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Genomic and transcriptomic analysis of sacred fig (Ficus religiosa)

BACKGROUND: Peepal/Bodhi tree (Ficus religiosa L.) is an important, long-lived keystone ecological species. Communities on the Indian subcontinent have extensively employed the plant in Ayurveda, traditional medicine, and spiritual practices. The Peepal tree is often thought to produce oxygen both d...

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Autores principales: Ashalatha, K. L., Arunkumar, Kallare P, Gowda, Malali
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10100241/
https://www.ncbi.nlm.nih.gov/pubmed/37046210
http://dx.doi.org/10.1186/s12864-023-09270-z
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author Ashalatha, K. L.
Arunkumar, Kallare P
Gowda, Malali
author_facet Ashalatha, K. L.
Arunkumar, Kallare P
Gowda, Malali
author_sort Ashalatha, K. L.
collection PubMed
description BACKGROUND: Peepal/Bodhi tree (Ficus religiosa L.) is an important, long-lived keystone ecological species. Communities on the Indian subcontinent have extensively employed the plant in Ayurveda, traditional medicine, and spiritual practices. The Peepal tree is often thought to produce oxygen both during the day and at night by Indian folks. The goal of our research was to produce molecular resources using whole-genome and transcriptome sequencing techniques. RESULTS: The complete genome of the Peepal tree was sequenced using two next-generation sequencers Illumina HiSeq1000 and MGISEQ-2000. We assembled the draft genome of 406 Mb, using a hybrid assembly workflow. The genome annotation resulted in 35,093 protein-coding genes; 53% of its genome consists of repetitive sequences. To understand the physiological pathways in leaf tissues, we analyzed photosynthetically distinct conditions: bright sunny days and nights. The RNA-seq analysis supported the expression of 26,479 unigenes. The leaf transcriptomic analysis of the diurnal and nocturnal periods revealed the expression of the significant number of genes involved in the carbon-fixation pathway. CONCLUSIONS: This study presents a draft hybrid genome assembly for F. religiosa and its functional annotated genes. The genomic and transcriptomic data-derived pathways have been analyzed for future studies on the Peepal tree. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-023-09270-z.
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spelling pubmed-101002412023-04-14 Genomic and transcriptomic analysis of sacred fig (Ficus religiosa) Ashalatha, K. L. Arunkumar, Kallare P Gowda, Malali BMC Genomics Research BACKGROUND: Peepal/Bodhi tree (Ficus religiosa L.) is an important, long-lived keystone ecological species. Communities on the Indian subcontinent have extensively employed the plant in Ayurveda, traditional medicine, and spiritual practices. The Peepal tree is often thought to produce oxygen both during the day and at night by Indian folks. The goal of our research was to produce molecular resources using whole-genome and transcriptome sequencing techniques. RESULTS: The complete genome of the Peepal tree was sequenced using two next-generation sequencers Illumina HiSeq1000 and MGISEQ-2000. We assembled the draft genome of 406 Mb, using a hybrid assembly workflow. The genome annotation resulted in 35,093 protein-coding genes; 53% of its genome consists of repetitive sequences. To understand the physiological pathways in leaf tissues, we analyzed photosynthetically distinct conditions: bright sunny days and nights. The RNA-seq analysis supported the expression of 26,479 unigenes. The leaf transcriptomic analysis of the diurnal and nocturnal periods revealed the expression of the significant number of genes involved in the carbon-fixation pathway. CONCLUSIONS: This study presents a draft hybrid genome assembly for F. religiosa and its functional annotated genes. The genomic and transcriptomic data-derived pathways have been analyzed for future studies on the Peepal tree. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-023-09270-z. BioMed Central 2023-04-12 /pmc/articles/PMC10100241/ /pubmed/37046210 http://dx.doi.org/10.1186/s12864-023-09270-z Text en © The Author(s) 2023 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
Ashalatha, K. L.
Arunkumar, Kallare P
Gowda, Malali
Genomic and transcriptomic analysis of sacred fig (Ficus religiosa)
title Genomic and transcriptomic analysis of sacred fig (Ficus religiosa)
title_full Genomic and transcriptomic analysis of sacred fig (Ficus religiosa)
title_fullStr Genomic and transcriptomic analysis of sacred fig (Ficus religiosa)
title_full_unstemmed Genomic and transcriptomic analysis of sacred fig (Ficus religiosa)
title_short Genomic and transcriptomic analysis of sacred fig (Ficus religiosa)
title_sort genomic and transcriptomic analysis of sacred fig (ficus religiosa)
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10100241/
https://www.ncbi.nlm.nih.gov/pubmed/37046210
http://dx.doi.org/10.1186/s12864-023-09270-z
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