The comparison of the complete chloroplast genome of Suaeda japonica Makino presenting different external morphology (Amaranthaceae)

Abstract

Suaeda japonica Makino is an annual herb found in the seashore in Korea and Japan. In this study, we presented second complete chloroplast genome of S. japonica which is 152,112 bp long and has four subregions: 83,620 bp of large single-copy (LSC) and 18,102 bp of small single-copy (SSC) regions are separated by 25,195 bp of inverted repeat (IR) regions including 128 genes (83 protein-coding genes, 8 rRNAs, and 37 tRNAs). The overall GC content of the chloroplast genome is 36.4% and those in the LSC, SSC, and IR regions are 34.2%, 29.2%, and 42.7%, respectively. Phylogenetic trees show that two S. japonica is monophyletic. This chloroplast genome suggests further investigation to find the relationship between morphological variations and genetic diversity.

Keywords:

• Suaeda japonica
• chloroplast genome
• Amaranthaceae
• Suaeda
• phylogeny

Suaeda japonica Makino (Amarathaeceae) is an annual halophyte, growing up to 20–50 cm with a woody stem (Chung 1992). It is distributed in a tidal flat in the West Sea of Korean peninsula and Kyushu in Japan (Hara and Kurosawa 1963; Chung 1992). Interestingly, two morphological types of S. japonica were identified: (i) more slender and slightly smaller stems and branches (Julpo type) and (ii) robust woody with thick stems and branches and slightly taller (Gwanghwa type) (Figure 1(B)). To understand the genetic diversity of the two types related to morphological differences, chloroplast genome of the latter was sequenced.

Figure 1. (A) Neighbor joining (bootstrap repeat is 10,000) and maximum likelihood (bootstrap repeat is 1,000) phylogenetic trees of 16 Amaranthaceae complete chloroplast genomes: Suaeda japonica (MK764271 in this study and MK558824 (Kim Y et al. 2019)), Suaeda malacosperma (NC_039180; Park J-S et al. 2018), Beta vulgaris (EF534108), Salicornia brachiate (NC_027224), Salicornia europaea (NC_027225), Salicornia bigelovii (NC_027226), Bienertia sinuspersici (KU726550; Kim B et al. 2016), Haloxylon ammodendron (NC_027668; Dong et al. 2016), Haloxylon persicum (NC_027669; Dong et al. 2016), Amaranthus tricolor (KX094399), Amaranthus hypochondriacus (NC_030770 and MG836505; Hong et al. 2019), Amaranthus caudatus (NC_040143; Hong et al. 2019), Amaranthus hybridus subsp. cruentus (MG836506 and MG836507; Hong et al. 2019), and Gymnocarpos przewalskii (NC_036812; Yang et al. 2018). Phylogenetic tree was drawn based on neighbor-joining tree. The numbers above branches indicate bootstrap support values of maximum likelihood phylogenetic tree. (B) displays S. japonica (Gwanghwa type). (C) shows S. japonica (Julpo type) used in the previous study.

Total DNA of Gwanghwa type of S. japonica isolated in Geonpyeong-ri, Ganghwa-gun, Incheon (Voucher in InfoBoss Cyber Herbarium (IN); IB-01021) was extracted from fresh leaves by using a DNeasy Plant Mini Kit (QIAGEN, Hilden, Germany). Genome sequencing was performed using HiSeqX at Macrogen Inc., Korea. De novo assembly and confirmation were done by Velvet 1.2.10 (Zerbino and Birney 2008), SOAPGapCloser 1.12 (Zhao et al. 2011), BWA 0.7.17 (Li 2013), and SAMtools 1.9 (Li et al. 2009). Geneious R11 11.1.5 (Biomatters Ltd., Auckland, New Zealand) was used for annotation based on S. japonica chloroplast Julpo type (MK558824; Kim et al. 2019).

Suaeda japonica chloroplast genome (MK764271) is 152,112 bp long (GC ratio is 36.4%) and has four subregions: 83,620 bp of large single-copy (LSC; 34.2%) and 18,102 bp of small single-copy (SSC; 29.2%) regions are separated by 25,195 bp of inverted repeat (IR; 42.7%) region. It contains 128 genes (83 protein-coding genes, 8 rRNAs, and 37 tRNAs); 17 genes (six protein-coding genes, four rRNAs, and seven tRNAs) are duplicated in IR regions.

In comparison to S. japonica Julpo type chloroplast genome, three single nucleotide polymorphisms (SNPs) and three insertions and deletions (INDELs) are identified: one SNP and two INDEL are intergenic in LSC. Two SNPs are synonymous in ndhA and non-synonymous in ycf1, respectively,and one INDEL is in ndhA intron. Number of variations of S. japonica chloroplast genomes are similar to those of Coffea arabica (Min, Kim, Xi, Heo, et al. 2019; Park, Kim, Xi, Heo 2019; Park, Kim, Xi, Nho, et al. 2019; Park, Xi, et al. 2019), Camellia japonica (Park, Kim, Xi, Oh, et al. 2019), Abeliophyllum distichum (Min, Kim, Xi, Jang, et al. 2019), and Marchantia polymorpha subsp. ruderalis (Kwon et al. 2019a) presenting less than 5 SNPs and INDELs; while Dysphania pumilio contains 25 SNPs and 2 INDELs (Kwon et al. 2019b). Although variations on organelle genomes of M. polymorpha subsp. ruderalis are very low (Kwon et al. 2019a, 2019b), its whole genome contains enough variations, so more investigations of S. japonica should be conducted.

Sixteen complete chloroplast genome sequences of Amaranthaceae including S. japonica were aligned by MAFFT 7.450 (Katoh and Standley 2013) for constructing bootstrapped neighbor joining and maximum likelihood trees using MEGA X (Kumar et al. 2018). Phylogenetic trees show that two S. japonica chloroplasts are clustered (Figure 1), indicating that the genetic distance between two types is low in contrast to that of their morphologies.

Disclosure statement

No potential conflict of interest was reported by the authors.