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

被引：56

作者：

Zhang, Yanzhen ^{[1
]}

Ma, Ji ^{[1
]}

Yang, Bingxian ^{[1
]}

Li, Ruyi ^{[1
]}

Zhu, Wei ^{[1
]}

Sun, Lianli ^{[1
]}

Tian, Jingkui ^{[1
]}

Zhang, Lin ^{[1
]}

机构：

[1] Zhejiang Univ, Coll Biomed Engn & Instrument Sci, Hangzhou 310003, Zhejiang, Peoples R China

来源：

GENE | 2014年 / 540卷 / 02期

基金：

美国国家科学基金会;

关键词：

Taxus chinensis var. mairei; Chloroplast genome; Large inversion; IR loss; SSRs; COMPLETE NUCLEOTIDE-SEQUENCE; RNA GENES; DNA; INSIGHTS; PACLITAXEL; COPIES;

D O I：

10.1016/j.gene.2014.02.037

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

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 (trnl-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 similar to 110 kb 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. (C) 2014 Elsevier B.V. All rights reserved.

引用

页码：201 / 209

页数：9

共 32 条

[11] REPuter: the manifold applications of repeat analysis on a genomic scale [J].

Kurtz, S ;

Choudhuri, JV ;

Ohlebusch, E ;

Schleiermacher, C ;

Stoye, J ;

Giegerich, R .

NUCLEIC ACIDS RESEARCH, 2001, 29 (22) :4633-4642

[12] Clustal W and clustal X version 2.0 [J].

Larkin, M. A. ;

Blackshields, G. ;

Brown, N. P. ;

Chenna, R. ;

McGettigan, P. A. ;

McWilliam, H. ;

Valentin, F. ;

Wallace, I. M. ;

Wilm, A. ;

Lopez, R. ;

Thompson, J. D. ;

Gibson, T. J. ;

Higgins, D. G. .

BIOINFORMATICS, 2007, 23 (21) :2947-2948

[13] The Complete Chloroplast Genome of Ginkgo biloba Reveals the Mechanism of Inverted Repeat Contraction [J].

Lin, Ching-Ping ;

Wu, Chung-Shien ;

Huang, Ya-Yi ;

Chaw, Shu-Miaw .

GENOME BIOLOGY AND EVOLUTION, 2012, 4 (03) :374-381

[14] OrganellarGenomeDRAW (OGDRAW): a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes [J].

Lohse, Marc ;

Drechsel, Oliver ;

Bock, Ralph .

CURRENT GENETICS, 2007, 52 (5-6) :267-274

[15] tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence [J].

Lowe, TM ;

Eddy, SR .

NUCLEIC ACIDS RESEARCH, 1997, 25 (05) :955-964

[16] SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler [J].

Luo, Ruibang ;

Liu, Binghang ;

Xie, Yinlong ;

Li, Zhenyu ;

Huang, Weihua ;

Yuan, Jianying ;

He, Guangzhu ;

Chen, Yanxiang ;

Pan, Qi ;

Liu, Yunjie ;

Tang, Jingbo ;

Wu, Gengxiong ;

Zhang, Hao ;

Shi, Yujian ;

Liu, Yong ;

Yu, Chang ;

Wang, Bo ;

Lu, Yao ;

Han, Changlei ;

Cheung, David W. ;

Yiu, Siu-Ming ;

Peng, Shaoliang ;

Zhu Xiaoqian ;

Liu, Guangming ;

Liao, Xiangke ;

Li, Yingrui ;

Yang, Huanming ;

Wang, Jian ;

Lam, Tak-Wah ;

Wang, Jun .

GIGASCIENCE, 2012, 1

[17] The microbial pan-genome [J].

Medini, D ;

Donati, C ;

Tettelin, H ;

Masignani, V ;

Rappuoli, R .

CURRENT OPINION IN GENETICS & DEVELOPMENT, 2005, 15 (06) :589-594

[18]

NIXON PJ, 1989, J BIOL CHEM, V264, P14129

[19]

ROWINSKY EK, 1993, SEMIN ONCOL, V20, P1

[20] PipMaker - A Web server for aligning two genomic DNA sequences [J].

Schwartz, S ;

Zhang, Z ;

Frazer, KA ;

Smit, A ;

Riemer, C ;

Bouck, J ;

Gibbs, R ;

Hardison, R ;

Miller, W .

GENOME RESEARCH, 2000, 10 (04) :577-586

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