The complete chloroplast genome of Zoysia macrostachya (Poaceae): Insights into intraspecific variations and species delimitation of the Zoysia species

Article information

Korean J. Pl. Taxon. 2021;51(3):326-331

Publication date (electronic) : 2021 September 30

doi : https://doi.org/10.11110/kjpt.2021.51.3.326

Sung-Dug OH, Seong-Kon LEE, Doh-Won YUN, Hyeon-Jin SUN¹, Hong-Gyu KANG¹, Hyo-Yeon LEE¹, Hong XI², Jongsun PARK^2,, Bumkyu LEE^3,

Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea

¹Subtropical Horticulture Research Institute, Jeju National University, Jeju 63243, Korea

²InfoBoss Inc. and InfoBoss Research Center, Gangnam-gu, Seoul 06278, Korea

³Department of Environmental Science & Biotechnology, Medicical Science, Jeonju University, Jeonju 55069, Korea

^*Author for correspondence: starflr@infoboss.co.kr (J. Park), leebk@jj.ac.kr (B. Lee)

Received 2021 August 5; Revised 2021 September 17; Accepted 2021 September 23.

Abstract

Materials and Methods

Results and Discussion

The chloroplast genome of Z. macrostachya (GenBank accession no. MZ233426) is 135,902 bp (GC ratio, 38.4%) and has four subregions: 81,546 bp of large single copy (LSC; 36.3%) and 12,586 bp of small single copy (SSC; 32.7%) regions are separated by 20,885 bp of inverted repeat (IR; 44.1%) (Fig. 1). Lengths of the complete Zoysia chloroplast genomes displayed 135,810 bp to 135,904 bp, similar to those of Tritichum, Oryza, and Avena genera (Ogihara et al., 2000; Wambugu et al., 2015; Liu et al., 2020) and displayed the short length among available Poaceae chloroplast genomes (from 129,905 bp [Rytidosperma semiannulare (Labill.) Connor & Edgar; NC_036701] to 162,086 bp [Paspalum ionanthum Chase; NC_039464] (Burke et al., 2018)). It contains 130 genes (83 protein-coding genes, eight rRNAs, 39 tRNAs, and one pseudogene); 19 genes (seven protein-coding genes, four rRNAs, and eight tRNAs) are duplicated in inverted repeat regions (Fig. 1). One pseudogene is a partial ndhF, same to that of the previously reported chloroplast genome of Z. macrostachya (Cheon et al., 2021).

Fig. 1.

Circular map of chloroplast genome of Zoysia macrostachya isolated in Korea. Gene shown outside are transcribed clockwise, and inside the circle are transcribed counter clockwise. Genes are color-coded to distinguish different functional groups. The dark grey and the light grey plot in the inner circle correspond to the GC content and AT content, respectively.

Thirty-nine SNPs and 11 INDEL regions (18 bp in total) were identified from pairwise alignment of two Z. macrostachya chloroplast genomes. The longest INDEL region is 6 bp long and two INDEL regions are 2-bp. Number of SNPs identified in Z. macrostachya is greater in number than that of Z. matrella (28 SNPs) (Lee and Park, 2021a); while number of the INDEL regions is smaller. In addition, both are smaller than those of Z. japonica (68 SNPs and 24 INDEL regions) (Lee and Park, 2021b), indicating that intraspecific variations of Z. macrostachya is the smallest among Zoysia species. These numbers are also smaller than those identified between the samples isolated in Korea: e.g., Campanula takesimana (Park et al., 2021a), Pseudostellaria palibiniana (Kim et al., 2019), Daphne genkwa (Yoo et al., 2021), Abeliophyllum distichum (Min et al., 2019; Park et al., 2019b, 2019c, 2021d), Chenopodium album (Park et al., 2021c), and Pyrus ussuriensis (Cho et al., 2019).

Two and one non-synonymous SNPs were found in psaB and psbK, respectively; while two, one, and one synonymous SNPs were identified in rpoC2, infA, and ccsA, respectively. In addition, one SNP was in trnQ, displaying 20.51% SNPs are in genic region. Number of genes containing SNPs in Z. macrostachya is smaller than that of Z. japonica, exhibiting different genes: rpoB, rpoC2, atpB, and ndhA contain one synonymous SNP each, petA covers three synonymous SNPs, rpoC1 and atpF have one non-synonymous SNP each (Lee and Park, 2021b). This distribution of intraspecific SNPs in the genic region can be developed as intraspecific molecular markers with additional experiments of validation. In addition, ycf1 which exhibits high nucleotide diversity in various plant species (Jiang et al., 2017; Park and Oh, 2020; Loeuille et al., 2021) was not found in this chloroplast genome, congruent to the other Zoysia chloroplast genomes (Tanaka et al., 2016; Cheon et al., 2021; Lee and Park, 2021a, 2021b).

ML and BI phylogenetic trees show that our Z. macrostachya was clustered with previous Z. macrostachya with high supportive values of all trees (Fig. 1). Interestingly, the branch length in Z. macrostachya clade is similar to the clade containing Z. japonica and Z. sinica (Fig. 2), suggesting the possible scenario that Z. sinica can be considered as Z. japonica together with similar morphological features of the two species (Yu et al., 1974). In addition, phylogenetic position of the Z. macrostachya clade was not supported by the BI tree (Fig. 2) and topology of Z. macrostachya and Z. macrantha presented in Cheon et al. (2021) was not also congruent with the three trees (Fig. 2), suggesting additional chloroplast genomes of neighbor species of Z. macrostachya are required to clarify the phylogenetic relationship. Taken together, our chloroplast genome provides the insight of intraspecific variations and species delimitation of Zoysia species.

Fig. 2.

Maximum-Likelihood (ML), Neighbor-Joining (NJ), and Bayesian inference (BI) phylogenetic trees of ten Zoysia and one outgroup complete chloroplast genomes. Phylogenetic tree was drawn based on ML tree. The numbers and hyphens above branches indicate support values of ML, NJ, and BI trees, and incongruent node in comparison to that of ML tree, respectively. BI tree was displayed separately without outgroup species which displayed too long branch length with blue colored shaded dotted rectangle.

Article information Continued