Identification of new polymorphic regions and differentiation of cultivated olives (Olea europaea L.) through plastome sequence comparison

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.

The quest to resolve recent radiations: Plastid phylogenomics of extinct and endangered Hawaiian endemic mints (Lamiaceae)

“…The sequence demonstrates the typical quadripartite structure of other angiosperms, with a large single copy (LSC) region of 81,364 bp and a small single copy (SSC) region of 17,499 bp, separated by a pair of inverted repeats (IRa and IRb) of 25,436 bp. The length and structure of the sequence is similar to other plastid genome sequences of members in the order Lamiales (Lukas and Novak, 2013;Mariotti et al, 2010;Qian et al, 2013) (Fig. 3, see also Fig.…”

“…The chloroplast genomes of the Hawaiian mints demonstrate the typical angiosperm quadripartite structure, and the gene content, order, and GC content were consistent with most other members of the Lamiales (Mariotti et al, 2010;Wicke et al, 2014;Zhang et al, 2013). The Hawaiian mint genome did not demonstrate any rearrangements or inversions, which have been found in Jasmin nudiflorum, Schwalbea americana, and a few other species (Welch et al, 2016) (Lee et al, 2007;Wicke et al, 2013).…”

“…First, we conducted a reference-guided assembly using YASRA 2.32 (Ratan, 2009) with olive (Olea europaea, NC_013707) (Mariotti et al, 2010) as the reference, which was the closest chloroplast genome sequence available at the time, and a setting of ≥75% identity between the reads and the reference. We also conducted de novo assembly of the shotgun data using default settings in SOAPdenovo v1.05 (Li et al, 2010).…”

Origin and History of the Olive

“…Whatever the techniques used to visualize the genetic diversity, the main feature is to aggregate data from the three DNA supports in the olive tree: the mitochondrial DNA (mt, ), the Chloroplast DNA (cp, [58] and the nuclear DNA (nu-, [15,59,60,61]. The information brought by the three compartments is not proportional to the length of the DNA, but by the mode of inheritance and by their mode of evolution.…”

Traceability of Origin and Authenticity of Olive Oil

“…A very important results, recently published, in Olea europaea L. genomic studies have been the DNA sequencing of the entire plastome of the Italian cultivar 'Frantoio' (Mariotti et al 2010). This sequence has a length of 155,889 bp and showed an organization and gene order that is conserved among numerous Angiosperms.…”