Alkaloid production and response to natural adverse conditions in <i>Peganum harmala</i>: <i>in silico</i> transcriptome analyses

Seyed Jazayeri; Mahtab Pooralinaghi; Yenny Torres-Navarrete; Byron Oviedo-Bayas; Ítalo Guerra; Dario Jácome; César Morán; Carlos Macias; Karime Escobar; Seyed Mohammad Hossein Ale Seyed Ghafoor; Gholamhasan Veiskarami; Pouria Jandaghi; Ronald Villamar Torres

doi:10.5114/bta.2022.120706

eISSN: 2353-9461
ISSN: 0860-7796

BioTechnologia

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RESEARCH PAPERS

**Alkaloid production and response to natural adverse conditions in Peganum harmala: in silico transcriptome analyses**

Seyed Mehdi Jazayeri

¹

,

Mahtab Pooralinaghi

²

,

Yenny Torres-Navarrete

³

,

Byron Oviedo-Bayas

⁴

,

Ítalo Espinoza Guerra

³

,

Dario Herrera Jácome

³

,

César Quinaluisa Morán

⁵

,

Carlos Salas Macias

⁶

,

Karime Montes Escobar

⁷

,

Seyed Mohammad Hossein Ale Seyed Ghafoor

⁸

,

Gholamhasan Veiskarami

⁹

,

Pouria Jandaghi

^{10, 11}

,

Ronald Oswaldo Villamar Torres

^{3, 5}

Departamento de Biología, Facultad de Ciencia, Universidad Nacional de Colombia
University of Payam Noor, Karaj, Alborz, Iran
Facultad de Ciencias Pecuarias y Biológicas, Universidad Técnica Estatal de Quevedo, Quevedo, Los Ríos, Ecuador
Facultad de Ciencias de la Ingeniería, Universidad Técnica Estatal de Quevedo, Los Rios, Ecuador
Carrera Tecnología Superior en Producción Agrícola, Instituto Superior Tecnológico “Ciudad de Valencia”, Ecuador
Departamento de Agronomía, Facultad de Ingeniería Agronómica, Universidad Técnica de Manabí, Ecuador
Departamento de Matemáticas y Estadística, Instituto de Ciencias Básicas, Universidad Técnica de Manabí, Ecuador
Department of Informatics, Faculty of Engineering, University of Arak, Arak, Iran
Center of Excellence in Phylogeny, Department and Plant Sciences, School of Biology, College of Science, University of Tehran, Tehran, Iran
Department of Human Genetics, McGill University, Montreal, Canada
McGill University and Genome Quebec Innovation Centre, Montreal, Canada

BioTechnologia vol. 103(4) ∙ pp. 355–384 ∙ 2022

DOI: https://doi.org/10.5114/bta.2022.120706

Online publish date: 2022/12/24

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AMA

Jazayeri SM, Pooralinaghi M, Torres-Navarrete Y, et al. Alkaloid production and response to natural adverse conditions in Peganum harmala: in silico transcriptome analyses. BioTechnologia. 2022;103(4):355-384. doi:10.5114/bta.2022.120706.

APA

Jazayeri, S. M., Pooralinaghi, M., Torres-Navarrete, Y., Oviedo-Bayas, B., Guerra, Í. E.,  & Jácome, D. H. et al. (2022). Alkaloid production and response to natural adverse conditions in Peganum harmala: in silico transcriptome analyses. BioTechnologia, 103(4), 355-384. https://doi.org/10.5114/bta.2022.120706

Chicago

Jazayeri, Seyed M, Mahtab Pooralinaghi, Yenny Torres-Navarrete, Byron Oviedo-Bayas, Ítalo E Guerra, Dario H Jácome,  and César Q Morán et al. 2022. "Alkaloid production and response to natural adverse conditions in Peganum harmala: in silico transcriptome analyses". BioTechnologia 103 (4): 355-384. doi:10.5114/bta.2022.120706.

Harvard

Jazayeri, S., Pooralinaghi, M., Torres-Navarrete, Y., Oviedo-Bayas, B., Guerra, Í., Jácome, D., Morán, C., Macias, C., Escobar, K., Ale Seyed Ghafoor, S., Veiskarami, G., Jandaghi, P.,  and Villamar Torres, R. (2022). Alkaloid production and response to natural adverse conditions in Peganum harmala: in silico transcriptome analyses. BioTechnologia, 103(4), pp.355-384. https://doi.org/10.5114/bta.2022.120706

MLA

Jazayeri, Seyed et al. "Alkaloid production and response to natural adverse conditions in Peganum harmala: in silico transcriptome analyses." BioTechnologia, vol. 103, no. 4, 2022, pp. 355-384. doi:10.5114/bta.2022.120706.

Vancouver

Jazayeri S, Pooralinaghi M, Torres-Navarrete Y, Oviedo-Bayas B, Guerra Í, Jácome D et al. Alkaloid production and response to natural adverse conditions in Peganum harmala: in silico transcriptome analyses. BioTechnologia. 2022;103(4):355-384. doi:10.5114/bta.2022.120706.

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Peganum harmala is a valuable wild plant that grows and survives under adverse conditions and produces pharmaceutical alkaloid metabolites. Using different assemblers to develop a transcriptome improves the quality of assembled transcriptome. In this study, a concrete and accurate method for detecting stress-responsive transcripts by comparing stress-related gene ontology (GO) terms and public domains was designed. An integrated transcriptome for P. harmala including 42656 coding sequences was created by merging de novo assembled transcriptomes. Around 35000 transcripts were annotated with more than 90% resemblance to three closely related species of Citrus, which confirmed the robustness of the assembled transcriptome; 4853 stress-responsive transcripts were identified. CYP82 involved in alkaloid biosynthesis showed a higher number of transcripts in P. harmala than in other plants, indicating its diverse alkaloid biosynthesis attributes. Transcription factors (TFs) and regulatory elements with 3887 transcripts comprised 9% of the transcriptome. Among the TFs of the integrated transcriptome, cystein2/histidine2 (C2H2) and WD40 repeat families were the most abundant. The Kyoto Encyclopedia of Genes and Genomes (KEGG) MAPK (mitogen-activated protein kinase) signaling map and the plant hormone signal transduction map showed the highest assigned genes to these pathways, suggesting their potential stress resistance. The P. harmala whole-transcriptome survey provides important resources and paves the way for functional and comparative genomic studies on this plant to discover stress-tolerance-related markers and response mechanisms in stress physiology, phytochemistry, ecology, biodiversity, and evolution. P. harmala can be a potential model for studying adverse environmental cues and metabolite biosynthesis and a major source for the production of various alkaloids.

keywords:

Alkaloid production and response to natural adverse conditions in Peganum harmala: in silico transcriptome analyses

SSR, model plant, transcription factor, RNA-Seq, halophyte

**Alkaloid production and response to natural adverse conditions in Peganum harmala: in silico transcriptome analyses**