基于全叶绿体基因组分析的栽培黄草乌基源研究

Complete chloroplast genome analysis based study on origins of cultivated Radix Aconitum Vilmoriniani

关键词:  栽培黄草乌, 叶绿体基因组, 序列特征, 系统发育分析, 物种鉴定

Key words:  cultivated Radix Aconitum Vilmoriniani, chloroplast genome, sequence characteristics, phylogenetic analysis, species identification

摘要:

为探究云南伤科用毒性药材黄草乌(Radix Aconitum Vilmoriniani)栽培品质量的影响因素,该研究利用Illumina HiSeq 4000高通量测序平台对来自10个不同栽培基地黄草乌样品的叶绿体基因组展开测序,经过对测序数据的组装、注释,利用生物信息学工具对其叶绿体基因组特征展开分析并构建系统发育树。结果表明:(1)10个栽培品的叶绿体基因组全长155 744～155 937 bp,大单拷贝区和小单拷贝区分别为86 363～86 548 bp、16 921～17 007 bp,反向重复区大小为26 170～26 236 bp,均注释到131个基因。(2)序列鉴定出60～73个SSR位点,基因组比较分析发现,10个栽培品叶绿体基因组显示出一定的扩张,并在其中发现了trnK-UUU-trnQ-UUG等变异热点区域。(3)基于2个数据集的系统发育分析均表明,JS-1-4、QJ-1-2、LX-1-3、LJ-3-2与黄草乌(Aconitum vilmorinianum)亲缘关系较近; LQ-1-3、GJ-1-3、NL-1-3、DC-2-2和滇南草乌(A. austroyunnanense)关系较近; 基于全叶绿体基因组序列构建的系统进化树中LJ-4-3与马耳山乌头(A. delavayi)亲缘关系近,LJ-1-2与宾川乌头(A. duclouxii)的亲缘关系较近; 而基于蛋白质编码基因序列构建的系统进化树中,LJ-4-3与西南乌头(A. episcopale)亲缘关系近,LJ-1-2则与苍山乌头(A. contortum)关系较近。综上认为,黄草乌的栽培种植存在种源混杂的客观问题,主要有黄草乌和滇南草乌两种植物,个别栽培基地还掺混了乌头属(Aconitum)的其他物种,这可能是黄草乌栽培品质量不稳定的因素之一。

Abstract:

To study the influencing factors on the quality of cultivated varieties of Radix Aconitum Vilmoriniani, a toxic medicinal material for traumatology in Yunnan Province, the chloroplast genomes of samples from 10 different cultivation bases were sequenced by Illumina HiSeq 4000 high-throughput sequencing platform. Then the sequencing data were assembled and annotated followed by analysis of the characteristics of the chloroplast genomes by bioinformatics tools and construction of the phylogenetic trees. The results were as follows:(1)The full length of chloroplast genome of the 10 cultivated varieties from different regions were 155 744-155 937 bp, the large single copy region(LSC)and small single copy region(SSC)were 86 363-86 548 bp and 16 921-17 007 bp, respectively, the size of the inverted repeat region(IR)was 26 170-26 236 bp. The GC content of chloroplast genome of 10 cultivated varieties was 38.1%, with obvious AT preference, and 131 genes were annotated, including 85 protein-coding genes, 37 tRNA genes and 8 rRNA genes.(2)These sequences identified 60-73 SSR sites, and genome comparative analysis found that the length of chloroplast genome of 10 cultivated varieties ranged from 155 744 to 155 937 bp with moderate expansion. Some variation hot spots were found, such as trnK-UUU-trnQ-UUG, trnY-GUA-trnE-UUC, trnC-GCA-trnT-GGU, ycf4-cemA, ycf1 and ndhF, etc.(3)Phylogenetic analysis based on the two datasets showed that JS-1-4, QJ-1-2, LX-1-3, LJ-3-2 were closely related to Aconitum vilmorinianum and LQ-1-3, GJ-1-3, NL-1-3, DC-2-2 were closely related to A. austroyunnanense. In the phylogenetic tree, which was constructed based on the complete chloroplast genomes, LJ-4-3 was closely related to A. delavayi and LJ-1-2 was closely related to A. duclouxii; while in the phylogenetic tree which was constructed based on the protein coding gene sequences(PCGs), LJ-4-3 was closely related to A. episcopale and LJ-1-2 was closely related to A. contortum. In summary, the hybrid origins of cultivation of Radix Aconitum Vilmoriniani include at least the two original plants: A. vilmorinianum and A. austroyunnanense, and other species of Aconitum even existed in individual cultivation bases. The mixed origins of cultivation may be one of the influencing factors on instability of the quality of Radix Aconitum Vilmoriniani.