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. 2019 Sep 3;4(2):2892–2893. doi: 10.1080/23802359.2019.1660274

Complete plastome sequence of Rumex japonicus (Polygonaceae) in Dok-do Island, Korea

Jin-Suk Youn a, JiYoung Yang a, Seung-Chul Kim b,✉, Jae-Hong Pak a,✉
PMCID: PMC7706998  PMID: 33365778

Abstract

We reported the complete chloroplast genome sequence of Rumex japonicus in Dok-do Island, Korea. The genome size was 159,223 bp in total length with one large single-copy (LSC; 84,962 bp), one small single-copy (SSC; 12,999 bp), and 2 inverted repeat (IR) regions (IRa and IRb, each with 30,631 bp). The overall GC content was 37.5% and the genome contained 131 genes, including 83 protein-coding, 38 transfer RNA and 8 ribosomal RNA genes. Phylogenetic analysis supported monophyly of subgenus Rumex and determined the phylogenetic position of R. japonicus as sister to the clade containing R. crispus and R. nepalensis.

Keywords: Chloroplast genome, Dok-do Island, Rumex japonicus, Polygonaceae

The docks and sorrels genus Rumex L. (Polygonaceae) is known for its diverse reproductive systems and sex-determining mechanism and comprises approximately 200 species distributed worldwide (Löve and Kapoor 1967; Mosyakin 2005; Navajas-Pérez et al. 2005). It is also known as one of the richest genera in natural hybrids, especially within the subgenus Rumex (Rechinger 1984; Daehler and Carino 2001). Given its large number of species and frequent hybridization, the genus Rumex has had a complicated taxonomic history, resulted in various infrageneric classification systems (e.g., Meisner 1856; Willkomm 1862; Dammer 1893; Rechinger 1964; Löve and Kapoor 1967). The molecular phylogenetic study of Rumex sensu lato recognized two large clades; one formed by the species of subgenus Rumex and the other composed of the species of subgenera Acetosa, Acetosella, and Platypodium (Navajas-Pérez et al. 2005). Rumex japoincus Houtt. is widely distributed in the Northeast Asia (China, Japan, and Korea), including Dok-do Island, which is located about 87.4 km away from Ulleung-do Island in East Sea. The Dok-do is oceanic volcanic island, consisting of two main islets (Seo-do; 88,740 m2 and Dong-do; 73,300 m2) and 89 annexed islets (the total area of 187,554 m2) (Sohn 1995). The Dok-do Island was formed from the early to late Pliocene (Sohn 1995). In Dok-do, about 60 native and introduced vascular plant species occur, one of which is R. japoincus, the most widely distributed species in both islets (Jung et al. 2014).

We sequenced the complete plastome of R. japonicus sampled from Dok-do Island (Voucher specimen; 37°14′26″ 131°52′10″, KNU-YJS20170714) to develop molecular markers for species identification and conduct phylogenetic and population genetic studies. Total DNA was isolated using the DNeasy plant Mini Kit (Qiagen, Carlsbad, CA, USA) and sequenced by the Illumina platform (Macrogen, Seoul, Korea). A total of 50,101,414 paired-end reads were obtained and assembled de nove with Velvet v. 1.2.10 using multiple k-mers (Zerbion and Birney 2008). The tRNAs were confirmed using tRNAscan-SE (Lower and Eddy 1997). The complete plastome of R. japonicus (MK058527) was 159,223 bp in total length with one large single-copy region (LSC; 84,962 bp), one small single-copy region (SSC; 12,999 bp), and two inverted repeat regions (IRa and IRb; 30,631 bp each). The overall GC content was 37.5% (LSC, 35.6%; SSC, 32.6%; IRs, 41.1%). The plastome contained 131 genes, including 83 protein-coding, 38 tRNA and 8 rRNA genes. The pairs of rpl23 gene located in IRs became pseudogene. The 16 genes contained one intron, while two genes (clpP and ycf3) contained two introns. A total of 18 genes were duplicated in IRs, including 7 tRNA, 4 rRNA, 6 protein-coding genes, and 1 pseudogene. Phylogenetic analysis of 13 representative species in the family Polygonaceae and one outgroup species (Plumbago auriculata, NC041245; Plumbaginaceae) was conducted using IQ-TREE v.1.4.2 (Nguyen et al. 2015) based on MAFFT v.7 (Katoh and Standley 2013) alignment. The ML tree (Figure 1) suggested that subgenus Rumex is monophyletic (100% bootstrap support) and that R. japonicus is sister to the clade containing R. nepalensis and R. crispus.

Figure 1.

Figure 1.

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The maximum-likelihood (ML) tree based on 13 representatives of Polygonaceae and one ougroup taxon, Plumbago auriculata (Plumbaginaceae). The bootstrap support value based on 1000 replicates is shown on each node.

Disclosure statement

The authors report no conflict of interest and are responsible for the content and writing of the paper alone.

References

  1. Daehler CC, Carino DA. 2001. Hybridization between native and alien plants and its consequences In: Lockwood JL and McKinney ML, editors. Biotic homogenization. New York, Kluwer Academic/Plenum Publishers; p. 81–102. [Google Scholar]
  2. Dammer U. 1893. Polygonaceae Vol 1a In: Engler HGA and Prantl KAE, editors. Die natürlichen Pflanzenfamilien. 3rd ed. Leipzig: Engelmann; p. 1–36. [Google Scholar]
  3. Jung SY, Byun JG, Park SH, Oh SH, Yang JC, Jang JW, Chang KS, Lee YM. 2014. The study of distribution characteristics of vascular and naturalized plants in Dokdo. South Korea J Asia Pac Biodivers. 7:197–205. [Google Scholar]
  4. Katoh K, Standley DM. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usabillty. Mol Bio Evol. 30:772–780. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Löve Á, Kapoor BM. 1967. A chromosome atlas of the collective genus Rumex. Cytologia. 32:328–342. [Google Scholar]
  6. Lower TM, Eddy SR. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25:955–964. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Meisner CF. 1856. Polygonaceae In: de Candolle A, editor. Prodromus systematis naturalis regni vegetabilis. Paris: Masson; p. 1–185. [Google Scholar]
  8. Mosyakin SL. 2005. Rumex Linnaeus. Flora of North America Editorial Committee, Flora of North America north of Mexico. New York: Oxford University Press; p. 489–533. [Google Scholar]
  9. Navajas-Pérez R, de la Herrán R, López González G, Jamilena M, Lozano R, Ruiz Rejón C, Ruiz Rejón M, Garrido-Ramos MA. 2005. The evolution of reproductive systems and sex-determining mechanisms within Rumex (Rolygonaceae) inferred from nuclear and chloroplastidal sequence data. Mol Biol Evol. 22:1929–1939. [DOI] [PubMed] [Google Scholar]
  10. Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ. 2015. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 32:268–274. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Rechinger KH. 1964. The genus Rumex L Vol. 2 In: Tutin TH, Heywood VH, Burges NA, Valentine DH, Walters SM, Webb DA, editors. Flora Europaea. Cambridge: University Press; p. 82–891. [Google Scholar]
  12. Rechinger KH. 1984. Rumex (Polygonaceae) in Australia: a reconsideration. Nuytsia. 5:75–122. [Google Scholar]
  13. Sohn YK. 1995. Geology of Tok Island, Korea: eruptive and depositional processes of a shoaling to emergent island volcano. Bull Volcanol. 56:660–674. [Google Scholar]
  14. Willkomm HM. 1862. Polygoneae In: Willkomm HM, Lange J, editors. Prodromus Florae Hispanicae, vol. 1. Sumtibus E. Schweizerbart (E. Koch), Stuttgartiae; p. 279–292. [Google Scholar]
  15. Zerbion DR, Birney E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18:821–829. [DOI] [PMC free article] [PubMed] [Google Scholar]

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