Abstract
The whole chloroplast (cp) genome sequence of Populus ilicifolia has been characterized from Illumina pair-end sequencing. The complete cp genome was 158,017 bp in length, containing a large single copy region (LSC) of 85,926 bp and a small single copy region (SSC) of 16,533 bp, which were separated by a pair of 27,780 and 27,778 bp inverted repeat regions (IRs). The genome contained 126 genes, including 82 protein-coding genes (75 PCG species), 36 tRNA genes (29 tRNA species) and 8 ribosomal RNA genes (4 rRNA species). The most of gene species occur as a single copy, while 18 gene species occur in double copies. The overall AT content of P. ilicifolia cp genome is 63.5 %, while the corresponding values of the LSC, SSC and IR regions are 65.7, 69.4 and 58.2 %, respectively. Further, phylogenetic analysis suggested that P. ilicifolia is closely related to P. euphratica.
References
Battiscombe E (1926) A descriptive catalogue of some of the common of some of the common trees and wood plants of Kenya colony. Nairobi, Kenya
Doyle JJ (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19:11–15
Huang DI, Cronk QCB (2015) Plann: a command-line application for annotating plastome sequences. Appl Plant Sci 3:1500026
International Union for Conservation of Nature (2016) The IUCN red list of threatened species: Populus ilicifolia (Tana River Poplar). doi:10.2305/IUCN.UK.1998.RLTS.T32882A9731782.en
Katoh K, Standley DM (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30:772–780
Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A et al (2012) Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28:1647–1649
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 Acids Res 41:W575–W581
Maundu P, Tengnas B (2005) Useful trees and shrubs for Kenya. Technical Handbook No. 35. World Agroforestry Centre, Nairobi, Kenya
Oballa PO (1996) Status of Populus ilicifolia in Kenya. Occasional Paper No. 3. A report on conservation initiatives. Kenya Forestry Research Institute, Nairobi
Stamatakis A (2014) RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:1312–1313
World Conservation Monitoring Centre (1998) Populus ilicifolia. In: IUCN 2012. IUCN Red List of Threatened Species. Version 2012.1. www.iucnredlist.org
Yang WL, Wang WW, Zhang L et al (2016) Characterization of the complete chloroplast genome of Idesia polycarpa. Conserv Genetics Res. doi:10.1007/s12686-016-0553-8
Zerbino DR, Birney E (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821–829
Zhang Q, Gao L (2016) The complete chloroplast genome sequence of desert poplar (Populus euphratica). Mitochondrial DNA 27:721–723
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This work was financially supported by the National Natural Science Foundation of China (31500502 and 31561123001).
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Chen, Z., Wang, W., Yang, W. et al. Characterization of the complete chloroplast genome of Populus ilicifolia . Conservation Genet Resour 8, 391–393 (2016). https://doi.org/10.1007/s12686-016-0566-3
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DOI: https://doi.org/10.1007/s12686-016-0566-3