阴地蕨属药用植物光合作用关键酶RuBisCO的核质协同进化研究  

The Cytonuclear Coordination Study of the Key Photosynthesis Enzyme RuBisCO in Botrychium Species

作　　者：曾宇灵 朱明玉 李伟 刘义飞 张景景 雷笛[1,2,3] 森林 ZENG Yuling;ZHU Mingyu;LI Wei;LIU Yifei;ZHANG Jingjing;LEI Di;SEN Lin(College of Pharmacy,Hubei University of Chinese Medicine,Wuhan 430065,China;Key Laboratory of Ministry of Education,Hubei University of Chinese Medicine,Wuhan 430065,China;Hubei Shizhen Laboratory,Wuhan 430065)

机构地区：[1]湖北中医药大学药学院,武汉430065 [2]湖北中医药大学教育部重点实验室,武汉430065 [3]湖北时珍实验室,武汉430065

出　　处：《世界科学技术-中医药现代化》2025年第1期84-97,共14页Modernization of Traditional Chinese Medicine and Materia Medica-World Science and Technology

基　　金：国家自然科学基金委员会青年基金项目(31500260):中国阴地蕨属药用草本植物系统学及分子进化研究,负责人:森林;刘合钢全国名老中医药专家传承工作室建设项目,负责人:刘合刚。

摘　　要：目的为深入探究药用阴地蕨属植物的系统发育关系、分子鉴定方法和光合作用关键酶RuBisCO的进化规律,采集阴地蕨(Botrychium ternatum(Thunb.)Sw.)和蕨萁(Botrychium virginianum(L.)Sw.)开展序列测定和数据挖掘。方法本研究结合二代短读长和三代长读长数据完整测定并混合组装了阴地蕨和蕨萁的叶绿体基因组。利用组装结果、GenBank库和SRA库中的公开数据,提取叶绿体基因组编码区和核基因rbcS编码区分别重建了18种蕨类植物的系统发育关系。随后开展光合作用关键酶RuBisCO大小亚基编码序列rbcL和rbcS的适应性进化及共进化分析。结果两种叶绿体基因组全长分别为139063 bp(NC_060644)和139372 bp(OR609363),物种之间有很高的共线性关系,物种内的反向重复区的共线性显著;分别蕴含着92个和78个cpSSR位点,具备作为分子标记的潜力。叶绿体基因组组装结果中的rbcL基因与转录组测序结果重建所得rbcS基因共进化分析表明:(1)蕨类植物中rbcL与rbcS基因存在显著的共进化网络;(2)RBCL、RBCS亚基中存在受到正选择的位点;(3)其中来自RBCL的位点11与RBCS的位点106既存在正选择又显示共进化,揭示蕨类植物的RuBisCO酶存在来自叶绿体基因组和核基因组的协同进化。结论本研究为药用阴地蕨属植物及近缘物种系统发育关系和分子鉴定提供了理论依据和数据支持,还为探索阴地蕨属植物RuBisCO酶的适应性进化与共进化提供了新视角,诠释了蕨类植物在长期适应地球环境变化中的细胞器与细胞核相互协同的进化规律。Objective To establish the phylogenic relationships among genus Botrychium,and to develop better molecular markers,along with to gain better understanding of cytonuclear coordination patterns of RuBisCO enzyme,the current article sampled two species(e.g.Botrychium ternatum(Thunb.)Sw.and Botrychium virginianum(L.)Sw.),and applied sequencing approaches for the data mining.Methods The assembly results of chloroplast(cp)genomes from B.ternatum and B.virginianum were determined via de novo hybrid assemble approach with the help of short reads(Illumina)and long reads(PacBio and Nanopore).Then the phylogenic relationships of 18 fern species were reconstructed based on the protein coding sequences from the cp genome and the rbcS gene,which were fished out of the RNA-seq data from SRA database,respectively.Then the adaptive selection and co-evolutionary analysis were employed to investigate the evolutionary trajectories of rbcL(cp genome)and rbcS(nuclear genome)genes.Results The full length of cp genome in the two genus Botrychium species were determined as 139063 bp(NC_060644)and 139372 bp(OR609363).Then 92 SSR sites and 78 SSR sites were identified in the current two cp genomes,respectively.The collinearity analysis showed high relevant relationship between the current two species,and significant relationship within both species among the inverted repeats regions.The adaptation and coevolution investigations illustrated the following results:(1)Coevolution network exists between RBCL and RBCS subunits from the fern RuBisCO enzyme.(2)Positively selected sites were significantly detected among both rbcL and rbcS genes.(3)Two coevolutionary pair sites from the two genes(e.g.site 11 in RBCL and site 106 in RBCS)were significantly positively selected,which may demonstrate a molecular pattern for the fern species fine-tuning the RuBisCO enzyme during the long earth history via the cytonuclear coordination.Conclusion Our current research shed a new light on the phylogenetic relationship of the genus Botrychium among the fern b

关 键 词：RuBisCO酶 阴地蕨属 叶绿体基因组 rbcS基因 共进化分析 

分 类 号：R282.71[医药卫生—中药学]