CNR - Institute of Plant Genetics, Perugia, Italy.
BMC Plant Biol. 2010 Sep 24;10:211. doi: 10.1186/1471-2229-10-211.
The 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.
The 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.
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.
栽培橄榄（Olea europaea L.）是木犀科中最重要的农业物种。尽管已经有许多关于质体多态性的研究来评估油橄榄亚种的分类学、系统发育和系统地理学，但仅鉴定出少数可区分农艺和经济重要性橄榄品种的多态性区域。本研究的目的是对橄榄的整个质体基因组进行测序，并分析许多潜在的多态性区域，以开发新的品种间遗传标记。
使用通用和新设计的 PCR 引物通过直接序列分析确定了橄榄品种 Frantoio 的完整质体基因组，这些引物设计用于扩增所有重叠区域。橄榄的叶绿体基因组在组织和基因顺序上在许多被子植物物种中是保守的，并且不包含在 Jasminum 和 Menodora 属的叶绿体基因组中发现的任何倒位、基因重复、插入、反向重复扩展和基因/内含子丢失，这两个属与 Olea 同科。注释序列用于评估编码基因的含量、重复和长散布序列的程度和分布以及核苷酸组成模式。这些分析为橄榄质体的结构、功能和比较基因组学研究提供了必要的信息。此外，将橄榄质体序列与其他品种和物种的序列进行比对，确定了栽培橄榄内 30 个新的细胞器多态性。
除了鉴定可能在改变橄榄品种代谢和适应方面发挥功能作用的突变外，新的叶绿体标记代表了一种评估橄榄品种间质体变异水平的有价值工具，可用于群体遗传分析、系统发育、品种特征和 DNA 食品追踪。
