The complete chloroplast genome sequence of Taxus chinensis var. mairei (Taxaceae): loss of an inverted repeat region and comparative analysis with related species

• Published in: Gene 2014-05, Vol.540 (2), p.201-209
• Main Authors: Zhang, Yanzhen, Ma, Ji, Yang, Bingxian, Li, Ruyi, Zhu, Wei, Sun, Lianli, Tian, Jingkui, Zhang, Lin
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; Base Sequence; Chloroplast genome; Codon - genetics; Cycas revoluta; DNA, Chloroplast - genetics; Gene Order; Genes, Plant; Genome, Chloroplast; Ginkgo biloba; Inverted Repeat Sequences - genetics; IR loss; Large inversion; Microsatellite Repeats; Molecular Sequence Annotation; Molecular Sequence Data; Plant Proteins - chemistry; Plant Proteins - genetics; Ribosomal Proteins - chemistry; Ribosomal Proteins - genetics; Sequence Analysis, DNA; Sequence Homology, Nucleic Acid; SSRs; Taxaceae; Taxus - genetics; Taxus chinensis; Taxus chinensis var. mairei
• ISSN: 0378-1119; 1879-0038
• DOI: 10.1016/j.gene.2014.02.037

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 129,513bp 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 30bp 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. •We sequenced the complete chloroplast genome of Taxus c. var. mairei.•One of the large IRs was lost in Taxus c. var. mairei.•Several genes (rpl32, clpP etc.) differ significantly with related species.•A 110kb inversion with gene contents unarranged was found.