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The Complete Chloroplast Genome of Common Walnut (Juglans Regia)

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MITOCHONDRIAL DNA: RESOURCES, 2016 http://dx.doi.org/10.1080/23802359.2015.1137804 MITOGENOME ANNOUNCEMENT The complete chloroplast genome of common walnut (Juglans regia) Yiheng Hua, Keith E. Woesteb, Meng Danga, Tao Zhoua, Xiaojia Fenga, Guifang Zhaoa, Zhanlin Liua, Zhonghu Lia and Peng Zhaoa aKey Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, China; bUSDA Forest Service Hardwood Tree Improvement and Regeneration Center (HTIRC), Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN, USA ABSTRACT ARTICLE HISTORY Common walnut (Juglans regia L.) is cultivated in temperate regions worldwide for its wood and nuts. Received 1 December 2015 The complete chloroplast genome of J. regia was sequenced using the Illumina MiSeq platform. This is Accepted 22 December 2015 the first complete chloroplast sequence for the Juglandaceae, a family that includes numerous species of economic importance. The chloroplast genome of J. regia was 160 367 bp in length, with 36.11% GC KEYWORDS Complete chloroplast content. It contains a pair of inverted repeats (26 035 bp) which were separated by a large single copy genome; economic tree; (89 872 bp) and a small single copy region (18 425 bp). A total of 137 genes were annotated, which Juglans regia included 86 protein-coding genes, three pseudogenes (two ycf15 and one infA), 40 tRNA genes and eight rRNA genes. The neighbour-joining phylogenetic analysis with the reported chloroplast genomes showed that common walnut chloroplasts are most closely related to those of the Fagaceae family. Juglans L. is one of the eight living genera in the family Blume; Lu et al. 2015). The large single copy (LSC) and small Juglandaceae consisting of 21 extant taxa (Manning 1978; single copy (SSC) contained 89 872 and 18 425 bp, respective- Aradhya et al. 2007). The common walnut (Juglans regia L.) is ly, while the inverted repeat (IR) was 26 035 bp in length. This the most economically important member of the genus chloroplast genome contained 137 functional genes, including Juglans because of its high-quality timber and nutritious nuts 86 protein-coding genes, three pseudogenes (two ycf15 and (Pollegioni et al. 2015). It is native to the mountainous regions one infA), 40 tRNA genes and eight rRNA genes. There were of central Asia, but it has become the most widespread tree 12 protein-coding genes, 14 tRNA and all eight rRNA genes nut cultivated in the world (Chen et al. 2014). duplicated in the IR regions. The LSC region contained 62 Chloroplasts play an important role in photosynthesis in protein-coding and 25 tRNA genes, whereas the SSC region green plants and participate in the biosynthesis of starch, contained 12 protein-coding and one tRNA gene. Fourteen fatty acids and amino acids (Neuhaus & Emes 2000). The DNA genes contained one or two introns, including the protein- sequence of the chloroplast genome can be used as a super coding genes, rps16, atpF, rpoC1, ycf3 (three introns), clpP, barcode or a resource for research in phylogeography, genetic petB, petD, rpl16, rpl2, ndhB and rps12. diversity and evolution. Although many members of the The phylogenetic relationship of J. regia to other plant Juglandaceae are economically important, no member of the families was evaluated by comparing the J. regia chloroplast family has had its complete chloroplast sequence published. to chloroplasts from 11 other species (eight species in the For this study, we collected the fresh, healthy leaves from Fagales), downloaded from NCBI). A neighbour-joining analysis J. regia growing in the orchard of Northwest University, was performed using the software Geneious version 8.0.2 Shaanxi, China. DNA was extracted using methods described (http://www.geneious.com/) (Figure 1). The phylogenetic tree by Zhao and Woeste (2011). We sequenced the complete showed that J. regia (Juglandaceae) was most closely related chloroplast genome of J. regia with the Illumina MiSeq to members of Fagaceae family and the genus Populus sequencing platform (Sangon Biotech, Shanghai, China). We (Figure 1). The newly characterized J. regia complete chloro- assembled the chloroplast genome using SPAdes (http://bio- plast genome will provide essential data for further study on inf.spbau.ru/spades) and annotated with software CpGAVAS the phylogeny and evolution of the genus Juglans and of the (http://www.biomedcentral.com/1471-2164/13/715) (Liu et al. Juglandaceae, for molecular breeding, and potentially for gen- 2012). We determined the complete chloroplast genome se- etic engineering. quence of J. regia was 160 367 bp in length (GenBank acces- sion number KT963008). The GC content was 36.11%. Declaration of interest Chloroplasts are typically AT-rich, and the GC content of the This work was supported by the National Natural Science Foundation of J. regia chloroplast was similar to values previously reported China (No. 41471038, No. 31200500 and No. J1210063), the Program for for most other vascular species (e.g., 36.9% in Quercus aliena Excellent Young Academic Backbones funding by Northwest University. CONTACT Peng Zhao [email protected] College of Life Sciences, Northwest University, 229 Northern Taibai Road, Xi’an 710069, China ß 2016 The Author(s). Published by Taylor & Francis. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/ licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 2 Y. HU ET AL. Figure 1. Phylogenetic relationships among 12 chloroplast genomes. The 12 species can be divided into three independent clades: Fagales, Salicales and Brassicales. Arabidopsis thaliana (Brassicales) was used as an outgroup. Bootstrap support values are given at the nodes. Chloroplast genome accession number used in this phyl- ogeny analysis: Arabidopsis thaliana: NC000932; Populus euphratica: NC024747; Populus trichocarpa: NC009143; Trigonobalanus doichangensis: KF990556; Quercus aquifo- lioides: NC026913; Quercus aliena: NC026790; Quercus rubra: JX970937; Quercus spinosa: NC026907; Lithocarpus balansae: KP299291; Castanea mollissima: NC014674; Castanopsise chinocarpa: NC023801. Mention of a trademark, proprietary product, or vendor does not consti- GenBank submission of completely sequenced chloroplast genome tute a guarantee or warranty of the product by the U.S. Department of sequences. BMC Genomics 13:715. Agriculture and does not imply its approval to the exclusion of other Lu S, Hou M, Du FK, Li J, Yin K. 2015. Complete chloroplast genome of products or vendors that also may be suitable. the Oriental white oak: Quercus aliena Blume. Mitochondrial DNA1–3. DOI: 10.3109/19401736.2015.1053074. Manning WE. 1978. The classification within the Juglandaceae. Ann Mo References Bot Gard. 65:1058–1087. Neuhaus HE, Emes MJ. 2000. Nonphotosynthetic metabolism in plastids. Aradhya MK, Potter D, Gao F, Simon CJ. 2007. Molecular phylogeny of Annu Rev Plant Physiol Plant Mol Biol. 51:111–140. Juglans (Juglandaceae): a biogeographic perspective. Tree Genet Pollegioni P, Woeste KE, Chiocchini F, Lungo SD, Olimpier I, Virginia T, Genom. 3:363–378. Clark J, Hemery GE, Mapelli S, Malvolti ME. 2015. Ancient humans influ- Chen LN, Ma QG, Chen YK, Wang BQ, Pei D. 2014. Identification of major enced the current spatial genetic structure of common walnut popula- walnut cultivars grown in China based on nut phenotypes and SSR tions in Asia. PLoS One 10:e0135980. markers. Sci Hortic. 168:240–248. Zhao P, Woeste KE. 2011. DNA markers identify hybrids between butter- Liu C, Shi L, Zhu Y, Chen H, Zhang J, Lin X, Guan X. 2012. CpGAVAS, an nut (Juglans cinerea L.) and Japanese awlnut (Juglans ailantifolia Carr.). integrated web server for the annotation, visualization, analysis, and Tree Genet Genom. 7:511–533..
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