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Complete chloroplast genome sequence of a major economic species, Ziziphus jujuba (Rhamnaceae)

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Abstract

Ziziphus jujuba is an important woody plant with high economic and medicinal value. Here, we analyzed and characterized the complete chloroplast (cp) genome of Z. jujuba, the first member of the Rhamnaceae family for which the chloroplast genome sequence has been reported. We also built a web browser for navigating the cp genome of Z. jujuba (http://bio.njfu.edu.cn/gb2/gbrowse/Ziziphus_jujuba_cp/). Sequence analysis showed that this cp genome is 161,466 bp long and has a typical quadripartite structure of large (LSC, 89,120 bp) and small (SSC, 19,348 bp) single-copy regions separated by a pair of inverted repeats (IRs, 26,499 bp). The sequence contained 112 unique genes, including 78 protein-coding genes, 30 transfer RNAs, and four ribosomal RNAs. The genome structure, gene order, GC content, and codon usage are similar to other typical angiosperm cp genomes. A total of 38 tandem repeats, two forward repeats, and three palindromic repeats were detected in the Z. jujuba cp genome. Simple sequence repeat (SSR) analysis revealed that most SSRs were AT-rich. The homopolymer regions in the cp genome of Z. jujuba were verified and manually corrected by Sanger sequencing. One-third of mononucleotide repeats were found to be erroneously sequenced by the 454 pyrosequencing, which resulted in sequences of 1–4 bases shorter than that by the Sanger sequencing. Analyzing the cp genome of Z. jujuba revealed that the IR contraction and expansion events resulted in ycf1 and rps19 pseudogenes. A phylogenetic analysis based on 64 protein-coding genes showed that Z. jujuba was closely related to members of the Elaeagnaceae family, which will be helpful for phylogenetic studies of other Rosales species. The complete cp genome sequence of Z. jujuba will facilitate population, phylogenetic, and cp genetic engineering studies of this economic plant.

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Acknowledgments

Funding for this work was provided by the Natural Science Foundation of China (31561123001, 31570662). The work was supported by the Program for Innovative Research Team of the Educational Department of China and in Universities of Jiangsu Province, the Priority Academic Program Development (PAPD) program, and the Doctorate Fellowship Foundation at Nanjing Forestry University.

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  1. The Southern Modern Forestry Collaborative Innovation Center, Nanjing Forestry University, Nanjing, 210037, China

    Qiuyue Ma, Shuxian Li, Zhaodong Hao & Congrui Sun

  2. The College of Information Science and Technology, Nanjing Forestry University, 159 Longpan Road, Nanjing, 210037, China

    Changwei Bi & Ning Ye

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  1. Qiuyue Ma
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Correspondence to Ning Ye.

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Communicated by M. Kupiec.

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294_2016_612_MOESM1_ESM.tif

Neighbor-joining phylogenetic tree based on 64 protein-coding genes from 24 plant taxa. The tree was obtained using the Poisson model. Numbers at the nodes are bootstrap support values. (TIFF 1943 kb)

Primers used for PCR amplification to fill gaps in the assembled Z. jujuba chloroplast sequence. (DOC 16 kb)

Seventeen genes in the Ziziphus jujuba chloroplast genome that contained introns. (DOC 35 kb)

Repeat sequences in the Ziziphus jujuba chloroplast genome. (DOC 77 kb)

Distribution of SSRs in the Ziziphus jujuba chloroplast genome. (DOC 191 kb)

Details of the chloroplast genome sequences used for the phylogenetic analysis. (DOC 48 kb)

Primers used for PCR amplification to test the accuracy of mononucleotide repeats. (XLS 41 kb)

Verification of the homopolymers in the Ziziphus jujuba cp genome. (DOC 25 kb)

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Ma, Q., Li, S., Bi, C. et al. Complete chloroplast genome sequence of a major economic species, Ziziphus jujuba (Rhamnaceae). Curr Genet 63, 117–129 (2017). https://doi.org/10.1007/s00294-016-0612-4

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