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An overview of the apple genome through BAC end sequence analysis

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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.

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Abbreviations

BAC:

Bacterial artificial chromosome

BES:

BAC end sequence

SSR:

Simple sequence repeat

TE:

Transposable element

EST:

Expressed seqeuence tag

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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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  1. Department of Natural Resources and Environmental Sciences, University of Illinois, Urbana, IL, 61801, USA

    Yuepeng Han & Schuyler S. Korban

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  1. Yuepeng Han
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  2. Schuyler S. Korban
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Correspondence to Schuyler S. Korban.

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Han, Y., Korban, S.S. An overview of the apple genome through BAC end sequence analysis. Plant Mol Biol 67, 581–588 (2008). https://doi.org/10.1007/s11103-008-9321-9

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