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

10.1080/23802359.2024.2397983
2397983
Version of Record
Data Note
Plastome Report
The complete plastome of Saxifraga giraldiana Engler and its phylogenetic analysis
X. Liang et al.
Liang Xin a
Yang Luxuan a
Xu Xiaoting a
Chi Xiulian b
a College of Life Sciences, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Sichuan University, Chengdu, China
b State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, PR China
Supplemental data for this article can be accessed online at https://doi.org/10.1080/23802359.2024.2397983.

CONTACT Xiulian Chi xiulian68@126.com State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, PR China
30 8 2024
2024
30 8 2024
9 9 11571161
17 1 2024
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-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits unrestricted non-commercial 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

Saxifraga giraldiana Engler is a common subalpine and alpine plant belonging to Saxifragaceae. However, the genetic diversity of this species has remained to be explored. In this study, we have assembled and characterized the complete chloroplast genome of S. giraldiana, filling this knowledge gap and uncovering its genetic composition. The chloroplast genome is 147,267 bp long and contains 131 genes, including 85 protein-coding genes, 38 tRNA genes, and eight rRNA genes. Furthermore, we have performed a phylogenetic analysis of 19 representative species within Saxifraga. As a result, we have found that S. giraldiana, together with S. implicans and S. stellariifolia, forms a monophyletic group. These findings have implications for the conservation and utilization of S. giraldiana.

Keywords

Saxifragaceae
chloroplast genome
phylogeny
Saxifraga giraldiana
Scientific and Technological Innovation Project of China Academy of Chinese Medical Sciences CI2021A03908 This study was supported by the Scientific and Technological Innovation Project of China Academy of Chinese Medical Sciences [CI2021A03908].
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pmcIntroduction

Saxifraga giraldiana Engler, 1901, is a perennial herb within the Saxifragaceae family. It exhibits distinctive characteristics during its flowering phase, notably the withering of basal and lower stem leaves, petals yellow, brown spotted, ovate or elliptic to oblong. This species thrives predominantly in understory habitats, alpine meadows, and mountain crevices at altitudes of 1000–4000 m (Wang et al. 2001). Morphologically, S. giraldiana was considered closely related to Saxifraga stellariifolia, primarily distinguished by sepals (Wang et al. 2001; Yuan, Li, et al. 2023).

However, relying solely on morphology for species differentiation presents challenges, urging the need for molecular data. Despite the transformative impact of high-throughput sequencing in phylogenetics (Li et al. 2022), the study on the chloroplast genome of S. giraldiana has been notably absent. Besides, many Saxifraga species are distributed in alpine regions, but genetic data are still lacking for some species, including S. giraldiana, hindering a comprehensive understanding of the phylogenetic position of the species, the phylogenetic relationships within the taxon, and the biogeographic history (Tkach et al. 2015). To fill this gap, this study assembled and characterized the complete chloroplast genome of S. giraldiana. This work can lay the foundation for future research on the evolution, protection, and potential medicinal applications of S. giraldiana.

Materials and methods

Fresh leaves for sequencing were harvested on 22 August 2018, from Xiling Snow Mountain, Dayi County, Chengdu City, Sichuan Province, China (104.716666 E, 30.702516 N) (Figure 1). The specimen, with the identification number QL-SC01-01, has been meticulously preserved in the herbarium of Sichuan University, with Xiao-Ting Xu (xiaotingxu@sc.edu.cn) serving as the contact person. The genomic DNA extraction followed the modified CTAB method (Porebski et al. 1997) and the quality was assessed using the Qubit 2.0 system. Then, the total genomic DNA was fragmented and subjected to paired-end sequencing with fragment length of 150 bps on the Illumina high-throughput sequencing platform NovaSeq 6000. Following quality control procedures, approximately 4.82 GB of clean paired-end reads were assembled using NOVOPlasty (v.2.7.1) (Dierckxsens et al. 2017). The annotation of the complete circular chloroplast genome was conducted by CPGAVAS2 (Shi et al. 2019) with reference to the S. stellariifolia chloroplast genome (NC_070511.1). Manual adjustments were performed using Geneious Primer (v2021.1.1.0). Finally, the annotated chloroplast genome was submitted to GenBank using Bankit and was assigned the accession number OR948604. The circular genome mapping of the newly sequenced chloroplast genome was illustrated using the CPGview (Liu et al. 2023) online tool. To ascertain the phylogenetic relationships of S. giraldiana, the chloroplast genomes of 19 additional Saxifraga species were downloaded from GenBank, including the morphological closely related species, Saxifraga stellariifolia, Saxifraga implicans, and Saxifraga insolens (Yuan, Li, et al. 2023). Another species in the sister branches of Saxifraga: Micranthes melanocentra was chosen as outgroup (Tkach et al. 2015; Yuan, Ma, et al. 2023). The entire chloroplast genome sequence was aligned using MAFFT (v7.487) (Katoh et al. 2002; Katoh and Standley 2013) under default parameters settings. Subsequently, a maximum-likelihood (ML) phylogenetic tree was constructed using IQ-TREE (v2.2.0) (Minh et al. 2020) using the best-fit model determined by ModelFinder (Kalyaanamoorthy et al. 2017) and 1000 ultrafast bootstrap replicates (Hoang et al. 2018).

Figure 1. Field photos of S. giraldiana shot the photo at the position of 104.716 E, 30.702 N. These photos were taken by Dr. Lei Zhang with the author’s approval for use. It exhibits distinctive characteristics during its flowering phase, notably the withering of basal and lower stem leaves, petals yellow, brown spotted, ovate or elliptic to oblong.

Results

The S. giraldiana complete chloroplast genome is 147,267 bp long with 38.1% GC content (Figure 2). The genome assembly is highly reliable with an average mapping depth of ×393 (Supplementary Figure 1). The genome has four subregions: a large single-copy (LSC) region (79,463 bp), a small single-copy (SSC) region (16,866 bp) regions, and two inverted repeat (IR) regions of 25,469 bp long each, showing a conserved quadripartite structure. A total of 131 genes are predicted, including 85 protein-coding genes, 38 tRNA genes, and eight rRNA genes (Figure 2). In the S. giraldiana chloroplast genome, six unique protein-coding genes (ndhB, rpl2, rpl23, rps12, rps7, and ycf2), six unique tRNA genes (trnA, tnrI, trnL, trnN, trnR, and trnV), and four unique rRNA genes (rrn16, rrn23, rrn4.5, and rrn5) are located at the IR regions. Seventeen genes possess two exons each (rps16, atpF, ndhA, two copies of ndhB, petB, petD, rpl16, ropC1, two copies of trnA, trnG, two trnI, trnK, trnL, trnV), while four genes (clpP, two copies of copies of rps12, and ycf3) comprise three exons. Eleven genes (rps16, atpF, rpoC1, ycf3, clpP, petB, petD, rpl16, two copies of ndhB, and ndhA) are cis-splicing genes (Supplementary Figure 2), and the rps12 gene is trans-splicing gene (Supplementary Figure 3).

Figure 2. The complete chloroplast genome map of S. giraldiana generated using CPGview. The map comprises six tracks. Dispersed repeats at the center, then short blue bars for long tandem repeats. Various-colored bars for microsatellite sequences in the third track. The fourth track is for small single-copy (SSC), inverted repeat (IRa and IRb), and large single-copy (LSC) regions. The fifth track illustrates GC. The sixth showcases genes, genes with inner ones in a clockwise and outer ones in an anticlockwise direction. Functional gene classifications are shown in the bottom left corner.

Our phylogenetic analysis, involving representative Saxifraga species, reveals that S. giraldiana forms a monophyletic group alongside S. implicans and S. stellariifolia (Figure 3). Notably, S. giraldiana and S. stellariifolia exhibit extreme morphological similarity (Wang et al. 2001). The bootstrap value for the sister species of S. girladiana and S. implicans is only 72, and the branch length is significantly shorter compared to other species. These findings contribute valuable insights to the conservation and utilization of S. giraldiana and enhance our understanding of the evolution and biogeography of the genus Saxifraga.

Figure 3. Maximum-likelihood (ML) phylogenetic tree of S. giraldiana (red font) and 19 Saxifraga species. Micranthes melanocentra was used as outgroup taxa. The bootstrap support values are shown at the branches in the cladogram tree (A). The corresponding phylogram tree is shown in panel B. GenBank accession number of each species was shown in brackets. The corresponding phylogram tree is shown in panel B. Sequences used for tree construction were as follows: S. giraldiana (OR948604.1, this study), Saxifraga implicans (NC_070476.1, Yuan, Ma, et al. 2023), Saxifraga stellariifolia (NC_070511.1, Yuan, Ma, et al. 2023), Saxifraga diversifolia var. angustibracteata (NC_070456.1, Yuan, Ma, et al. 2023), Saxifraga xiaozhongdianensis (NC_070526.1, Yuan, Ma, et al. 2023), Saxifraga viscidula (NC_070523.1, Yuan, Ma, et al. 2023), Saxifraga insolens (NC_070477.1, Yuan, Ma, et al. 2023), Saxifraga tangutica (NC_070514.1, Yuan, Ma, et al. 2023), Saxifraga sinomontana (MN104589.1, Li et al. 2019), Saxifraga congestiflora (NC_070453.1, Yuan, Ma, et al. 2023), Saxifraga maxionggouensis (NC_070484.1, Yuan, Ma, et al. 2023), Saxifraga moorcroftiana (NC_070488.1, Yuan, Ma, et al. 2023), Saxifraga signata (NC_070507.1, Yuan, Ma, et al. 2023), Saxifraga gemmigera (NC_070464.1, Yuan, Ma, et al. 2023), Saxifraga signatella (NC_070508.1, Yuan, Ma, et al. 2023), Saxifraga umbellulata var. pectinata (NC_058983.1), Saxifraga substrigosa (NC_070513.1, Yuan, Ma, et al. 2023), Saxifraga cinerascens (NC_070452.1, Yuan, Ma, et al. 2023), Saxifraga nangxianensis (NC_070492.1, Yuan, Ma, et al. 2023), Saxifraga cernua (NC_070450.1, Yuan, Ma, et al. 2023), and Micranthes melanocentra (NC_056191.1).

Discussion and conclusions

This study represents the first sequencing and characterization of the chloroplast genome of S. giraldiana, revealing a conserved quadripartite structure with a size of 147,267 bp and 131 predicted genes. Phylogenetic analysis positions S. giraldiana in close relation to S. implicans and S. stellariifolia, forming a monophyletic group with notably short branch lengths. This consistent with previous studies that identify S. stellariifolia as a sister species to the clade housing S. implicans, supported by RAD sequences, albeit with limited support (Yuan, Li, et al. 2023). The bootstrap value between S. girladiana and S. implicans for each other’s sister species is low, suggesting a minimal level of differentiation in the chloroplast genome’s CDS region. This low variation between species may necessitate a more extensive sampling of nuclear genes for accurate phylogenetic analysis. Increasing the density of nuclear gene data could help elucidate phylogenetic relationships between species and facilitate the detection of hybrid introgression within the evolutionary network. Overall, this study contributes valuable insights into the genomics and evolutionary relationships of S. giraldiana, emphasizing the need for further research, especially involving nuclear genomes, to enhance understanding of speciation processes and intricate phylogenetic associations among Saxifraga species.

Supplementary Material

Saxifraga giraldiana_S_20240815.docx

Acknowledgements

The authors would like to thank Dr. Lei Zhang for his help in sampling and taking photographs of the samples in this paper.

Author contributions

Xiaoting Xu and Xiulian Chi conceived the project, Xin Liang and Luxuan Yang carried out experiments and data analysis. Xin Liang and Xiaoting Xu wrote the manuscript. Xiulian Chi revised the manuscript. All authors have read and agreed to the published version of the manuscript.

Ethical approval

This study includes no human, animal, or endangered plant samples, and the sampling site was not in the natural reserve. No permissions are needed during the collection of samples.

Disclosure statement

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

Data availability statement

The genome sequence data that support the findings of this study are openly available in GenBank of NCBI at https://www.ncbi.nlm.nih.gov/ under the accession number OR948604. The associated BioProject, SRA, and Bio-Sample numbers are PRJNA1051492, SRX22864841, and SAMN38773424, respectively.
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