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

Abstract

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.

Unraveling the complexity of faba bean (Vicia faba L.) transcriptome to reveal cold-stress-responsive genes using long-read isoform sequencing technology

“…Despite the advantages of long-read sequencing, developing unified and practical approaches to analyzing the data remains a significant challenge. Previous studies applied standard Iso-seq bioinformatic pipelines to generate high-quality isoforms 34 , 35 . In the current study, we modified the standard pipeline by incorporating the Cogent tool 36 and the Cupcake ToFU package to refine and reconstruct the coding genome to obtain a comprehensive faba bean transcriptome atlas.…”

Genome-Wide Association Study for Agronomic Traits in Gamma-Ray-Derived Mutant Kenaf (Hibiscus cannabinus L.)

“…The high levels of phenolic compounds, such as anthocyanin, observed in the previous study for the purple genotypes and their antioxidant activity are approximately 4~5 times higher than other cultivars caused by anthocyanin [ 14 ]. In the kenaf plant, the genes of phenylpropanoid biosynthetic enzymes, including HcPAL , Hc4CL , HcC4H , and HcCHS , have been isolated in previous studies [ 38 , 39 ]. Recent progress, including NGS technology, has facilitated various transcriptome analyses in kenaf.…”

Global transcriptome analysis reveals genes associated with seedling advance growth traits in a selfed family of Chinese fir (Cunninghamia lanceolata)

“…Based on previous studies, a hypothetical partial pathway of cellulose biosynthesis is presented in Fig. 9B (Kimura & Kondo, 2002;Huang et al, 2012;Lyu et al, 2020). Recently, analysis in A. thaliana revealed that AtCesA6-null mutants presented a reduced cell elongation of young seedlings with little effect on cell division, thus affecting the cellular integrity and biomass yield in mature plants (Hu et al, 2018).…”