Chloroplast Genome Variation and Evolutionary Analysis of Olea europaea L.

Abstract

Olive (Olea europaea L.) is a very important woody tree and favored by consumers because of the fruit’s high-quality olive oil. Chloroplast genome analysis will provide insights into the chloroplast variation and genetic evolution of olives. The complete chloroplast genomes of three accessions (O. europaea subsp. cuspidata isolate Yunnan, O. europaea subsp. europaea var. sylvestris, and O. europaea subsp. europaea var. frantoio) were obtained by next-generation sequencing technology. A total of 133 coding regions were identified in the three chloroplast genomes without rearrangement. O. europaea subsp. europaea var. sylvestris and O. europaea subsp. europaea var. frantoio had the same sequences (155,886 bp), while O. europaea subsp. cuspidata isolate Yunnan (155,531 bp) presented a large gap between rps16 and trnQ-UUG genes with six small gaps and fewer microsatellites. The whole chloroplast genomes of 11 O. europaea were divided into two main groups by a phylogenetic tree and O. europaea subsp. cuspidata formed a separate group (Cuspidata group) with the other subspecies (Mediterranean/North African group). Identification of consistency and diversity among O. europaea subspecies will benefit the exploration of domestication events and facilitate molecular-assisted breeding for O. europaea.

Comparative chloroplast genomes of Prunus subgenus Cerasus (Rosaceae): insights into sequence variations and phylogenetic relationships

“…2004). In the cp genomes of 23 Prunus species here analyzed, mononucleotide SSRs were the most abundant, while SSRs with repeat motifs of two or more base pairs were scarce or absent, as have been reported in other angiosperms (Iram et al 2019;Niu et al 2020;Zeb et al 2020;Yik et al 2021). Among the mononucleotide SSRs, A/T repeats were found to be the most abundant, while G/C repeats were quite rare, similar to the previously reported cp genomes (Khan et al 2019;Chincoya et al 2020;Niu et al 2020;Roy et al 2020;Liu et al 2021), and this might be due to the AT-rich composition in the cp genome (Abdullah et al 2019).…”

“…In the cp genomes of 23 Prunus species here analyzed, mononucleotide SSRs were the most abundant, while SSRs with repeat motifs of two or more base pairs were scarce or absent, as have been reported in other angiosperms (Iram et al 2019;Niu et al 2020;Zeb et al 2020;Yik et al 2021). Among the mononucleotide SSRs, A/T repeats were found to be the most abundant, while G/C repeats were quite rare, similar to the previously reported cp genomes (Khan et al 2019;Chincoya et al 2020;Niu et al 2020;Roy et al 2020;Liu et al 2021), and this might be due to the AT-rich composition in the cp genome (Abdullah et al 2019). Most of the SSRs were located in the LSC region compared to SSC and IR regions; this result is consistent with several other studies in Artemisia scoparia (Iram et al 2019), Firmiana (Abdullah et al 2019), Lycium chinense (Yang et al 2019), Mammillaria (Chincoya et al 2020), and Olea europaea (Niu et al 2020).…”

“…In angiosperms, IGSs 3'trnV-UAC-ndhC, rpl32-trnL-UAG , trnQ- UUG-5'rps16, rps4-trnT-UGU , psbZ-trnG-GCC , rpl33-rps18, psbL-trnS-GCU , psbM-trnD-GUC , trnM-CAU-aptE, accD-trnM, rrn5-rrn4.5, infA-rps8, etc. (Shaw et al 2007;Wu et al 2018;Chincoya et al 2020;Khan et al 2020;Li et al 2020a;Niu et al 2020;Mekbib et al 2020) and rpl16 intron (Kelchner et al 1997) have proven to be highly variable in different species. However, these so-called highly variable regions may exhibit unequal levels of variation across different taxonomic groups of angiosperms, and even do not show high levels of variation in some genus.…”

How to Choose a Good Marker to Analyze the Olive Germplasm (Olea europaea L.) and Derived Products

“…europaea and cuspidata from Australia and Hawaii [197], and using both ribosomal and cytoplasmic sequences, Besnard et al [198] revised the correlations within the Oleaceae family. More recently, other authors have analyzed chloroplast genome variation to perform O. europaea L. evolutionary analysis [199,200], confirming the wide potential of these markers.…”

Complete chloroplast genome sequence of historical olive (Olea europaea subsp. europaea) cultivar Mehras, in Jordan

“…Several chloroplast genomes were identified and investigated from Olea spp. adapted to different habitats (Besnard et al 2011;Niu et al 2020). In this study, we assembled the complete chloroplast genome in Mehras using next generation sequencing.…”