Comparative transcriptome analyses of genes involved in sulforaphane metabolism at different treatment in Chinese kale using full-length transcriptome sequencing

Wu, Qiuyun; Wang, Junwei; Mao, Shuxiang; Xu, Hongyan; Wu, Qi; Liang, Mantian; Yuán, Yǒulù; Liu, Mingyue; Huang, Ke

doi:10.1186/s12864-019-5758-2

Cited by 25 publications

(15 citation statements)

References 44 publications

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“…The use of high-throughput transcriptome technologies enables to investigate the genetic responses that organisms deploy in alternative environments (Roy et al, 2010). So far, RNA-seq was employed to evaluate the changes induced by different treatments (Zheng et al, 2013;Alfonso-Parra et al, 2016;Wu et al, 2019).…”

Section: Discussionmentioning

confidence: 99%

Transcriptome Analysis of Ophraella communa Male Reproductive Tract in Indirect Response to Elevated CO2 and Heat Wave

et al. 2020

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Increase in atmospheric CO 2 directly affects the insect physiology and behavior, and indirectly affects the herbivorous insects by affecting their hosts. The increase in atmospheric CO 2 is accompanied by an increase in temperature and heat waves. Ophraella communa LeSage is a natural enemy of Ambrosia artemisiifolia (common ragweed). The development and reproduction of this beetle is weakened upon eating common ragweed grown under stress conditions. As female behavior and physiology alter after mating, the reproductive tract of males is likely to modulate reproduction and development in this species. Herein, the transcriptional profiles of testes and accessory glands from male O. communa individuals feeding on common ragweed under conditions of high CO 2 concentration and heat waves and that grown under ambient CO 2 concentration were compared. Differentially expressed genes (DEGs) were identified between the same tissues from beetles fed on common ragweed grown under different stress conditions. There were 3, 2, 3, 1and 5 genes related to decomposition and transport of macromolecular substances, host location, stress response, reproduction, and poisonous food-utilization. No expected response was observed in the male reproductive tract, but some of the identified DEGs might control the development of the population. The results presented here should be helpful in guiding future studies on deciphering the indirect response of other organs to high CO 2 concentration and heat waves, as well as the functions of seminal fluid proteins in O. communa.

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Section: Discussionmentioning

confidence: 99%

Transcriptome Analysis of Ophraella communa Male Reproductive Tract in Indirect Response to Elevated CO2 and Heat Wave

et al. 2020

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“…In general, terpenoids are regarded as phytoanticipins, which are involved in responding to biotic and abiotic stresses ( Dixon, 2001 ). Salicylic acid (SA) is an endogenous signal substance that exists universally in plants ( Wu et al, 2019 ). It exhibit that SA is perceived by the Non-expresser of PR (NPRs) receptors, and functions directly in the activation of defense responses ( Sawai and Saito, 2011 ).…”

Section: Introductionmentioning

confidence: 99%

“…RNA-seq has been performed to identify the putative genes involved in terpenoid biosynthesis in multiple plants ( Luo et al, 2011 ; Ma et al, 2016 ; Wang et al, 2017 ; Zhou et al, 2017 ; Choudhri et al, 2018 ; Shan et al, 2020 ). Nevertheless, the short read lengths from RNA-seq restrict the construction of completely assembled transcripts, making it difficult to obtain full-length sequences ( Wu et al, 2019 , 2020 ). As a third-generation sequencing technique, single-molecule real-time (SMRT) sequencing can generate full-length cDNA sequences without post-sequencing assembly, which basically overcomes the limitation of RNA-seq ( Wu et al, 2019 , 2020 ).…”

Section: Introductionmentioning

confidence: 99%

“…Nevertheless, the short read lengths from RNA-seq restrict the construction of completely assembled transcripts, making it difficult to obtain full-length sequences ( Wu et al, 2019 , 2020 ). As a third-generation sequencing technique, single-molecule real-time (SMRT) sequencing can generate full-length cDNA sequences without post-sequencing assembly, which basically overcomes the limitation of RNA-seq ( Wu et al, 2019 , 2020 ). Thus, SMRT sequencing could provide an accurate technique for gene annotation, novel gene discovery and long non-coding RNA (lncRNA) identification.…”

Section: Introductionmentioning

confidence: 99%

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Full-Length Transcriptome Analyses of Genes Involved in Triterpenoid Saponin Biosynthesis of Psammosilene tunicoides Hairy Root Cultures With Exogenous Salicylic Acid

Qiu

et al. 2021

Front. Genet.

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Triterpenoid saponins constitute a diverse class of bioactive compounds in medicinal plants. Salicylic acid (SA) is an efficient elicitor for secondary metabolite production, but a transcriptome-wide regulatory network of SA-promoted triterpenoid saponin biosynthesis remains little understood. In the current study, we described the establishment of the hairy root culture system for Psammosilene tunicoides, a triterpenoid saponin-producing medicinal herb in China, using genetic transformation by Agrobacterium rhizogenes. Compared to controls, we found that total saponin content was dramatically increased (up to 2.49-fold) by the addition of 5 mg/L SA in hairy roots for 1 day. A combination of single-molecule real-time (SMRT) and next-generation sequencing (Illumina RNA-seq) was generated to analyze the full-length transcriptome data for P. tunicoides, as well as the transcript profiles in treated (8 and 24 h) and non-treated (0 h) groups with 5 mg/L SA in hairy roots. A total of 430,117 circular consensus sequence (CCS) reads, 16,375 unigenes and 4,678 long non-coding RNAs (lncRNAs) were obtained. The average length of unigenes (2,776 bp) was much higher in full-length transcriptome than that derived from single RNA-seq (1,457 bp). The differentially expressed genes (DEGs) were mainly enriched in the metabolic process. SA up-regulated the unigenes encoding SA-binding proteins and antioxidant enzymes in comparison with controls. Additionally, we identified 89 full-length transcripts encoding enzymes putatively involved in saponin biosynthesis. The candidate transcription factors (WRKY, NAC) and structural genes (AACT, DXS, SE, CYP72A) might be the key regulators in SA-elicited saponin accumulation. Their expression was further validated by quantitative real-time PCR (qRT-PCR). These findings preliminarily elucidate the regulatory mechanisms of SA on triterpenoid saponin biosynthesis in the transcriptomic level, laying a foundation for SA-elicited saponin augmentation in P. tunicoides.

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“…Functional enrichment analysis showed that DEGs between the Control and WFS groups were associated with 34 KEGG pathways, including starch and sucrose metabolism, metabolic pathways, retinol metabolism, glycolysis-gluconeogenesis and lysosome ( Figure 5), which were reported to be linked to pathogen interaction (Wu et al, 2019).…”

Section: Transcriptome Difference Between Control and Wfsmentioning

confidence: 99%

Identification of Multigene Biomarker for Shrimp White Feces Syndrome by Full-Length Transcriptome Sequencing

et al. 2020

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The pacific white shrimp, Litopenaeus vannamei, with the largest shrimp industry production in the world, is currently threatened by a severe disease, white feces syndrome (WFS), which cause devastating losses globally, while its causal agents remain largely unknown. Herein, compared to the Control shrimp by metagenomic analysis, we firstly investigated that the altered functions of intestinal microbial community in WFS shrimp were the enrichment of bacterial chemotaxis and flagellar assembly pathways, hinting at a potential role of pathogenic bacteria for growth and development, which might be related to WFS occurrence. Single-molecule real-time (SMRT) sequencing was to further identify the gene structure and gene regulation for more clues in WFS aetiology. Totally 50,049 high quality transcripts were obtained, capturing 39,995 previously mapped and 10,054 newly detected transcripts, which were annotated to 30,554 genes. A total of 158 differentially expressed genes (DEGs) were characterized in WFS shrimp. These DEGs were strongly associated with various immune related genes that regulated the expression of multiple antimicrobial peptides (e.g., antilipopolysaccharide factors, penaeidins, and crustin), which were further experimentally validated using quantitative PCR on transcript level. Collectively, multigene biomarkers were identified to be closely associated with WFS, especially those functional alterations in microbial community and the upregulated immune related gene with antibacterial activities. Our finding not only inspired our cogitation on WFS aetiology from both microbial and host immune response perspectives with combined metagenomic and full-length transcriptome sequencing, but also provided valuable information for enhancing shrimp aquaculture.

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Comparative transcriptome analyses of genes involved in sulforaphane metabolism at different treatment in Chinese kale using full-length transcriptome sequencing

Cited by 25 publications

References 44 publications

Transcriptome Analysis of Ophraella communa Male Reproductive Tract in Indirect Response to Elevated CO2 and Heat Wave

Transcriptome Analysis of Ophraella communa Male Reproductive Tract in Indirect Response to Elevated CO2 and Heat Wave

Full-Length Transcriptome Analyses of Genes Involved in Triterpenoid Saponin Biosynthesis of Psammosilene tunicoides Hairy Root Cultures With Exogenous Salicylic Acid

Identification of Multigene Biomarker for Shrimp White Feces Syndrome by Full-Length Transcriptome Sequencing

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