The complete chloroplast genome of Juniperus microsperma, a rare endemic conifer from the Qinghai-Tibet Plateau whose current status satisfies the IUCN Red List criteria of endangered species, was determined in this study. The genome size is 127,409 bp in length. The genome contained 119 genes, including 82 protein-coding genes, four ribosomal RNA genes and 33 transfer RNA genes. The most of genes occur as a single copy, while two genes occur in double copies (trnL-CAU and trnQ-UUG). In these genes, eight genes (atpF, ndhA, ndhB, rpoC1, petD, petB, rpl16 and rpl2) have a single intron, while two genes (rps12 and ycf3) harbor two introns. There are no inverted repeat sequences in this genome. The GC content of this cp genome is 35.0%. Phylogenomic analysis revealed a close relationship among J. microsperma, J. virginiana, J. scopulorum and J. bermudiana.
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This work was supported by the National Natural Science Foundation of China (Grants 31622015, 31590821, 31370261), Science & Technology Basic Resources Investigation Program of China (Grant 2017FY100100), Sichuan Provincial Department of Science and Technology (Grant 2015JQ0018), Natural Science Foundation of the Tibet Autonomous Region (Grant XZ2017ZRG-04).
Adams RP (2000) Systematics of the one seeded Juniperus of the eastern hemisphere based on leaf essential oils and random amplified polymorphic DNAs (RAPDs). Biochem Syst Ecol 28(6):529–543CrossRefGoogle Scholar
Adams RP (2014) Junipers of the world: the genus Juniperus: Trafford Publishing, BloomingtonGoogle Scholar
Adams RP, Mao KS, Liu JQ (2013) The volatile leaf oil of Juniperus microsperma and its taxonomy. Phytologia 95:87–93Google Scholar
Dierckxsens N, Mardulyn P, Smits G (2017) NOVOPlasty: de novo assembly of organelle genomes from whole genome data. Nucleic Acids Res 45(4):e18–e18Google Scholar
Doyle JJ (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19:11–15Google Scholar
Guo Q, Bianba D, Zheng W (2016) Characterization of the complete chloroplast genome of Juniperus cedrus (Cupressaceae). Mitochondrial DNA A 27(6):4355–4356CrossRefGoogle Scholar
Huang DI, Cronk QC (2015) Plann: a command-line application for annotating plastome sequences. Appl Plant Sci 3(8):1500026CrossRefGoogle Scholar
International Union for Conservation of Nature (IUCN) (2012) IUCN Red List categories and criteria, version 3.1, 2nd edn. IUCN Gland, Switzerland, p 32Google Scholar
Katoh K, Standley DM (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30(4):772–780CrossRefGoogle Scholar
Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C (2012) Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28(12):1647–1649CrossRefGoogle Scholar
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25(16):2078–2079CrossRefGoogle Scholar
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(W1):W575–W581CrossRefGoogle Scholar
Mao K, Hao G, Liu J, Adams RP, Milne RI (2010) Diversification and biogeography of Juniperus (Cupressaceae): variable diversification rates and multiple intercontinental dispersals. New Phytol 188(1):254–272CrossRefGoogle Scholar
Shang H-Y, Li Z-H, Dong M, Adams RP, Miehe G, Opgenoorth L, Mao K-S (2015) Evolutionary origin and demographic history of an ancient conifer (Juniperus microsperma) in the Qinghai-Tibetan Plateau. Sci Rep 5:10216CrossRefGoogle Scholar
Stamatakis A (2014) RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30(9):1312–1313CrossRefGoogle Scholar