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Characterization of the Complete Chloroplast Genome of Platycarya

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Characterization of the Complete Chloroplast Genome of Platycarya Conservation Genet Resour DOI 10.1007/s12686-016-0624-x TECHNICAL NOTE Characterization of the complete chloroplast genome of Platycarya strobilacea (Juglandaceae) Jing Yan1 · Kai Han1 · Shuyun Zeng1 · Peng Zhao1 · Keith Woeste2 · Jianfang Li1 · Zhan-Lin Liu1 Received: 1 September 2016 / Accepted: 4 October 2016 © Springer Science+Business Media Dordrecht 2016 Abstract. The whole chloroplast genome (cp genome) The overall AT content of the cp genome is 64 %, and the sequence of Platycarya strobilacea was characterized corresponding values of the LSC, SSC and IR regions are from Illumina pair-end sequencing data. The complete cp 66.4, 70.1 and 57.5 %, respectively. Phylogenetic analysis genome was 160,994 bp in length and contained a large confirmed the placement of P. strobilacea near to Juglans. single copy region (LSC) of 90,225 bp and a small single copy region (SSC) of 18,371 bp, which were separated Keywords Platycarya strobilacea · Hickory · China · by a pair of inverted repeat regions (IRs, 26,199 bp). The Conservation · Chloroplast genome genome contained 130 genes, including 85 protein-coding genes (80 PCG species), 36 tRNA genes (29 tRNA spe- cies) and 8 ribosomal RNA genes (4 rRNA species). Most Platycarya strobilacea, the only species in the monotypic genes occur as a single copy, but 15 genes are duplicated. genus Platycarya (Juglandaceae), mainly grows as scat- tered individuals in evergreen forests of South China (Chen et al. 2012). As one of main components of the local vegeta- tion, this species plays a key role in the forest ecosystems. Zhan-Lin Liu Extracts of its fruit contain compounds used for anti-aging [email protected] cosmetics (Kim et al. 2010). However, due to anthropogenic Jing Yan over-exploitation and fragmentation of its natural habitat, [email protected] wild resources of P. strobilacea have dramatically declined Kai Han and need urgent protection and restoration. An improved [email protected] understanding of its genetics would contribute to the formu- Shuyun Zeng lation of conservation strategies. In this study, we assembled [email protected] and characterized the complete chloroplast genome of P. Peng Zhao strobilacea from Illumina sequencing data. [email protected] Fresh leaves of an individual were collected from Zheng- Keith Woeste pin (Shaanxi, China; 31°53′N, 109°31′E), and were used for [email protected] total genomic DNA isolation. A shotgun library was pre- Jianfang Li pared and sequenced on the Illumina Hiseq 2500 Sequenc- [email protected] ing System (Illumina, CA, USA). In total, 8.2G raw reads 1 Key Laboratory of Resource Biology and Biotechnology were obtained, quality-trimmed and assembled for the chlo- in Western China (Ministry of Education), College of roplast genome using the program MITObim v1.8 (Hahn Life Science, Northwest University, Xi’an 710069, et al. 2013) with Juglans regia (GenBank: NC_028617.1) Shaanxi Province, China (Potter et al. 2002) as the initial reference. The genome 2 USDA Forest Service Hardwood Tree Improvement and was annotated by aligning with the reference chloro- Regeneration Center (HTIRC), Department of Forestry and Natural Resources, Purdue University, 715 West State Street, plast genome. A map of the genome was generated using West Lafayette, IN 47907, USA OGDRAW (http://ogdraw.mpimp-golm.mpg.de/) (Lohse et 1 3 2 Conservation Genet Resour trnS-G trnL-UAA trnF-GAA GA GT trnG-GCC psbZ t rnM-CAT psbC psbD trnT-G N p et ycf3 s p rbcL rps4 aA trnT-TGT trnC-GCA A psaB ndhJ accD trnV-UA atp trnS-TG psaI a 14 M tp E s b yc B p f ndhK r ps ce 4 C ndhC TC A mA fM-CAT C T n - T pet tr oB A nE Y-GT rp tr rn t LSC trnD-G petL 1 pet poC G r rpl33 rps18 psaJ psbJ rpoC2 psbL psbF rps2 psbE pI trnW at rpl2 trnP-TGG-CCA 0 rps12 atpH clpP atpF trnR-TCT psbB atpA A psbT trnS-CG psbH psbN psbI petB trnS-GCT psbK petD Platycarya strobilacea trnQ-TTG rpoA rps16 rps11 rpl36 chloroplast genome rps8 rpl14 matK rpl16 rps3 160,994 bp rpl22 psbA rps12 trnH-GTG rps19 rpl2 rpl23 trnI-CAT rpl2 rpl23 trn I-CAT ycf2 I R B A R ycf2 I CAA trnL- ndhB trnL ycf15 ps7 2 tr r s1 n -CAA photosystem I rp V -GAC n photosystem II SSC trnR trnI-GAU dh tr B r n - rn5S cytochrome b/f complex A A r rrn16S - ps7 C U rps1 ATP synthase G G S C 2 NADH dehydrogenase S C rrn23 RubisCO large subunit A rrn16S psaC ndhE -G rrn4.5 ndhG RNA polymerase trnN-GTT yc rps15 rnV ndhH t n f ndhI 1 ribosomal proteins (SSU) ndhF dh A ndhD rrn23 ribosomal proteins (LSU) trnI-GAU rrn4.5 clpP, matK trnA-UGC S tr n other genes N-GTT S hypothetical chloroplast reading frames (ycf) ycf1 2 ORFs rpl3 transfer RNAs rrn5S ccsA trnL-TAG ribosomal RNAs trnR-ACG origin of replication introns polycistronic transcripts Fig. 1 Gene map of the whole chloroplast genome of Platycarya strobilacea Fig. 2 Phylogeny of nine species in Fagales based on the neighbor- mollissima HQ336406.1, Quercus baronii NC_029490.1, Quercus joining (NJ) analysis of the concatenated coding sequences of 80 chlo- spinose KM841421.1, Trigonobalanus doichangensis NC_023959.1, roplast PCGs. The bootstrap values are indicated next to the branches. Ostrya rehderiana NC_028349.1, Platycarya strobilacea KX868670, Quercus rubra JX970937, Quercus aliena NC_026790.1, Castanea Juglans regia NC_028617.1 1 3 Conservation Genet Resour 3 al. 2013). The annotated cp genome has been deposited into Acknowledgments This study was financially supported by the GenBank with the accession number KX868670. National Natural Science Foundation of China (31670219, 31370353, J1210063) and Natural Science Basic Research Plan in Shaanxi Prov- The cp genome of P. strobilacea is 160,994 bp in ince of China (2015JM3106). Mention of a trademark, proprietary length, and is comprised of a pair of inverted repeat (IR) product, or vendor does not constitute a guarantee or warranty of the regions (26,199 bp each), a large single-copy (LSC) region product by the U.S. Department of Agriculture and does not imply its of 90,225 bp, and a small single-copy (SSC) region of approval to the exclusion of other products or vendors that also may be suitable. 18,371 bp (Fig. 1). The chloroplast genome harbors 130 genes, including 85 protein-coding genes (80 PCG species), 36 transfer RNA genes (29 tRNA species) and 8 ribosomal References RNA genes (4 rRNA species). The majority of the gene spe- cies are single copy, but 15 gene species located within the Chen SC, Zhang L, Zeng J, Shi F, Yang H, Mao YR, Fu CX (2012) IR regions are duplicated, including 5 PCG species (rpl2, Geographic variation of chloroplast DNA in Platycarya strobila- rpl23, rps7, rps12, ycf2), 6 tRNA species (trnA-UGC, trnI- cea (Juglandaceae). J Syst Evol 50:374–385 CAT, trnL-CAA, trnN-GTT, trnR-ACG, trnV-GAC), and all Hahn C, Bachmann L, Chevreux B (2013) Reconstructing mitochon- drial genomes directly from genomic next-generation sequencing rRNA species (4.5S, 5S, 16S, 23S rRNA). The base compo- reads—a baiting and iterative mapping approach. Nucleic Acids sition is asymmetric (31.7 % A, 18.3 % C, 17.7 % G, 32.3 % Res 41:e129 T) with an overall A+T content of 64 %. The A+T contents Kim YH, Kim HK, Han CS, Yang HC, Park SH, Jang HI, Kim JW, of the LSC, SSC and IR regions are 66.4, 70.1 and 57.5 %, Choi YS, Lee NH (2010) Anti-wrinkle activity of Platycarya strobilacea extract and its application as a cosmeceutical ingredi- respectively. ent. J Cosmet Sci 61:211–223 To identify the phylogenetic position of Platycarya Lohse M, Drechsel O, Kahlau S, Bock R (2013) OrganellarGenome- strobilacea, a neighbor-joining (NJ) phylogenetic tree was DRAW-a suite of tools for generating physical maps of plastid reconstructed using the concatenated coding sequences of and mitochondrial genomes and visualizing expression data sets. Nucleic Acids Res 41:W575–W581 80 chloroplast PCGs from nine taxa of Fagales (see Fig. 2 Potter D, Gao FY, Baggett S, McKenna RJ, McGranahan HG (2002) for details) with MEGA6 (Tamura et al. 2013). The topology Defining the sources of Paradox: DNA sequence markers for of the phylogenetic tree was consistent with the traditional North American walnut (Juglans L.) species and hybrids. Sci Hortic 94:157–170 tribe-level taxonomy of Fagales. The two Juglandaceae spe- Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) cies (Platycarya strobilacea, Juglans regia) grouped into MEGA6: molecular evolutionary genetics analysis version 6.0. one clade and formed a sister to Ostrya rehderiana. Mol Biol Evol 30:2725–2729 1 3.
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