Abstract
BackgroundSweet cherry (Prunus avium) is one of the most popular of the temperate fruits. Previous studies have demonstrated that there were several haplotypes in the chloroplast genome of sweet cherry cultivars. However, none of chloroplast genome of a sweet cherry cultivar were yet released, and the phylogenetic relationships among Prunus based on chloroplast genome data were unclear.MethodsIn this study, we assembled and annotated the complete chloroplast genome of a sweet cherry cultivar P. avium ‘Summit’ from high-throughput sequencing data. Gene Ontology (GO) terms were assigned to classify the function of the annotated genes. Maximum likelihood (ML) trees were constructed to reveal the phylogenetic relationships within Prunus species, using LSC (large single-copy) regions, SSC (small single-copy) regions, IR (inverted repeats) regions, CDS (coding sequences), intergenic regions, and whole cp genome datasets, respectively.ResultsThe complete plastid genome was 157, 886 bp in length with a typical quadripartite structure of LSC (85,990 bp) and SSC (19,080 bp) regions, separated by a pair of IR regions (26,408 bp). It contained 131 genes, including 86 protein-coding genes, 37 transfer RNA genes and 8 ribosomal RNA genes. A total of 77 genes were assigned to three major GO categories, including molecular function, cellular component and biological process categories. Comparison with other Prunus species showed that P. avium ‘Summit’ was quite conserved in gene content and structure. The non-coding regions, ndhc-trnV, rps12-trnV and rpl32-trnL were the most variable sequences between wild Mazzard cherry and ‘Summit’ cherry. A total of 73 simple sequence repeats (SSRs) were identified in ‘Summit’ cherry and most of them were mononucleotide repeats. ML phylogenetic tree within Prunus species revealed four clades: Amygdalus, Cerasus, Padus, and Prunus. The SSC and IR trees were incongruent with results using other cp data partitions. These data provide valuable genetic resources for future research on sweet cherry and Prunus species.
Highlights
Chloroplast is generally situated in the cytoplasmic matrix and plays an important role in photosynthesis and fatty acid, starch, and amino acid synthesis (Wicke et al, 2011)
It is a typical quadripartite structure that consists of large single copy (LSC) region, small single copy (SSC) region, and two inverted repeats (IR) regions; It is well known that the cp genome is usually highly conserved in gene structure and content
When the six phylogenetic trees were compared with each other, we found that the topological structures based on LSC region, CDS region, intergenic region and whole cp genome datasets were similar (Fig. 5)
Summary
Chloroplast (cp) is generally situated in the cytoplasmic matrix and plays an important role in photosynthesis and fatty acid, starch, and amino acid synthesis (Wicke et al, 2011). As early as in 1,700, six subgenera within Prunus were recognized based on fruit morphology: Amygdalus L., Armeniaca Mill., Cerasus Mill., Laurocerasus Duhamel, Persica Mill., and Prunus sensu stricto (Bouhadida et al, 2007). We assembled and annotated the complete chloroplast genome of a sweet cherry cultivar P. avium ‘Summit’ from high-throughput sequencing data. Maximum likelihood (ML) trees were constructed to reveal the phylogenetic relationships within Prunus species, using LSC (large single-copy) regions, SSC (small single-copy) regions, IR (inverted repeats) regions, CDS (coding sequences), intergenic regions, and whole cp genome datasets, respectively. The SSC and IR trees were incongruent with results using other cp data partitions These data provide valuable genetic resources for future research on sweet cherry and Prunus species
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