Bioinformatics in the plant genomic and phenomic domain: The German contribution to resources, services and perspectives.

Plant genetic resources are a substantial opportunity for plant breeding, preservation and maintenance of biological diversity. As part of the German Network for Bioinformatics Infrastructure (de.NBI) the German Crop BioGreenformatics Network (GCBN) focuses mainly on crop plants and provides both data and software infrastructure which are tailored to the needs of the plant research community. Our mission and key objectives include: (1) provision of transparent access to germplasm seeds, (2) the delivery of improved workflows for plant gene annotation, and (3) implementation of bioinformatics services that link genotypes and phenotypes. This review introduces the GCBN's spectrum of web-services and integrated data resources that address common research problems in the plant genomics community.

[1]  Alfredo Ferro,et al.  OCDB: a database collecting genes, miRNAs and drugs for obsessive-compulsive disorder , 2015, Database J. Biol. Databases Curation.

[2]  Erik Schultes,et al.  The FAIR Guiding Principles for scientific data management and stewardship , 2016, Scientific Data.

[3]  Thomas Nussbaumer,et al.  RNASeqExpressionBrowser - a web interface to browse and visualize high-throughput expression data , 2014, Bioinform..

[4]  S. Okay.  Identification of Gene Families Using Genomics and/or Transcriptomics Data , 2016 .

[5]  Stephan Weise,et al.  GBIS: the information system of the German Genebank , 2015, Database J. Biol. Databases Curation.

[6]  Thomas Nussbaumer,et al.  PGSB PlantsDB: updates to the database framework for comparative plant genome research , 2015, Nucleic Acids Res..

[7]  Uwe Scholz,et al.  PGP repository: a plant phenomics and genomics data publication infrastructure , 2016, Database J. Biol. Databases Curation.

[8]  U. Sonnewald,et al.  Differences and commonalities of plant responses to single and combined stresses , 2017, The Plant journal : for cell and molecular biology.

[9]  Binxiao Feng,et al.  Epigenetic map and genetic map basis of complex traits in cassava population , 2017, Scientific Reports.

[10]  B. Usadel,et al.  Plant Pathway Databases. , 2016, Methods in molecular biology.

[11]  John K. McCooke,et al.  A chromosome conformation capture ordered sequence of the barley genome , 2017, Nature.

[12]  Monya Baker,et al.  Reproducibility: Seek out stronger science , 2016, Nature.

[13]  Uwe Scholz,et al.  Measures for interoperability of phenotypic data: minimum information requirements and formatting , 2016, Plant Methods.

[14]  K. Mayer,et al.  PGSB/MIPS PlantsDB Database Framework for the Integration and Analysis of Plant Genome Data. , 2017, Methods in molecular biology.

[15]  Joseph M. Awika,et al.  Major Cereal Grains Production and Use around the World , 2011 .

[16]  Janet M Thornton,et al.  ELIXIR: a distributed infrastructure for European biological data. , 2012, Trends in biotechnology.

[17]  Karl G. Kugler,et al.  chromoWIZ: a web tool to query and visualize chromosome-anchored genes from cereal and model genomes , 2014, BMC Plant Biology.

[18]  Edward S. Buckler,et al.  Crop genomics: advances and applications , 2011, Nature Reviews Genetics.

[19]  U. Scholz,et al.  BARLEX - the Barley Draft Genome Explorer. , 2015, Molecular plant.

[20]  A. Greenberg,et al.  Next-generation phenotyping: requirements and strategies for enhancing our understanding of genotype–phenotype relationships and its relevance to crop improvement , 2013, Theoretical and Applied Genetics.

[21]  Mark Stitt,et al.  Mercator: a fast and simple web server for genome scale functional annotation of plant sequence data. , 2014, Plant, cell & environment.

[22]  Matthias Lange,et al.  Towards recommendations for metadata and data handling in plant phenotyping. , 2015, Journal of experimental botany.

[23]  Xiaofeng Cao,et al.  The effect of transposable elements on phenotypic variation: insights from plants to humans , 2016, Science China Life Sciences.

[24]  Uwe Scholz,et al.  Towards a whole‐genome sequence for rye (Secale cereale L.) , 2017, The Plant journal : for cell and molecular biology.

[25]  Yu Wang,et al.  DroughtDB: an expert-curated compilation of plant drought stress genes and their homologs in nine species , 2015, Database J. Biol. Databases Curation.

[26]  Jing Zhang,et al.  Erratum to: The real cost of sequencing: scaling computation to keep pace with data generation , 2016, Genome Biology.

[27]  Theo van Hintum,et al.  EURISCO: The European search catalogue for plant genetic resources , 2016, Nucleic Acids Res..

[28]  M. Bayer,et al.  Exome sequencing of geographically diverse barley landraces and wild relatives gives insights into environmental adaptation , 2016, Nature Genetics.

[29]  Uwe Scholz,et al.  Quantitative monitoring of Arabidopsis thaliana growth and development using high-throughput plant phenotyping , 2016, Scientific Data.

[30]  Anne E. Carpenter,et al.  ProtocolNavigator: emulation-based software for the design, documentation and reproduction biological experiments , 2014, Bioinform..

[31]  Anil S. Thanki,et al.  transPLANT Resources for Triticeae Genomic Data , 2016, The plant genome.

[32]  Uwe Scholz,et al.  From RNA-seq to large-scale genotyping - genomics resources for rye (Secale cereale L.) , 2011, BMC Plant Biology.

[33]  P. Tudzynski,et al.  Cross-talk of the biotrophic pathogen Claviceps purpurea and its host Secale cereale , 2017, BMC Genomics.

[34]  J. Batley,et al.  A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome , 2014, Science.

[35]  Uwe Scholz,et al.  e!DAL - a framework to store, share and publish research data , 2014, BMC Bioinformatics.

[36]  Uwe Scholz,et al.  LAILAPS: The Plant Science Search Engine , 2014, Plant & cell physiology.

[37]  Marie E. Bolger,et al.  Plant genome sequencing - applications for crop improvement. , 2014, Current opinion in biotechnology.

[38]  K. Mayer,et al.  PGSB/MIPS Plant Genome Information Resources and Concepts for the Analysis of Complex Grass Genomes. , 2016, Methods in molecular biology.

[39]  David C. Nickle,et al.  ViroBLAST: a stand-alone BLAST web server for flexible queries of multiple databases and user's datasets , 2007, Bioinform..

[40]  Adam M Phillippy,et al.  New advances in sequence assembly , 2017, Genome research.

[41]  Anne E. Trefethen,et al.  Toward interoperable bioscience data , 2012, Nature Genetics.

[42]  Uwe Scholz,et al.  From plant genomes to phenotypes. , 2017, Journal of biotechnology.

[43]  J. Chapman,et al.  Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ) , 2013, The Plant journal : for cell and molecular biology.

[44]  B. Gaut,et al.  A triptych of the evolution of plant transposable elements. , 2010, Trends in plant science.

[45]  Uwe Scholz,et al.  OPTIMAS-DW: A comprehensive transcriptomics, metabolomics, ionomics, proteomics and phenomics data resource for maize , 2012, BMC Plant Biology.

[46]  S. Jackson,et al.  The First 50 Plant Genomes , 2013 .

[47]  Mihaela M. Martis,et al.  A physical, genetic and functional sequence assembly of the barley genome. , 2022 .