The complete chloroplast genome of Limonium tetragonum (Plumbaginaceae) isolated in Korea

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Korean J. Pl. Taxon. 2021;51(3):337-344

Publication date (electronic) : 2021 September 30

doi : https://doi.org/10.11110/kjpt.2021.51.3.337

Yongsung KIM, Hong XI¹, Jongsun PARK^1,

Honam National Institute of Biological Resources, Mokpo 58762, Korea

¹InfoBoss Inc. and InfoBoss Research Center, Seoul 06278, Korea

^*Author for correspondence: starflr@infoboss.co.kr

Received 2021 June 27; Revised 2021 August 16; Accepted 2021 September 7.

Abstract

Materials and Methods

Results and Discussion

The chloroplast genome of L. tetragonum (GenBank accession of MN044572) isolated in Korea is 154,689 bp long (GC ratio of 37.0%) and had four subregions: 84,572 bp of large single copy (35.3%) and 12,813 bp of small single copy (31.5%) regions are separated by 28,562 bp of inverted repeat (IR; 40.9%) (Table 1), which is similar to those of the previously reported L. tetragonum chloroplast genome (MW085088) (Table 1). It contained 128 genes (83 protein-coding genes [PCGs], eight rRNAs, and 37 tRNAs); 14 genes (five PCGs, four rRNAs, and five tRNAs) were duplicated in the IR regions, which is also same to those of the previously reported L. tetragonum chloroplast genome (MW085088) (Fig. 1, Table 1).

Table 1.

List of two available chloroplast genomes of Limonium tetragonum.

Fig. 1.

Circular map of chloroplast genome of Limonium tetragonum isolated in Korea. Genes shown outside are transcribed clockwise, and those 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.

Based on the pair-wise sequence alignment with the previously reported L. tetragonum chloroplast genome (MW085088) (Darshetkar et al., 2021), 35 SNPs and 33 INDELs regions (88 bp in total) were identified. The longest INDEL region was 18-bp located between trnT and trnL. The inserted sequence was 18-bp repetitive sequences. In addition, two chloroplast genomes of Limonium bicolor (Bunge) Kuntze (Darshetkar et al., 2021) display extremely divergent manner, no SNP and 116 INDEL regions (15,840 bp in length), which is similar to the case of Phedimus takesimensis chloroplast genomes (129 SNPs and 112 INDEL regions (8,506 bp in length) (Park et al., in preparation).

Numbers of these intraspecific variations of L. tetragonum were smaller than those of Pseudostellaria palibiniana (Takeda) Ohwi (84 SNPs and 125-bp INDELs), Pyrus ussuriensis Maxim. (1,221 SNPs and 781-bp INDELs), Goodyera schlechtendaliana Rchb. f. (200 SNPs and 511-bp INDELs), Gastrodia elata Blume (324 SNPs and 630-bp INDELs) isolated in Korea; while they were larger than those of Artemisia fukudo Makino (seven SNPs and 12-bp INDELs) (Min et al., 2019b), Fagus multinervis Nakai (two SNPs and 2-bp INDELs) (Park and Oh, 2020), Aconitum coreanum (H. Lév.) Rapaics (five to 19 SNPs and 52-bp to 950bp INDELs) (Kim et al., 2019d), Viburnum erosum Thunb. (16 SNPs and 50-bp INDELs) (Choi et al., 2020), and Veronica nakaiana Ohwi (seven SNPs and 4-bp INDELs) (Lee et al., 2021). In addition, seven PCGs contained at least one SNP or INDELs, among which two synonymous SNPs were found in psbA and psaA (Table 2) and four non-synonymous SNPs were identified in rpl20, rpl32, and ycf2 located in the IR region (Table 2). The ratio of synonymous to non-synonymous SNPs was 0.5, which is different from the normal ratio, like Chenopodium album L. (Park et al., 2021a). One INDEL region was identified in the genic region of rpoC2, resulting the extension of rpoC2 length in comparison to the previously sequenced chloroplast genome (MW085088) (Table 2).

Table 2.

List of intraspecific variations identified from the two Limonium tetragonum chloroplast genomes.

Sixteen chloroplast genomes were used for constructing ML and BI phylogenetic trees. Both phylogenetic trees displayed that two L. tetragonum, collected from the East and West coastal areas of Korean peninsula, respectively, were clustered with high bootstrap value (Fig. 2). The sister species of L. tetragonum is controversial: L. tetragonum formed a sister group with Limonium aureum (L.) Mill. in both trees (Fig. 2), whereas it was clustered with L. bicolor in the previous study using chloroplast genomes (Darshetkar et al., 2021). The close relative of L. tetragonum was not clearly confirmed because the phylogenetic study using chloroplast and nuclear loci could not determine the relationship with Limonium sinense (Girard) Kuntze, Limonium tenellum (Turczaninow) Kuntze, and Limonium flexuosum (Linnaeus) Kuntze (Koutroumpa et al., 2018) and the study with the complete chloroplast genome of L. tetragonum displayed that L. bicolor was sister species (Darshetkar et al., 2021), however, number of taxa used in this study was limited due to lack of complete chloroplast genomes and L. bicolor was not included in the previous study. This incongruency of the phylogenetic relationship might be caused by different sequences in both studies. Moreover, the supportive value of the clade of L. tetragonum and L. bicolor was 73%, which was lower than those (100%) in this study (Fig. 2), suggesting that L. aureum might be a sister species of L. tetragonum. Most of Limonium phylogenetic studies were conducted with the lack of East Asian Limonium species (Lledó et al., 2005; Malekmohammadi et al., 2017; Koutroumpa et al., 2018), requiring the additional phylogenetic studies including East Asian Limonium species.

Fig. 2.

Maximum-likelihood (ML) and Bayesian inference (BI) phylogenetic trees of 16 chloroplast genomes. Phylogenetic tree was drawn based on ML tree. The numbers above branches indicate support values of ML and BI trees, respectively.

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