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Databases and Tools for the Analysis of the Barley Genome

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The Barley Genome

Part of the book series: Compendium of Plant Genomes ((CPG))

Abstract

Ever-increasing advances seen in barley genome sequencing over the last years have enabled scientists to generate databases and tools specially designed in helping researchers and breeders. Both genomic as well as expressed sequences were obtained through various experimental setups ranging from BAC sequencing over Illumina iSelect 9k SNP chip to RNA-Seq to form heterogeneous datasets. Where possible datasets were crosslinked and enriched in information to build a basis for further research. Ensembl Plants, a web portal designed for exploring genomic data for various plant species, have been utilized to explore differences and similarities between barley and its related species. Furthermore, the barley genome explorer BARLEX was constructed to be the central repository and hub of genomic sequences of barley sequencing efforts. Powerful visualizations of interconnected BACs and other sequencing information enable to backtrack every position that makes up the barley reference sequence and help in understanding the connection to other datasets. Further tools utilizing other barley data are discussed and described for more specialized use cases. Last but not least a list of URLs is given for a comprehensive overview of barley-centric resources.

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Abbreviations

AA:

Amino acid

AGP:

A golden path (filetype)

AHRD:

Automatic assignment of human-readable description

BAC:

Bacterial artificial chromosome

BLAST:

Basic local alignment search tool

CDS:

Coding sequence

cDNA:

Copy DNA

CSH:

Cold Spring Harbor laboratory

DNA:

Deoxyribonucleic acid

EBI:

European Bioinformatics Institute

EI:

Earlham Institute (formerly TGAC)

EST:

Expressed sequence tag

FPC:

Fingerprinted contig

FTP:

File transfer protocol

GO:

Gene ontology

HC:

High confidence

HTML:

Hypertext markup language

IBSC:

International Barley Genome Sequencing Consortium

IPK:

Leibniz Institute of Plant Genetics and Crop Plant Research

Iso-Seq:

Isoform sequencing

JHI:

James Hutton Institute

LC:

Low confidence

PGSB:

Plant Genome and Systems Biology unit at the Helmholtz Center Munich

QTL:

Quantitative trait loci

RNA:

Ribonucleic acid

RNA-Seq:

RNA sequencing

SNP:

Single nucleotide polymorphism

TAIR:

The Arabidopsis Information Resource

TCAP:

Triticeae Coordinated Agricultural Project

TGAC:

The Genome Analysis Centre

WGS:

Whole genome shotgun

XML:

Extensible markup language

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Authors and Affiliations

  1. Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466, Seeland, Germany

    Sebastian Beier & Uwe Scholz

  2. European Molecular Biology Lab, The European Bioinformatics Institute, Wellcome Trust Genome Campus, CB10 1SD, Hinxton, Cambridge, UK

    Daniel M. Bolser & Paul J. Kersey

  3. Plant Genome and Systems Biology (PGSB), Helmholtz Center Munich, 85764, Neuherberg, Germany

    Manuel Spannagl

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  1. Sebastian Beier
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  2. Daniel M. Bolser
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  3. Uwe Scholz
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  4. Manuel Spannagl
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  5. Paul J. Kersey
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Correspondence to Uwe Scholz .

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Editors and Affiliations

  1. Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Sachsen-Anhalt, Germany

    Nils Stein

  2. Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota, USA

    Gary J. Muehlbauer

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Beier, S., Bolser, D.M., Scholz, U., Spannagl, M., Kersey, P.J. (2018). Databases and Tools for the Analysis of the Barley Genome. In: Stein, N., Muehlbauer, G. (eds) The Barley Genome. Compendium of Plant Genomes. Springer, Cham. https://doi.org/10.1007/978-3-319-92528-8_21

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