation revealed by integrative analysis of a plant-defense related specialized metabolic pathway

Gaurav D Moghe, Bryan J Leong, Steven M Hurney, A Daniel Jones, Robert L Last
2017 eLife  
Our results reveal hundreds of acylsugars produced across the Solanaceae family and even within a single plant, built on simple sugar cores.  ...  To understand how this novelty is generated, we investigated the evolution of the Solanaceae family-specific, trichome-localized acylsugar biosynthetic pathway using a combination of mass spectrometry,  ...  T32-GM110523 to BL ADJ acknowledges support from the USDA National Institute of Food and Agriculture, Hatch project MICL-02143.  ... 
doi:10.7554/elife.28468 pmid:28853706 pmcid:PMC5595436 fatcat:dma3wzmfzzblhi7mwziwgrvtnu
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