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Databases and Tools for the Analysis of the Barley Genome

  • Sebastian Beier
  • Daniel M. Bolser
  • Uwe Scholz
  • Manuel Spannagl
  • Paul J. Kersey
Chapter
Part of the Compendium of Plant Genomes book series (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.

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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Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  • Sebastian Beier
    • 1
  • Daniel M. Bolser
    • 2
  • Uwe Scholz
    • 1
  • Manuel Spannagl
    • 3
  • Paul J. Kersey
    • 2
  1. 1.Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenSeelandGermany
  2. 2.European Molecular Biology LabThe European Bioinformatics Institute, Wellcome Trust Genome CampusHinxton, CambridgeUK
  3. 3.Plant Genome and Systems Biology (PGSB), Helmholtz Center MunichNeuherbergGermany

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