Abstract
Rosa chinensis var. spontanea, an endemic and endangered plant of China, is one of the key ancestors of modern roses and a source for famous traditional Chinese medicines against female diseases, such as irregular menses and dysmenorrhea. In this study, the complete chloroplast (cp) genome of R. chinensis var. spontanea was sequenced, analyzed, and compared to congeneric species. The cp genome of R. chinensis var. spontanea is a typical quadripartite circular molecule of 156,590 bp in length, including one large single copy (LSC) region of 85,910 bp and one small single copy (SSC) region of 18,762 bp, separated by two inverted repeat (IR) regions of 25,959 bp. The GC content of the whole genome is 37.2%, while that of LSC, SSC, and IR is 42.8%, 35.2% and 31.2%, respectively. The genome encodes 129 genes, including 84 protein-coding genes (PCGs), 37 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. Seventeen genes in the IR regions were found to be duplicated. Thirty-three forward and five inverted repeats were detected in the cp genome of R. chinensis var. spontanea. The genome is rich in SSRs. In total, 85 SSRs were detected. A genome comparison revealed that IR contraction might be the reason for the relatively smaller cp genome size of R. chinensis var. spontanea compared to other congeneric species. Sequence analysis revealed that the LSC and SSC regions were more divergent than the IR regions within the genus Rosa and that a higher divergence occurred in non-coding regions than in coding regions. A phylogenetic analysis showed that the sampled species of the genus Rosa formed a monophyletic clade and that R. chinensis var. spontanea shared a more recent ancestor with R. lichiangensis of the section Synstylae than with R. odorata var. gigantea of the section Chinenses. This information will be useful for the conservation genetics of R. chinensis var. spontanea and for the phylogenetic study of the genus Rosa, and it might also facilitate the genetics and breeding of modern roses.
Highlights
Molecular data have suggested that Rosa chinensis Jacq. var. spontanea
A genome comparison revealed that inverted repeat (IR) contraction might be the reason for the relatively smaller cp genome size of R. chinensis var. spontanea compared to other congeneric species
The complete cp genome of R. chinensis var. spontanea represents a typical quadripartite circular molecule that is 156,590 bp in length. It is composed by a large single copy (LSC) region of 85,910 bp and a small single copy (SSC) region of 18,762 bp, separated by two IR regions of 25,959 bp (Table 1 and Figure 1)
Summary
Molecular data have suggested that Rosa chinensis Jacq. var. spontanea (Rehder et. Wilson) Yü et Ku is the maternal parent of R. chinensis and the possible paternal parent of R. odorata (Andrews) Sweet [1], which gave characters of recurrent flowering, tea scent, and multiple floral colors to modern roses [2,3]. Spontanea originates from China and is endemic to the Hubei, Sichuan, Chongqing, and Guizhou provinces [5,6] It has been overharvested by local people and pharmaceutical companies because of its medicinal usefulness and has become rare in its wild habitats. It was uncertain whether it still existed as a wild-living species because investigators failed to collect samples of this species in the field [1]. Spontanea, including analyses of the repeats and SSRs. we carried out comparative sequence analysis studies of cp sequences in the genus Rosa. We carried out comparative sequence analysis studies of cp sequences in the genus Rosa This information will be useful for the conservation genetics of R. chinensis var. It might benefit the genetics and breeding of modern roses
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