The complete chloroplast genome sequence of an economically important plant, Zanthoxylum bungeanum (Rutaceae)
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TeCHNICAL NOte
The complete chloroplast genome sequence of an economically important plant, Zanthoxylum bungeanum (Rutaceae) Yulin Liu1 · Anzhi Wei1
Received: 23 August 2016 / Accepted: 30 August 2016 © Springer Science+Business Media Dordrecht 2016
Abstract The complete chloroplast genome (cp genome) sequence of Zanthoxylum bungeanum has been assembled from Illumina pair-end sequencing. This genome was 158,401 bp in length, consisting of a pair of inverted repeats (IRs) of 27,446 bp which separated by a large single copy (LSC) region and a small single copy (SSC) region (85,898 and 17,611 bp in length, respectively). There are 132 genes, including 87 protein-coding genes (78 PCG species), 37 rRNA genes (30 rRNA species) and eight tRNA genes (four tRNA species) in the cp genome. The overall GC content of the whole genome is 38.6 %, while the corresponding values of the LSC, SSC, and IR regions are 36.87, 33.51 and 42.54 %, respectively. Phylogenetic analysis indicated that the cp genome of Z. bungeanum is closely related to that of congeneric Zanthoxylum piperitum. Keywords Zanthoxylum bungeanum · Chloroplast genome · Illumina sequencing
Zanthoxylum bungeanum is an aromatic tree or shrub belonging to the Rutaceae family and native to China. This species have high economic and ecological values due to its strong tolerance for cold and drought and its pericarps have been utilized as a pungent foodstuff and also as a kind
Anzhi Wei [email protected] Yulin Liu [email protected] 1
College of Foresty, Northwest A&F University, Yangling 712100, Shaanxi, People’s Republic of China
of traditional Chinese medicine for treatment of vomiting, toothache, stomach ache etc. for 1000 years (Cheng et al. 2015; Huang et al. 2012). However, lots of germplasm resources of Z. bungeanum were lost gradually due to the long period artificial selection and woodcutting. Thus, to protect and make use of the germplasm resources become urgent and necessary. Genome information is helpful to its effective management, conservation and exploitation. In this study, the complete cp genome sequence of Z. bungeanum has been assembled based on high-throughput sequencing data and its annotated genomic sequence has been submitted to GenBank with the accession number KX497031. The whole genomic DNA of Z. bungeanum was extracted from fresh leaves of an individual collected from Fengxian (Shannxi, China; 33°58′N, 106°38′E), using DNeasy Plant Mini Kit (QIAGEN, German). Then, an Illumina pair-end library was constructed and sequenced by the Illumina Hiseq 2500 platform. After filtered out the low-quality reads by CLC Genomics Workbench v7.5 (http://www.clcbio. com), the clean reads were used for the cp genome assembly by MITObim v1.8 (Hahn et al. 2013) by comparing with the congeneric Zanthoxylum piperitum (KT153018) (Lee et al. 2016) as the reference. The annotation of cp genome was conducted on the program GENEIOUS R9 (Biomatters Ltd., Auckland, New Zealand) by comparing with the cp genome of Z. piperitum (KT153018) and Citrus sinensis (DQ8
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