Comparative analysis and functional annotation of a large expressed sequence tag collection of apple

Authors: GASIC, KSENIJA - UNIV OF IL; CLEMSON UNIV; GONZALEZ, DELKIN - UNIV OF IL, URBANA, IL; THIMMAPURAM, JYOTHI - UNIV OF IL, URBANA, IL; MALNOY, MICKAEL - CORNELL UNIV, GENEVA, NY; GONG, GEORGE - UNIV OF IL, URBANA, IL; HAN, YUEPENG - UNIV OF IL, URBANA, IL; VODKIN, LILA - UNIV OF IL, URBANA, IL; LEI, LIU - UNIV OF IL, URBANA, IL; ALDWINCKLE, HERB - CORNELL UNIV, GENEVA, NY; CARROLL, NATALIE - PURDUE UNIV, INDIANA; ORVIS, KATHRYN - PURDUE UNIV, INDIANA; GOLDSBROUGH, PETER - PURDUE UNIV, INDIANA; CLIFTON, SANDRA - WASHINGTON UNIV, ST.LOUIS; PAPE, DEANA - WASHINGTON UNIV, ST.LOUIS; FULTON, LUCINDA - WASHINGTON UNIV, ST.LOUIS; MARTIN, JOHN - WASHINGTON UNIV, ST.LOUIS; THEISING, BRENDA - WASHINGTON UNIV, ST.LOUIS; Wisniewski, Michael; Fazio, Gennaro; KORBAN, SCHUYLER - UNIV OF IL, URBANA, IL

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/14/2008
Publication Date: 2/13/2009
Citation: Gasic, K., Gonzalez, D.O., Thimmapuram, J., Malnoy, M., Gong, G., Han, Y., Vodkin, L.O., Lei, L., Aldwinckle, H.S., Carroll, N., Orvis, K., Goldsbrough, P., Clifton, S., Pape, D., Fulton, L., Martin, J., Theising, B., Wisniewski, M.E., Fazio, G., Korban, S.S. 2009. Comparative analysis and functional annotation of a large expressed sequence tag collection of apple. The Plant Genome. 2(1):23-38.

Interpretive Summary: Economically important traits in fruit crops are determined by the genetic composition of the specific cultivar and the regulation and expression of those genes. The expression of specific sets of genes in particular tissue at a particular time or developmental stage will determine if a tree is dwarfed or tall, columnar or spreading, resistant or susceptible to disease, and have big fruit or little fruit, sweet or sour fruit, etc. Expressed sequence tags (ESTs) provide a picture of all the genes that are being expressed in a specific tissue at any given point in time and are invaluable to discovering and identifying the role of specific genes in defining economically important traits. ESTs are invaluable for gene discovery, genome annotation, and comparative genomics. The present study identified and sequenced over 190,000 ESTs from different tissues and cultivars of apple at various developmental stages or exposed to biotic or abiotic stress conditions. Sequence analysis of these ESTS revealed that they could be combined into 23,442 contigs (multiple sequences representing the same gene) and over 9,400 singletons (sequences that could not be coalesced) for a total of over 33,800 unigenes. Comparative analysis showed a high degree of homology with the poplar genome. There were over 3,000 protein matches unique to apple-poplar without homology in other species database. These genes may represent tree-specific genes and their functional role should be explored. The information obtained from this study can be used for identifying specific genes that are responsible for economically-important traits in apple and other tree fruit crops.

Technical Abstract: A total of 34 apple cDNA libraries were constructed from root, leaf, bud, shoot, flower, and fruit tissues, at varying developmental stages and/or under biotic or abiotic stress conditions, and of several genotypes. From these libraries, 190,425 clones were partially sequenced from the 5’ end and 42,619 clones were sequenced from the 3’ end, and a total of 182,241 high quality expressed sequence tags (ESTs) were obtained. These coalesced into 23,442 tentative contigs and 9,843 singletons, for a total of 33,825 apple unigenes. Functional annotation of this unigene set revealed an even distribution of apple sequences among the three main GO categories. Of approximately 33,000 apple unigenes, 8,437 (25%) had no detectable homologs (E greater than 0.1) in the Arabidopsis genome. When the entire apple unigene set was compared with the entire citrus unigene set and the poplar predicted proteome, both members of the core eudicot and rosids clade, 13,521 of the apple unigenes matched one or more sequences in citrus; while 25,817 had counterparts in the poplar protein database. Apple-Arabidopsis-Citrus-Poplar comparisons revealed closer evolutionary relationships between apple and poplar than with the other two species. Genes involved in basic metabolic pathways appear to be largely conserved among apple, citrus, poplar, and Arabidopsis.