The complete chloroplast genome of <i>Limonium tetragonum</i> (Plumbaginaceae) isolated in Korea

Yongsung KIM; Hong XI; Jongsun PARK

doi:10.11110/kjpt.2021.51.3.337

Korean J. Pl. Taxon > Volume 51(3); 2021 > Article

KIM, XI, and PARK: The complete chloroplast genome of Limonium tetragonum (Plumbaginaceae) isolated in Korea

Short Communication

Korean Journal of Plant Taxonomy 2021; 51(3): 337-344.

Published online: September 30, 2021

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

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

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 June 27, 2021 Revised August 16, 2021 Accepted September 7, 2021

(open-access):

This is an open-access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

The chloroplast genome of Limonium tetragonum (Thunb.) Bullock, a halophytic species, was sequenced to understand genetic differences based on its geographical distribution. The cp genome of L. tetragonum was 154,689 bp long (GC ratio is 37.0%) and has four subregions: 84,572 bp of large single-copy (35.3%) and 12,813 bp of small single-copy (31.5%) regions were separated by 28,562 bp of inverted repeat (40.9%) regions. It contained 128 genes (83 protein-coding genes, eight rRNAs, and 37 tRNAs). Thirty-five single-nucleotide polymorphisms and 33 INDEL regions (88 bp in length) were identified. Maximum-likelihood and Bayesian inference phylogenetic trees showed that L. tetragonum formed a sister group with L. aureum, which is incongruent with certain previous studies, including a phylogenetic analysis.

Keywords: Limonium tetragonum, chloroplast genome, phylogenetic analysis, intraspecific variation, Plumbaginaceae

Limonium, belonging to Plumbaginaceae family, is a cosmopolitan halophytic genus, and a few species inhabit alkaline soil away from the coastal area (Kubitzki, 1993; Morgan and Funnell, 2018). Limonium tetragonum (Thunb.) Bullock, distributed in coastal areas of Korea and Japan, is a biennial halophytic species with radical leaves (8–15 × 1.5–3 cm) and yellow corolla (Owhi, 1965; Park, 2007; Lee et al., 2011; Park et al., 2020a). The crude extracts and solvent-partitioned fractions of whole plants of L. tetragonum display antioxidant (Lee et al., 2011) and anti-cancer activities (Kong et al., 2008); ethyl acetate soluble fraction of aerial parts exhibits anti-liver fibrosis (Kim et al., 2016); that of whole plants shows anti-alcohol toxicity (Kim et al., 2015); and its methanol extracts of whole plants present hepatoprotective activities (Yang et al., 2014). We sequenced L. tetragonum from the western coastal area of Korea for investigating intraspecific variations on chloroplast genomes with chloroplast of L. tetragonum isolated in eastern seashore of Korea.

Materials and Methods

Plant material

We collected L. tetragonum in Aphaedo island in Shinan-gun, Jeollanam-do, Korea (34.8612N, 126.32629E). A voucher specimen and genomic DNA were deposited in the InfoBoss Cyber Herbarium (IN, the voucher number IB-00899).

DNA extraction and chloroplast genome determination

The total genomic DNA was extracted from fresh leaf by using a DNeasy Plant Mini Kit (QIAGEN, Hilden, Germany). Genome sequencing was performed using HiSeqX at Macrogen Inc., Korea, and de novo assembly was done by Velvet v1.2.10 (Zerbino and Birney, 2008) and GapCloser v1.12 (Zhao et al., 2011). Assembled sequences were confirmed by BWA v0.7.17 (Li, 2013) and SAMtools v1.9 (Li et al., 2009). All bioinformatic analyses were conducted in the Genome Information System (http://geis.infoboss.co.kr/) utilized in the previous studies (Kim et al., 2018, 2019a, 2019b, 2019c, 2021; Bum et al., 2020; Park et al., 2021c).

Genome annotation was conducted based on another L. tetragonum chloroplast (MW085088.1) with Geneious R11 v11.0.5 (Biomatters Ltd, Auckland, New Zealand). A circular map of L. tetragonum chloroplast genome was drawn using OGDRAW v1.31 (Greiner et al., 2019).

Identification of intraspecific variations

Single nucleotide polymorphisms (SNPs) and insertions and deletions (INDELs) were identified using the ‘Find variations/SNPs’ function implemented in the Geneious R11 v11.0.5 (Biomatters Ltd, Auckland, New Zealand) based on the pairwise alignment of the two chloroplast genomes of L. tetragonum conducted by MAFFT 7.450 (Katoh and Standley, 2013). This method has been used in the previous studies (Kim et al., 2019a; Min et al., 2019a; Choi et al., 2021; Park et al., 2021b, 2021d). INDEL region was defined as the continuous INDELs.

Phylogenetic analysis

Maximum-likelihood (ML) and Bayesian inference (BI) phylogenetic trees were constructed based on the multiple sequence alignment of all available nine Plumbaginaceae chloroplast genomes and the seven chloroplast genomes of non-core Caryophyllales clade (Crawly and Hilu, 2012; Yao et al., 2019) by MAFFT v7.450 (Katoh and Standley, 2013). The chloroplast genome of Nepenthes graciliflora Elmer (1912) (Yao et al., 2019) was marked as outgroup species. The ML tree was reconstructed in IQ-TREE v1.6.12 (Nguyen et al., 2015) with 1,000 bootstrap repeats. In the ML analysis, a heuristic search was used with nearest-neighbor interchange branch swapping, GTR+F + R4 model determined as the best fit model by the ModelFinder implemented in IQ-TREE, and uniform rates among sites. All other options used the default settings. The posterior probability of each node was estimated by the BI using MrBayes v3.2.6 (Huelsenbeck and Ronquist 2001). The HKY85 model with gamma rates was used as a molecular model. A Markov chain Monte Carlo algorithm was employed for 1,100,000 generations, sampling trees every 200 generations, with four chains running simultaneously. Trees from the first 100,000 generations were discarded as burn-in.

Data availablity

Chloroplast genome sequence can be accessed via accession number of MN044572 in GenBank of NCBI at https://www.ncbi.nlm.nih.gov. The associated BioProject, SRA, and Bio-Sample numbers are PRJNA737051, SAMN19678692, and SRR14793527, respectively.

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).

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).

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.

ACKNOWLEDGMENTS

This study was carried out with the support of the Honam National Institute of Biological Resources (HNIBR202101107).

NOTES

Conflict of Interest

The authors declare that there are no conflicts of interest.

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.

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.

Table 1.

List of two available chloroplast genomes of Limonium tetragonum.

GenBank accession	Length (bp)				GC contents				No. of genes

	Whole	LSC	SSC	IR	Whole (%)	LSC (%)	SSC (%)	IR (%)	No. of PCGs	No. of tRNAs	No. of rRNAs
MN044572	154,689	84,572	13,013	28,562	37.0	35.3	31.5	40.9	83	37	8
MW085088	154,691	84,568	12,997	28,563	37.0	35.3	31.5	40.9	83	37	8

LSC, large single copy; SSC, small single copy; IR, inverted repeat ; PCG, protein-coding gene.

Table 2.

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

No.	Type	Changed bases		Coordination		Type	Position	SNP type

		MN044572	MW085088	MN044572	MW085088
1	SNP	G	A	485	485	Genic	psbA	Synonymous SNP
2	INDEL	-	AA	4,316	4,316–4,317	Intergenic	trnK-rps16
3	SNP	G	A	4,549	4,551	Intergenic	trnK-rps16
4	INDEL	T	-	6,256	6,258	Intergenic	rps16-trnQ
5	INDEL	-	AA	6,670	6,671–6,672	Intergenic	trnQ-psbK
6	INDEL	-	AAA	7,214	7,217–7,219	Intergenic	psbK-psbI
7	INDEL	-	T	7,866	7,872	Intergenic	trnS-trnG
8	INDEL	-	CGGGTCA	7,966	7,973–7,979	Intergenic	trnS-trnG
9	INDEL	-	A	8,224	8,238	Intergenic	trnS-trnG
10	INDEL	T	-	15,561	15,576	Intergenic	rps2-rpoC2
11	INDEL	-	T	15,898	15,912	Genic	rpoC2	Frameshift
12	SNP	T	G	27,306	27,321	Intergenic	rpoB-trnC
13	SNP	T	G	27,307	27,322	Intergenic	rpoB-trnC
14	SNP	C	G	27,308	27,323	Intergenic	rpoB-trnC
15	SNP	C	A	27,309	27,324	Intergenic	rpoB-trnC
16	SNP	C	A	27,310	27,325	Intergenic	rpoB-trnC
17	INDEL	-	A	28,271	28,286	Intergenic	trnC-petN
18	INDEL	A	-	31,349	31,435	Intergenic	trnE-trnT
19	INDEL	-	AA	31,472	31,487-31,488	Intergenic	trnE-trnT
20	SNP	C	A	31,768	31,785	Intergenic	trnE-trnT
21	SNP	A	G	32,417	32,434	Intergenic	trnT-psbD
22	INDEL	AAAG	-	36,846–36,849	36,863	Intergenic	psbZ-trnG
23	SNP	G	A	42,109	42,122	Genic	psaA	Synonymous SNP
24	SNP	A	T	42,931	42,944	Intergenic	psaA-ycf3
25	SNP	A	T	42,932	42,945	Intergenic	psaA-ycf3
26	INDEL	ATATATTTATAT ATTATA	-	47,679–47,696	47,692	Intergenic	trnT-trnL
27	INDEL	-	TAAT	47,873	47,868–47,871	Intergenic	trnT-trnL
28	INDEL	ATTTAAA	-	48,687–48,693	48,686	Intronic	trnL
29	SNP	A	G	49,304	49,296	Intergenic	trnF-ndhJ
30	INDEL	-	AAAA	55,296	55288–55,291	Intergenic	atpB-rbcL
31	INDEL	-	T	55,474	55,470	Intergenic	atpB-rbcL
32	INDEL	-	A	57,897	57,894	Intergenic	rbcL-accD
33	INDEL	A	-	61,499	61,497	Intergenic	ycf4-cemA
34	INDEL	-	TCTA	63,882	63,879-63,882	Intergenic	petA-psbJ
35	SNP	G	T	64,137	64,138	Intergenic	petA-psbJ
36	SNP	A	T	64,138	64,139	Intergenic	petA-psbJ
37	SNP	A	T	64,139	64,140	Intergenic	petA-psbJ
38	SNP	T	G	64,140	64,141	Intergenic	petA-psbJ
39	SNP	G	T	64,141	64,142	Intergenic	petA-psbJ
40	SNP	A	T	64,142	64,143	Intergenic	petA-psbJ
41	SNP	G	T	64,143	64,144	Intergenic	petA-psbJ
42	SNP	A	C	64,146	64,147	Intergenic	petA-psbJ
43	SNP	A	T	64,147	64,148	Intergenic	petA-psbJ
44	SNP	A	C	64,148	64,149	Intergenic	petA-psbJ
45	SNP	C	A	64,149	64,150	Intergenic	petA-psbJ
46	SNP	A	T	64,150	64,151	Intergenic	petA-psbJ
47	SNP	A	T	64,151	64,152	Intergenic	petA-psbJ
48	SNP	A	C	64,152	64,153	Intergenic	petA-psbJ
49	INDEL	T	-	65,511	65,512	Intergenic	psbE-petL
50	INDEL	T	-	66,150	66,150	Intergenic	petL-petG
51	INDEL	TA	-	68,210-68,211	68,209	Intergenic	rpl33-rps18
52	INDEL	-	C	68,295	68,292	Intergenic	rpl33-rps18
53	SNP	T	G	69,126	69,124	Genic	rpl20	Non-synomynous SNP
54	INDEL	CTTT	-	69,359-69,362	69,357	Intergenic	rpl20-rps12
55	SNP	C	A	71,121	71,115	Intronic	clpP
56	INDEL	A	-	75,382	75,376	Intergenic	psbH-petB
57	INDEL	A	-	80,610	80,603	Intergenic	rps8-rpl14
58	INDEL	-	AAAA	81,060	81,052–81,055	Intergenic	rpl14-rpl16
59	SNP	C	A	86,943	86,939	Genic	ycf2	Non-synomynous SNP
60	INDEL	-	G	92,158	92,154	Intergenic	ycf2-trnL
61	SNP	A	T	106,466	106,463	Intergenic	trnR-trnN
62	SNP	A	T	115,749	115,746	Intergenic	ndhF-rpl32
63	SNP	G	A	116,280	116,277	Genic	rpl32	Non-synomynous SNP
64	INDEL	-	T	116,808	116,805	Intergenic	rpl32-trnL
65	INDEL	-	TTT	123,377	123,375-123,377	Intronic	ndhA
66	SNP	T	A	132,796	132,797	Intergenic	trnN-trnR
67	INDEL	-	C	147,096	147,097	Intergenic	trnL-ycf2
68	SNP	G	T	152,319	152,321	Genic	ycf2	Non-synomynous SNP

SNP, single nucleotide polymorphism; INDEL, insertions and deletion.

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