The complete chloroplast genome sequence of Taxus chinensis var. mairei (Taxaceae): loss of an inverted repeat region and comparative analysis with related species
Introduction
Since the first report of the complete chloroplast (cp) genome sequences of the tobacco and the liverwort (Shinozaki et al., 1986), a number of land plant chloroplast genomic sequences have been determined. These recent determination of complete cp genomic sequence of various plant species have enabled numerous comparative analyses as well as advancements in plant and genome evolutionary studies, including transcriptome analysis and pangenomes that are based on these data (Medini et al., 2005). Although the published complete cp genome sequence of gymnosperm species were few in number, unique characteristics such as genome-scale genomic rearrangement and a more frequent gene lost and gain events were found in them (Jansen et al., 2007). The probability of genomic rearrangements and gene loss events of a land plant cp genome during evolutionary progress was thought to have intimate relationship with the size of IRs (Wu et al., 2007). Large IRs can help stabilize the cp genome and reduce the possibility of gene loss and rearrangements (Xiao et al., 2008). In most angiosperms such as date palm (Phoenix dactylifera L.), the relative size of LSC, SSC and IRs remains constant, the gene order and organization are almost the same with inferred ancestral angiosperm cp genomes (Yang et al., 2010). However, some clades of gymnosperm such as Pinaceae and Cupressaceae have lost one of the large inverted repeats, which lead to more gene loss and structural rearrangements in their cp genomes (Kolodner and Tewari, 1979).
Taxus chinensis var. mairei is a variety of the Taxus genus, yew family (Taxaceae) in domestic China. Its secondary metabolite paclitaxel (taxol) is a chemotherapy drug given to treat ovarian, breast and non-small cell lung cancer, which is one of the most promising antineoplastic agents of the last decade, with demonstrated activity in advanced and refractory ovarian, breast, lung, and head and neck cancers (Rowinsky et al., 1993). Paclitaxel was first isolated from the bark of pacific yew tree in 1970s, but leaves of Taxus were also examined as a source of paclitaxel and related toxoids (Ketchum et al., 1999). As the breast cancer rate increases, the unique medicinal value of Taxus was gradually recognized. The access to plastid genome information of T. chinensis var. mairei will provide usage of information for further transcriptomic and proteomic analysis, and pave the way to study the enzymes that catalyze the biosynthesis of the natural compounds in chloroplast.
Currently, the gene content and genomic structure of some species of gymnosperms are still little known, because there are only 3 published complete cp genome sequences of Taxaceae in GenBank (http://www.ncbi.nlm.nih.gov). Here, we report the complete cp genome sequence of Taxus c. var. mairei, the first reported cp genome in the Taxus genus. In this report, we described details of the genome assembly, annotation, and simple sequence repeats (SSRs). Dot-plot analyses and genomic comparative analyses were also performed in order to better understand the unique structure of the cp genome of T. c. var. mairei.
Section snippets
DNA sequencing and genome assembly
Fresh leaves of T. chinensis var. mairei were collected for the preparation of genomic DNA extraction. 5 μg purified DNA was used for the construction of cp DNA libraries. Solexa high-throughput sequencing system (Illumina Genome Analyzer II) was used to generate raw sequence reads for this project.
Since the original sequence reads are a mixture of DNA from nucleus and organelles, BLAT (Kent, 2002) software was used to isolate chloroplast-related reads from the raw reads based on known reference
Genome assembly and validation
Using the Illumina Hiseq 2000 system, 49,743,352 paired-end reads were generated to assemble the cp genome of T. chinensis var. mairei. After filtering low-quality reads (≤ Q20 bases) and aligning with reference cp genomes, we collected 1,802,286 reads (3.62% of total) reaching 95 × coverage over the cp genome (Supplementary Table 1). The unassembled reads (~ 96.38%) were mostly from the nuclear genome due to the raw reads which was a collection of DNA from nucleus and organelles. We have manually
Gene content differences between T. chinensis var. mairei and other gymnosperms
There are marked differences in gene content between T. chinensis var. mairei and several other gymnosperm cp genomes. The gene rps16 was absent from the cp genome of T. chinensis var. mairei. The absence of rps16 is also found in the cp genome of P. thunbergii (Tsudzuki et al., 1992), an early divergent plant of the Pinaceae family.
Another gene psbG, positioned between ndhJ and ndhK in C. wilsoniana (Wu et al., 2011) and G. biloba (Lin et al., 2012), is completely absent from the cp genome of
Conclusions
The complete chloroplast genome sequence of the T. chinensis var. mairei has revealed that the Taxus species has a distinct cp genome compared to previously reported gymnosperm cp genomes, lost one of the large inverted repeats (IRs), making more gene loss events and structural rearrangements happened in its cp genome. The deleted large IRs and the numerous genome rearrangements that have occurred in the cp genome of T. chinensis var. mairei provided new insights into the evolutionary lineage
Conflict of interest
There is no conflict of interest.
Acknowledgments
This work was supported by the National Science Foundation of China (Grant Nos. 81274033, 81202424) and the Research Project of Chinese Ministry of Education (Grant No. 113037A).
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These authors contributed equally to this work.