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Article

The Complete Chloroplast Genome of a Key Ancestor of Modern Roses, Rosa chinensis var. spontanea, and a Comparison with Congeneric Species

by
Hong-Ying Jian
1,*,†,
Yong-Hong Zhang
2,†,
Hui-Jun Yan
1,
Xian-Qin Qiu
1,
Qi-Gang Wang
1,
Shu-Bin Li
1 and
Shu-Dong Zhang
3,*
1
National Engineering Research Center for Ornamental Horticulture/Flower Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China
2
School of Life Sciences, Yunnan Normal University, Kunming 650500, China
3
School of Biological Sciences and Technology, Liupanshui Normal University, Liupanshui 553004, China
*
Authors to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Molecules 2018, 23(2), 389; https://doi.org/10.3390/molecules23020389
Submission received: 19 January 2018 / Revised: 6 February 2018 / Accepted: 7 February 2018 / Published: 12 February 2018
(This article belongs to the Section Molecular Diversity)
Browse Figures
Versions Notes

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.

1. Introduction

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]. As one of the key ancestors of modern roses, R. chinensis var. spontanea is not only a precious germplasm resource for improving modern roses but also valuable plant material for the genetic research of recurrent flowering and the study of the biosynthesis of flower scent components. Furthermore, with the effect of “promoting blood circulation for removing blood stasis” and “subdhing swelling and detoxicating”, R. chinensis var. spontanea is also a source for famous traditional Chinese medicines that treat female diseases such as irregular menses and dysmenorrhea [4].
Rosa chinensis var. 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]. It has been listed as an endangered (EN) species in a recent biodiversity report [7]. Fortunately, during systematic and integrative field investigations focusing on this species, we recently found several populations in the wild.
It is important to mention that little information is available about R. chinensis var. spontanea except the fact that it is a diploid plant [8] and that it emits 1,3,5-trimethoxybenzene, together with methyleugenol and isomethyleugenol, as minor floral scent compounds [9], resulting from O-methytransferas genes [10]. The chloroplasts (cps) play important functional roles in the photosynthesis, biosynthesis, and metabolism of starch and fatty acids throughout the plant’s life cycle [11]. Typically, the cp genomes of angiosperm are circulars, with a characteristic quadripartite structure that is comprised of two inverted repeats (IRs) and two single copy regions: a large single copy region (LSC) and a small single copy region (SSC). The genetic composition of cp genome in angiosperm is more or less conserved, containing 110 to 120 genes including protein-coding genes (PCGs), transfer RNA (tRNA) genes and ribosomal RNA (rRNA) genes. In spite of the generally high conservation of gene order and gene content, cp genomes in angiosperm have undergone size changes, structure rearrangement, contraction and expansion of IRs, and even pseudogenization due to adaptations, even within genera, to the host plants’ environments [12].
Here we report the sequence and structural analyses of the complete cp genome of R. chinensis var. spontanea, including analyses of the repeats and SSRs. Furthermore, 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. spontanea, as well as for the phylogenetic study of the genus Rosa. It might also benefit the genetics and breeding of modern roses.

2. Results and Discussion

2.1. Characteristics of Chloroplast Genome of R. chinensis var. spontanea

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 LSC region of 85,910 bp and a SSC region of 18,762 bp, separated by two IR regions of 25,959 bp (Table 1 and Figure 1). The GC content of the total cp DNA sequence is 37.2%, similar to that of R. odorata (Andr.) Sweet var. gigantea (Crép) Rehd. et Wils.(KF753637) [13], R. praelucens Byhouwer (MG450565) [14] and R. roxburghii Tratt. (KX768420). The GC content of the IR regions is 42.8%, while the LSC and SSC regions exhibit lower GC content (35.2% and 31.2%, respectively) (Table 1). The complete cp genome includes 57.8% coding sequences (50.2% PCGs, 1.8% tRNAs, and 5.8% rRNAs) and 42.2% non-coding sequences (11.8% introns and 30.4% intergenic spacers). Among PCGs, the AT content of the first, second, and third positions is 54.7%, 62.5%, and 69.7%, respectively (Table 1). This kind of bias towards a higher AT content at the third position of the codons is used to discriminate cp DNA from nuclear and mitochondrial DNA [15] and has been widely reported in other plant cp genomes [16,17,18].
The cp genome of R. chinensis var. spontanea contains 129 genes, including 84 PCGs, 37 tRNAs, and eight rRNAs (Table S1). Six PCGs (ndhB, rpl2, rpl23, rps7, rps12 and ycf2), four rRNAs (rrn16, rrn23, rrn 4.5 and rrn5) and seven tRNAs (trnA-UGC, trnI-CAU, trnI-GAU, trnL-CAA, trnN-GUU, trnR-ACG, and trnV-GAC) within the IR regions are completely duplicated. The LSC region contains 62 PCGs and 22 tRNAs. The SSC region contains one tRNA and 12 PCGs. Additionally, 14 genes, namely trnK-UUU, rps16, trnG-GCC, rpoC1, trnL-UAA, trnV-UAC, petB, rpl16, rp12, ndhB, trnI-GAU, trnA-UGC, ndhA, and petD, contain one intron, whereas the ycf3, rps12 and clpP genes contain two introns. Despite that, there are 17–20 group II introns within tRNA and protein-coding genes in land plant cp genomes [19], so far only the intron of trnL has been characterized as a group I intron in chloroplasts [20]. Thus, all these introns of R. chinensis var. spontanea, except the trnL-UAA intron, might be group II introns. The rps12 gene is trans-spliced in the cp genome of R. chinensis var. spontanea. C-terminal exon 2 and 3 of rps12 are located in the IR regions. Exon 1 is 28,259 bp downstream of the nearest copy of exons 2 and 3 while 72,017 bp away from the distal copy of exons 2 and 3 (Table S1). The trnK-UUU gene had the largest intron with a 2498 bp length, in which the matK gene was located. The matK gene encodes MatK, the maturase which is derived from reverse transcriptase and has been proved to be an essential splice factor for both the group I and group II introns [20,21].
Based on the sequences of PCGs and tRNAs, the frequency of codon usage of the cp genome of R. chinensis var. spontanea was estimated (Table 2). In total, 27,525 codons were found in all the coding sequences. Among these, leucine is the most frequent amino acid, representing 10.4% (2,871) of the total codons, while cysteine is the least frequent one with 1.2% (320) of the codons. A- and U-ending codons are common. Except for trnL-CAA, trnS-GGA and a stop codon (UAG), all types of preferred synonymous codons (RSCU > 1) ended with A or U.

2.2. Repeat and SSR Analysis

For the repeat structure analysis, 33 forward and five inverted repeats with a minimal repeat size of 20 bp were detected in the cp genome of R. chinensis var. spontanea (Table 3). Most of these repeats are between 20 and 30 bp. The longest forward repeat is 41 bp in length, located in the intergenic region between the genes psbE and petL. Most of the repeats were found in the LSC region. Among them, repeat No. 5 is related to trnS-GCU and trnS-UGA (Table 3). Repeat No. 7 is related to trnG-GCU and trnG-UCC. Repeat No. 13 is associated with psa genes. Six forward repeats were located in IR regions, including two repeats associated with ycf2 genes and one repeat related to the ndhB gene. In addition, there were several repeat pairs with either repeated sequence located in a distinct region, e.g., each of the two sequences of repeat No. 16, 25, and 26 are located in the gene introns of LSC and SSC, respectively.
As chloroplast-specific SSRs are uniparentally inherited and exhibit a high level of intraspecific polymorphism, they are widely used in population genetics, species identification, evolutionary processes research of wild plants [22,23], and as markers for linkage map construction and the breeding of crop plants [24,25]. In total, 85 SSRs were identified in the cp genome of R. chinensis var. spontanea, most of which were detected in the LSC region (Table 4). Among them, 55 (64.7%) are mononucleotide SSRs, ten (11.8%) are dinucleotide SSRs, seven (8.2%) are trinucleotide SSRs, 10 (11.8%) are tetranucleotide SSRs, one (1.2%) is a pentanucleotide SSR, and two (2.4%) are hexanucleotide SSRs. Only 22 SSRs are located in genes and the others are in the intergenic regions. Fifty two (94.5%) of the mononucleotide SSRs belong to the A/T type, which is consistent with the hypothesis that cp SSRs are generally composed of short polyadenine (poly A) or polythymine (poly T) repeats and rarely contain tandem guanine (G) or cytosine (C) repeats. These cp SSR markers can be used in the conservation genetics of R. chinensis var. spontanea, as well as and in both the linkage map construction and molecular-marker-assisted selection of modern roses.

2.3. Comparative Analysis of the Chloroplast Genomes of the Genus Rosa

The complete cp genome sequence of R. chinensis var. spontanea was compared to that of R. odorata var. gigantea [13], R. roxburghii (KX768420) and R. praelucens (MG450565) [14]. Rosa chinensis var. spontanea has the smallest cp genome with the smallest IR region (25,959 bp), while R. praelucens has the largest cp genome with the largest LSC, at 86,313 bp (Table S2). No significant differences were found in the sequence lengths of SSC among the four species. The main reason for the length differences in cp genomes of different rose species is the size variation of the LSC and IR regions (Table S2).
Sequence comparisons revealed that the LSC and the SSC regions were more divergent than the IR regions, and that higher divergence could be found in non-coding regions than in coding regions (Figure 2). Significant variations could be found in coding regions of some genes including rps19 and ycf1. The highest divergence in non-coding regions was found in the intergenic regions of the trnK-rps16, rps16-trnQ, trnS-trnG, trnR-atpA, atpF-atpH, rps2-rpoC2, rpoB-trnC, trnC-petN, trnT-psbD, psbZ-trnG, rps4-trnT, psbE-petL, trnP-psaJ, ndhF-rpl32, and ccsA-ndhD. The introns of rpl2, rps16, ndhA, trnV, clpP, and ndhA were relatively highly divergent, too. These results might indicate that these regions evolve rapidly in the genus Rosa, as well as in other Rosaceae plants [26,27].

2.4. IR Contraction in the Chloroplast Genome of R. chinensis var. spontanea

Although IRs are the most conserved regions of the cp genomes, contraction and expansion at the borders of IR regions are common evolutionary events, and are hypothesized to be the main reason for size differences between cp genomes [28]. Detailed comparisons of the IR-SSC and IR-LSC boundaries among the cp genomes of the above four rose species were presented in Figure 3. IR regions are relatively highly conserved in the genus Rosa, but compared to other congeneric species, some position changes occurred in the IR/LSC regions of R. chinensis var. Spontanea. The rpl2 gene in the cp genome shifted by 31 bp from IRb to LSC at the LSC/IRb border, and that gene also shifted by 31 bp from IRa to LSC at the IRa/LSC border, indicating the IR contraction in the cp genome of this species. This contraction is mainly caused by the fragment deletions in the intergenic regions of the rps12-trnV, rrn4.5-rrn5, and trnR-trnN genes, and leads to the relatively smaller size of its IR regions and consequently a smaller size of the cp genome (Figure 3, Table S2).
Generally, the IRa/LSC border is located between the rpl2 and trnH genes in the rose family with rpl2 in IRa and trnH in LSC [27], like in R. roxburghii and R. odorata var. gigantea. The trnH gene of R. praelucens extends only one bp from LSC to IRa, but its LSC region was much larger than that of other species (Table S2). One 505 bp insertion in the intergenic region between the genes psbM and trnD was detected according to the result of the MAFFT alignment. This large insertion leads to the largest LSC region of R. praelucens and thus the largest cp genome among these four rose species. The extraction and contraction of the IR region at the IR-SSC boundaries among these species were not significant. Accordingly, the extension and contraction of IR regions at the IR/LSC borders, along with the large insertion/deletion in the LSC region, might be the main reason for the cp genome size variation in the genus Rosa.

2.5. Phylogenetic Analysis

There have been many attempts to reconstruct the phylogeny of the genus Rosa. Most of them suggested that the extant classification system was artificial [29,30] and that interspecies relationships within the genus remained ambiguous. The specific relationships within the sections Chinenses and Synstylae were still obscure due to limited sampling, low genetic variation of molecular markers, and complex evolutionary histories [31]. The availability of the complete cp genomes will provide additional informative data for the reconstruction of a robust phylogenetic model for the rose species. The phylogenetic tree (Figure 4) based on the LSC, SSC and one-IR regions in the cp genomes of 22 species from Rosaceae showed that species from Rosaceae were monophyletic and that the intra-family relationships were almost in compliance with that found by Zhang et al. [32]. Species from the genus Rosa formed a monophyletic clade with 100% support. The representative of the subgenus Hulthemia, R. persica Michx. [33,34], was a sister to the clade composed by the other five rose species, supporting the subgenus position of Hulthemia. In the subgenus Rosa, R. chinensis var. spontanea from section Chinenses was sister to R. lichiangensis from section Synstylae, and then clustered with another species from section Chinenses, R. odorata var. gigantean, confirming that R. sections Chinenses and Synstylae, defined in the traditional taxonomic system, shared a more recent ancestor and could be merged as one section in the genus Rosa [30].

3. Materials and Methods

3.1. DNA Sequencing and Chloroplast Genome Assembly

Dry leaves of R. chinensis var. spontanea collected from Yichang of Hubei (111°10′ E, 30°47′ N, 400 m) were used to extract the total genomic DNA. A shotgun library was prepared and sequenced using the Illumina Hiseq 2000 (Illumina, CA, USA) at Novogene (Beijing, China). Approximately 3.68 Gb raw data of 150 bp paired-end reads were generated. The raw reads were filtered to obtain high-quality clean reads by using NGS QC Toolkit v2.3.3 with default parameters [35]. The cp genome was de novo assembled using the GetOrganelle pipeline (https://github.com/Kinggerm/GetOrganelle).

3.2. Gene Annotation and Sequence Analysis

The genome was automatically annotated by using the CpGAVAS pipeline [36]. The annotation was adjusted and confirmed by Geneious 8.1 [37]. Sequence data was deposited into GenBank under the accession number MG523859. The circular cp map of R. chinensis var. spontanea was generated by OGDRAW [38]. Codon usage analysis, calculation of relative synonymous codon usage values (RSCU), and measurement of AT content were carried out by using MEGA 6.06 [39].

3.3. Genome Comparison

MUMer [40] was used to perform pairwise sequence alignments of cp genomes. The mVISTA [41] program was applied to compare the complete cp genome of R. chinensis var. spontanea to the other published cp genomes of its congeneric species, i.e., R. odorata var. gigantea, R. roxburghii and R. praelucens, using the shuffle-LAGAN mode [42] and using the annotation of R. chinensis var. spontanea as reference.

3.4. Repeats and Simple Sequence Repeats (SSRs)

REPuter [43] was used to find forward and inverted tandem repeats ≥ 20 bp with a minimum alignment score and maximum period size of 100 and 500, respectively. The minimum identity of repeats was limited to 85% (Hamming distance of 3). IMEx [44] was used to identify SSRs with the minimum repeat number set to 10, 5, 4, 3, 3 and 3 for mono-, di-, tri-, tetra-, penta- and hexanucleotides, respectively.

3.5. Phylogenetic Analysis

To identify the phylogenetic position of R. chinensis var. spontanea in Rosa, 21 published cp genomes of Rosaceae were used to construct a phylogeny tree, using Berchemiella wilsonii (C. K. Schneid.) Nakai (Rhamnaceae) as the outgroup. The LSC, SSC, and one-IR regions of the total 23 cp genomes were all aligned using MAFFT 7.308 [45]. The maximum likelihood (ML) tree was reconstructed by RAxML 8.2.11 [46] with the nucleotide substitution model of GTR + Gamma; node support was conducted by means of a bootstrap analysis with 1000 replicates.

4. Conclusions

In this study, we report and analyze the first complete cp genome of R. chinensis var. spontanea, one of the key ancestors of modern roses and a source for famous traditional Chinese medicines against female diseases. Compared to the cp genomes of other rose species, the cp genome of R. chinensis var. spontanea is the smallest, most likely due to the contraction of IR regions by 31 bps on each IR/LSC border. The cp genome of R. chinensis var. spontanea is rich in SSRs, which are valuable sources for developing new molecular markers. Our phylogenetic analysis showed that sampled species of the genus Rosa formed a monophyletic clade. Rosa 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 supported the hypothesis that, in the traditional taxonomic system, Rosa sections Chinenses and Synstylae were closely related and could be merged to a single section within the genus Rosa. This information will be useful for the conservation genetics of R. chinensis var. spontanea and the phylogenetic study of genus Rosa, and might also facilitate the genetics and breeding of modern roses.

Supplementary Materials

Supplementary materials are available online.

Acknowledgments

This study was supported by the National Natural Scientific Foundation of China (Grant 31760087), the Strategic Priority Research Program of the Chinese Academy of Sciences (Grant XDPB0201), and the Academic and Technical Talent Training Project of Yunnan Province, China (Grant 2013HB092).

Author Contributions

Hong-Ying Jian and Shu-Dong Zhang conceived and designed the research framework; Hong-Ying Jian wrote the paper; Shu-Dong Zhang and Yong-Hong Zhang assembled and annotated the genome; Hong-Ying Jian, Yong-Hong Zhang, and Hui-Jun Yan analyzed the data; Hong-Ying Jian, Hui-Jun Yan, and Xian-Qin Qiu performed the experiments. Hong-Ying Jian, Yong-Hong Zhang, Qi-Gang Wang, Shu-Bin Li, and Shu-Dong Zhang collected the samples and made revisions to the final manuscript. All authors have read and approved the final manuscript.

Conflicts of Interest

The authors declare no conflict of interest.

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Sample Availability: Sequence data of Rosa chinensis var. spontanea has been deposited into GenBank and are available from the authors.
Molecules 23 00389 g001 550
Figure 1. Chloroplast genome map of Rosa chinensis var. spontanea. Genes inside the circle are transcribed clockwise, and those outside are counterclockwise. Genes of different functions are color-coded. The darker gray in the inner circle shows the GC content, while the lighter gray shows the AT content.
Figure 1. Chloroplast genome map of Rosa chinensis var. spontanea. Genes inside the circle are transcribed clockwise, and those outside are counterclockwise. Genes of different functions are color-coded. The darker gray in the inner circle shows the GC content, while the lighter gray shows the AT content.
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Molecules 23 00389 g002 550
Figure 2. Complete chloroplast genome comparison of four rose species using the chloroplast genome of R. chinensis var. spontanea as a reference. The grey arrows and thick black lines above the alignment indicate the gene orientation. The y-axis represents the identity from 50% to 100%.
Figure 2. Complete chloroplast genome comparison of four rose species using the chloroplast genome of R. chinensis var. spontanea as a reference. The grey arrows and thick black lines above the alignment indicate the gene orientation. The y-axis represents the identity from 50% to 100%.
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Molecules 23 00389 g003 550
Figure 3. Comparison of the LSC, SSC and IR regions in chloroplast genomes of four species. Ψ: pseudogenes, →: distance from the edge.
Figure 3. Comparison of the LSC, SSC and IR regions in chloroplast genomes of four species. Ψ: pseudogenes, →: distance from the edge.
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Molecules 23 00389 g004 550
Figure 4. Phylogeny of 22 species within Rosaceae based on the ML analysis of the chloroplast genome’s LSC, SSC, and one-IR regions with Berchemiella wilsonii (Rhamnaceae) as the outgroup. The position of R. chinensis var. spontanea is shown in block letters.
Figure 4. Phylogeny of 22 species within Rosaceae based on the ML analysis of the chloroplast genome’s LSC, SSC, and one-IR regions with Berchemiella wilsonii (Rhamnaceae) as the outgroup. The position of R. chinensis var. spontanea is shown in block letters.
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Table
Table 1. Base composition in the chloroplast genome of Rosa chinensis var. spontanea.
Table 1. Base composition in the chloroplast genome of Rosa chinensis var. spontanea.
Region AT (U)GCLength
LSC 31.733.117.218.085,910
SSC 34.434.315.116.318,762
IRB 28.728.522.220.625,959
IRA 28.728.522.220.625,959
Total 31.031.818.618.7156,590
PCGs30.631.420.317.779,773
1st position30.72426.918.726,591
2nd position29.53317.720.226,591
3rd position31.73816.414.126,591
PCGs: protein-coding genes.
Table
Table 2. Condon-anticodon recognition patterns and codon usage of the Rosa chinensis var. spontanea chloroplast genome.
Table 2. Condon-anticodon recognition patterns and codon usage of the Rosa chinensis var. spontanea chloroplast genome.
Amino AcidCodonCountRSCUtRNAAmino AcidCodonCountRSCUtRNA
PheUUU10151.3 SerUCU5801.62
PheUUC5450.7trnF-GAASerUCC3701.03trnS-GGA
LeuUUA8971.87 SerUCA4061.13trnS-UGA
LeuUUG5801.21trnL-CAASerUCG2220.62
LeuCUU5951.24 ProCCU4241.45
LeuCUC2170.45 ProCCC2410.82
LeuCUA3800.79 ProCCA3201.09trnP-UGG
LeuCUG2020.42 ProCCG1870.64
IleAUU11361.48 ThrACU5421.55
IleAUC4510.59trnI-CAUThrACC2690.77trnT-GGU
IleAUA7160.93 ThrACA4181.19trnT-UGU
MetAUG6351trnM-CAUThrACG1710.49
ValGUU5501.44 AlaGCU6451.76
ValGUC1930.5trnV-GACAlaGCC2440.67
ValGUA5671.48 AlaGCA3911.07
ValGUG2230.58 AlaGCG1830.5
TyrUAU7981.6 CysUGU2371.48
TyrUAC1980.4trnY-GUACysUGC830.52trnC-GCA
stopUAA591.38 stopUGA210.49
stopUAG481.13 TrpUGG4841trnW-CCA
HisCAU4761.49 ArgCGU3621.28trnR-ACG
HisCAC1610.51trnH-GUGArgCGC1200.43
GlnCAA7341.51trnQ-UUGArgCGA3851.36
GlnCAG2360.49 ArgCGG1440.51
AsnAAU10031.52 SerAGU4201.17
AsnAAC3170.48 SerAGC1560.43trnS-GCU
LysAAA10821.48 ArgAGA4881.73trnR-UCU
LysAAG3850.52 ArgAGG1940.69
AspGAU8901.62 GlyGGU6121.3
AspGAC2070.38trnD-GUCGlyGGC2090.44trnG-GCC
GluGAA10521.46trnE-UUCGlyGGA6941.48
GluGAG3900.54 GlyGGG3650.78
RSCU: Relative Synonymous Codon Usage.
Table
Table 3. Repeat sequences in the Rosa chinensis var. spontanea chloroplast genome.
Table 3. Repeat sequences in the Rosa chinensis var. spontanea chloroplast genome.
IDRepeat Start 1TypeSize (bp)Repeat Start 2Mismatch (bp)E-ValueGeneRegion
14426F2945,071−28.74 × 10−5IGS; ycf3(intron)LSC
24427F304428−36.56 × 10−4IGSLSC
34428F2845,072−38.47 × 10−3IGSLSC
44432F2645,072−24.48 × 10−3IGSLSC
58329F2936,077−28.74 × 10−5trnS-GCU; trnS-UGALSC
68873F20889506.27 × 10−3IGSLSC
79804F2737,135−13.10 × 10−5trnG-GCU; trnG-UCCLSC
813,510F2089,60606.27 × 10−3IGS; ycf2LSC; IRa
914,236F2029,56006.27 × 10−3IGSLSC
1027,619F2427,64302.45 × 10−5IGSLSC
1129,555F2429,556−11.76 × 10−3IGSLSC
1233,157F2033,17706.27 × 10−3IGSLSC
1339,390F3041,614−36.56 × 10−4psaB; psaALSC
1442,625F25147,248−14.59 × 10−4IGSLSC; IRb
1544,406F39100,26202.28 × 10−14ycf3(intron); IGSLSC; IRa
1644,406F38122,33209.13 × 10−14ycf3(intron); ndhA(intron)LSC; SSC
1745,075F24142,008−11.76 × 10−3ycf3(intron); IGSLSC; IRb
1847,622F2547,64506.13 × 10−6IGSLSC
1958,656F3458,68702.34 × 10−11IGSLSC
2066,712F4166,75201.43 × 10−15IGSLSC
2166,939F2066,95806.27 × 10−3IGSLSC
2268,033F2168,05201.57 × 10−3IGSLSC
2371,232F2084,92806.27 × 10−3IGSLSC
2480,953F2780,966−21.21 × 10−3IGSLSC
2583,166F29122,320−32.36 × 10−3rpl16(intron); ndhA(intron)LSC;SSC
2683,172F28122,326−38.47 × 10−3rpl16(intron); ndhA(intron)LSC;SSC
2790,610F2990,631−28.74 × 10−5ycf2IRa
2897,630F31144,839−31.81 × 10−4ndhB(intron)IRa; IRb
29100,260F40122,33005.70 × 10−15IGS; ndhA(intron)IRa; SSC
30101,012F23101,03309.80 × 10−5IGSIRa
31141,437F30141,458−22.34 × 10−5IGSIRb
32141,444F23141,46509.80 × 10−5IGSIRb
33151,840F29151,861−28.74 × 10−5ycf2IRb
346406I2071,23106.27 × 10−3IGSLSC
356408I2471,228−11.76 × 10−3IGSLSC
368622I2645,073−24.48 × 10−3IGSLSC
378625I2345,077−16.76 × 10−3IGSLSC
3871,232I2084,93006.27 × 10−3IGSLSC
F: Forward; I: Inverted; IGS: intergenic space.
Table
Table 4. Simple sequence repeats (SSRs) in the Rosa chinensis var. spontanea chloroplast genome.
Table 4. Simple sequence repeats (SSRs) in the Rosa chinensis var. spontanea chloroplast genome.
IDRepeat MotifLength (bp)StartEndRegionGeneIDRepeat MotifLength (bp)StartEndRegionGene
1(A)1111279289LSC 44(TTTA)41250,46850,479LSC
2(T)111141084118LSC 45(TA)51052,74252,751LSC
3(A)191944284446LSC 46(T)101055,81155,820LSCatpB
4(A)101044494458LSC 47(AAAT)31255,91155,922LSC
5(A)101048874896LSC 48(TAAT)31258,36658,377LSC
6(T)101050235032LSC 49(T)141460,81060,823LSC
7(TATAT)31561026116LSCrps1650(TC)51062,28062,289LSCcemA
8(T)171764076423LSC 51(T)111164,51364,523LSC
9(AATA)31265256536LSC 52(T)101069,68969,698LSC
10(AG)51067556764LSC 53(A)161669,73969,754LSC
11(A)111169456955LSC 54(T)181871,23571,252LSC
12(TAA)41282578268LSC 55(T)151571,93371,947LSCclpP
13(A)101086398648LSC 56(A)101072,73372,742LSCclpP
14(AT)61210,09310,104LSC 57(AT)61273,63273,643LSC
15(TAT)41210,34310,354LSC 58(A)121279,23179,242LSC
16(T)111112,15712,167LSC 59(A)141479,39379,406LSC
17(T)101012,91512,924LSC 60(T)101079,42979,438LSCrpoA
18(A)101013,18413,193LSC 61(ATGT)31279,52979,540LSCrpoA
19(C)101014,23714,246LSC 62(T)111181,58681,596LSC
20(T)101014,24714,256LSC 63(A)101082,64182,650LSC
21(T)111118,36118,371LSCrpoC264(A)121283,42283,433LSCrpl16
22(TA)51019,73019,739LSCrpoC265(A)111183,49883,508LSCrpl16
23(T)101026,08026,089LSCrpoB66(T)181884,93184,948LSC
24(T)121228,92528,936LSC 67(TAT)41286,61986,630IRarpl2
25(C)151529,55629,570LSC 68(TAGAAG)31893,98794,004IRaycf2
26(T)101029,57129,580LSC 69(T)1111101,618101,628IRa
27(AAT)41230,50430,515LSC 70(AGGT)312107,843107,854IRarrn23
28(T)141430,51930,532LSC 71(TATT)312110,028110,039IRa
29(A)101030,66630,675LSC 72(TGT)412111,869111,880SSC
30(TA)51036,31336,322LSC 73(T)1010115,507115,516SSC
31(T)111136,47336,483LSC 74(TAA)412115,558115,569SSC
32(AT)51237,07037,079LSC 75(A)1313115,612115,624SSC
33(C)131337,30337,315LSC 76(T)1010120,845120,854SSC
34(A)111137,31637,326LSC 77(AT)714121,678121,691SSC
35(AT)51043,68243,691LSCycf378(A)1616122,551122,566SSCndhA
36(A)151545,07345,087LSCycf379(T)1515122,804122,818SSCndhA
37(A)101045,39245,401LSC 80(T)1010129,830129,839SSCycf1
38(T)101045,93145,940LSC 81(ATAA)312132,463132,474IRb
39(A)111147,29647,306LSC 82(CTAC)312134,645134,656IRbrrn23
40(TAAT)31248,11248,123LSC 83(A)1111140,873140,883IRb
41(T)141448,30648,319LSC 84(CTTCTA)318148,497148,514IRbycf2
42(A)121248,42048,431LSC 85(ATA)412155,871155,882IRb
43(TA)51048,50048,509LSC

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Jian, H.-Y.; Zhang, Y.-H.; Yan, H.-J.; Qiu, X.-Q.; Wang, Q.-G.; Li, S.-B.; Zhang, S.-D. The Complete Chloroplast Genome of a Key Ancestor of Modern Roses, Rosa chinensis var. spontanea, and a Comparison with Congeneric Species. Molecules 2018, 23, 389. https://doi.org/10.3390/molecules23020389

AMA Style

Jian H-Y, Zhang Y-H, Yan H-J, Qiu X-Q, Wang Q-G, Li S-B, Zhang S-D. The Complete Chloroplast Genome of a Key Ancestor of Modern Roses, Rosa chinensis var. spontanea, and a Comparison with Congeneric Species. Molecules. 2018; 23(2):389. https://doi.org/10.3390/molecules23020389

Chicago/Turabian Style

Jian, Hong-Ying, Yong-Hong Zhang, Hui-Jun Yan, Xian-Qin Qiu, Qi-Gang Wang, Shu-Bin Li, and Shu-Dong Zhang. 2018. "The Complete Chloroplast Genome of a Key Ancestor of Modern Roses, Rosa chinensis var. spontanea, and a Comparison with Congeneric Species" Molecules 23, no. 2: 389. https://doi.org/10.3390/molecules23020389

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