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Characterization of the complete chloroplast genome of two sister species of salt cress (Brassicaceae)

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Abstract

The complete chloroplast genomes from two salt cresses (Eutrema halophilum and Eutrema botschantzevii), plants known to tolerate high levels of salt, are determined in this study. The genome sizes were 153,312 and 153,280 bp. Both genomes containing a large single copy region (LSC) of 84k bp and a small single copy region (SSC) of 18k bp, which were separated by a pair of 25,928 bp inverted repeat regions (IRs). The cpDNA contained 125 genes, including 87 protein-coding genes (79 PCG species), 30 tRNA genes (25 tRNA species) and eight ribosomal RNA genes (4 rRNA species). The most of gene species occur as a single copy, while 17 gene species occur in double copies. These complete chloroplast genomes can be subsequently used for population studies of Eutrema, and provide valuable insight into conservation and restoration efforts for this endangered species.

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References

  • Amtmann A, Bohnert HJ, Bressan RA (2005) Abiotic stress and plant genome evolution. Search for new models. Plant Physiol 138(1):127–130

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Champigny MJ, Sung WW, Catana V, Salwan R, Summers PS, Dudley SA, Provart NJ, Cameron RK, Golding GB, Weretilnyk EA (2013) RNA-Seq effectively monitors gene expression in Eutrema salsugineum plants growing in an extreme natural habitat and in controlled growth cabinet conditions. BMC Genom 14(1):578

    Article  CAS  Google Scholar 

  • Huang DI, Cronk QC (2015) Plann: a command-line application for annotating plastome sequences. Appl Plant Sci 3(8):1500026

    Article  Google Scholar 

  • Katoh K, Standley DM (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30(4):772–780

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C, Thierer T, Ashton B, Meintjes P, Drummond A (2012) Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinforma 28(12):1647–1649

    Article  Google Scholar 

  • Lee YP, Babakov A, de Boer B, Zuther E, Hincha DK (2012) Comparison of freezing tolerance, compatible solutes and polyamines in geographically diverse collections of Thellungiella sp. and Arabidopsis thaliana accessions. BMC Plant Biol 12(1):131

    Article  PubMed  PubMed Central  Google Scholar 

  • Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows–Wheeler transform Bioinforma 25(16):1754–1760

    Article  CAS  Google Scholar 

  • Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup (2009) The sequence alignment/map format and SAMtools. Bioinforma 25(16):2078–2079

    Article  Google Scholar 

  • Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30(12):2725–2729

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang XJ, Shi DC, Wang XY, Wang J, Sun YS, Liu JQ (2015) Evolutionary migration of the disjunct salt cress Eutrema salsugineum (= Thellungiella salsuginea, Brassicaceae) between Asia and North America. PLoS ONE 10(5):e0124010

    Article  PubMed  PubMed Central  Google Scholar 

  • Wu HJ, Zhang Z, Wang JY, Oh DH, Dassanayake M, Liu B, Huang Q, Sun HX, Xia R, Wu Y et al (2012) Insights into salt tolerance from the genome of Thellungiella salsuginea. Proc Natl Acad Sci USA 109(30):12219–12224

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zerbino DR, Birney E (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18(5):821–829

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

This work was supported by the National Natural Science Foundation of China (91331102).

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Authors and Affiliations

  1. Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria

    Huiying Shang

  2. MOE Key Laboratory of Bio-Resources and Eco-Environment, College of Life Science, Sichuan University, Chengdu, China

    Yuanshuo Li, Xinyi Guo & Xiaojuan Wang

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  1. Huiying Shang
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  2. Yuanshuo Li
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  3. Xinyi Guo
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  4. Xiaojuan Wang
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Correspondence to Xiaojuan Wang.

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Shang, H., Li, Y., Guo, X. et al. Characterization of the complete chloroplast genome of two sister species of salt cress (Brassicaceae). Conservation Genet Resour 9, 237–239 (2017). https://doi.org/10.1007/s12686-016-0661-5

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  • DOI: https://doi.org/10.1007/s12686-016-0661-5

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