Abstract
Background Prinsepia utilis Royle is a wild woody oil species of Rosaceae that yields edible oil which has been proved to possess particular benefits for human health and medical therapy. However, the lack of bred varieties has largely impeded exploiting immense potentials for high quality of its seed oil. It is urgently needed to enlarge the knowledge of genetic basis of the species and develop genetic markers to enhance modern breeding programs.ResultsHere we reported the complete chloroplast (cp) genome of 156,328 bp. Comparative cp sequence analyses of P . utilis along with other four Rosaceae species resulted in similar genome structures, gene orders, and gene contents. Contraction/expansion of inverted repeat regions (IRs) explained part of the length variation in the Rosaceae cp genomes. Genome sequence alignments revealed that nucleotide diversity was associated with AT content, and large single copy regions (LSC) and small single copy regions (SSC) harbored higher sequence variations in both coding and non-coding regions than IRs. Simple sequence repeats (SSRs) were detected in the P . utilis and compared with those of the other four Rosaceae cp genomes. Almost all the SSR loci were composed of A or T, therefore it might contribute to the A-T richness of cp genomes and be associated with AT biased sequence variation. Among all the protein-coding genes, ycf1 showed the highest sequence divergence, indicating that it could accomplish the discrimination of species within Rosaceae as well as within angiosperms better than other genes.ConclusionsWith the addition of this new sequenced cp genome, high nucleotide substitution rate and abundant deletions/insertions were observed, suggesting a greater genomic dynamics than previously explored in Rosaceae. The availability of the complete cp genome of P . utilis will provide chloroplast markers and genetic information to better enhance the conservation and utilization of this woody oil plant.
Highlights
Rosaceae, containing about 3,000 species in over 100 genera, is the third economically important plant family in temperate regions [1]
The cp genome of P. utilis exhibited a circular DNA molecule of 156,328 bp with a typical quadripartite structure resembling to the majority of land plant cp genomes
It consisted of two inverted repeat regions (IRa and IRb) of 26,302 bp separated by large (LSC) and small (SSC) single-copy regions of 85,239 and 18,485 bp, respectively (Figure 1)
Summary
Rosaceae, containing about 3,000 species in over 100 genera, is the third economically important plant family in temperate regions [1]. Five nucleic genomes, Fragaria vesca (strawberry) [4], Malus×domestica (apple) [5], Pyrus bretschneideri (pear) [6], Prunus persica (peach), and P. mume [7], were completely sequenced. Comparative cp sequence analyses of P. utilis along with other four Rosaceae species resulted in similar genome structures, gene orders, and gene contents. Genome sequence alignments revealed that nucleotide diversity was associated with AT content, and large single copy regions (LSC) and small single copy regions (SSC) harbored higher sequence variations in both coding and non-coding regions than IRs. Simple sequence repeats (SSRs) were detected in the P. utilis and compared with those of the other four Rosaceae cp genomes. The availability of the complete cp genome of P. utilis will provide chloroplast markers and genetic information to better enhance the conservation and utilization of this woody oil plant
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