Analyses of Expressed Sequence Tags from Apple

Abstract

The domestic apple (Malus domestica; also known as Malus pumila Mill.) has become a model fruit crop in which to study commercial traits such as disease and pest resistance, grafting, and flavor 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 collection from various tissues of apple, focusing on fruit tissues of the cultivar Royal Gala. Over 150,000 expressed sequence tags 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 nonredundant sequences comprising 17,460 tentative contigs and 25,478 singletons, together representing what we predict are approximately one-half the expressed genes from apple. Many potential molecular markers are abundant in the apple transcripts. Dinucleotide repeats are found in 4,018 nonredundant sequences, mainly in the 5#-untranslated region 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 are highly abundant with one found, on average, every 706 bp of transcribed DNA. Predictions of the numbers of representatives from protein families indicate 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 (Arabidopsis thaliana) suggest 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.

Identification of Genes with Potential Roles in Apple Fruit Development and Biochemistry through Large-Scale Statistical Analysis of Expressed Sequence Tags

“…The number of unique sequences derived from the combined set of clusters and singletons (approximately 44,000) is similar to the number of unique sequences (approximately 43,000) determined by Newcomb et al (2006) from clustering of approximately 150,000 apple ESTs, but substantially greater than the 6,928 unique sequences identified by the most recent National Center for Biotechnology Information (NCBI) UniGene apple assembly (http://www.ncbi.nlm.nih.gov/UniGene; UniGene Build No. 13).…”

“…Public sequence databanks contain in excess of approximately 200,000 apple EST sequences. The majority of the ESTs were contributed through large-scale sequencing efforts in the United States and New Zealand (Korban et al, 2004;Newcomb et al, 2006). The entire available EST dataset resulted from the efforts of at least 20 contributors and was derived from more than 70 cDNA libraries representing diverse transcriptional profiles from a variety of organs, fruit parts, developmental stages, biotic and abiotic stresses, and from at least nine cultivars (Table I; Supplemental Table I).…”

“…For example, in apple, Newcomb et al (2006) recently analyzed approximately 150,000 ESTs from 43 libraries for the presence of potential molecular markers useful for genetic mapping and undertook a census of representatives of common protein families and genes potentially important for fruit quality. An additional attractive use of EST data is as an entry point for gene expression analysis.…”

Towards the identification of flower-specific genes in Citrus spp

“…This could indicate that reproductive development of woody perennials would share, at least to some extent, particular motifs not found among herbaceous-derived proteins. This observation has also been reported for other woody species such as Eucalyptus (Dornelas and Rodriguez, 2005) and apple (Newcomb et al, 2006).…”

The genome of the domesticated apple (Malus × domestica Borkh.)

“…In Rosaceae, photosynthesis-derived carbohydrates are transported mainly as sorbitol 23,24 . Compared with other plant genomes, apple has considerably more copies of key genes related to sorbitol metabolism.…”