Plant Molecular Biology

, Volume 67, Issue 6, pp 581–588 | Cite as

An overview of the apple genome through BAC end sequence analysis

Article

Abstract

The apple, Malus × domestica Borkh., is one of the most important fruit trees grown worldwide. A bacterial artificial chromosome (BAC)-based physical map of the apple genome has been recently constructed. Based on this physical map, a total of ∼2,100 clones from different contigs (overlapping BAC clones) have been selected and sequenced at both ends, generating 3,744 high-quality BAC end sequences (BESs) including 1,717 BAC end pairs. Approximately 8.5% of BESs contain simple sequence repeats (SSRs), most of which are AT/TA dimer repeats. Potential transposable elements are identified in ∼21% of BESs, and most of these elements are retrotransposons. About 11% of BESs have homology to the Arabidopsis protein database. The matched proteins cover a broad range of categories. The average GC content of the predicted coding regions of BESs is 42.4%; while, that of the whole BESs is 39%. A small number of BES pairs were mapped to neighboring chromosome regions of A. thaliana and Populus trichocarpa; whereas, no pairs are mapped to the Oryza sativa genome. The apple has a higher degree of synteny with the closely related Populus than with the distantly related Arabidopsis. BAC end sequencing can be used to anchor a small proportion of the apple genome to the Populus and possibly to the Arabidopsis genomes.

Keywords

Apple Bacterial artificial chromosome BAC end sequences Simple sequence repeats Synteny 

Abbreviations

BAC

Bacterial artificial chromosome

BES

BAC end sequence

SSR

Simple sequence repeat

TE

Transposable element

EST

Expressed seqeuence tag

Notes

Acknowledgements

This project was supported by the USDA Cooperative State Research, Education and Extension Service—National Research Initiative—Plant Genome Program grant No. 2005-35300-15538

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Copyright information

© Springer Science+Business Media B.V. 2008

Authors and Affiliations

  1. 1.Department of Natural Resources and Environmental SciencesUniversity of IllinoisUrbanaUSA

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