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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.


Expression pattern of 2,162 differentially expressed transcripts between genotypes IACSP04-627 (high-lignin) and IACSP04-065 (low-lignin).The number (N) indicates the amount of transcripts presented in each cluster. The y-axis shows the reads count, on log2 scale, of each transcript. Cluster 1 (C1) represents the profile of transcripts that increased in IACSP04-065 sugarcane genotype. Cluster 2 shows the profile of transcripts that had a minimal abundance in IACSP04-627 and high abundance in IACSP04-065. Cluster 3 and Cluster 4 shows an inverted pattern, where transcripts are more abundant in IACSP04-627 genotype.
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pone.0134909.g003: Expression pattern of 2,162 differentially expressed transcripts between genotypes IACSP04-627 (high-lignin) and IACSP04-065 (low-lignin).The number (N) indicates the amount of transcripts presented in each cluster. The y-axis shows the reads count, on log2 scale, of each transcript. Cluster 1 (C1) represents the profile of transcripts that increased in IACSP04-065 sugarcane genotype. Cluster 2 shows the profile of transcripts that had a minimal abundance in IACSP04-627 and high abundance in IACSP04-065. Cluster 3 and Cluster 4 shows an inverted pattern, where transcripts are more abundant in IACSP04-627 genotype.

Mentions: Besides the expression profile of phenylpropanoid biosynthetic genes, the transcriptome obtained from both contrasting genotypes was also analyzed for the whole differential expression. This analysis resulted in 2,162 differentially expressed transcripts (S3 File) that were clustered by self-organizing maps (Fig 3). This clustering analysis shows four different expression patterns for these 2,162 differentially expressed transcripts. The Cluster 1 (C1, with 425 sugarcane transcripts) represents the profile of transcripts with higher expression levels in the IACSP04-065 sugarcane genotype. Cluster 2 (C2, n = 604) has the profile of transcripts that had a minimal abundance in IACSP04-627. Cluster 3 (C3, n = 629) and Cluster 4 (C4, n = 504) shows the opposite of C1 and C2, where transcripts are more abundant in the IACSP04-627 genotype.


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)

Expression pattern of 2,162 differentially expressed transcripts between genotypes IACSP04-627 (high-lignin) and IACSP04-065 (low-lignin).The number (N) indicates the amount of transcripts presented in each cluster. The y-axis shows the reads count, on log2 scale, of each transcript. Cluster 1 (C1) represents the profile of transcripts that increased in IACSP04-065 sugarcane genotype. Cluster 2 shows the profile of transcripts that had a minimal abundance in IACSP04-627 and high abundance in IACSP04-065. Cluster 3 and Cluster 4 shows an inverted pattern, where transcripts are more abundant in IACSP04-627 genotype.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0134909.g003: Expression pattern of 2,162 differentially expressed transcripts between genotypes IACSP04-627 (high-lignin) and IACSP04-065 (low-lignin).The number (N) indicates the amount of transcripts presented in each cluster. The y-axis shows the reads count, on log2 scale, of each transcript. Cluster 1 (C1) represents the profile of transcripts that increased in IACSP04-065 sugarcane genotype. Cluster 2 shows the profile of transcripts that had a minimal abundance in IACSP04-627 and high abundance in IACSP04-065. Cluster 3 and Cluster 4 shows an inverted pattern, where transcripts are more abundant in IACSP04-627 genotype.
Mentions: Besides the expression profile of phenylpropanoid biosynthetic genes, the transcriptome obtained from both contrasting genotypes was also analyzed for the whole differential expression. This analysis resulted in 2,162 differentially expressed transcripts (S3 File) that were clustered by self-organizing maps (Fig 3). This clustering analysis shows four different expression patterns for these 2,162 differentially expressed transcripts. The Cluster 1 (C1, with 425 sugarcane transcripts) represents the profile of transcripts with higher expression levels in the IACSP04-065 sugarcane genotype. Cluster 2 (C2, n = 604) has the profile of transcripts that had a minimal abundance in IACSP04-627. Cluster 3 (C3, n = 629) and Cluster 4 (C4, n = 504) shows the opposite of C1 and C2, where transcripts are more abundant in the IACSP04-627 genotype.

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.