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Open Access Highly Accessed Research article

Analysis of 90 Mb of the potato genome reveals conservation of gene structures and order with tomato but divergence in repetitive sequence composition

Wei Zhu14, Shu Ouyang1, Marina Iovene2, Kimberly O'Brien15, Hue Vuong1, Jiming Jiang2 and C Robin Buell3*

  • * Corresponding author: C Robin Buell buell@msu.edu

  • † Equal contributors

Author Affiliations

1 J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA

2 Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA

3 Department of Plant Biology, Michigan State University, 166 Plant Biology Building, East Lansing, MI 48824, USA

4 Translational Sciences, MedImmune, Inc., One MedImmune Way, Gaithersburg, MD, 20878, USA

5 Institute for Genome Sciences, University of Maryland School of Medicine, 20 Penn Street HSF-II, Baltimore, MD 21201, USA

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BMC Genomics 2008, 9:286  doi:10.1186/1471-2164-9-286

Published: 13 June 2008

Abstract

Background

The Solanaceae family contains a number of important crop species including potato (Solanum tuberosum) which is grown for its underground storage organ known as a tuber. Albeit the 4th most important food crop in the world, other than a collection of ~220,000 Expressed Sequence Tags, limited genomic sequence information is currently available for potato and advances in potato yield and nutrition content would be greatly assisted through access to a complete genome sequence. While morphologically diverse, Solanaceae species such as potato, tomato, pepper, and eggplant share not only genes but also gene order thereby permitting highly informative comparative genomic analyses.

Results

In this study, we report on analysis 89.9 Mb of potato genomic sequence representing 10.2% of the genome generated through end sequencing of a potato bacterial artificial chromosome (BAC) clone library (87 Mb) and sequencing of 22 potato BAC clones (2.9 Mb). The GC content of potato is very similar to Solanum lycopersicon (tomato) and other dicotyledonous species yet distinct from the monocotyledonous grass species, Oryza sativa. Parallel analyses of repetitive sequences in potato and tomato revealed substantial differences in their abundance, 34.2% in potato versus 46.3% in tomato, which is consistent with the increased genome size per haploid genome of these two Solanum species. Specific classes and types of repetitive sequences were also differentially represented between these two species including a telomeric-related repetitive sequence, ribosomal DNA, and a number of unclassified repetitive sequences. Comparative analyses between tomato and potato at the gene level revealed a high level of conservation of gene content, genic feature, and gene order although discordances in synteny were observed.

Conclusion

Genomic level analyses of potato and tomato confirm that gene sequence and gene order are conserved between these solanaceous species and that this conservation can be leveraged in genomic applications including cross-species annotation and genome sequencing initiatives. While tomato and potato share genic features, they differ in their repetitive sequence content and composition suggesting that repetitive sequences may have a more significant role in shaping speciation than previously reported.