Abstract
We report the complete chloroplast DNA (cpDNA) of Populus qiongdaoensis T. Hong et P. Luo, which is an endangered tree species, by employing next-generation sequencing reads and de novo assembly. The chloroplast genome of P. qiongdaoensis is 1,56,074 bp in length, with 36.70 % GC content. It contains a pair of inverted repeats (27,548 bp) which were separated by a large single copy (84,467 bp) and a small single copy region (16,512 bp). A total of 131 genes were annotated, which included 86 protein-coding genes, 37 tRNA genes and eight rRNA genes. A neighbor joining tree based on the reported chloroplast genomes of Populus showed that the chloroplast of the P. qiongdaoensis is most closely related to the P. tremula and P. rotundifolia.
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References
Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19:11–15
Katoh K, Misawa K, Kuma K, Miyata T (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acid Res 30(14):3059–3066
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. Bioinformatics 28(12):1647–1649
Kersten B, Faivre Rampant P, Mader M, Le Paslier M-C, Bounon R, Berard A (2016) Genome sequences of Populus tremula chloroplast and mitochondrion: implications for holistic poplar breeding. PLoS One 11(1):e0147209
Liang JH, Fang FZ (2012) Survey on wild Populus qiongdaoensis T. Hong et P. Luo resource. Tropical. Forestry 40(1):32–34
Lohse M, Drechsel O, Kahlau S, Bock R (2013) OrganellarGenomeDRAW—a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets. Nucleic Acid Res gkt289
Luo P, Hong T (1987) A new species of Populus in tropical forests from Hainan. Bull Botanical Res 7(3):67–70
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
Zerbino DR, Birney E (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18(5):821–829
Acknowledgments
This work was financially supported by the National Key Project for Research and Development (2016YFD0600101).
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Tianjing Wang, Liqiang Fan have contributed equally to this work.
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Wang, T., Fan, L., Guo, X. et al. Characterization of the complete chloroplast genome of Populus qiongdaoensis T. Hong et P. Luo. Conservation Genet Resour 8, 435–437 (2016). https://doi.org/10.1007/s12686-016-0590-3
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DOI: https://doi.org/10.1007/s12686-016-0590-3