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Characterization of Gene Isoforms Related to Cellulose and Lignin Biosynthesis in Kenaf (Hibiscus cannabinus L.) Mutant

Kenaf is a source of fiber and a bioenergy crop that is considered to be a third world crop. Recently, a new kenaf cultivar, "Jangdae," was developed by gamma irradiation. It exhibited distinguishable characteristics such as higher biomass, higher seed yield, and earlier flowering than the...

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Autores principales: Lyu, Jae Il, Ramekar, Rahul, Kim, Dong-Gun, Kim, Jung Min, Lee, Min-Kyu, Hung, Nguyen Ngoc, Kim, Jin-Baek, Ahn, Joon-Woo, Kang, Si-Yong, Choi, Ik-Young, Park, Kyoung-Cheul, Kwon, Soon-Jae
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7285769/
https://www.ncbi.nlm.nih.gov/pubmed/32423146
http://dx.doi.org/10.3390/plants9050631
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author Lyu, Jae Il
Ramekar, Rahul
Kim, Dong-Gun
Kim, Jung Min
Lee, Min-Kyu
Hung, Nguyen Ngoc
Kim, Jin-Baek
Ahn, Joon-Woo
Kang, Si-Yong
Choi, Ik-Young
Park, Kyoung-Cheul
Kwon, Soon-Jae
author_facet Lyu, Jae Il
Ramekar, Rahul
Kim, Dong-Gun
Kim, Jung Min
Lee, Min-Kyu
Hung, Nguyen Ngoc
Kim, Jin-Baek
Ahn, Joon-Woo
Kang, Si-Yong
Choi, Ik-Young
Park, Kyoung-Cheul
Kwon, Soon-Jae
author_sort Lyu, Jae Il
collection PubMed
description Kenaf is a source of fiber and a bioenergy crop that is considered to be a third world crop. Recently, a new kenaf cultivar, "Jangdae," was developed by gamma irradiation. It exhibited distinguishable characteristics such as higher biomass, higher seed yield, and earlier flowering than the wild type. We sequenced and analyzed the transcriptome of apical leaf and stem using Pacific Biosciences single-molecule long-read isoform sequencing platform. De novo assembly yielded 26,822 full-length transcripts with a total length of 59 Mbp. Sequence similarity against protein sequence allowed the functional annotation of 11,370 unigenes. Among them, 10,100 unigenes were assigned gene ontology terms, the majority of which were associated with the metabolic and cellular process. The Kyoto encyclopedia of genes and genomes (KEGG) analysis mapped 8875 of the annotated unigenes to 149 metabolic pathways. We also identified the majority of putative genes involved in cellulose and lignin-biosynthesis. We further evaluated the expression pattern in eight gene families involved in lignin-biosynthesis at different growth stages. In this study, appropriate biotechnological approaches using the information obtained for these putative genes will help to modify the desirable content traits in mutants. The transcriptome data can be used as a reference dataset and provide a resource for molecular genetic studies in kenaf.
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spelling pubmed-72857692020-06-15 Characterization of Gene Isoforms Related to Cellulose and Lignin Biosynthesis in Kenaf (Hibiscus cannabinus L.) Mutant Lyu, Jae Il Ramekar, Rahul Kim, Dong-Gun Kim, Jung Min Lee, Min-Kyu Hung, Nguyen Ngoc Kim, Jin-Baek Ahn, Joon-Woo Kang, Si-Yong Choi, Ik-Young Park, Kyoung-Cheul Kwon, Soon-Jae Plants (Basel) Article Kenaf is a source of fiber and a bioenergy crop that is considered to be a third world crop. Recently, a new kenaf cultivar, "Jangdae," was developed by gamma irradiation. It exhibited distinguishable characteristics such as higher biomass, higher seed yield, and earlier flowering than the wild type. We sequenced and analyzed the transcriptome of apical leaf and stem using Pacific Biosciences single-molecule long-read isoform sequencing platform. De novo assembly yielded 26,822 full-length transcripts with a total length of 59 Mbp. Sequence similarity against protein sequence allowed the functional annotation of 11,370 unigenes. Among them, 10,100 unigenes were assigned gene ontology terms, the majority of which were associated with the metabolic and cellular process. The Kyoto encyclopedia of genes and genomes (KEGG) analysis mapped 8875 of the annotated unigenes to 149 metabolic pathways. We also identified the majority of putative genes involved in cellulose and lignin-biosynthesis. We further evaluated the expression pattern in eight gene families involved in lignin-biosynthesis at different growth stages. In this study, appropriate biotechnological approaches using the information obtained for these putative genes will help to modify the desirable content traits in mutants. The transcriptome data can be used as a reference dataset and provide a resource for molecular genetic studies in kenaf. MDPI 2020-05-14 /pmc/articles/PMC7285769/ /pubmed/32423146 http://dx.doi.org/10.3390/plants9050631 Text en © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Lyu, Jae Il
Ramekar, Rahul
Kim, Dong-Gun
Kim, Jung Min
Lee, Min-Kyu
Hung, Nguyen Ngoc
Kim, Jin-Baek
Ahn, Joon-Woo
Kang, Si-Yong
Choi, Ik-Young
Park, Kyoung-Cheul
Kwon, Soon-Jae
Characterization of Gene Isoforms Related to Cellulose and Lignin Biosynthesis in Kenaf (Hibiscus cannabinus L.) Mutant
title Characterization of Gene Isoforms Related to Cellulose and Lignin Biosynthesis in Kenaf (Hibiscus cannabinus L.) Mutant
title_full Characterization of Gene Isoforms Related to Cellulose and Lignin Biosynthesis in Kenaf (Hibiscus cannabinus L.) Mutant
title_fullStr Characterization of Gene Isoforms Related to Cellulose and Lignin Biosynthesis in Kenaf (Hibiscus cannabinus L.) Mutant
title_full_unstemmed Characterization of Gene Isoforms Related to Cellulose and Lignin Biosynthesis in Kenaf (Hibiscus cannabinus L.) Mutant
title_short Characterization of Gene Isoforms Related to Cellulose and Lignin Biosynthesis in Kenaf (Hibiscus cannabinus L.) Mutant
title_sort characterization of gene isoforms related to cellulose and lignin biosynthesis in kenaf (hibiscus cannabinus l.) mutant
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7285769/
https://www.ncbi.nlm.nih.gov/pubmed/32423146
http://dx.doi.org/10.3390/plants9050631
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