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Comparative genomics analysis in Prunoideae to identify biologically relevant polymorphisms.
MedLine Citation:
PMID:  23763653     Owner:  NLM     Status:  Publisher    
Abstract/OtherAbstract:
Prunus is an economically important genus with a wide range of physiological and biological variability. Using the peach genome as a reference, sequencing reads from four almond accessions and one sweet cherry cultivar were used for comparative analysis of these three Prunus species. Reference mapping enabled the identification of many biological relevant polymorphisms within the individuals. Examining the depth of the polymorphisms and the overall scaffold coverage, we identified many potentially interesting regions including hundreds of small scaffolds with no coverage from any individual. Non-sense mutations account for about 70 000 of the 13 million identified single nucleotide polymorphisms (SNPs). Blast2GO analyses on these non-sense SNPs revealed several interesting results. First, non-sense SNPs were not evenly distributed across all gene ontology terms. Specifically, in comparison with peach, sweet cherry is found to have non-sense SNPs in two 1-aminocyclopropane-1-carboxylate synthase (ACS) genes and two 1-aminocyclopropane-1-carboxylate oxidase (ACO) genes. These polymorphisms may be at the root of the nonclimacteric ripening of sweet cherry. A set of candidate genes associated with bitterness in almond were identified by comparing sweet and bitter almond sequences. To the best of our knowledge, this is the first report in plants of non-sense SNP abundance in a genus being linked to specific GO terms.
Authors:
Tyson Koepke; Scott Schaeffer; Artemus Harper; Federico Dicenta; Mark Edwards; Robert J Henry; Birger L Møller; Lee Meisel; Nnadozie Oraguzie; Herman Silva; Raquel Sánchez-Pérez; Amit Dhingra
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Publication Detail:
Type:  JOURNAL ARTICLE     Date:  2013-6-13
Journal Detail:
Title:  Plant biotechnology journal     Volume:  -     ISSN:  1467-7652     ISO Abbreviation:  Plant Biotechnol. J.     Publication Date:  2013 Jun 
Date Detail:
Created Date:  2013-6-14     Completed Date:  -     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  101201889     Medline TA:  Plant Biotechnol J     Country:  -    
Other Details:
Languages:  ENG     Pagination:  -     Citation Subset:  -    
Copyright Information:
© 2013 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.
Affiliation:
Department of Horticulture, Washington State University, Pullman, WA, USA; Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA, USA.
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