Analyzing and characterization of the chloroplast genome of Salix suchowensis
Author and article information
Abstract
By screening sequence reads from the chloroplast (cp) genome of S. suchowensis that generated by the next generation sequencing platforms, we built the complete circular pseudomolecule for its cp genome. This pseudomolecule is 155,508 bp in length, which has a typical quadripartite structure containing 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 cp genome of S. suchowensis encoded 119 unique genes, including 4 ribosome RNA genes, 30 transfer RNA genes, 82 protein-coding genes and 3 pseudogenes. Analyzing the repetitive sequences detected 15 tandem repeats, 16 forward repeats and 5 palindromic repeats. In addition, a total of 188 perfect microsatellites were detected, which were characterized as A/T predominance in nucleotide compositions. Significant shifting of the IR/SSC boundaries was revealed by comparing this cp genome with that of other rosids plants. We also built phylogenetic trees to demonstrate the phylogenetic position of S. suchowensis in Rosidae, with 66 orthologous protein-coding genes presented in the cp genomes of 32 species. By sequencing 30 amplicons based on the pseudomolecule, experimental verification achieved accuracy up to 99.84% for the cp genome assembly of S. suchowensis. In conclusion, this study built a high quality pseudomolecule for the cp genome of S. suchowensis, which is a useful resource for facilitating the development of this shrub willow into a more productive bioenergy crop.
Cite this as
2016. Analyzing and characterization of the chloroplast genome of Salix suchowensis. PeerJ Preprints 4:e2388v1 https://doi.org/10.7287/peerj.preprints.2388v1Author comment
This is a submission to PeerJ for review.
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Supplemental Information
Figure S1
Figure S1 The neighbor joining (NJ) phylogenetic tree
Table S1
Table S1 Primer sequences and results of sequences alignment of the amplicons<?xml:namespace prefix = o ns = "urn:schemas-microsoft-com:office:office" />
Table S2
Table S2 Statistics of tandem repeats, forward repeats and palindromic repeats in S. suchowensis chloroplast genome<?xml:namespace prefix = o ns = "urn:schemas-microsoft-com:office:office" />
Table S3
Table S3 Distribution of SSRs in the S. suchowensis chloroplast genome<?xml:namespace prefix = o ns = "urn:schemas-microsoft-com:office:office" />
Table S4
Table S4 Species classification in phylogenetic tree and GenBank accession numbers of the cp genome <?xml:namespace prefix = o ns = "urn:schemas-microsoft-com:office:office" />
Additional Information
Competing Interests
The authors declare that they have no competing interests.
Author Contributions
Congrui Sun performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables.
Jie Li performed the experiments.
Xiaogang Dai analyzed the data.
Yingnan Chen conceived and designed the experiments, wrote the paper, reviewed drafts of the paper.
DNA Deposition
The following information was supplied regarding the deposition of DNA sequences:
GenBank, Accession No. KU341117
Data Deposition
The following information was supplied regarding data availability:
The raw data was included in an early publication of our group (Dai et al., 2014).
Funding
This work was supported by the Key Forestry Public Welfare Project (201304102), 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. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
