Skip to main content
NCBI home page
Mitochondrial DNA. Part B, Resources logoLink to Mitochondrial DNA. Part B, Resources
. 2020 Feb 7;5(1):1079–1080. doi: 10.1080/23802359.2020.1722037

The complete chloroplast genome and phylogenetic analysis of Cuminum cyminum

Jing Zhou a, Zhenwen Liu b,✉
PMCID: PMC7748533  PMID: 33366883

Abstract

Cuminum cyminum (Apiaceae) is an economically important plant, whose fruits are usually used as flavoring, and also have pharmacological activities such as antioxidant, antibacterial, hypolipidemic, and so on. In this study, we assembled and annotated complete chloroplast (cp) genome sequence of C. cyminum. The results showed that the complete cp genome of C. cyminum was 157,839 bp in length, consisting of a large single-copy (LSC) region of 83,927bp, a small single-copy (SSC) region of 17,598bp, and two inverted repeat regions (IRa and IRb) of 28,157bp. In total, 131 genes were annotated, comprising of 86 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The phylogenetic analysis indicated that C. cyminum belongs to the tribe Scandiceae, and showed close relationship with Daucus carota.

Keywords: Cuminum cyminum, complete chloroplast genome, phylogeny

Cuminum cyminum L., an economically important plant belonging to the family Apiaceae, is indigenous to SW Asia and the Mediterranean region, but is today widely cultivated. Its aromatic fruits (cumin) are popular for its flavor, and has been used in Chinese and Ayurvedic medicine for the treatment of dyspepsia, diarrhea, and jaundice (Sheh et al. 2005; Srivsatava et al. 2011). Studies on this species have focused on describing its chemical constituents (Yan et al. 2002; Hashemi et al. 2009; Zhou et al. 2011) and pharmacological activity (Lee 2005; Sultana et al. 2010; Chen et al. 2011), rarely involved in its genomes. Here, the complete chloroplast (cp) genome sequence of C. cyminum is characterized, and its phylogenetic relationships with related taxa in Apiaceae are revealed.

The total genomic DNA was extracted from the leaves of C. cyminum collected from Kuerle (41°36′5.34″N, 86°03′25.66″E), Xinjiang of China using a Universal Genomic DNA Extraction kit (Tiangen Biotech, Beijing, China) following the manufacturer’s protocol. Voucher specimen was deposited in KUN (Kunming Institute of Botany, Chinese Academy of Sciences, ZJ1706). Then, the genome sequencing were performed with Illumina Hiseq 2500 (Majorbio, Shanghai, China) platform with pair-end (2 × 300) library. The raw data were filtered using Trimmomatic with default settings (Bolger et al. 2014). Then paired-end reads of clean data were assembled into circular contigs using GetOrganelle.py (Jin et al. 2018) with Daucus carota (No. NC_008325) as reference. Finally, the plastome was annotated by the Dual Organellar Genome Annotator (DOGMA; http://dogma.ccbb.utexas.edu/) (Wyman et al. 2004) and tRNAscan-SE (Lowe and Chan 2016) with manual adjustment using Geneious (Kearse et al. 2012), and the physical map was drawn by OGDRAW (Lohse et al. 2007).

The plastomes of C. cyminum (GenBank accession number: MN901636) show the typical properties of Apiaceae and most other eudicot plastid DNAs in its structural organization, gene content, and gene arrangement. The total length of the chloroplast genome was 157,389 bp, with 37.80% overall GC content. With typical quadripartite structure, a pair of IRs (inverted repeats) of 28,157 bp was separated by a small single-copy (SSC) region of 17,598 bp and a large single-copy (LSC) region of 83,927 bp. The cp genome contained 131 genes, including 86 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Among these, 18 genes were duplicated in the inverted repeat regions.

To investigate its phylogenetic placement, a total of 30 cp genome sequences of Apiaceae were downloaded from the NCBI database. All sequences were aligned using the MAFFT (Katoh and Standley 2013) webserver (http://mafft.cbrc.jp/alignment/server/), a maximum likelihood (ML) analysis was constructed using RAxML (Stamatakis 2014) with 1000 bootstrap replicates, and Bupleurum boissieuanum used as outgroup (NC_036017). The results showed that C. cyminum belongs to the tribe Scandiceae, and it was closely related to Daucus carota (Figure 1). Meanwhile, the phylogenetic relationship in Apiaceae was consistent with previous studies, and this will be beneficial to construct a more reasonable phylogeny of Apiaceae.

Figure 1.

Figure 1.

Open in a new tab

Maximum likelihood (ML) tree of 30 species in the family Apiaceae based on the complete chloroplast sequences using Bupleurum boissieuanum (NC_036017) as an outgroup. Numbers on the nodes are bootstrap values from 1000 replicates.

Funding Statement

This work was supported by the National Natural Science Foundation of China [No. 31460052 and 31960048] and the Hundred-Talent Program of Kunming Medical University [60118260127].

Disclosure statement

The authors declare no conflicts of interest and are responsible for the content of the article.

References

  1. Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 30(15):2114–2120. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Chen QQ, Gan ZL, Dai YQ, Yang Y, Ni YY. 2011. Antioxidant activity and kinetics analysis of cumin oleoresin and its main components in vitro. Sci Technol Food Industry. 32:111–113. [Google Scholar]
  3. Hashemi P, Shamizadeh M, Badiei A, Ghiasvand A R, Azizi K. 2009. Study of the essential oil composition of cumin seeds by an amino ethyl-functionallized nanoporous SPME fiber. Chromatographia. 70(7–8):1147–1157. [Google Scholar]
  4. Jin JJ, Yu WB, Yang JB, Song Y, Yi TS, Li DZ. 2018. GetOrganelle: a simple and fast pipeline for de novo assembly of a complete circular chloroplast genome using genome skimming data. bioRxiv. 1–11. [Google Scholar]
  5. Katoh K, Standley D. 2013. MAFFT multiple sequence alignment softwareversion improvements in performance and usability. Mol Biol Evol. 30(4):772–780. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C, et al. 2012. Geneious basic: an integratedand extendable desktop software platform for the organization andanalysis of sequence data. Bioinformatics. 28(12):1647–1649. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Lohse M, Drechsel O, Bock R. 2007. Organellar Genome DRAW (OGDRAW): a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes. Curr Genet. 52(5–6):267–274. [DOI] [PubMed] [Google Scholar]
  8. Lowe TM, Chan PP. 2016. tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes. Nucleic Acids Res. 44(W1):W54–W57. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Lee HS. 2005. Cuminaldehyde: aldose reductase and α-glucosidase inhibitor derived from Cuminum cyminum L. seeds. J Agric Food Chem. 53(7):2446–2450. [DOI] [PubMed] [Google Scholar]
  10. Sheh ML, Pu FD, Pan ZH, Watson MF, Cannon JFM, Holmes-Smith I, Kljuykov EV, Phillippe LR, Pimenov MG. 2005. Apiaceae. In: Flora of China Editorial Committee , editor. Flora of China, vol. 14. St. Louis MI: Missouri Botanical Garden Press; p. 1–205. [Google Scholar]
  11. Srivsatava R, Srivastava SP, Prakash S, Jaiswal N, Mishra A, Maurya R, Srivastava AK. 2011. Antidiabetic and antidyslipidemic activities of Cuminum cyminum L. in validated animal models. Med Chem Res. 20(9):1656–1666. [Google Scholar]
  12. Stamatakis A. 2014. RAxML version 8: a tool for phylogenetic analysis andpost-analysis of large phylogenies. Bioinformatics. 30(9):1312–1313. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Sultana S, Ripa FA, Hamid K. 2010. Comparative antioxidant activity study of some commonly used spices in Bangladesh. Pak J Biol Sci. 13(7):340–343. [DOI] [PubMed] [Google Scholar]
  14. Wyman SK, Jansen RK, Boore JL. 2004. Automatic annotation of organel-lar genomes with DOGMA. Bioinformatics. 20(17):3252–3255. [DOI] [PubMed] [Google Scholar]
  15. Yan JH, Tang KW, Zhong M, Deng NH. 2002. Determination of chemical components of volatile oil from Cuminum cyminum L. by gas chromatography-mass spectrometry. Se Pu. 20(6):569–572. [PubMed] [Google Scholar]
  16. Zhou JW, Huang JX, Huang L, Liu L. 2011. Column chromatography separation and GC-MS determination of essential oil components of Cuminum cyminum L. J Anhui Agri Sci. 39:9840–9841. [Google Scholar]

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

RESOURCES