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. 2019 Jul 13;4(2):2475–2476. doi: 10.1080/23802359.2019.1638329

Characterization of the complete plastome of Atriplex centralasiatica (Chenopodiaceae), an annual halophytic herb

Xue-Jie Zhang 1, Ning Wang 1, Luo-Yan Zhang 1, Shou-Jin Fan 1, Xiao-Jian Qu 1,✉
PMCID: PMC7687555  PMID: 33365589

Abstract

Atriplex centralasiatica, an annual halophytic herb, is one of the most important Chinese herbal medicines, forages and indicator plants for saline-alkali soil. In this study, we report the complete plastome of A. centralasiatica. The plastome was 152,237 bp in length and comprises a large single-copy region (83,721 bp), a small single-copy region (18,096 bp), and a pair of inverted repeats (25,210 bp). It encodes 113 unique genes, including 79 protein-coding genes (PCGs), 30 tRNAs and 4 rRNAs. The overall GC content of this plastome was 37.3%. Phylogenomic analysis based on 21 plastomes revealed that A. centralasiatica was closely related to the genus Chenopodium.

Keywords: Atriplex centralasiatica, plastome, phylogenomics

Atriplex centralasiatica, an annual halophytic herb, is one of the most important indicator plants in the saline-alkali region of China (Zhang et al. 2010; Yuan et al. 2016). This species, together with other halophytes as Suaeda salsa and Thellungiella halophila, play an important role in investigating the physiological mechanisms of salt tolerance in halophytes (Sui et al. 2010; Han et al. 2011; Guo, Jia et al. 2012; Guo, Wang et al. 2012; Han et al. 2012; Li, Liu et al. 2012; Li, Pang et al. 2012; Xu et al. 2013; Cheng et al. 2014; Feng et al. 2014; Sui and Han 2014; Guo et al. 2015; Wang et al. 2017; Cui et al. 2018; Guo et al. 2018). Photosynthesis in Chenopodiaceae C4 plants is considered to help improve the adaptability of C4 plants in saline environments (Qi et al. 2010; Guo, Wang et al. 2012). Atriplex centralasiatica is one of the representative C4 halophytes in Chenopodiaceae. Yet, its photosynthetic characteristics under salt stress have seldom been investigated. In this study, we reported the plastome of A. centralasiatica, the first one in genus Atriplex, which would provide fundamental genetic resource for studying this important species.

Fresh leaves of A. centralasiatica were collected from the Yellow River Delta (Shandong, China; 37°29'N, 118°43'E). Voucher specimen (XLC47) was deposited at College of Life Sciences, Shandong Normal University. Total genomic DNA was extracted by the modified CTAB method described in Wang et al. (2013). Due to limited fresh sample, the plastid DNA was not directly extracted (Liu et al. 2017). The total genomic DNA was used for library preparation and paired-end (PE) sequencing by the Illumina MiSeq instrument at Novogene (Beijing, China). The plastome was assembled using OGA-Organelle Genome Assembler (https://github.com/quxiaojian/OGA; Qu 2019). Annotation was performed with PGA-Plastid Genome Annotator (Qu et al. 2019), coupled with manual correction using Geneious v8.0.2 (https://www.geneious.com). To determine the phylogenetic placement of A. centralasiatica, a maximum likelihood (ML) tree was reconstructed using RAxML v8.2.10 (Stamatakis 2014), including tree robustness assessment using 1000 rapid bootstrap replicates with the GTRGAMMA substitution model, based on the alignment of 79 shared PCGs using MAFFT v7.313 (Katoh and Standley 2013).

The complete plastome of A. centralasiatica (GenBank accession number: MK867774) was 152,237 bp in length and comprises a large single-copy region (LSC: 83,721 bp), a small single-copy region (SSC: 18,096 bp), and a pair of inverted repeats (IR: 25,210bp). The overall GC content was 37.3%. A total of 113 unique genes were annotated in this plastome, including 79 protein-coding genes (PCGs), 30 tRNAs and 4 rRNAs. Among them, eleven PCGs and six tRNAs contained introns, in which nine PCGs and six tRNAs contained one intron and two PCGs contained two introns. There were 18 duplicated genes in the IR. The ML phylogenetic tree showed that A. centralasiatica was closely related to the genus Chenopodium (Figure 1).

Figure 1.

Figure 1.

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A maximum likelihood (ML) tree inferred from 79 plastome genes is shown. Four Amaranthus species from Amaranthaceae are used as outgroup. The numbers on branches are bootstrap support values.

Disclosure statement

No potential conflict of interest was reported by the authors.

References

  1. Cheng S, Yang Z, Wang MJ, Song J, Sui N, Fan H. 2014. Salinity improves chilling resistance in Suaeda salsa. Acta Physiol Plant. 36:1823–1830. [Google Scholar]
  2. Cui F, Sui N, Duan G, Liu Y, Han Y, Liu S, Wan S, Li G. 2018. Identification of metabolites and transcripts involved in salt stress and recovery in peanut. Front Plant Sci. 9:217. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Feng ZT, Deng YQ, Fan H, Sun QJ, Sui N, Wang BS. 2014. Effects of NaCl stress on the growth and photosynthetic characteristics of Ulmus pumila L. seedlings in sand culture. Photosynthetica. 52:313–320. [Google Scholar]
  4. Guo JR, Li YD, Han GL, Song J, Wang BS. 2018. NaCl markedly improved the reproductive capacity of the euhalophyte Suaeda salsa. Funct Plant Biol. 45:350–361. [DOI] [PubMed] [Google Scholar]
  5. Guo JR, Suo SS, Wang BS. 2015. Sodium chloride improves seed vigour of the euhalophyte Suaeda salsa. Seed Sci Res. 25:335–344. [Google Scholar]
  6. Guo YH, Jia WJ, Song J, Wang DA, Chen M, Wang BS. 2012. Thellungiella halophila is more adaptive to salinity than Arabidopsis thaliana at stages of seed germination and seedling establishment. Acta Physiol Plant. 34:1287–1294. [Google Scholar]
  7. Guo YH, Wang D, Jia WJ, Song J, Yang JC, Wang BS. 2012. Effects of seed vernalisation and photoperiod on flowering induction in the halophyte Thellungiella halophila. Aust J Bot. 60:743–748. [Google Scholar]
  8. Han N, Lan WJ, He X, Shao Q, Wang BS, Zhao XJ. 2012. Expression of a Suaeda salsa vacuolar H+/Ca2+ transporter gene in Arabidopsis contributes to physiological changes in salinity. Plant Mol Biol Rep. 30:470–477. [Google Scholar]
  9. Han N, Shao Q, Bao HY, Wang BS. 2011. Cloning and characterization of a Ca2+/H+ antiporter from halophyte Suaeda salsa L. Plant Mol Biol Rep. 29:449–457. [Google Scholar]
  10. Katoh K, Standley DM. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 30:772–780. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Li K, Pang CH, Ding F, Sui N, Feng ZT, Wang BS. 2012. Overexpression of Suaeda salsa stroma ascorbate peroxidase in Arabidopsis chloroplasts enhances salt tolerance of plants. S Afr J Bot. 78:235–245. [Google Scholar]
  12. Li X, Liu Y, Chen M, Song YP, Song J, Wang BS, Feng G. 2012. Relationships between ion and chlorophyll accumulation in seeds and adaptation to saline environments in Suaeda salsa populations. Plant Biosystems. 146:142–149. [Google Scholar]
  13. Liu F, Jin Z, Wang Y, Bi YP, Melton JT. 2017. Plastid genome of Dictyopteris divaricata (Dictyotales, Phaeophyceae): understanding the evolution of plastid genomes in brown algae. Mar Biotechnol. 19:627–637. [DOI] [PubMed] [Google Scholar]
  14. Qi YC, Wang FF, Zhang H, Liu WQ. 2010. Overexpression of suadea salsa S-adenosylmethionine synthetase gene promotes salt tolerance in transgenic tobacco. Acta Physiol Plant. 32:263–269. [Google Scholar]
  15. Qu XJ, Moore MJ, Li DZ, Yi TS. 2019. PGA: a software package for rapid, accurate, and flexible batch annotation of plastomes. Plant Methods. 15:50. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Qu XJ. 2019. Complete plastome sequence of an Endangered species, Calocedrus rupestris (Cupressaceae). Mitochondr DNA B. 4:762–763. [Google Scholar]
  17. Stamatakis A. 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 30:1312–1313. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Sui N, Han GL. 2014. Salt-induced photoinhibition of PSII is alleviated in halophyte Thellungiella halophila by increases of unsaturated fatty acids in membrane lipids. Acta Physiol Plant. 36:983–992. [Google Scholar]
  19. Sui N, Li M, Li K, Song J, Wang BS. 2010. Increase in unsaturated fatty acids in membrane lipids of Suaeda salsa L. enhances protection of photosystem II under high salinity. Photosynthetica. 48:623–629. [Google Scholar]
  20. Wang HY, Jiang DF, Huang YH, Wang PM, Li T. 2013. Study on the phylogeny of Nephroma helveticum and allied species. Mycotaxon. 125:263–275. [Google Scholar]
  21. Wang J, Zhang Q, Cui F, Hou L, Zhao S, Xia H, Qiu J, Li T, Zhang Y, Wang X, et al. 2017. Genome-wide analysis of gene expression provides new insights into cold responses in Thellungiella salsuginea. Front Plant Sci. 8:713. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Xu J, Li Y, Ma X, Ding J, Wang K, Wang S, Tian Y, Zhang H, Zhu XG. 2013. Whole transcriptome analysis using next-generation sequencing of model species Setaria viridis to support C4 photosynthesis research. Plant Mol Biol. 83:77–87. [DOI] [PubMed] [Google Scholar]
  23. Yuan F, Leng B, Wang B. 2016. Progress in studying salt secretion from the salt glands in recretohalophytes: how do plants secrete salt?. Front Plant Sci. 7:977. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Zhang SR, Song J, Wang H, Feng G. 2010. Effect of salinity on seed germination, ion content and photosynthesis of cotyledons in halophytes or xerophyte growing in Central Asia. J Plant Ecol. 3:259–267. [Google Scholar]

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