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Analysis and characterization of the Salix suchowensis chloroplast genome

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Abstract

By screening sequence reads from the Salix suchowensis chloroplast (cp) genome that were generated by next-generation sequencing platforms, we assembled a complete circular pseudomolecule for the cp genome. This pseudomolecule is 155,508 bp long and has a typical quadripartite structure that contains two single copy regions, a large single copy region (LSC, 84,385 bp), and a small single copy region (SSC, 16,209 bp) separated by inverted repeat regions (IRs, 27,457 bp). Gene annotation revealed that the S. suchowensis cp genome encoded 119 unique genes, including four ribosome RNA genes, 30 transfer RNA genes, 82 protein-coding genes, and three pseudogenes. Analysis of the repetitive sequences revealed 31 tandem repeats, 16 forward repeats, and five palindromic repeats. In addition, a total of 148 perfect microsatellites, which were characterized as A/T dominant in nucleotide composition, were detected. Significant shifting of the IR/SSC boundaries was revealed by comparing this cp genome with those of other rosid plants. We also constructed phylogenetic trees to demonstrate the phylogenetic position of S. suchowensis in Rosidae based on 66 orthologous protein-coding genes present in the cp genomes of 32 species. Sequencing 30 amplicons based on the pseudomolecule for experimental verification revealed 99.88% accuracy for the S. suchowensis cp genome assembly. Therefore, we assembled a high-quality pseudomolecule of the S. suchowensis cp genome, which is a useful resource for facilitating development of this shrub willow into a more productive bioenergy crop.

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Authors and Affiliations

  1. Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, 210037, People’s Republic of China

    Congrui Sun, Jie Li, Xiaogang Dai & Yingnan Chen

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  1. Congrui Sun
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  2. Jie Li
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  3. Xiaogang Dai
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  4. Yingnan Chen
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Correspondence to Yingnan Chen.

Additional information

Project Funding: This work was supported by the Key Forestry Public Welfare Project (201304102), and the Natural Science Foundation of China (31400564 and 315005533). It was also enabled by the Innovative Research Team of the Educational Department of China and the PAPD (Priority Academic Program Development) program at Nanjing Forestry University.

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Corresponding Editor: Yu Lei.

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Sun, C., Li, J., Dai, X. et al. Analysis and characterization of the Salix suchowensis chloroplast genome. J. For. Res. 29, 1003–1011 (2018). https://doi.org/10.1007/s11676-017-0531-3

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  • DOI: https://doi.org/10.1007/s11676-017-0531-3

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