Complete chloroplast genome data of Ranunculus membranaceus (Ranunculaceae), an important medicinal plant species

The perennial alpine herb Ranunculus membranaceus (Ranunculaceae) has significant medicinal value. The complete chloroplast genome of R. membranaceus was sequenced by high-throughput Illumina sequencing Platform Illumina NovaSeq 6000. The circular genome is 156,028 bp in size, including two inverted repeats (IRs) of 25,361 bp, a large single-copy (LSC) region of 85,491 bp, and a small single-copy (SSC) region of 19,815 bp. A total of 128 genes were annotated, namely 84 protein-coding genes (PCGs), 36 tRNA genes, and eight rRNA genes. Two phylogenetic trees of 18 species of the tribe Ranunculeae species were constructed with Meconopsis punicea as the outgroup based on the whole chloroplast genomes and the concatenated sequence of PCGs, respectively. Phylogeny showed that R. membranaceus was closely related to R. yunnanensis. These data enrich knowledge of Ranunculaceae genetics and will contribute to further studies of R. membranaceus in molecular breeding, genetic transformation, species identification, genetic engineering and phylogenetic research.


a b s t r a c t
The perennial alpine herb Ranunculus membranaceus (Ranunculaceae) has significant medicinal value. The complete chloroplast genome of R. membranaceus was sequenced by high-throughput Illumina sequencing Platform Illumina No-vaSeq 60 0 0. The circular genome is 156,028 bp in size, including two inverted repeats (IRs) of 25,361 bp, a large single-copy (LSC) region of 85,491 bp, and a small singlecopy (SSC) region of 19,815 bp. A total of 128 genes were annotated, namely 84 protein-coding genes (PCGs), 36 tRNA genes, and eight rRNA genes. Two phylogenetic trees of 18 species of the tribe Ranunculeae species were constructed with Meconopsis punicea as the outgroup based on the whole chloroplast genomes and the concatenated sequence of PCGs, respectively. Phylogeny showed that R. membranaceus was closely related to R. yunnanensis . These data enrich knowledge of Ranunculaceae genetics and will contribute to further studies of R. membranaceus in molecular breeding, ge-netic transformation, species identification, genetic engineering and phylogenetic research.
© 2023 The Author(s

Value of the Data
• Ranunculus membranaceus has significant medicinal value, and its complete chloroplast genome data will be useful in phylogenetic comparisons with the related species. • The data will be useful to clarify the genus's chloroplast genome structure and in phylogenomic studies of R. membranaceus . • The detected simple sequence repeats can be used in the development of potentially useful molecular markers and evaluation of genetic diversity in R. membranaceus populations and closely related species.

Objective
Ranunculus membranaceus Royle is an alpine perennial herb of the family Ranunculaceae, mainly distributed in the Qinghai-Tibet Plateau of China, northern India, Nepal, and Pakistan at altitudes between 2700 and 5000 m [1] . The whole plant, especially flowers, of Ranunculus membranaceus is commonly used in traditional Chinese medicine. The species is used to treat dyspepsia, laryngitis, abdominal lumps and hydrops, and arthritis. Its population declines due to grassland degradation and over-collection in the wild. Here, the complete chloroplast genome of R. membranaceus is described in order to provide a basis for resource management, conservation, breeding and investigating genetics of this medicinal species.

Data Description
R. membranaceus is a species characterized by having fibrous roots, reduced sheathing basal leaves, deeply divided stem leaves, dense whitish-tomentose indument on all parts of the plant, and yellow flowers ( Fig. 1 ) [1] . The whole plant, especially flowers, is commonly used in traditional Chinese medicine to warm the middle abdomen to dispel cold, invigorate the stomach and digestion, and clear damp to promote diuresis. It is used for dyspepsia, laryngitis, abdominal lumps and hydrops, and yellow water disease [2] . Here, the complete chloroplast genome of R. membranaceus is described, along with phylogenetic analysis of the cpDNA sequence information with 17 other species of the tribe Ranunculeae. The R. membranaceus chloroplast genome ( Fig. 2 ) was found to be 156,028 bp long. The mean coverage was 100.85x and the GC content was 37.9%. The assembled genome exhibited a tetrad structure with a large single-copy (LSC) region of 85,491 bp, two inverted repeats (IRs) of 25,361 bp, and a small single-copy (SSC) region of 19,815 bp. The GC contents of these regions differed, being highest in the IRs (43.5%), and lowest (36.1% and 31.5%) in the LSC and SSC regions, respectively. One hundred and twenty-eight genes were observed ( Table 1 ). Of these, 84 coded for protein, 36 for tRNA, and 8 for rRNA. Two copies of each of the tRNA genes trnA-UGC, trnI-CAU, trnL-CAA, trnV-GAC, trnI-GAU , and trnR-ACG were observed. Similarly, two copies of the rRNA genes rrn4.5s and rrn5s were identified. The rpl2, rps7, rpl23 , and ndhB protein-coding genes also had two copies, while rps12 had three copies. Three hundred and nineteen simple sequence repeats (SSRs) were found, of which dinucleotides were the most common SSR markers, representing 52.7% of the total. The remaining SSRs were composed of 117 (36.7%) mono-, 17 (5.3%) tetra-, 16 (5.0%) tri-, and 1 (0.3%) hexa-SSRs ( Fig. 3 ).
Two phylogenetic trees were constructed for R. membranaceus and 17 other species of the tribe Ranunculeae with Meconopsis punicea as the outgroup based on the whole chloroplast genomes and the concatenated sequence of PCGs, respectively. The phylogenetic tree based on the concatenated sequence of PCGs has a higher support rate than the phylogenetic tree based on the whole chloroplast genome. The topological structure of two phylogenetic trees is similar.  It is apparent ( Fig. 4 ) that R. membranaceus is closely related to R. yunnanensis with 100% bootstrap support in two phylogenetic trees. These findings enrich our knowledge of Ranunculaceae genetics, and provide a basis for resource management, breeding, and further investigations into the genetics of R. membranaceus .

Experimental Design, Materials and Methods
Fresh samples were collected from the Qinghai Haibei National Field Research Station of Alpine Grassland Ecosystem (altitude 3200 m, 37.617 °N, 101.200 °E), which is situated at Menyuan, Qinghai Province, China, in the north-eastern Qinghai-Tibet plateau [3] . A voucher specimen was deposited at the Forestry Herbarium, College of Agriculture and Animal Husbandry, Qinghai University, Xining, China under the voucher number HB210330 0 01.
The chloroplast genome data of 17 other species of the tribe Ranunculeae from NCBI were downloaded for the phylogenetic tree reconstruction. These species account for 61.2% of the total of species reported in the genus Ranunculus, and account for 20.2% in the tribe Ranunculeae. A phylogenetic tree of tribe Ranunculeae species was constructed using the maximum likelihood method with Berberis amurensis (GenBank: NC030062) as the outgroup. MAFFT [10 , 11] (online version: https://mafft.cbrc.jp/alignment/server/ ) was used to align the sequences using default settings and the tree was created using MEGA7 with the general time reversible (GTR) model with 10 0 0 bootstraps [12] . After aligned, it was found that, the percentage of missing data is 39.5 %, the number of parsimony informative sites is 24568 (see the alignment in Appendix 1). For comparison with the ML phylogenetic tree based on complete chloroplast genomes, a ML phylogenetic tree based on the concatenated PCGs of 19 Ranunculaceae species was created using IQ-tree v1.6.8 [13] with 10 0 0 bootstraps in PhyloSuite v1.2.2 [14] . Alignments were trimmed with PhyloSuite v1.2.2 [14] and manually edited where necessary. We used Partition-Finder2 in PhyloSuite v1.2.2 for optimal partitioning strategy and evolutionary model selection (see the best selected models in Appendix 2). Phylograms were visualized with FigTree v1.4.4 ( http://tree.bio.ed.ac.uk/ ).

Ethics Statements
This study did not require an official ethics review.

CRediT Author Statement
All authors contributed to the design of the study and the writing of the manuscript. Material preparation and collection were performed by Chunhui Zhang, Lin Wu and Zhen Ma. The data analysis was performed by Yanmei Ren, Ji-zhong Wan, Mengyan Wang and Zuoyi Wang. The draft of the manuscript was written by Yanmei Ren. Huakun Zhou and Ji-Zhong Wan revisited critically for intellectual content and Chunhui Zhang and Zhen Ma reviewed the final version of our manuscript.

Declaration of Competing Interest
The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Data Availability
Characterization of the complete chloroplast genome of Ranunculus membranaceus (Ranunculaceae) (Original data) (NCBI).