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

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.

[1]  Ching-Ping Lin,et al.  Loss of Different Inverted Repeat Copies from the Chloroplast Genomes of Pinaceae and Cupressophytes and Influence of Heterotachy on the Evaluation of Gymnosperm Phylogeny , 2011, Genome biology and evolution.

[2]  S. Eddy,et al.  tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. , 1997, Nucleic acids research.

[3]  Patrick J. Biggs,et al.  SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data , 2010, BMC Bioinformatics.

[4]  Glenn Tesler,et al.  GRIMM: genome rearrangements web server , 2002, Bioinform..

[5]  C. Lemieux,et al.  The complete chloroplast DNA sequence of the green alga Nephroselmis olivacea: insights into the architecture of ancestral chloroplast genomes. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[6]  B. Lang,et al.  Mitochondrial genomes: anything goes. , 2003, Trends in genetics : TIG.

[7]  P. Xiao,et al.  Interspecific relationships and origins of Taxaceae and Cephalotaxaceae revealed by partitioned Bayesian analyses of chloroplast and nuclear DNA sequences , 2008, Plant Systematics and Evolution.

[8]  R. Gibbs,et al.  PipMaker--a web server for aligning two genomic DNA sequences. , 2000, Genome research.

[9]  R. Varshney,et al.  Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.) , 2003, Theoretical and Applied Genetics.

[10]  E. Eisenhauer,et al.  Clinical toxicities encountered with paclitaxel (Taxol). , 1993, Seminars in oncology.

[11]  R. Kolodner,et al.  Inverted repeats in chloroplast DNA from higher plants. , 1979, Proceedings of the National Academy of Sciences of the United States of America.

[12]  M. Sugiura,et al.  Chloroplast DNA of black pine retains a residual inverted repeat lacking rRNA genes: nucleotide sequences of trnQ, trnK, psbA, trnI and trnH and the absence of rps16 , 1992, Molecular and General Genetics MGG.

[13]  T. Kondo,et al.  Complete nucleotide sequence of the Cryptomeria japonica D. Don. chloroplast genome and comparative chloroplast genomics: diversified genomic structure of coniferous species , 2008, BMC Plant Biology.

[14]  Robert K. Jansen,et al.  Automatic annotation of organellar genomes with DOGMA , 2004, Bioinform..

[15]  H. Tettelin,et al.  The microbial pan-genome. , 2005, Current opinion in genetics & development.

[16]  J. Stoye,et al.  REPuter: the manifold applications of repeat analysis on a genomic scale. , 2001, Nucleic acids research.

[17]  psbG is not a photosystem two gene but may be an ndh gene. , 1989, The Journal of biological chemistry.

[18]  W. J. Kent,et al.  BLAT--the BLAST-like alignment tool. , 2002, Genome research.

[19]  F. Takaiwa,et al.  The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression , 1986, The EMBO journal.

[20]  Masaru Fujimoto,et al.  Loss of the rpl32 gene from the chloroplast genome and subsequent acquisition of a preexisting transit peptide within the nuclear gene in Populus. , 2007, Gene.

[21]  Chung-Shien Wu,et al.  Chloroplast genome (cpDNA) of Cycas taitungensis and 56 cp protein-coding genes of Gnetum parvifolium: insights into cpDNA evolution and phylogeny of extant seed plants. , 2007, Molecular biology and evolution.

[22]  D. Gibson,et al.  EFFICIENT EXTRACTION OF PACLITAXEL AND RELATED TAXOIDS FROM LEAF TISSUE OF TAXUS USING A POTABLE SOLVENT SYSTEM , 1999 .

[23]  Ching-Ping Lin,et al.  The Complete Chloroplast Genome of Ginkgo biloba Reveals the Mechanism of Inverted Repeat Contraction , 2012, Genome biology and evolution.

[24]  Rodrigo Lopez,et al.  Clustal W and Clustal X version 2.0 , 2007, Bioinform..

[25]  Bo Wang,et al.  The Complete Chloroplast Genome Sequence of Cephalotaxus oliveri (Cephalotaxaceae): Evolutionary Comparison of Cephalotaxus Chloroplast DNAs and Insights into the Loss of Inverted Repeat Copies in Gymnosperms , 2013, Genome biology and evolution.

[26]  Ralph Bock,et al.  OrganellarGenomeDRAW (OGDRAW): a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes , 2007, Current Genetics.

[27]  Jun Yu,et al.  The Complete Chloroplast Genome Sequence of Date Palm (Phoenix dactylifera L.) , 2010, PloS one.

[28]  James Leebens-Mack,et al.  Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns , 2007, Proceedings of the National Academy of Sciences.

[29]  Jian Wang,et al.  SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler , 2012, GigaScience.

[30]  K. H. Wolfe,et al.  When gene marriages don't work out: divorce by subfunctionalization. , 2007, Trends in genetics : TIG.

[31]  M. Sugiura,et al.  Loss of all ndh genes as determined by sequencing the entire chloroplast genome of the black pine Pinus thunbergii. , 1994, Proceedings of the National Academy of Sciences of the United States of America.