De novo and comparative transcriptomic analysis explain morphological differences in Panax notoginseng taproots

BMC Genomics

Yuan Liu¹  Panpan Wang¹  Lifang Yang¹  Xiuming Cui¹  Hanye Wang¹  Luqi Huang²  Mingju Gao³ 

[1] Faculty of Life Science and Technology, Kunming University of Science and Technology;National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences;Wenshan University;

关键词: Panax notoginseng;    Taproot;    Phenotypic differences;    De novo assembly transcriptome;    Differentially expressed genes;   

DOI  :  10.1186/s12864-021-08283-w

来源: DOAJ

【 摘 要 】

Abstract Background Panax notoginseng (Burk.) F. H. Chen (PN) belonging to the genus Panax of family Araliaceae is widely used in traditional Chinese medicine to treat various diseases. PN taproot, as the most vital organ for the accumulation of bioactive components, presents a variable morphology (oval or long), even within the same environment. However, no related studies have yet explained the molecular mechanism of phenotypic differences. To investigate the cause of differences in the taproot phenotype, de novo and comparative transcriptomic analysis on PN taproot was performed. Results A total of 133,730,886 and 114,761,595 paired-end clean reads were obtained based on high-throughput sequencing from oval and long taproot samples, respectively. 121,955 unigenes with contig N50 = 1,774 bp were generated by using the de novo assembly transcriptome, 63,133 annotations were obtained with the BLAST. And then, 42 genes belong to class III peroxidase (PRX) gene family, 8 genes belong to L-Ascorbate peroxidase (APX) gene family, and 55 genes belong to a series of mitogen-activated protein kinase (MAPK) gene family were identified based on integrated annotation results. Differentially expressed genes analysis indicated substantial up-regulation of PnAPX3 and PnPRX45, which are related to reactive oxygen species metabolism, and the PnMPK3 gene, which is related to cell proliferation and plant root development, in long taproots compared with that in oval taproots. Furthermore, the determination results of real-time quantitative PCR, enzyme activity, and H2O2 content verified transcriptomic analysis results. Conclusion These results collectively demonstrate that reactive oxygen species (ROS) metabolism and the PnMPK3 gene may play vital roles in regulating the taproot phenotype of PN. This study provides further insights into the genetic mechanisms of phenotypic differences in other species of the genus Panax.

【 授权许可】

Unknown