title: The complete chloroplast genome sequence of Taxus chinensis var. mairei (Taxaceae): loss of an inverted repeat region and comparative analysis with related species.
abstract: Taxus chinensis var. mairei (Taxaceae) is a domestic variety of yew species in local China. This plant is one of the sources for paclitaxel, which is a promising antineoplastic chemotherapy drugs during the last decade. We have sequenced the complete nucleotide sequence of the chloroplast (cp) genome of T. chinensis var. mairei. The T. chinensis var. mairei cp genome is 129,513 bp in length, with 113 single copy genes and two duplicated genes (trnI-CAU, trnQ-UUG). Among the 113 single copy genes, 9 are intron-containing. Compared to other land plant cp genomes, the T. chinensis var. mairei cp genome has lost one of the large inverted repeats (IRs) found in angiosperms, fern, liverwort, and gymnosperm such as Cycas revoluta and Ginkgo biloba L. Compared to related species, the gene order of T. chinensis var. mairei has a large inversion of ~110kb including 91 genes (from rps18 to accD) with gene contents unarranged. Repeat analysis identified 48 direct and 2 inverted repeats 30 bp long or longer with a sequence identity greater than 90%. Repeated short segments were found in genes rps18, rps19 and clpP. Analysis also revealed 22 simple sequence repeat (SSR) loci and almost all are composed of A or T.
authors.affiliation: College of Biomedical Engineering & Instrument Science, Zhejiang University, 38 Zheda Road, Hangzhou, Zhejiang, China.
authors.forename: Yanzhen
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: College of Biomedical Engineering & Instrument Science, Zhejiang University, 38 Zheda Road, Hangzhou, Zhejiang, China.
authors.forename: Ji
authors.initials: J
authors.lastname: Ma
authors.affiliation: College of Biomedical Engineering & Instrument Science, Zhejiang University, 38 Zheda Road, Hangzhou, Zhejiang, China.
authors.forename: Bingxian
authors.initials: B
authors.lastname: Yang
authors.affiliation: College of Biomedical Engineering & Instrument Science, Zhejiang University, 38 Zheda Road, Hangzhou, Zhejiang, China.
authors.forename: Ruyi
authors.initials: R
authors.lastname: Li
authors.affiliation: College of Biomedical Engineering & Instrument Science, Zhejiang University, 38 Zheda Road, Hangzhou, Zhejiang, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Zhu
authors.affiliation: College of Biomedical Engineering & Instrument Science, Zhejiang University, 38 Zheda Road, Hangzhou, Zhejiang, China.
authors.forename: Lianli
authors.initials: L
authors.lastname: Sun
authors.affiliation: College of Biomedical Engineering & Instrument Science, Zhejiang University, 38 Zheda Road, Hangzhou, Zhejiang, China.
authors.forename: Jingkui
authors.initials: J
authors.lastname: Tian
authors.affiliation: College of Biomedical Engineering & Instrument Science, Zhejiang University, 38 Zheda Road, Hangzhou, Zhejiang, China. Electronic address: zhanglin@zju.edu.cn.
authors.forename: Lin
authors.initials: L
authors.lastname: Zhang
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D003062:Codon / Q000235:genetics; D018742:DNA, Chloroplast / Q000235:genetics; D023061:Gene Order; D017343:Genes, Plant; D054628:Genome, Chloroplast; D055029:Inverted Repeat Sequences / Q000235:genetics*; D018895:Microsatellite Repeats; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D010940:Plant Proteins / Q000737:chemistry / Q000235:genetics; D012269:Ribosomal Proteins / Q000737:chemistry / Q000235:genetics; D017422:Sequence Analysis, DNA; D012689:Sequence Homology, Nucleic Acid; D020946:Taxus / Q000235:genetics*
chemical_list: D003062:Codon; D018742:DNA, Chloroplast; D010940:Plant Proteins; D012269:Ribosomal Proteins
keywords: Chloroplast genome; IR loss; Large inversion; SSRs; Taxus chinensis var. mairei