Characterization of the complete plastid genome of Quercus sichourensis
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Abstract
Quercus sichourensis is an endemic species in China, and is critically endangered. The complete plastid genome of Q. sichourensis was generated by Illumina pair-end sequencing in the current study. The whole plastome had a length of 160,681 bp, consisting of two copies of inverted repeat regions (25,835 bp), a large single copy region (90,154 bp) and a small single copy region (18,857 bp). The plastome encoded a total of 134 genes, comprising 86 protein-coding genes (79 PCG species), 40 tRNA genes (33 tRNA species), and 8 rRNA genes (4 rRNA species). The overall GC content of Q. sichourensis plastome is 36.9%. The maximum likelihood phylogenetic analysis based on 30 complete plastomes revealed that Q. sichourensis was strictly related to Quercus edithiae with 100% bootstrap support value.
Keywords
Quercus sichourensis Critically endangered species Plastid genome Phylogenetic relationshipNotes
Acknowledgements
This work was financially supported by the National Natural Science Foundation of China (31770229).
References
- Alexander LW, Woeste KE (2014) Pyrosequencing of the northern red oak (Quercus rubra L.) chloroplast genome reveals high quality polymorphisms for population management. Tree Genet Genomes 10:803–812CrossRefGoogle Scholar
- Chen WY, Ji YH, Deng M, Chen ST, Zhou ZK (2007) Cyclobalanopsis sichourensis, a new record species of Fagaceae in Gnizhou. Acta Bot Yunnanica 29:395–396Google Scholar
- Chevreux B, Pfisterer T, Drescher B, Driesel AJ, Müller WE, Wetter T, Suhai S (2004) Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs. Genome Res 14:1147–1159CrossRefPubMedPubMedCentralGoogle Scholar
- Doyle JJ (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19:11–15Google Scholar
- Hahn C, Bachmann L, Chevreux B (2013) Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—a baiting and iterative mapping approach. Nucleic Acids Res 41:e129–e129CrossRefPubMedPubMedCentralGoogle Scholar
- Hu HH (1951) Additional notes on the Fagaceae of Yunnan I. Acta Phytotax Sin 1:103–118Google Scholar
- Jansen RK, Saski C, Lee SB, Hansen AK, Daniell H (2011) Complete plastid genome sequences of three rosids (Castanea, Prunus, Theobroma): evidence for at least two independent transfers of rpl22 to the nucleus. Mol Biol Evol 28:835–847CrossRefPubMedGoogle Scholar
- Katoh K, Standley DM (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30:772–780CrossRefPubMedPubMedCentralGoogle 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 41:575–581CrossRefGoogle Scholar
- Ma YP, Chen G, Grumbine RE, Dao ZL, Sun WB, Guo HJ (2013) Conserving plant species with extremely small populations (PSESP) in China. Biodivers Conserv 22:803–809CrossRefGoogle Scholar
- Patel RK, Jain M (2012) NGS QC Toolkit: a toolkit for quality control of next generation sequencing data. PLoS ONE 7:e30619CrossRefPubMedPubMedCentralGoogle Scholar
- Stamatakis A (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analysis with thousands of taxa and mixed models. Bioinformatics 22:2688–2690CrossRefPubMedGoogle Scholar
- Wyman SK, Jansen RK, Boore JL (2004) Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20:3252–3255CrossRefPubMedGoogle Scholar
- Xia K, Fan L, Sun WB, Chen WY (2016) Conservation and fruit biology of Sichou oak (Quercus sichourensis, Fagaceae)—a critically endangered species in China. Plant Divers 38:233–237CrossRefGoogle Scholar