药学学报, 2019, 54(1): 173-181
杨俏俏, 姜梅, 王立强, 陈海梅, 刘昶, 黄林芳. 药食两用藠头叶绿体基因组解析、比较基因组学及系统发育研究[J]. 药学学报, 2019, 54(1): 173-181.
YANG Qiao-qiao, JIANG Mei, WANG Li-qiang, CHEN Hai-mei, LIU Chang, HUANG Lin-fang. Complete chloroplast genome of Allium chinense: comparative genomic and phylogenetic analysis[J]. Acta Pharmaceutica Sinica, 2019, 54(1): 173-181.

杨俏俏, 姜梅, 王立强, 陈海梅, 刘昶, 黄林芳
中国医学科学院、北京协和医学院药用植物研究所, 国家中医药管理局中药资源保护重点研究室, 北京 100193
藠头(Allium chinense)为百合科葱属常用药食两用植物。为探究部分葱属植物系统发育关系不明确及该属物种鉴别通用DNA条形码匮乏的问题,本研究应用高通量测序技术对藠头叶绿体全基因组进行测序、组装、注释及系统进化研究。结果显示藠头叶绿体基因组为152 525 bp,呈典型的四分状结构,共编码116个基因,其中蛋白质编码基因81个,转运RNA(transfer RNA)基因31个和核糖体RNA(ribosome RNA)基因4个。对6个葱属植物叶绿体基因组比较分析发现了7个变异较大的区间,包括基因编码区ndhAycf1,以及非编码区rps16-trnQtrnT-trnFndhF-rpl32rpl32-trnLrpl16-rps3。利用葱属和非葱属53个物种的58个共有蛋白序列构建了进化树,发现除百合属、重楼属外其余各属物种所在分枝的支持率都达到66%~100%,有效地解决该类植物的系统进化与分类问题。此外,利用EcoPrimer软件成功发现了7个可用于葱属物种鉴定的候选DNA条形码序列并设计了引物。本研究首次获得了藠头叶绿体基因组序列,明确葱属物种间的亲缘关系,发现了一系列葱属物种特异的DNA条形码序列,为深入研究葱属植物的系统进化、分类及物种鉴定提供科学依据。
关键词:    藠头      叶绿体基因组      分子标记      系统发育      DNA条形码     
Complete chloroplast genome of Allium chinense: comparative genomic and phylogenetic analysis
YANG Qiao-qiao, JIANG Mei, WANG Li-qiang, CHEN Hai-mei, LIU Chang, HUANG Lin-fang
Key Research Laboratory of Traditional Chinese Medicine Resources Protection, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plants, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
Allium chinense belongs to the genus Alliums of the lily family. It can be used both as medicine and food. To date, the phylogenetic relationship of Allium species have not be resolved completely. Furthermore, there has been a lack of DNA barcode to distinguish closely related species. In this study, the complete chloroplast genome of A. chinense was obtained using next generation DNA sequencing and bioinformatic analysis, and compared with that from other Allium species. The genome is a circular molecule of 152 525 bp with a typical quadripartite structure. Genome annotation identified a total of 116 genes, including 81 protein-coding genes, 31 tRNA genes, and 4 rRNA genes. Analyses of sequences from six Allium species showed that the most diverse regions are found in the protein coding regions such as ndhA and ycf1 genes, and in the intergenic regions, such as ps16-trnQ, trnT-trnF, ndhF-rpl32, rpl32-trnL and rpl16-rps3. A phylogenetic tree was constructed using 58 protein coding sequences from 53 species. All branches showed strong support with bootstrap scores reaching 66%-100%, except those for the Lilium and Paris. Our results suggest that the completed chloroplast genome could solve the classification problems of these species. Using EcoPrimer software, we identified seven markers from the chloroplast genomes, which can be used to differentiate congeneric species. In summary, we have sequenced the complete chloroplast genome of A. chinense, carried out phylogenetic analysis and identified a series of genus specific DNA barcode sequences. The results have laid the foundation for the systematical determination of the phylogenetic relationship of Allium species and the differentiation of species using the genus specific primers.
Key words:    Allium chinense    complete chloroplast genome    molecular marker    phylogenetic analysis    DNA barcode   
收稿日期: 2018-09-29
DOI: 10.16438/j.0513-4870.2018-0887
基金项目: 国家自然科学基金资助项目(81274013,81473315);中国医学科学院医学与健康科技创新工程协同创新团队:"本草基因组"(2016-I2M-3-016).
通讯作者: 刘昶,Tel:86-10-62811448,E-mail:lfhuang@implad.ac.cn;黄林芳,E-mail:cliu6688@yahoo.com
Email: lfhuang@implad.ac.cn;cliu6688@yahoo.com
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