title: Complete chloroplast genome sequence of a major economic species, Ziziphus jujuba (Rhamnaceae).
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.
authors.affiliation: The Southern Modern Forestry Collaborative Innovation Center, Nanjing Forestry University, Nanjing, 210037, China.
authors.forename: Qiuyue
authors.initials: Q
authors.lastname: Ma
authors.affiliation: The Southern Modern Forestry Collaborative Innovation Center, Nanjing Forestry University, Nanjing, 210037, China.
authors.forename: Shuxian
authors.initials: S
authors.lastname: Li
authors.affiliation: The College of Information Science and Technology, Nanjing Forestry University, 159 Longpan Road, Nanjing, 210037, China.
authors.forename: Changwei
authors.initials: C
authors.lastname: Bi
authors.affiliation: The Southern Modern Forestry Collaborative Innovation Center, Nanjing Forestry University, Nanjing, 210037, China.
authors.forename: Zhaodong
authors.initials: Z
authors.lastname: Hao
authors.affiliation: The Southern Modern Forestry Collaborative Innovation Center, Nanjing Forestry University, Nanjing, 210037, China.
authors.forename: Congrui
authors.initials: C
authors.lastname: Sun
authors.affiliation: The College of Information Science and Technology, Nanjing Forestry University, 159 Longpan Road, Nanjing, 210037, China. yening@njfu.edu.cn.
authors.forename: Ning
authors.initials: N
authors.lastname: Ye
mesh_terms: D001482:Base Composition; D003062:Codon; D019295:Computational Biology / Q000379:methods; D019143:Evolution, Molecular; D023061:Gene Order; D017343:Genes, Plant; D054628:Genome, Chloroplast; D018895:Microsatellite Repeats; D058977:Molecular Sequence Annotation; D016366:Open Reading Frames; D010802:Phylogeny; D012091:Repetitive Sequences, Nucleic Acid; D017422:Sequence Analysis, DNA; D031957:Ziziphus / Q000145:classification / Q000235:genetics*
chemical_list: D003062:Codon
keywords: Chloroplast; Evolution; Genome; Rhamnaceae; Rosales; Ziziphus jujuba