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Transcriptome characterization of Larrea tridentata and identification of genes associated with phenylpropanoid metabolic pathways

Larrea tridentata (Sesse and Moc. ex DC.) Coville (family: Zygophyllaceae) is an aromatic evergreen shrub with resin-covered leaves, known to use in traditional medicine for diverse ailments. It also has immense pharmacological significance due to presence of powerful phenylpropanoids antioxidant, n...

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Autores principales: Ali, Mohammad Ajmal, Alhemaid, Fahad, Farah, Mohammad Abul, Elangbam, Meena, Gurung, Arun Bahadur, Al-Anazi, Khalid Mashay, Lee, Joongku
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8916640/
https://www.ncbi.nlm.nih.gov/pubmed/35275977
http://dx.doi.org/10.1371/journal.pone.0265231
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author Ali, Mohammad Ajmal
Alhemaid, Fahad
Farah, Mohammad Abul
Elangbam, Meena
Gurung, Arun Bahadur
Al-Anazi, Khalid Mashay
Lee, Joongku
author_facet Ali, Mohammad Ajmal
Alhemaid, Fahad
Farah, Mohammad Abul
Elangbam, Meena
Gurung, Arun Bahadur
Al-Anazi, Khalid Mashay
Lee, Joongku
author_sort Ali, Mohammad Ajmal
collection PubMed
description Larrea tridentata (Sesse and Moc. ex DC.) Coville (family: Zygophyllaceae) is an aromatic evergreen shrub with resin-covered leaves, known to use in traditional medicine for diverse ailments. It also has immense pharmacological significance due to presence of powerful phenylpropanoids antioxidant, nordihydroguaiaretic acid (NDGA). The RNA sequence/transcriptome analyses connect the genomic information into the discovery of gene function. Hence, the acquaint analysis of L. tridentata is in lieu to characterize the transcriptome, and to identify the candidate genes involved in the phenylpropanoid biosynthetic pathway. To gain molecular insight, the bioinformatics analysis of transcriptome was performed. The total bases covered 48,630 contigs of length greater than 200 bp and above came out to 21,590,549 with an average GC content of 45% and an abundance of mononucleotide, SSR, including C3H, FAR1, and MADS transcription gene families. The best enzyme commission (EC) classification obtained from the assembled sequences represented major abundant enzyme classes e.g., RING-type E3 ubiquitin transferase and non-specific serine/threonine protein kinase. The KEGG pathway analysis mapped into 377 KEGG different metabolic pathways. The enrichment of phenylpropanoid biosynthesis pathways (22 genes i.e., phenylalanine ammonia-lyase, trans-cinnamate 4-monooxygenase, 4-coumarate-CoA ligase, cinnamoyl-CoA reductase, beta-glucosidase, shikimate O-hydroxycinnamoyl transferase, 5-O-(4-coumaroyl)-D-quinate 3’-monooxygenase, cinnamyl-alcohol dehydrogenase, peroxidase, coniferyl-alcohol glucosyltransferase, caffeoyl shikimate esterase, caffeoyl-CoA O-methyltransferase, caffeate O-methyltransferase, coniferyl-aldehyde dehydrogenase, feruloyl-CoA 6-hydroxylase, and ferulate-5-hydroxylase), and expression profile indicated antioxidant, anti-arthritic, and anticancer properties of L. tridentata. The present results could provide an important resource for squeezing biotechnological applications of L. tridentata.
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spelling pubmed-89166402022-03-12 Transcriptome characterization of Larrea tridentata and identification of genes associated with phenylpropanoid metabolic pathways Ali, Mohammad Ajmal Alhemaid, Fahad Farah, Mohammad Abul Elangbam, Meena Gurung, Arun Bahadur Al-Anazi, Khalid Mashay Lee, Joongku PLoS One Research Article Larrea tridentata (Sesse and Moc. ex DC.) Coville (family: Zygophyllaceae) is an aromatic evergreen shrub with resin-covered leaves, known to use in traditional medicine for diverse ailments. It also has immense pharmacological significance due to presence of powerful phenylpropanoids antioxidant, nordihydroguaiaretic acid (NDGA). The RNA sequence/transcriptome analyses connect the genomic information into the discovery of gene function. Hence, the acquaint analysis of L. tridentata is in lieu to characterize the transcriptome, and to identify the candidate genes involved in the phenylpropanoid biosynthetic pathway. To gain molecular insight, the bioinformatics analysis of transcriptome was performed. The total bases covered 48,630 contigs of length greater than 200 bp and above came out to 21,590,549 with an average GC content of 45% and an abundance of mononucleotide, SSR, including C3H, FAR1, and MADS transcription gene families. The best enzyme commission (EC) classification obtained from the assembled sequences represented major abundant enzyme classes e.g., RING-type E3 ubiquitin transferase and non-specific serine/threonine protein kinase. The KEGG pathway analysis mapped into 377 KEGG different metabolic pathways. The enrichment of phenylpropanoid biosynthesis pathways (22 genes i.e., phenylalanine ammonia-lyase, trans-cinnamate 4-monooxygenase, 4-coumarate-CoA ligase, cinnamoyl-CoA reductase, beta-glucosidase, shikimate O-hydroxycinnamoyl transferase, 5-O-(4-coumaroyl)-D-quinate 3’-monooxygenase, cinnamyl-alcohol dehydrogenase, peroxidase, coniferyl-alcohol glucosyltransferase, caffeoyl shikimate esterase, caffeoyl-CoA O-methyltransferase, caffeate O-methyltransferase, coniferyl-aldehyde dehydrogenase, feruloyl-CoA 6-hydroxylase, and ferulate-5-hydroxylase), and expression profile indicated antioxidant, anti-arthritic, and anticancer properties of L. tridentata. The present results could provide an important resource for squeezing biotechnological applications of L. tridentata. Public Library of Science 2022-03-11 /pmc/articles/PMC8916640/ /pubmed/35275977 http://dx.doi.org/10.1371/journal.pone.0265231 Text en © 2022 Ali et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Ali, Mohammad Ajmal
Alhemaid, Fahad
Farah, Mohammad Abul
Elangbam, Meena
Gurung, Arun Bahadur
Al-Anazi, Khalid Mashay
Lee, Joongku
Transcriptome characterization of Larrea tridentata and identification of genes associated with phenylpropanoid metabolic pathways
title Transcriptome characterization of Larrea tridentata and identification of genes associated with phenylpropanoid metabolic pathways
title_full Transcriptome characterization of Larrea tridentata and identification of genes associated with phenylpropanoid metabolic pathways
title_fullStr Transcriptome characterization of Larrea tridentata and identification of genes associated with phenylpropanoid metabolic pathways
title_full_unstemmed Transcriptome characterization of Larrea tridentata and identification of genes associated with phenylpropanoid metabolic pathways
title_short Transcriptome characterization of Larrea tridentata and identification of genes associated with phenylpropanoid metabolic pathways
title_sort transcriptome characterization of larrea tridentata and identification of genes associated with phenylpropanoid metabolic pathways
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8916640/
https://www.ncbi.nlm.nih.gov/pubmed/35275977
http://dx.doi.org/10.1371/journal.pone.0265231
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