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

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...

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Autores principales: Yang, Lifang, Wang, Hanye, Wang, Panpan, Gao, Mingju, Huang, Luqi, Cui, Xiuming, Liu, Yuan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8802446/
https://www.ncbi.nlm.nih.gov/pubmed/35100996
http://dx.doi.org/10.1186/s12864-021-08283-w
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author Yang, Lifang
Wang, Hanye
Wang, Panpan
Gao, Mingju
Huang, Luqi
Cui, Xiuming
Liu, Yuan
author_facet Yang, Lifang
Wang, Hanye
Wang, Panpan
Gao, Mingju
Huang, Luqi
Cui, Xiuming
Liu, Yuan
author_sort Yang, Lifang
collection PubMed
description 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 H(2)O(2) 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-021-08283-w.
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spelling pubmed-88024462022-02-02 De novo and comparative transcriptomic analysis explain morphological differences in Panax notoginseng taproots Yang, Lifang Wang, Hanye Wang, Panpan Gao, Mingju Huang, Luqi Cui, Xiuming Liu, Yuan BMC Genomics Research 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 H(2)O(2) 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-021-08283-w. BioMed Central 2022-01-31 /pmc/articles/PMC8802446/ /pubmed/35100996 http://dx.doi.org/10.1186/s12864-021-08283-w Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research
Yang, Lifang
Wang, Hanye
Wang, Panpan
Gao, Mingju
Huang, Luqi
Cui, Xiuming
Liu, Yuan
De novo and comparative transcriptomic analysis explain morphological differences in Panax notoginseng taproots
title De novo and comparative transcriptomic analysis explain morphological differences in Panax notoginseng taproots
title_full De novo and comparative transcriptomic analysis explain morphological differences in Panax notoginseng taproots
title_fullStr De novo and comparative transcriptomic analysis explain morphological differences in Panax notoginseng taproots
title_full_unstemmed De novo and comparative transcriptomic analysis explain morphological differences in Panax notoginseng taproots
title_short De novo and comparative transcriptomic analysis explain morphological differences in Panax notoginseng taproots
title_sort de novo and comparative transcriptomic analysis explain morphological differences in panax notoginseng taproots
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8802446/
https://www.ncbi.nlm.nih.gov/pubmed/35100996
http://dx.doi.org/10.1186/s12864-021-08283-w
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