紫花地丁与其他堇菜属植物叶绿体基因组比较及系统发育分析  

Comparison and Phylogenetic Analysis of Chloroplast Genomes of Viola philippica and Other Viola L. Species

作　　者：秦楠 张娜郡 陈超 胡楠 李冠文 缪文玉[2] Qin Nan;Zhang Najun;Chen Chao;Hu Nan;Li Guanwen;Miao Wenyu(College of Pharmaceutical and Food Engineering,Shanxi University of Chinese Medicine,Yuci,030619;Taiyuan City Vocational and Technical College Management Engineering Department,Taiyuan,030027)

机构地区：[1]山西中医药大学中药与食品工程学院,榆次030619 [2]太原城市职业技术学院管理工程系,太原030027

出　　处：《分子植物育种》2022年第24期8099-8111,共13页Molecular Plant Breeding

基　　金：山西省教育厅创新项目(2019L0729);山西省自然科学基金面上项目(201801D121256);企业横向项目-复合沙棘口服液特医食品研究开发基金项目(20200727)共同资助。

摘　　要：紫花地丁(Viola philippica)为堇菜科(Violaceae)堇菜属(Viola L.)植物,也是一种传统中药材。本研究对紫花地丁叶绿体基因组进行测序,并完成其特征解析。通过结合近缘植物叶绿体基因组数据,分析紫花地丁叶绿体基因组的密码子偏好性、重复序列及系统发育。紫花地丁叶绿体基因组全长157 417 bp,总GC含量为36.25%,包括1个大单拷贝区(large single-copy, LSC),1个小单拷贝区(small single-copy, SSC)和2个反向重复序列(inverted repeats, IR),共注释得到111个功能基因,其中77个蛋白质编码基因,30个tRNA基因,4个rRNA基因;共检测到23个SSRs,以单核苷酸重复为主,多由A或T碱基重复组成;系统发育分析显示,紫花地丁与Viola seoulensis亲缘关系最近;所选紫花地丁在内的6个堇菜属植物叶绿体基因组在非编码区变异程度较高,核苷酸多态性分析(Pi)获得8个高变区热点,均处于LSC及SSC区域;叶绿体基因组边界分析显示6种堇菜属植物叶绿体基因组IR区基因排列顺序较为保守,扩张和收缩程度相差不大。本研究为后续紫花地丁及堇菜属植物遗传多样性、物种鉴定及相关中药资源开发提供了理论依据。Viola philippica is a plant of the genus Viola L. in the Violaceae family, also a kind of traditional Chinese herbal medicine. In this study, we sequenced the choroplast genome sequence of Viola philippica and analyzed the characterization of chloroplast genome structure analyzed. By combining the chloroplast genome data of closely related species, the codon usage, repeat sequence and phylogenetic relationship of the chloroplast genome of Viola philippica were analyzed. The length of Viola philippica chloroplast genome was 157 417 bp,with an average GC content of 36.25%. The genotypes showed a typical tetrad chloroplast genome, including a pair of inverted repeats encoding the same but opposite direction sequences, a large single copy(LSC) region, and a small single copy(SSC) region. The Viola philippica chloroplast genome contains 111 unique genes of which 77and 30 are protein coding and transfer RNA(tRNA) genes respectively and also 4 ribosomal RNA genes(rRNA).Repeat analyses of Viola philippica chloroplast genome revealed a total of 23 repeats, and identified A/T mononucleotides as majority SSRs. The phylogenetic analysis showed a relationship in Viola philippica and Viola seoulensis was the closest. Comparison of the whole chloroplast genome among the 6 cultivars, including Viola philippica, showed that noncoding regions had sequence variations. Based on nucleotide polymorphism(Pi) analysis, 8 high mutation regions which are all located in region of LSC and SSC were determined. The IR boundary of the 6 genotypes of Viola L. showed a similar degree of expansion. Based on this study, the genetic diversity, species identification and development of traditional Chinese medicine resources of the genus Viola L. can be established.

关 键 词：紫花地丁(Viola philippica) 堇菜属 叶绿体基因组 系统发育 比较基因组 

分 类 号：S567.239[农业科学—中草药栽培]