Abstract
BackgroundThe cultivated olive (Olea europaea L.) is the most agriculturally important species of the Oleaceae family. Although many studies have been performed on plastid polymorphisms to evaluate taxonomy, phylogeny and phylogeography of Olea subspecies, only few polymorphic regions discriminating among the agronomically and economically important olive cultivars have been identified. The objective of this study was to sequence the entire plastome of olive and analyze many potential polymorphic regions to develop new inter-cultivar genetic markers.ResultsThe complete plastid genome of the olive cultivar Frantoio was determined by direct sequence analysis using universal and novel PCR primers designed to amplify all overlapping regions. The chloroplast genome of the olive has an organisation and gene order that is conserved among numerous Angiosperm species and do not contain any of the inversions, gene duplications, insertions, inverted repeat expansions and gene/intron losses that have been found in the chloroplast genomes of the genera Jasminum and Menodora, from the same family as Olea.The annotated sequence was used to evaluate the content of coding genes, the extent, and distribution of repeated and long dispersed sequences and the nucleotide composition pattern. These analyses provided essential information for structural, functional and comparative genomic studies in olive plastids. Furthermore, the alignment of the olive plastome sequence to those of other varieties and species identified 30 new organellar polymorphisms within the cultivated olive.ConclusionsIn addition to identifying mutations that may play a functional role in modifying the metabolism and adaptation of olive cultivars, the new chloroplast markers represent a valuable tool to assess the level of olive intercultivar plastome variation for use in population genetic analysis, phylogenesis, cultivar characterisation and DNA food tracking.
Highlights
The cultivated olive (Olea europaea L.) is the most agriculturally important species of the Oleaceae family
In addition to identifying mutations that may play a functional role in modifying the metabolism and adaptation of olive cultivars, the new chloroplast markers represent a valuable tool to assess the level of olive intercultivar plastome variation for use in population genetic analysis, phylogenesis, cultivar characterisation and DNA food tracking
Five repeats were located within coding regions (CDS), two repeats were found in the introns of the ycf3 and ndhA
Summary
The cultivated olive (Olea europaea L.) is the most agriculturally important species of the Oleaceae family. The Olea genus includes two sections, Olea and Ligustroides The former comprises the six recognised subspecies of the olive complex, which can be found throughout the Mediterranean area as well as the temperate and subtropical regions of Africa and Asia. Chloroplast genome sequencing of species belonging to this family from the tribe of Jasmineae revealed that two genera, Jasminum and Menodora, carry several distinctive rearrangements, including inversions, gene duplications, insertions, inverted repeat expansions and gene/intron losses [2]. One of these genomic features involves the duplication of the rpl protein-coding gene in Jasminum.
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