Comparative transcriptome analysis reveals a gene expression profile that contributes to rhizome swelling in <i>Panax japonicus</i> var. <i>major</i>

Tang, Jun; Lu, Ying; Gao, Zheng; Song, Wan Ling; Wei, Kun Hua; Zhao, Yan; Tang, Q.; Li, Xue Jiao; Chen, Jun Wen; Zhang, Guanghui; Long, Guang Qiang; Fan, Wei; Yang, Sheng Chao

doi:10.1080/11263504.2019.1651774

Cited by 7 publications

(3 citation statements)

References 46 publications

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“…Potato has become a model system for understanding the molecular basis of USO development, and numerous studies have demonstrated the complex roles of plant hormones such as auxin, abscisic acid, cytokinin, and gibberellin on the tuber induction process (reviewed in Hannapel et al, 2017). These hormones have been additionally identified in USO formation in other tuberous root crops including sweet potato (Dong et al, 2019; Noh et al, 2010) and cassava (Melis & van Staden, 1985; Sojikul et al, 2015), in rhizome formation in Panax japonicus (Tang et al, 2019) and Nelumbo nucifera (Cheng, Li, Yin, et al, 2013; Yang et al, 2015), and in corm formation in Sagittaria trifolia (Cheng, Li, Xu, et al, 2013), suggesting that shared processes trigger tuberization in both root‐ and stem‐originating USOs.…”

Section: Introductionmentioning

confidence: 99%

Comparative transcriptomics of a monocotyledonous geophyte reveals shared molecular mechanisms of underground storage organ formation

Tribble

Martínez‐Gómez

Alzate‐Guarín

et al. 2021

Evolution and Development

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Many species from across the vascular plant tree‐of‐life have modified standard plant tissues into tubers, bulbs, corms, and other underground storage organs (USOs), unique innovations which allow these plants to retreat underground. Our ability to understand the developmental and evolutionary forces that shape these morphologies is limited by a lack of studies on certain USOs and plant clades. We take a comparative transcriptomics approach to characterizing the molecular mechanisms of tuberous root formation in Bomarea multiflora (Alstroemeriaceae) and compare these mechanisms to those identified in other USOs across diverse plant lineages; B. multiflora fills a key gap in our understanding of USO molecular development as the first monocot with tuberous roots to be the focus of this kind of research. We sequenced transcriptomes from the growing tip of four tissue types (aerial shoot, rhizome, fibrous root, and root tuber) of three individuals of B. multiflora. We identified differentially expressed isoforms between tuberous and non‐tuberous roots and tested the expression of a priori candidate genes implicated in underground storage in other taxa. We identify 271 genes that are differentially expressed in root tubers versus non‐tuberous roots, including genes implicated in cell wall modification, defense response, and starch biosynthesis. We also identify a phosphatidylethanolamine‐binding protein, which has been implicated in tuberization signalling in other taxa and, through gene‐tree analysis, place this copy in a phylogenetic context. These findings suggest that some similar molecular processes underlie the formation of USOs across flowering plants despite the long evolutionary distances among taxa and non‐homologous morphologies (e.g., bulbs vs. tubers). (Plant development, tuberous roots, comparative transcriptomics, geophytes).

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Section: Introductionmentioning

confidence: 99%

Comparative transcriptomics of a monocotyledonous geophyte reveals shared molecular mechanisms of underground storage organ formation

Tribble

Martínez‐Gómez

Alzate‐Guarín

et al. 2021

Evolution and Development

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“…Specific primers for each gene were designed for RT-qPCR amplification using Primer-BLAST ( https://www.ncbi.nlm.nih.gov/tools/primer-blast/ ). Actin was used as an internal reference gene to normalize the mRNA expression levels of target genes in each sample [ 59 ]. The specific primers for the target genes and actin are listed in Supplementary Table 1 .…”

Section: Methodsmentioning

confidence: 99%

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

Yang

Wang

et al. 2022

BMC Genomics

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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.

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“…Speci c primers for each gene were designed for RT-qPCR ampli cation using Primer-BLAST (https://www.ncbi.nlm.nih.gov/tools/primer-blast/). Actin was used as an internal reference gene to normalize the mRNA expression levels of target genes in each sample [54]. The speci c primers for the target genes and actin are listed in Supplementary Table 2.…”

Section: Rt-qpcr Validation Of Unigenesmentioning

confidence: 99%

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

Yang

Wang

et al. 2021

Preprint

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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. The annotation results showed 38,313 BLASTX hits and 24,820 BLASTP hits. KEGG analysis identified 52 genes encoding class III peroxidase (PRX) family members, 13 genes encoding L-Ascorbate peroxidase (APX) family members, and 99 genes encoding a series of mitogen-activated protein kinase (MAPK) family members. Differentially expressed genes analysis indicated substantial upregulation of genes encoding APX3 and PRX45 enzymes, which are related to reactive oxygen species metabolism, and the MPK3 enzyme, 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 MPK3 enzyme 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.

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Comparative transcriptome analysis reveals a gene expression profile that contributes to rhizome swelling in Panax japonicus var. major

Cited by 7 publications

References 46 publications

Comparative transcriptomics of a monocotyledonous geophyte reveals shared molecular mechanisms of underground storage organ formation

Comparative transcriptomics of a monocotyledonous geophyte reveals shared molecular mechanisms of underground storage organ formation

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

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

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