Complete plastome sequence of <i>Paeonia lactiflora</i> Pall. (Paeoniaceae: Saxifragales)

Samigullin, Tahir H.; Logacheva, Maria D.; Degtjareva, Galina V.; Ефимов, С.В.; Terentieva, E.I.; Vallejo-Roman, Carmen M.

doi:10.1080/23802359.2018.1501311

Cited by 7 publications

(6 citation statements)

References 6 publications

(8 reference statements)

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“…In this study, comparative analysis showed that these two gene loss events occurred in all eleven plastomes of Paeoniaceae. A possible explanation is that the two functional genes have been transferred to the nucleus [8,47,54,55,56,57,58,59,60]. Furthermore, Dong et al [8] observed that the intron of rpl2 was completely lost in Saxifraga stolonifera .…”

Section: Resultsmentioning

confidence: 99%

Next-Generation Genome Sequencing of Sedum plumbizincicola Sheds Light on the Structural Evolution of Plastid rRNA Operon and Phylogenetic Implications within Saxifragales

Ding

Zhu

Dong

et al. 2019

Plants

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The genus Sedum, with about 470 recognized species, is classified in the family Crassulaceae of the order Saxifragales. Phylogenetic relationships within the Saxifragales are still unresolved and controversial. In this study, the plastome of S. plumbizincicola was firstly presented, with a focus on the structural analysis of rrn operon and phylogenetic implications within the order Saxifragaceae. The assembled complete plastome of S. plumbizincicola is 149,397 bp in size, with a typical circular, double-stranded, and quadripartite structure of angiosperms. It contains 133 genes, including 85 protein-coding genes (PCGs), 36 tRNA genes, 8 rRNA genes, and four pseudogenes (one ycf1, one rps19, and two ycf15). The predicted secondary structure of S. plumbizincicola 16S rRNA includes three main domains organized in 74 helices. Further, our results confirm that 4.5S rRNA of higher plants is associated with fragmentation of 23S rRNA progenitor. Notably, we also found the sequence of putative rrn5 promoter has some evolutionary implications within the order Saxifragales. Moreover, our phylogenetic analyses suggested that S. plumbizincicola had a closer relationship with S. sarmentosum than S. oryzifolium, and supported the taxonomic revision of Phedimus. Our findings of the present study will be useful for further investigation of the evolution of plastid rRNA operon and phylogenetic relationships within Saxifragales.

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Section: Resultsmentioning

confidence: 99%

Next-Generation Genome Sequencing of Sedum plumbizincicola Sheds Light on the Structural Evolution of Plastid rRNA Operon and Phylogenetic Implications within Saxifragales

Ding

Zhu

Dong

et al. 2019

Plants

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“…Furthermore, all published five P. lactiflora and three P. veitchii complete chloroplast genomes in GenBank database were simultaneously taken into consideration for comparative analyses ( Zhang et al, 2016 ; Samigullin et al, 2018 ; Lee et al, 2019 ; Gao et al, 2020 ; Tables 2 , 3 ). The result showed that the two Chishao chloroplast genomes exhibited high similarity with previously published data in genome size and structure, gene number, as well as GC content.…”

Section: Resultsmentioning

confidence: 99%

“…In this study, we (1) sequenced, assembled, and annotated the complete chloroplast genome sequence of P. lactiflora and P. veitchii from our herbal materials, and compared them with those reported previously in terms of genome size, gene structure and guanine-cytosine (GC) content ( Zhang et al, 2016 ; Samigullin et al, 2018 ; Lee et al, 2019 ; Gao et al, 2020 ), and then search for hypervariable regions in protein-coding sequences to design mini-barcodes; (2) to combine the mini-barcode with DNA metabarcoding method to examine whether the former could be used for the qualitative and quantitative analysis of P. lactiflora and P. veitchii ; (3) take “cerebral thrombosis tablets” as an example to confirm the applicability of designed mini-barcode in proprietary Chinese medicines.…”

Section: Introductionmentioning

confidence: 99%

Development of Mini-Barcode Based on Chloroplast Genome and Its Application in Metabarcoding Molecular Identification of Chinese Medicinal Material Radix Paeoniae Rubra (Chishao)

Xia

Zhang

et al. 2022

Front. Plant Sci.

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Radix Paeoniae Rubra (Chishao), a typical multi-origin Chinese medicinal material, originates from the dried roots of Paeonia lactiflora or P. veitchii. The previous study suggested that these two commonly used Chishao showed variation in their chemical compositions and clinical efficacies. Therefore, accurate identification of different Chishao species was of great significance for the guide of clinical medication, and timely treatment of patients. In this study, the chloroplast genome sequences of P. lactiflora and P. veitchii were obtained by next-generation sequencing (NGS) technology, and then the hypervariable regions were selected to design two mini-barcode candidates for species identification. Combined with DNA metabarcoding technology, we performed qualitative and quantitative analysis on the artificially mixed samples of P. lactiflora and P. veitchii and evaluated the identification ability of these mini-barcode candidates. Furtherly, the mini-barcode with good performance was applied to distinguish the Chinese patent medicine “cerebral thrombosis tablets” containing Chishao. The results indicated that the chloroplast genomes of P. lactiflora and P. veitchii were 152,750 and 152,527 bp, respectively. As published previously, they exhibited a typical quadripartite structure including a large single-copy region (LSC), a small single-copy region (SSC) and a pair of inverted repeat regions (IRs). The nucleotide polymorphism analysis revealed seven variable protein-coding regions as petL, psaI, psbJ, rpl16, ycf1b, psaC, and ndhF, and two mini-barcodes were developed from ycf1b and ndhF respectively. The result suggested that both two mini-barcodes performed well distinguishing P. lactiflora from P. veitchii. Besides, P. lactiflora was the only raw material of Chishao in all collected “cerebral thrombosis tablets” samples. In general, this study has established a method to realize the qualitative and quantitative identification of Chishao as multi-origin Chinese medicinal materials, which can be applied to Chinese patent medicines containing Chishao.

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“… 2023 ), P. lactiflora MZ636553 (unpublished), P. mairei MZ617462 (unpublished), P. veitchii NC_032401 (Samigullin et al. 2018 ), P. intermedia MT210547 (Chen et al. 2023 ), P. ovovata NC_026076 (Samigullin et al.…”

Section: Resultsmentioning

confidence: 99%

The complete chloroplast genome of the first registered Paeonia Itoh hybrid cv. Hexie in China

Duan,

Dai,

Hao

et al. 2024

Mitochondrial DNA Part B

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Complete plastome sequence of Paeonia lactiflora Pall. (Paeoniaceae: Saxifragales)

Cited by 7 publications

References 6 publications

Next-Generation Genome Sequencing of Sedum plumbizincicola Sheds Light on the Structural Evolution of Plastid rRNA Operon and Phylogenetic Implications within Saxifragales

Next-Generation Genome Sequencing of Sedum plumbizincicola Sheds Light on the Structural Evolution of Plastid rRNA Operon and Phylogenetic Implications within Saxifragales

Development of Mini-Barcode Based on Chloroplast Genome and Its Application in Metabarcoding Molecular Identification of Chinese Medicinal Material Radix Paeoniae Rubra (Chishao)

The complete chloroplast genome of the first registered Paeonia Itoh hybrid cv. Hexie in China

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