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Large-Scale Transcriptome Analysis of Two Sugarcane Genotypes Contrasting for Lignin Content.

Vicentini R, Bottcher A, Brito Mdos S, Dos Santos AB, Creste S, Landell MG, Cesarino I, Mazzafera P - PLoS ONE (2015)

Bottom Line: We generated a set of 85,151 transcripts of sugarcane using RNA-seq and de novo assembling.More than 2,000 transcripts showed differential expression between the genotypes, including several genes involved in the lignin biosynthetic pathway.This information can give valuable knowledge on the lignin biosynthesis and its interactions with other metabolic pathways in the complex sugarcane genome.

View Article: PubMed Central - PubMed

Affiliation: Systems Biology Laboratory, Centre for Molecular Biology and Genetic Engineering, State University of Campinas, Campinas, SP, Brazil.

ABSTRACT
Sugarcane is an important crop worldwide for sugar and first generation ethanol production. Recently, the residue of sugarcane mills, named bagasse, has been considered a promising lignocellulosic biomass to produce the second-generation ethanol. Lignin is a major factor limiting the use of bagasse and other plant lignocellulosic materials to produce second-generation ethanol. Lignin biosynthesis pathway is a complex network and changes in the expression of genes of this pathway have in general led to diverse and undesirable impacts on plant structure and physiology. Despite its economic importance, sugarcane genome was still not sequenced. In this study a high-throughput transcriptome evaluation of two sugarcane genotypes contrasting for lignin content was carried out. We generated a set of 85,151 transcripts of sugarcane using RNA-seq and de novo assembling. More than 2,000 transcripts showed differential expression between the genotypes, including several genes involved in the lignin biosynthetic pathway. This information can give valuable knowledge on the lignin biosynthesis and its interactions with other metabolic pathways in the complex sugarcane genome.

No MeSH data available.


Transcript levels of lignin genes in the contrasting sugarcane genotypes.(*) indicates transcripts that are significantly (p-value ≤ 1e-4) different in abundance between the two sugarcane genotypes.
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pone.0134909.g001: Transcript levels of lignin genes in the contrasting sugarcane genotypes.(*) indicates transcripts that are significantly (p-value ≤ 1e-4) different in abundance between the two sugarcane genotypes.

Mentions: The RNA-seq data were used to quantify and study sugarcane genome-wide changes in gene expression related with the phenylpropanoid biosynthesis, in particular the lignin biosynthetic pathway. Applying the previously described orthology workflow [25] it was possible to identify 21 sugarcane transcripts that encode for enzymes involved in lignin biosynthesis (Fig 1), including 2 PALs (EC 4.3.1.5), 3 C4Hs (EC 1.14.13.11), 2 4CLs (EC 6.2.1.12), 1 HCT (EC 2.3.1.133), 2 C3Hs (EC 1.14.13.36), 3 CCoAOMTs (EC 2.1.1.104), 1 CCR (EC 1.2.1.44), 2 COMTs (EC 2.1.1.68), 1 F5H, and 4 CADs (EC 1.1.1.195). The total number of identified phenylpropanoid-monolignol transcripts represents the members of lignin gene families expressed in sugarcane stems, but most likely does not represent the total number of lignin genes present in the highly polyploidy sugarcane genome. Accordingly, the total number of lignin genes present in closely related species is significantly higher. Xu and colleagues [40] performed a comparative genome analysis of lignin biosynthesis gene families across the plant kingdom, including representative species from Bryophytes, Lycophytes, Dicot Angiosperms and Monocot Angiosperms. While Arabidopsis genome harbors 63 lignin genes, a total of 141, 149 and 157 genes were found for sorghum, poplar and rice, respectively. Noteworthy, the results of Xu et al. [40] differ significantly from the data previously published by Raes et al. [41] and Shi et al. [42], in which 34 and 95 genes were annotated as monolignol genes in Arabidopsis and poplar, respectively. This observation highlights the fact that different approaches applied to identify homolog genes in a given genome leads to significantly different outputs.


Large-Scale Transcriptome Analysis of Two Sugarcane Genotypes Contrasting for Lignin Content.

Vicentini R, Bottcher A, Brito Mdos S, Dos Santos AB, Creste S, Landell MG, Cesarino I, Mazzafera P - PLoS ONE (2015)

Transcript levels of lignin genes in the contrasting sugarcane genotypes.(*) indicates transcripts that are significantly (p-value ≤ 1e-4) different in abundance between the two sugarcane genotypes.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4524650&req=5

pone.0134909.g001: Transcript levels of lignin genes in the contrasting sugarcane genotypes.(*) indicates transcripts that are significantly (p-value ≤ 1e-4) different in abundance between the two sugarcane genotypes.
Mentions: The RNA-seq data were used to quantify and study sugarcane genome-wide changes in gene expression related with the phenylpropanoid biosynthesis, in particular the lignin biosynthetic pathway. Applying the previously described orthology workflow [25] it was possible to identify 21 sugarcane transcripts that encode for enzymes involved in lignin biosynthesis (Fig 1), including 2 PALs (EC 4.3.1.5), 3 C4Hs (EC 1.14.13.11), 2 4CLs (EC 6.2.1.12), 1 HCT (EC 2.3.1.133), 2 C3Hs (EC 1.14.13.36), 3 CCoAOMTs (EC 2.1.1.104), 1 CCR (EC 1.2.1.44), 2 COMTs (EC 2.1.1.68), 1 F5H, and 4 CADs (EC 1.1.1.195). The total number of identified phenylpropanoid-monolignol transcripts represents the members of lignin gene families expressed in sugarcane stems, but most likely does not represent the total number of lignin genes present in the highly polyploidy sugarcane genome. Accordingly, the total number of lignin genes present in closely related species is significantly higher. Xu and colleagues [40] performed a comparative genome analysis of lignin biosynthesis gene families across the plant kingdom, including representative species from Bryophytes, Lycophytes, Dicot Angiosperms and Monocot Angiosperms. While Arabidopsis genome harbors 63 lignin genes, a total of 141, 149 and 157 genes were found for sorghum, poplar and rice, respectively. Noteworthy, the results of Xu et al. [40] differ significantly from the data previously published by Raes et al. [41] and Shi et al. [42], in which 34 and 95 genes were annotated as monolignol genes in Arabidopsis and poplar, respectively. This observation highlights the fact that different approaches applied to identify homolog genes in a given genome leads to significantly different outputs.

Bottom Line: We generated a set of 85,151 transcripts of sugarcane using RNA-seq and de novo assembling.More than 2,000 transcripts showed differential expression between the genotypes, including several genes involved in the lignin biosynthetic pathway.This information can give valuable knowledge on the lignin biosynthesis and its interactions with other metabolic pathways in the complex sugarcane genome.

View Article: PubMed Central - PubMed

Affiliation: Systems Biology Laboratory, Centre for Molecular Biology and Genetic Engineering, State University of Campinas, Campinas, SP, Brazil.

ABSTRACT
Sugarcane is an important crop worldwide for sugar and first generation ethanol production. Recently, the residue of sugarcane mills, named bagasse, has been considered a promising lignocellulosic biomass to produce the second-generation ethanol. Lignin is a major factor limiting the use of bagasse and other plant lignocellulosic materials to produce second-generation ethanol. Lignin biosynthesis pathway is a complex network and changes in the expression of genes of this pathway have in general led to diverse and undesirable impacts on plant structure and physiology. Despite its economic importance, sugarcane genome was still not sequenced. In this study a high-throughput transcriptome evaluation of two sugarcane genotypes contrasting for lignin content was carried out. We generated a set of 85,151 transcripts of sugarcane using RNA-seq and de novo assembling. More than 2,000 transcripts showed differential expression between the genotypes, including several genes involved in the lignin biosynthetic pathway. This information can give valuable knowledge on the lignin biosynthesis and its interactions with other metabolic pathways in the complex sugarcane genome.

No MeSH data available.