The complete chloroplast genome of Atriplex gmelinii C. A. Mey. ex Bong. (Amaranthaceae)

Abstract

Atriplex gmelinii C. A. Mey. Ex Bong._1838 is an annual halophytic herb found in East Asia and North America. The chloroplast genome of A. gmelinii was successfully sequenced. The assembled genome (151,852 bp; GC ratio, 37.3%) is composed of four subregions, with the large single copy (LSC; 83,872 bp; 35.4%) and small single copy (SSC; 17,812 bp; 30.9%) regions separated by two regions of inverted repeat regions (25,084 bp; 42.8%). A total of 130 genes were predicted with 85 protein-coding genes, 8 rRNAs, and 37 tRNAs. The phylogenetic analyses inferred from whole chloroplast genomes of 35 species, including 34 species in Amaranthaceae and one outgroup species, suggest a close relationship between A. gmelinii and A. centralasiatica.

Keywords:

• Chloroplast genome
• Atriplex gmelinii
• phylogenetic analysis
• Amaranthaceae

Atriplex gmelinii C. A. Mey. ex Bong._1838, belonging to subfamily Chenopodioideae of family Amaranthaceae, is a halophytic annual plant found in coastal areas of Korea, China, Japan, Russia, and North America (Bassett and Crompton 1973; Park et al. 2020) and is a C₄ plant (Kim et al. 2011). The pharmaceutical usefulness of plant extracts from A. gemelinii has been investigated by testing its antioxidant (Bae et al. 2003; Jeong et al. 2016), anticancer (Park et al. 2019), and anti-inflammation properties (Jeong et al. 2017), as well as its enhancement of osteoblast differentiation (Karadeniz et al. 2020). Here, we completed the chloroplast genome of A. gmelinii collected in Korea.

Total DNA of A. gmelinii collected on Apahedo Island, Shinan-gun, Jeollanam-do, Korea, (34.818343 N, 126.336961E) was extracted from fresh leaves with a DNeasy Plant Mini Kit (QIAGEN, Hilden, Germany). The voucher was deposited in the InfoBoss Cyber Herbarium (IN; http://herbarium.infoboss.co.kr/; Voucher number: IB-00686; Contact: Jongsun Park; [email protected]). Genome sequencing was conducted using HiSeqX at Macrogen Inc., Korea, and de novo assembly and sequence confirmation were done by Velvet v1.2.10 (Zerbino and Birney 2008), GapCloser v1.12 (Zhao et al. 2011), BWA v0.7.17 (Li 2013), and SAMtools v1.9 (Li et al. 2009) in the Genome Information System (GeIS; http://geis.infoboss.co.kr/), which has been utilized in previous organelle genomic studies (Kwon et al. 2019; Oh and Park 2020; Park et al. 2020; Kim et al. 2021; Park et al. 2021). Geneious Prime^® v2020.2.4 (Biomatters Ltd., Auckland, New Zealand) was used for chloroplast genome annotation based on Chenopodium ficifolium SM_1800 chloroplast genome (NC_041200) (Kim et al. 2019a).

The chloroplast genome of A. gmelinii (GenBank accession: MT810472) is 151,852 bp and has four subregions: 83,872 bp of LSC and 17,812 bp of SSC regions are separated by two IR regions of 25,084 bp. It contains 130 genes (85 protein-coding genes, eight rRNAs, and 37 tRNAs); 19 genes (8 protein-coding genes, 4 rRNAs, and 7 tRNAs) are duplicated in IR regions. The number of genes in A. gmelinii is the same as that of Atriplex centralasiatica Iljin_1936 (Zhang et al. 2019). However, the other Chenopodioideae chloroplast genomes showed slightly different numbers of genes: those of Chenopodium and Dysphania chloroplast genomes have 84 (Hong et al. 2017; Kim et al. 2019; Park and Kim 2019; Kim et al. 2019a, 2019b; Park et al. 2021), with the exception of Dysphania botrys (L.) Mosyakin & Clemants_2002, which has 83 genes (Chen and Yang 2018) and one Chenopodium album L._1753 (MF418659), which has 89 genes (Jashmi and Biseshwori 2017). The C. album (MF418659) may have been misidentified due to a different configuration from the rest of C. album (Park et al. 2021). The overall GC content is 37.3% and those in the LSC, SSC, and IR regions are 35.4%, 30.9%, and 42.8%, respectively, which is similar to those of Chenopodium species (Hong et al. 2017; Kim et al. 2019a; Park et al. 2021).

Thirty-four Chenopodioideae (Amaranthaceae) chloroplast genomes and one outgroup species, Gymnocarpos przewalski Maxim._1880 (Caryophyllaceae), were used for phylogenetic analysis. We used MEGA X (Kumar et al. 2018) to construct a Maximum-Likelihood (ML) tree and MrBayes v3.2.6 (Ronquist and Huelsenbeck 2003) to carry out Bayesian Inference (BI) after aligning whole chloroplast genomes by MAFFT v7.450 (Katoh and Standley 2013). A heuristic search was used with nearest-neighbor interchange branch swapping, the Tamura-Nei model, and uniform rates among sites to construct an ML phylogenetic tree with default values for other options. To estimate the node confidences, bootstrap analysis with 1,000 pseudoreplicates was conducted. For the Bayesian inferences, the GTR model with gamma rates was used as a molecular model and a Markov-Chain Monte Carlo algorithm was employed for 1,000,000 generations with four chains running simultaneously. To build the consensus tree of BI we sampled trees every 200 generations after removing 100 K generations as a ‘burn-in.’ All phylogenetic trees inferred from ML and BI methods showed that A. gmelinii is strongly grouped with A. centralasiatica (Figure 1). The Atriplex group is a sister to the group composed of three species (C. album, C. ficifolium, and Chenopodium quinoa Willd._1798) in the genus Chenopodium.

Figure 1. The phylogenetic tree inferred from 34 whole chloroplast genomes of 23 species in the subfamily Chenopodioideae (Amaranthaceae) and one outgroup species in Caryophyllaceae. The ML tree is presented with the bootstrap values calculated from a ML search (1,000 bootstrap replication) and with the posterior probabilities from Bayesian inference.

Ethical statements

Authors declare that there is no ethical or legal violation in obtaining the study materials and preforming research. The species used in this study is not listed in the IUCN Red List and plant materials were collected in the location that was not designated as a protective area in Korea. Authors confirmed that the plant materials for this study were not subjected to be approved from Institutional Review Board (IRB) in the Catholic University of Korea.

Author contributions

JP and STK conceptualized the project and designed the experiment. JP, YK generated sequencing data. JP, JM and STK analyzed the data. JP and STK wrote the manuscript with input from all other authors. All authors have read and agreed to the published version of the manuscript.

Disclosure statement

No potential conflict of interest was reported by the authors.

Data availability statement

Chloroplast genome sequence can be accessed via accession number of MT810472 in GenBank of NCBI at https://www.ncbi.nlm.nih.gov. The associated BioProject, BioSample, and SRA study numbers are PRJNA692662, SAMN17360090 (SRS8042657), and SRP302073(SRR13449797), respectively.

Additional information

Funding

This study was supported by the InfoBoss Research Grant [IBG-0010] to Jongsun Park and by The Catholic University of Korea under new faculty support Grant [M-2020-B0014-00004] to Sang-Tae Kim.