Analyzing and characterization of the chloroplast genome of Salix suchowensis
- Published
- Accepted
- Subject Areas
- Bioinformatics, Genomics, Plant Science
- Keywords
- genome structure, chloroplast, Salix suchowensis, gene content, phylogenetic tree
- Copyright
- © 2016 Sun et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
- Cite this article
- 2016. Analyzing and characterization of the chloroplast genome of Salix suchowensis. PeerJ Preprints 4:e2388v1 https://doi.org/10.7287/peerj.preprints.2388v1
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.
Author Comment
This is a submission to PeerJ for review.
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" />