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本研究系统解析了伞形目（apiales）植物中阿魏酸（ferulic Acid, FA）生物合成的分子调控机制及其进化特征。全面整合了伞形目植物的基因组及转录组数据，结合生物信息学方法，对阿魏酸合成途径中的关键基因进行了全面分析。利用10种伞形目物种和2种外类群，构建了物种进化树，以阐明伞形目物种的系统进化关系。为明确阿魏酸合成途径中的关键酶基因，对8个关键酶基因进行了家族基因的鉴定及筛选。以拟南芥的参考序列为查询序列，共筛选出544个相关基因。进一步，选取合成通路中的2个关键酶：咖啡酸-O-甲基转移酶（caffeic Acid O-methyltransferase,COMT）和咖啡酰辅酶A-O-甲基转移酶（caffeoyl-CoA O-methyltransferase,CCoAOMT）进行深入分析。研究分别对鉴定出的66个COMT基因和91个CCoAOMT基因进行系统发育分析、理化性质分析、染色体定位分析、保守基序分析和基因表达模式分析等。本研究为深入理解伞形目植物阿魏酸合成途径的进化机制及其在植物适应性中的作用提供了分子层面的参考依据，为后续研究及功能验证与应用奠定了基础。
Abstract：This study comprehensively integrates genomic and transcriptomic data of Apiales plants and employs bioinformatics methods to conduct a thorough analysis of key genes in the Ferulic Acid synthesis pathway. Firstly, by using 10 Apiales species and 2 reference species, a phylogenetic tree was constructed to clarify the phylogenetic relationships among Apiales species. Then, the key enzyme genes in the Ferulic Acid synthesis pathway were identified, and the gene families of 8 key enzyme genes were determined and screened. With Arabidopsis thaliana reference sequences as query sequences, 544 relevant genes were screened out. Subsequently, two key enzymes in the synthesis pathway, caffeic acid O-methyltransferase(COMT) and caffeoyl-CoA O-methyltransferase(CCoAOMT), were analyzed in depth. The study performed phylogenetic analysis, physicochemical property analysis, chromosome localization analysis,conserved motif analysis, and gene expression pattern analysis on the 66 identified COMT genes and 91CCoAOMT genes. This study provides a molecular-level reference for understanding the evolutionary mechanism of the Ferulic Acid synthesis pathway in Apiales plants and its role in plant adaptability, and lays the foundation for subsequent research and functional validation and application studies.
[1]GROUP T A P,CHASE M W,CHRISTENHUSZ M J M,et al.An update of the angiosperm phylogeny group classification for the orders and families of flowering plants:APGⅣ[J].Botanical Journal of the Linnean Society,2016,181(1):1-20.
[2]SONG X,NIE F,CHEN W,et al.Coriander genomics database:a genomic,transcriptomic,and metabolic database for coriander[J].Horticulture Research,2020,7:55.
[3]SONG X,WANG J,LI N,et al.Deciphering the high-quality genome sequence of coriander that causes controversial feelings[J].Plant Biotechnology Journal,2020,18(6):1444-1456.
[4]SONG X,SUN P,YUAN J,et al.The celery genome sequence reveals sequential paleo-polyploidizations,karyotype evolution and resistance gene reduction in apiales[J].Plant Biotechnology Journal,2021,19(4):731-744.
[5]QUE F,HOU X L,WANG G L,et al.Advances in research on the carrot,an important root vegetable in the apiaceae family[J].Horticulture Research,2019,6(1):69.
[6]姚璇,胡婉莹,梁宗锁,等.人参属植物转录因子调控的研究进展[J].中药材,2023,46(6):1579-1584.
[7]BRISKIN D P.Medicinal plants and phytomedicines.Linking plant biochemistry and physiology to human health[J].Plant Physiology,2000,124(2):507-514.
[8]黄华永.阿魏酸及其类似物的合成与抗氧化活性研究[D].汕头:汕头大学,2006.
[9]BABBAR R,DHIMAN S,GROVER R,et al.A comprehensive review on therapeutic applications of ferulic acid and its novel analogues:a brief literature[J].Mini-Reviews in Medicinal Chemistry,2021,21(12):1578-1593.
[10]LI M,CUI X,JIN L,et al.Bolting reduces ferulic acid and flavonoid biosynthesis and induces root lignification in angelica sinensis[J].Plant Physiology and Biochemistry,2022,170:171-179.
[11]RAES J,ROHDE A,CHRISTENSEN J H,et al.Genome-wide characterization of the lignification toolbox in arabidopsis[J].Plant Physiology,2003,133(3):1051-1071.
[12]许雯雯,高换超,韩菲菲,等.葡萄COMT基因家族的鉴定与表达分析[J].果树学报,2023,40(10):2061-2075.
[13]ZHU X,WU J,LI S,et al.Artificial biosynthetic pathway for efficient synthesis of vanillin,a feruloyl-coa-derived natural product from eugenol[J].Journal of Agricultural and Food Chemistry,2024,72(12):6463-6470.
[14]HUANG X C,TANG H,WEI X,et al.The gradual establishment of complex coumarin biosynthetic pathway in apiaceae[J].Nature Communications,2024,15(1):6864.
[15]HAN X,LI C,SUN S,et al.The chromosome-level genome of female ginseng (angelica sinensis) provides insights into molecular mechanisms and evolution of coumarin biosynthesis[J].Plant Journal,2022,112(5):1224-1237.
[16]WANG Y,ZHANG H,RI H C,et al.Deletion and tandem duplications of biosynthetic genes drive the diversity of triterpenoids in aralia elata[J].Nature Communications,2022,13(1):2224.
[17]SHI X,CAO S,WANG X,et al.The complete reference genome for grapevine (Vitis vinifera L.) genetics and breeding[J].Horticulture Research,2023,10(5):246-258.
[18]MICHAEL T P,JUPE F,BEMM F,et al.High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell[J].Nature Communications,2018,9(1):541.
[19]WANG Z H,WANG X F,LU T,et al.Reshuffling of the ancestral core-eudicot genome shaped chromatin topology and epigenetic modification in panax[J].Nature Communications,2022,13(1):1902.
[20]FAN G,LIU X,SUN S,et al.The chromosome level genome and genome-wide association study for the agronomic traits of panax notoginseng[J].iScience,2020,23(9):101538.
[21]EMMS D M,KELLY S.Orthofinder:phylogenetic orthology inference for comparative genomics[J].Genome Biology,2019,20(1):238.
[22]KATOH K,STANDLEY D M.Mafft multiple sequence alignment software version 7:improvements in performance and usability[J].Molecular Biology and Evolution,2013,30(4):772-780.
[23]CAPELLA-GUTI RREZ S,SILLA-MART NEZ J M,GABALD N T.Trimal:a tool for automated alignment trimming in large-scale phylogenetic analyses[J].Bioinformatics,2009,25(15):1972-1973.
[24]STAMATAKIS A.Raxml version 8:a tool for phylogenetic analysis and post-analysis of large phylogenies[J].Bioinformatics,2014,30(9):1312-1313.
[25]YANG Z.Paml 4:phylogenetic analysis by maximum likelihood[J].Molecular Biology And Evolution,2007,24(8):1586-1591.
[26]KUMAR S,STECHER G,SULESKI M,et al.Timetree:a resource for timelines,timetrees,and divergence times[J].Molecular Biology and Evolution,2017,34(7):1812-1819.
[27]Chen C,Chen H,Zhang Y,et al.Tbtools:an integrative toolkit developed for interactive analyses of big biological data[J].Molecular Plant,2020,13(8):1194-1202.
[28]CHEN S,ZHOU Y,CHEN Y,et al.Fastp:an ultra-fast all-in-one fastq preprocessor[J].Bioinformatics,2018,34(17):884-890.
[29]BOLGER A M,LOHSE M,USADEL B.Trimmomatic:a flexible trimmer for illumina sequence data[J].Bioinformatics,2014,30(15):2114-2120.
[30]KIM D,PAGGI J M,PARK C,et al.Graph-based genome alignment and genotyping with hisat2 and hisat-genotype[J].Nature Biotechnology,2019,37(8):907-915.
[31]LIAO Y,SMYTH G K,SHI W.Featurecounts:an efficient general purpose program for assigning sequence reads to genomic features[J].Bioinformatics,2014,30(7):923-930.
[32]张璐,赵月强,付家锋,等.玉米咖啡酸O-甲基转移酶的全基因组鉴定与功能分析[J].福建农业学报,2023,38(11):1259-1266.
[33]WANG Y,WANG T,QI S,et al.Genome-wide identification,expression profiling,and protein interaction analysis of the ccoaomt gene family in the tea plant (camellia sinensis)[J].BMC Genomics,2024,25(1):238.
[34]ROCKMAN M V,SKROVANEK S S,KRUGLYAK L.Selection at linked sites shapes heritable phenotypic variation in c.Elegans[J].Science,2010,330(6002):372-376.
[35]BHATTACHARJEE P,CAMASSES A,GALI H,et al.The budding yeast heterochromatic protein sir3 modulates genome-wide gene expression through transient direct contacts with euchromatin[J].bioRxiv,2023:603-613.
基本信息:
DOI：
中图分类号:Q943.2
引用信息:
[1]付艳红,张晨浩,宋小明.伞形目植物阿魏酸合成途径相关基因的鉴定及进化分析[J].华北理工大学学报(自然科学版),2025,47(03):34-42.
基金信息:
国家自然科学基金面上项目（32172583)：大白菜耐热lncRNA功能验证、ceRNA调控网络解析及组学数据库平台搭建; 河北省杰出青年基金（C2022209010）：冰菜基因组解析及蔬菜组学数据共享及分析平台搭建