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The Complete Chloroplast Genome Sequence of an Endangered Plant Torreya Jackii (Pinales, Taxaceae)

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The Complete Chloroplast Genome Sequence of an Endangered Plant Torreya Jackii (Pinales, Taxaceae) Conservation Genet Resour DOI 10.1007/s12686-017-0855-5 TECHNICAL NOTE The complete chloroplast genome sequence of an endangered plant Torreya jackii (Pinales, Taxaceae) Jian‑hui Li1,2,3 · Hai‑xiang Cheng2 · Li‑li Liu1 · Xiao‑yan Wang3 · Tao Pan4 · Xin Hong4 Received: 27 July 2017 / Accepted: 28 August 2017 © Springer Science+Business Media B.V. 2017 Abstract Torreya jackii, endemic to eastern China, is a Cephalotaxaceae) when only sterile foliage is observed. species of conifer listed as Endangered (EN) on the IUCN Jack’s nutmeg tree is endemic to eastern China, including Red List of Threatened Species. Here, we report the com- Zhejiang, Fujian, and Jiangxi Provinces (Li and Liu 2016). plete chloroplast (cp) genome sequence and the cp genomic Its preferred environment is warm temperate to subtropical features of Torreya jackii. The genome was 136720 bp long under the southeast monsoon system, with a mean annual with 119 genes comprising 82 protein-coding genes, 33 temperature of 17–20 °C (with an absolute minimum of tRNA genes, and 4 rRNA genes. Phylogenetic analysis sug- −10 °C) and annual precipitation of 1350–1600 mm. Areas gested that Torreya species formed a monophyletic clade with rocky granitic or rhyolitic substrates or acidic mountain within the Taxaceae family, and the status of T. jackii is yellow earth with low pH of 4.2–5 are the most suitable closely related to that of congeneric T. fargesii. habitats for T. jackii (Li and Liu 2016). Historically, this species has undergone significant reductions in popualtion Keywords Torreya jackii · Chloroplast genome · size (population reduction exceeded 50%) during the past Taxaceae · Phylogeny 150 years because of habitat clearance for expanding agri- culture and general clearance of all such habitat in the past (Li and Liu 2016; Li and Jin 2007). Jack’s nutmeg tree (Torreya jackii), a small tree that grows In this study, we sequenced the complete chloroplast (cp) in evergreen broad-leaved forests, is a species of conifer genome and reported the cp genomic features of T. jackii. in the family Cephalotaxaceae. It is found at much lower The samples of T. jackii were collected from the Baiyunyuan elevations than other Torreya species (altitudinal range: Forest Park, Tonglu Country, Zhejiang Province (29°45′N, 120–1320 m above sea level; http://www.efloras.org/). It has 119°50′E; 350 m). The sequence of the T. jackii cp genome morphological similarity to Cephalotaxus fortunei (Pinales, has been deposited in public databases (Genbank Accession Number: KY369757). Total genomic DNA was extracted from the fresh mature leaves of T. jackii, and sequenced on * Tao Pan an Illumina Hiseq 2500 platform (San Diego, CA, USA.). [email protected] Genome sequences were screened out and assembled with * Xin Hong Velvet v1.2.07 (Zerbino and Birney 2008). The total length [email protected] of tung tree cp genome was determined to be 136,720 bp 1 Quzhou Academy of Agricultural Sciences, Quzhou 324000, with the circular structure similar to other Taxaceae cp Zhejiang, China genomes Fig. 1. The genome is structured with 119 unique 2 College of Chemistry and Materials Engineering of Quzhou genes including 82 distinct protein-coding genes, 4 dis- University, Quzhou 324000, Zhejiang, China tinct rRNA genes and 33 distinct tRNA genes. Among the 3 Zhejiang Provincial Key Laboratory of Plant Evolutionary protein-coding genes, 33 were distributed on the H-strand Ecology and Conservation, Taizhou 318000, Zhejiang, and 49 on the L-strand. In addition, there are seven protein- China coding genes duplicated. The genes coding for proteins, 4 Anhui University, Hefei 230601, Anhui, China rRNA and tRNA are 73,992, 4502, and 2412 bp, which Vol.:(0123456789)1 3 Conservation Genet Resour Fig. 1 Gene map of the Torreya jackii chloroplast genome. Genes lying outside of the outer circle are transcribed in the clockwise direction whereas genes inside are transcribed in the counterclockwise direction represent 54.12, 3.29 and 1.76% of the cp genome, respec- clustered together and T. jackii showed itself to be closely tively. The base composition of cp genomes was A (32.5%), related to the other species (T. fargesii) in Torreya (Fig.2). G (17.9%), C (17.7%), and T (32%), so the percentage of Ever since the first reports of the complete chloroplast A and T (64.5%) was higher than that of G and C (35.6%). (cp) genome sequences of tobacco and liverwort (Shinozaki To confirm the phylogenetic position of T. jackii (Kang and et al. 1986), a number of land plant chloroplast genomic Tang 1995; Li et al. 2001), a molecular phylogenetic tree sequences have been described. However, the cp genomes was constructed with MEGA 6.0 (Tamura et al. 2013) based of several species in Taxaceae have been reported, including on the maximum likelihood method using a dataset of the those of T. fargesii (Tao et al. 2015), Taxus mairei (Zhang complete genome sequences of 13 individuals of ten spe- et al. 2014), Amentotaxus formosana (Hsu et al. 2014) and A. cies from Coniferopsida. The five species in Taxaceae were argotaenia (Li et al. 2016). This newly reported chloroplast 1 3 Conservation Genet Resour References Hsu CY, Wu CS, Chaw SM (2014) Ancient nuclear plastid DNA in the yew family (Taxaceae). Genome Biol Evol 6:2111–2121 Kang N, Tang ZX (1995) Studies on the taxonomy of the genus Tor- reya. Bull Bot Res 15:349–362 Li JM, Jin ZX (2007) Genetic variation and differentiation in Torreya jackii Chun, an endangered plant endemic to China. Plant Sci 172:1048–1053 Li JH, Liu LL (2016) Research progress of Torreya jackii, a rare and endangered Plant endemic to China. Chin Wild Plant Resour 35:31 Li JH, Davis CC, Donoghue MJ, Kelley S, Pdel T (2001) Phylogenetic relationships of Torreya (Taxaceae) inferred from sequences of nuclear ribosomal DNA its region. Harv Papers Bot 6:275–281 Li J, Gao L, Tao K, Su YJ, Wang T (2016) The complete chloroplast genome sequence of Amentotaxus argotaenia (Taxaceae). Mito- chondrial DNA Part A 4:2919–2920 Shinozaki K et al (1986) The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression. EMBO J 5:2043–2049 Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: Fig. 2 Phylogenetic position of Torreya jackii inferredby maximum molecular evolutionary genetics analysis version 6.0. Mol Biol likelihood (ML)of complete cp genome. The bootstrap values were Evol 30:2725–2729 based on 1000 replicates, and are shown next to the nodes Tao K, Gao L, Li J, Chen SS, Su YJ, Wang T (2015) The complete chloroplast genome of Torreya fargesii (Taxaceae). Mitochondrial DNA Part A 27:3512–3513 genome provides a good foundation for the identification and Zerbino DR, Birney E (2008) Velvet: algorithms for de novo short genotyping of Taxaceae species. read assembly using de Bruijn graphs. Genome Res 18:821–829 Zhang YZ et al (2014) The complete chloroplast genome sequence of Taxus chinensis var. mairei (Taxaceae): loss of an inverted Acknowledgements This research was supported by the Natural Sci- repeat region and comparative analysis with related species. Gene ence Foundation of China (No. 31400321), Opening Project of Zhe- 540:201–209 jiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation (No. EEC2014-01), Anhui University Doctor Startup Found, Key University Science Research Project of Anhui Province (No. KJ2017A022), Fund of Guangxi Key Laboratory of Plant Conser- vation and Restoration Ecology in Karst Terrain (16-B-01-01). 1 3.
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