Skip to main content
NCBI home page
Mitochondrial DNA. Part B, Resources logoLink to Mitochondrial DNA. Part B, Resources
. 2021 Mar 11;6(3):753–754. doi: 10.1080/23802359.2021.1878953

Plastomes of two Rehmannia species： comparative genomic and phylogenetic analyses

Jing Sun a, Mengqi Sun a, Danchou Wang a, Kailun Xu a, Renyong Hu a,b,✉, Yonghua Zhang a,b,✉
PMCID: PMC7954473  PMID: 33763569

Abstract

Phylogenetic relationships within Rehmannia have not been well solved. Here, we assembled and reported two new complete plastomes of R. glutinosa and R. chingii by de novo assembly. The complete plastomes of R. glutinosa and R. chingii were 153,797 and 153,328 bp in length, respectively. These two plastomes had 98.8% sequence identity and a total of 401 SNPs, 137 indels and 6 inversions. They were highly conserved in GC content (43.1%), gene order, and gene content (133 genes), including 88 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The phylogenomic analysis confirmed the monophyly of Rehmannieae and supported R. chingii as the basal taxon of Rehmannia.

Keywords: Chloroplast genome, phylogenomics, Rehmannia glutinosa, Rehmannia chingii, Rehmannieae

Rehmannia Libosch. ex Fisch. et Mey., a small genus of tribe Rehmannieae (Orobanchaceae), is endemic to China (Rix 1987; Zeng et al. 2017). R. glutinosa (Gaert.) Libosch. ex Fisch. et Mey. is distributed from North China to Korea (Rix 1987), whose root is usually used as traditional medicine (Kim et al. 2008; Zhang et al. 2008). Rehmannia chingii H.L. Li, located in Tianmu mountains and adjacent areas of Southeast China, was seriously threatened by human activities (Zeng et al. 2016). Although the phylogenetic tree of all six Rehmannia species with complete plastomes has been reconstructed before, the phylogenetic relationship within Rehmannia remains controversial (Xia et al. 2009; Zeng et al. 2017). Here, we reported two new plastomes of R. glutinosa and R. chingii with further comparative genomic and phylogenomic analyses.

Samples of R. glutinosa and R. chingii were collected from Dahongzai (Henan, China, 34°14′16.91″N, 113° 5′23.44″E) and Mt. Tianmu (Zhejiang, China, 30°19′9.23″N, 119°26′33.20″E), respectively. Voucher specimens (Minqi Cai CMQ16223, Yonghua Zhang ZYH160425) were deposited in the Herbarium of Wenzhou University (WZU). Genomic DNAs were extracted from silica-dried leaves with modified CTAB method (Doyle and Doyle 1987). Then 125-bp Paired-end reads were sequenced on the Illumina HiSeq2500 platform. Complete plastomes were assembled and confirmed using NOVOPlasty (Dierckxsens et al. 2017) and CLC Genomics Workbench 11 (Zhang et al. 2019; Liu et al. 2020). Gene annotation was performed using program PGA (Qu et al. 2019) with Rehmannia henryi (GenBank accession numbers: KX636158) as a reference.

The complete plastomes of R. glutinosa and R. chingii (GenBank accession numbers: MW013795, MW013796) are 153,797 and 153,328 bp in genome sizes, respectively. Their plastomes contain a large single copy (LSC) region (84,672–84,257 bp), a small single copy (SSC) region (17,607–17,587 bp), and a pair of inverted repeats (IRs) (25,759–25,742 bp). The two plastomes have 98.8% sequence identity and a total of 401 SNPs, 137 indels and 6 inversions. They are highly conserved in GC content (43.1%), gene order, and gene content (133 genes, including 88 protein-coding genes, 37 tRNA genes, and 8 rRNA genes).

Maximum likelihood (ML) analysis was conducted on a dataset that included 113 genes for 14 taxa (13 Orobanchaceae species, one Lamiaceae species as the outgroup) using RAxML-HPC BlackBox (8.2.12) on CIPRES (http://www.phylo.org). The phylogeny of Orobanchaceae was well resolved and supported R. chingii (from Mt. Tianmu) as the basal taxon of the genus (Figure 1), which is consistent with the phylogenetic result using DNA fragments (Xia et al. 2009). Compared with the study of Zeng et al. (2016, 2017), we think that the former sequenced plastome of R. chingii (collected from Lishui, Zhejiang, China; GenBank accession number KX426347) was most likely misidentified based on our field investigation.

Figure 1.

Figure 1.

Open in a new tab

Phylogenetic tree of 14 taxa based on 113 genes of their plastomes using maximum likelihood (ML) method. Numbers near the nodes represent ML bootstrap value (≥90).

Funding Statement

This research was supported by the Basic Research Project of Wenzhou (Grant No. N20180004), the Natural Science Foundation of Zhejiang Province (Grant No. LY21C030002) and the National Natural Science Foundation of China (Grant No. 31800309).

Disclosure statement

The authors are really grateful to the open raw genome data from public database. The authors report no conflicts of interest and are responsible for the content and writing of the paper.

Data availability statement

The genome sequence data of Rehmannia glutinosa and Rehmannia chingii that support the findings of this study are openly available in GenBank of NCBI at (https://www.ncbi.nlm.nih.gov/) under the accession no. MW013795-MW013796. The associated BioProject and Sequence Read Archive (SRA) numbers are PRJNA664281, SRR12667759, and PRJNA664316, SRR12667977, respectively.

References

  1. Dierckxsens N, Mardulyn P, Smits G.. 2017. NOVOPlasty: de novo assembly of organelle genomes from whole genome data. Nucleic Acids Res. 45(4):e18. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Doyle JJ, Doyle JL.. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull. 19:11–15. [Google Scholar]
  3. Kim DH, Park CH, Park HW, Park CG, Sung JS, Yu HS, Kim GS, Seong NS, Kim JC, Kim MS, Bae SG, et al. 2008. A new high-quality, disease resistance and high-yielding Rehmannia glutinosa cultivar “Kokang”. Kor J Breed Sci. 40:84–87. [Google Scholar]
  4. Liu LX, Du YX, Folk RA, Wang SY, Soltis DE, Shang FD, Li P.. 2020. Plastome evolution in Saxifragaceae and multiple plastid capture events involving Heuchera and Tiarella. Front Plant Sci. 11:361. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Qu XJ, Moore MJ, Li DZ, Yi TS.. 2019. PGA: a software package for rapid, accurate, and flexible batch annotation of plastomes. Plant Methods. 15:50. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Rix M. 1987. The genus Rehmannia. Plantsman. 8:193–195. [Google Scholar]
  7. Xia Z, Wang YZ, Smith JF.. 2009. Familial placement and relations of Rehmannia and Triaenophora (Scrophulariaceae sl) inferred from five gene regions. Am J Bot. 96(2):519–530. [DOI] [PubMed] [Google Scholar]
  8. Zeng SY, Zhao JH, Han K, Liu ZL.. 2016. Complete chloroplast genome sequences of Rehmannia chingii, an endemic and endangered herb. Conserv Genet Resour. 8(4):407–409. [Google Scholar]
  9. Zeng SY, Zhou T, Han K, Yang YC, Zhao JH, Liu ZL.. 2017. The complete chloroplast genome sequences of six Rehmannia species. Genes, 8 8(3):103. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Zhang YH, Lee JK, Liu XL, Sun ZS.. 2019. The first complete chloroplast genome of Hylomecon japonica and its phylogenetic position within Papaveraceae. Mitochondrial DNA Part B. 4(2):2349–2350. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Zhang RX, Li MX, Jia ZP.. 2008. Rehmannia glutinosa: review of botany, chemistry and pharmacology. J Ethnopharmacol. 117(2):199–214. [DOI] [PubMed] [Google Scholar]

Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Data Availability Statement

The genome sequence data of Rehmannia glutinosa and Rehmannia chingii that support the findings of this study are openly available in GenBank of NCBI at (https://www.ncbi.nlm.nih.gov/) under the accession no. MW013795-MW013796. The associated BioProject and Sequence Read Archive (SRA) numbers are PRJNA664281, SRR12667759, and PRJNA664316, SRR12667977, respectively.

Articles from Mitochondrial DNA. Part B, Resources are provided here courtesy of Taylor & Francis

RESOURCES