Plant Physiology Preview
Published on March 10, 2006; 10.1104/pp.105.076208
Received January 11, 2006
Returned for revision February 6, 2006
Accepted February 22, 2006
Analyses of Expressed Sequence Tags from Apple (Malus x domestica)
Richard D. Newcomb *, Ross N. Crowhurst , Andrew P. Gleave , Erik H.A. Rikkerink , Andrew C. Allan , Lesley L. Beuning , Judith H. Bowen , Emma Gera , Kim R. Jamieson , Bart J. Janssen , William A. Laing , Steve McArtney , Bhawana Nain , Gavin S. Ross , Kimberley C. Snowden , Edwige J.F. Souleyre , Eric F. Walton , and Yar-Khing Yauk
The Horticultural and Food Research Institute of New Zealand Ltd., Mt Albert Research Centre, Private Bag 92169, Auckland, New Zealand
* Corresponding author; email: rnewcomb{at}hortresearch.co.nz.
The domestic apple (Malus x domestica, also known as M. pumila, Mill.) has become a model fruit crop in which to study commercial traits such as disease and pest resistance, grafting, and flavour and health compound biosynthesis. To speed the discovery of genes involved in these traits, develop markers to map genes, and breed new cultivars, we have produced a substantial expressed sequence tag (EST) collection from various tissues of apple, focusing on fruit tissues of the cultivar Royal Gala. Over 150,000 ESTs have been collected from 43 different cDNA libraries representing 34 different tissues and treatments. Clustering of these sequences results in a set of 42,938 non redundant sequences (NRs) comprising 17,460 tentative contigs and 25,478 singletons together representing what we predict are approximately half the expressed genes from apple. Many potential molecular markers are abundant in the apple transcripts. Dinucleotide repeats are found in 4018 NRs, mainly in the 5'UTR of the gene, with a bias toward one repeat type (containing AG, 88%) and against another (repeats containing CG, 0.1%). Trinucleotide repeats are most common in the predicted coding regions and do not show a similar degree of sequence bias in their representation. Bi-allelic single nucleotide polymorphisms (SNPs) are highly abundant with one found, on average, every 706 bp of transcribed DNA. Predictions of the numbers of representatives from protein families indicates the presence of many genes involved in disease resistance and the biosynthesis of flavor and health-associated compounds. Comparisons of some of these gene families with Arabidopsis suggests instances where there have been duplications in the lineages leading to apple of biosynthetic and regulatory genes that are expressed in fruit. This resource paves the way for a concerted functional genomics effort in this important temperate fruit crop.
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