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Mitochondrial DNA B Resour
Mitochondrial DNA B Resour
Mitochondrial DNA. Part B, Resources
2380-2359
Taylor & Francis

10.1080/23802359.2024.2397986
2397986
Version of Record
Data Note
Plastome Report
The complete chloroplast genome sequence of red raspberry (Rubus idaeus L.) and phylogenetic analysis
H. Zhou and H. Zhang
Zhou Hao a
Zhang Huajie bcd
a Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
b CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
c Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, China
d Wuhan Botanical Garden, University of Chinese Academy of Sciences, Beijing, China
Supplemental data for this article can be accessed online at https://doi.org/10.1080/23802359.2024.2397986.

CONTACT Huajie Zhang zhanghuajie@wbgcas.cn CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, China; Wuhan Botanical Garden, University of Chinese Academy of Sciences, Beijing, China
30 8 2024
2024
30 8 2024
9 9 11521156
27 11 2023
24 8 2024
KnowledgeWorks Global Ltd.29 8 2024
published online in a building issue29 8 2024
© 2024 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.
2024
The Author(s)
https://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The terms on which this article has been published allow the posting of the Accepted Manuscript in a repository by the author(s) or with their consent.

Abstract

Red raspberries, Rubus idaeus L. 1753 are famous fruits which possess high value bioactive compounds. In this study, we report the complete chloroplast genome of R. idaeus, it displayed a typical quadripartite structure with 155687 bp in length. The genome encodes 127 genes including 79 protein coding genes, 8 rRNA genes and 40 tRNA genes, the overall GC content is 37.2%. Phylogenetic analysis revealed a close relationship between R. idaeus and R. sachalinensis in Section Malaehobatus.

Keywords

Phylogeny
plastome
Rosaceae
Rubus idaeus
China Postdoctoral Science Foundation 10.13039/501100002858 2022M713333 This study was supported by grants from the Project funded by China Postdoctoral Science Foundation (2022M713333).
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pmcIntroduction

Red raspberries, Rubus idaeus L. 1753 are perennial shrubs 1–2 m tall in Rosaceae, it is native fruit from Europe (Figure 1) (Ispiryan et al. 2021; Lopez-Corona et al. 2022). As an important commercial fruit crop, red raspberries are widely cultivated in all temperate regions of the world now (Ispiryan et al. 2021; Davik et al. 2022). This berry has been shown to be rich in anthocyanins and other phenolic compounds with a strong antioxidant capacity (Kähkönen et al. 2001; Kafkas et al. 2008; Çekiç and Özgen, 2010). It also comprises rich health-beneficial nutrients such as minerals, vitamins and organic acids (Beekwilder et al. 2005; Pantelidis et al. 2007). The raspberry seed oil displays anti-inflammatory activity, which can be used to prevent gingivitis and skin lesions and is therefore added to products such as sunscreen and toothpaste (Oomah et al. 2000; Ispiryan et al. 2021; Lopez-Corona et al. 2022).

Figure 1. The photo of the whole plant Rubus idaeus. (A) The whole plant. (B) The fruits. (C) The flower. Morphology and habitat map of R. idaeus from Heicha Mountain, Xihui Village, Xing Town, Lvliang City, Shanxi Province, China (38°23′48″ N; 111°27′44″ E), photograph by Huajie Zhang.

Rubus is a large genus in Rosaceae which contains plentiful species with similar morphologies, causing complicated arguments on the species delimitation (Wang et al. 2016; Carter et al. 2019). Molecular identification is an efficient approach for species-level differentiation via standard DNA barcodes. Up to now, the complete plastid sequences of many Rubus species have been assembled and reported to construct the phylogeny of Rubus (Yu et al. 2022). The chromosome-level genome sequence of red raspberries was also detected (Davik et al. 2022). However, no complete chloroplast genome research has been conducted for the important fruit crop red raspberries. Here, we sequenced and assembled the complete chloroplast genome of wild accessions of red raspberries R. idaeus, it can not only provide genomic molecular maker to clarify the phylogenetic position of this species within Rubus, but also can help to explore the genetic diversity and promote the breeding programs.

Materials and methods

The sample of Rubus idaeus was collected from Heicha Mountain in northwestern Shanxi Province (38°23′48″ N; 111°27′44″ E). The specimen was deposited in Wuhan botanical Garden with the specific identifying number of HSM-2023fu (contacts: Guangwan Hu, guangwanhu@wbgcas.cn). We collected fresh leaves in silica gel to extract total genomic DNA. 1.5 µg of DNA of sample was sequenced using illumine Hiseq Platform, a minimum 5GB of raw sequencing data was finally obtained. The chloroplast genome of R. idaeus was assembled with NOVOPlasty (Dierckxsens et al. 2017), the read coverage depths of the assembled genome can be seen in Supplementary Figure 1. Then we annotated the genome with Goseq (https://chlorobox.mpimp‐golm.mpg.de/geseq.html) and manually checked and modified the start/stop codons of genes in Geneious v9.0.2 (Kearse et al. 2012). The complete chloroplast genome of R. idaeus was submitted to Genbank with the accession number of OR698909. Simple Sequence Repeats (SSRs) were detected in MISA with default parameters (Beier et al. 2017).

The complete genome sequences of R. idaeus and other 39 representative species from Rosaceae family were downloaded from NCBI, two species in Rosa were selected as outgroups (Figure 3). We extracted the sequences of large single copy (LSC) region, small single copy (SSC) region and one repeat of inverted repeated (IR) region of each species separately, then concatenated sequences into a super-matrix in Geneious v9.0.2 (Kearse et al. 2012). Concatenated sequences were then aligned with MAFFT v7.5(Katoh and Standley 2013). We conducted the maximum-likelihood (ML) analysis with RAxML v8.2.12 (Stamatakis 2014) with the model GTRGAMMA, 1000 rapid bootstrap replicates were conducted. We also detected the nucleotide diversity (pi) of the super-matrix in DnaSP 6 (Rozas et al. 2017) with a step size 400 bp and a window length 600 bp.

Results

The length of the complete chloroplast genome of R. idaeus was 155687 bp, with an LSC region of 85038 bp, an SSC region of 18717 bp and two separated IR regions of 25966 bp (Figure 2). A total of 127 genes were identified in the cp of R. idaeus, including 79 protein-coding genes, 40 tRNA genes, and 8 rRNA genes. Twelve genes contain introns, rps12 is a trans-splicing gene (Supplementary Figures 2 & 3). The overall GC content was 37.2%, and the corresponding contents for LSC, SSC and IR regions were 35.2%, 31.3% and 42.8%, respectively. The genome included 20 duplicated genes in the IR region including ycf1, trnN-GUU, trnL-CAG, trnR-ACG, rrn5, rrn4.5, rrn23, trnA-UGC, trnE-UUC, rrn16, trnV-GAC, rps12, rps7, ndhB, trnL-CAA, ycf2, trnI_CAU, trnM-CAU, rpl23 and rpl2, which exhibited 50.6% protein-coding sequences. Moreover, a total of 46 SSRs were identified in the chloroplast genome of R. idaeus. The phylogenetic results revealed that both Sect. Malaehobatus and Sect. Idaeobatua are polyphyletic groups, which is corresponding with previous research (Wang et al. 2016). Phylogenetic analysis also demonstrated a close relationship between R. idaeus and R. sachalinensis with 100% bootstrap support value (Figure 3). The nucleotide diversity analysis revealed four highly divergent intergenic regions (pi > 0.03), including rps16-trnQ, trnT-trnL, petA-psbL and rpl32-trnL (Supplementary Figure 4).

Figure 2. Circular maps of the Rubus idaeus chloroplast genome. Genes shown inside the circle are transcribed clockwise, and those outside the circle are counterclockwise transcribed. The light grey and the darker grey in the inner circle correspond to at and GC content, respectively. Different functional groups are signed according to the colored legend. LSC: large single copy, SSC: small single copy; IRA/IRB: Inverted repeat regions a/B.

Figure 3. Chloroplast phylogeny of 38 Rubus species using maximum likelihood (ML) method based on the concatenated LSC, SSC and an IR region. The red fonts represent R. idaeus in this study. Two Rosa species (Rosa sertata and Rosa glomerata) were selected as outgroups. Genbank IDs were listed after the species’ names. Maximum likelihood bootstrap values (BS) are shown at nodes. Branches with no values listed have 100% BS. The following sequences were used: Rubus parvifolius OK127884 (Yu et al. 2022), Rubus innominatus OK127883 (Yu et al. 2022), Rubus niveus NC056930, Rubus biflorus NC080344, Rubus phoenicolasius MW115432 (Zhang et al. 2021), Rubus pileatus NC056947, Rubus irritans NC057600 (Han et al. 2023), Rubus amabilis NC047211, Rubus sachalinensis NC056965 (Liu et al. 2021), Rubus idaeus OR698909 (this study), Rubus corchorifolius NC056942, Rubus chingii NC050296 (Wang et al. 2020), Rubus trianthus NC060616 (Yu et al. 2022), Rubus hirsutus OK127882 (Yu et al. 2022), Rubus tsangii NC056940, Rubus rosifolius OL435124 (Yang et al. 2022), Rubus crataegifolius NC039704 (Yang et al. 2017), Rubus peltatus NC056937, Rubus xanthocarpus NC056938, Rubus leucanthus MK105853, Rubus columellaris NC056932, Rubus ellipticus NC056929, Rubus wallichianus NC056933, Rubus rufus NC056798, Rubus cochinchinensis NC056289, Rubus pacificus NC064142 (Xiong et al. 2022), Rubus ichangensis NC056935, Rubus lambertianus OK127886 (Yu et al. 2022), Rubus buergeri NC072261, Rubus hunanensis OK127885 (Yu et al. 2022), Rubus tephrodes NC060615 (Yu et al. 2022), Rubus swinhoei OQ411240, Rubus bambusarum NC056916, Rubus henryi NC056945, Rubus setchuenensis NC056946, Rubus lineatus NC056943, Rubus pentagonus NC056936, Rubus quinquefoliolatus NC063615, Rosa sertata NC066975, Rosa glomerata NC062462 (Chen et al. 2022).

Discussion and conclusion

Raspberry has important medicinal and therapeutic value, it can be used in food, pharmaceutical, cosmetic and chemical industries. In this study, we successfully sequenced and assembled the complete chloroplast genome of R. idaeus and constructed the phylogenetic tree of Rubus, revealed that Sect. Malaehobatus and Sect. Idaeobatua are polyphyletic clades, and clarified the close relationships between R. idaeus and R. sachalinensis. The phylogenetic tree is consistent with previous research (Wang et al. 2016) with higher bootstrap support values, it shows that chloroplast genome sequence is an effective tool to construct the phylogenetic relationships of Rosaceae. The SSRs and the nucleotide diversity analysis can help to detect the population structure of wild populations. Four highly divergent intergenic regions can be used for phylogeny and evolution analysis in future studies. The first complete chloroplast genome will be beneficial to the identification and development of germplasm resources of raspberry in further research.

Supplementary Material

The supplemental figures.docx

Figure S2.jpg

Figure S3.jpg

Figure S1.jpeg

Ethical approval

No approval or permission was necessary when obtaining the materials and performing the research. Therefore, there are no ethical issues in this study.

Authors’ contributions

Huajie Zhang designed and conceived the article; Hao Zhou and Huajie Zhang collected and identified and the samples in fields, assembled and annotated the chloroplast genome; Hao Zhou finished the phylogenetic analysis and drafted the manuscript; All authors reviewed the final manuscript and agreed to be accountable for all aspects of the work.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Data availability statement

The genome sequence data supporting the funding is available in the GenBank of NCBI at https://www.ncbi.nlm.nih.gov/ under accession number OR698909. The associated BioProject, SRA and Bio-Sample numbers are PRJNA1033369, SRR26558505 and SAMN38031542, respectively.
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