Open Access Highly Accessed Research article

Low-pass shotgun sequencing of the barley genome facilitates rapid identification of genes, conserved non-coding sequences and novel repeats

Thomas Wicker1, Apurva Narechania2, Francois Sabot3, Joshua Stein2, Giang TH Vu56, Andreas Graner5, Doreen Ware24 and Nils Stein5*

Author Affiliations

1 Institute of Plant Biology, University Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland

2 Cold Spring Harbor Laboratory, 1 Bungtown Rd., Cold Spring Harbor, NY 11724, USA

3 Laboratoire Génome et Développement des Plantes, UMR 5096 CNRS-IRD-Université de Perpignan, 52 Avenue Paul Alduy, F-66860 Perpignan, France

4 United States Department of Agriculture-Agricultural Research Service (USDA-ARS) North Atlantic Area (NAA) Plant, Soil & Nutrition Laboratory Research Unit, Ithaca, New York 15853, USA

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

6 Institute of Biological, Environmental and Rural Sciences (IBERS), Edward Llwyd Buiding, Aberystwyth University, Ceredigion, SY23 3DA, UK

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BMC Genomics 2008, 9:518  doi:10.1186/1471-2164-9-518

Published: 31 October 2008

Abstract

Background

Barley has one of the largest and most complex genomes of all economically important food crops. The rise of new short read sequencing technologies such as Illumina/Solexa permits such large genomes to be effectively sampled at relatively low cost. Based on the corresponding sequence reads a Mathematically Defined Repeat (MDR) index can be generated to map repetitive regions in genomic sequences.

Results

We have generated 574 Mbp of Illumina/Solexa sequences from barley total genomic DNA, representing about 10% of a genome equivalent. From these sequences we generated an MDR index which was then used to identify and mark repetitive regions in the barley genome. Comparison of the MDR plots with expert repeat annotation drawing on the information already available for known repetitive elements revealed a significant correspondence between the two methods. MDR-based annotation allowed for the identification of dozens of novel repeat sequences, though, which were not recognised by hand-annotation. The MDR data was also used to identify gene-containing regions by masking of repetitive sequences in eight de-novo sequenced bacterial artificial chromosome (BAC) clones. For half of the identified candidate gene islands indeed gene sequences could be identified. MDR data were only of limited use, when mapped on genomic sequences from the closely related species Triticum monococcum as only a fraction of the repetitive sequences was recognised.

Conclusion

An MDR index for barley, which was obtained by whole-genome Illumina/Solexa sequencing, proved as efficient in repeat identification as manual expert annotation. Circumventing the labour-intensive step of producing a specific repeat library for expert annotation, an MDR index provides an elegant and efficient resource for the identification of repetitive and low-copy (i.e. potentially gene-containing sequences) regions in uncharacterised genomic sequences. The restriction that a particular MDR index can not be used across species is outweighed by the low costs of Illumina/Solexa sequencing which makes any chosen genome accessible for whole-genome sequence sampling.