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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.


Simplified scheme of the phenylpropanoid biosynthesis pathway with genes identified in sugarcane transcriptome.Pair-wise comparisons were made between both genotypes. Each heatmap represent lignin transcript sequences identified in RNA-seq. The log2 (IACSP04-627 / IACSP04-065) expression ratio values were false color-coded using a scale of -1 to 1 and indicate the genotype that showed highest expression for each transcript. The intensity of green and red indicates the degree of down- and up-regulation of the corresponding lignin gene.
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pone.0134909.g002: Simplified scheme of the phenylpropanoid biosynthesis pathway with genes identified in sugarcane transcriptome.Pair-wise comparisons were made between both genotypes. Each heatmap represent lignin transcript sequences identified in RNA-seq. The log2 (IACSP04-627 / IACSP04-065) expression ratio values were false color-coded using a scale of -1 to 1 and indicate the genotype that showed highest expression for each transcript. The intensity of green and red indicates the degree of down- and up-regulation of the corresponding lignin gene.

Mentions: Despite of the orthology relationship previously showed, the use of high-throughput sequencing technology can also be useful to estimate the diversity of transcripts isoforms and gene families. As sugarcane is a polyploid species, polymorphisms can be generated from a different number of allelic copies present in each genotype [27]. Therefore, sugarcane cultivars are highly heterozygous, with several different alleles at each locus, and this high level of genetic complexity creates challenges during conventional and molecular breeding [67]. Some studies showed that a mutation in a single lignin biosynthesis gene can affect the expression of several other genes of the exact same biosynthetic pathway [16,68,69]. In this type of study with sugarcane it is possible to detect many transcripts that show high homology to functional genes. The MapMan analysis of sugarcane transcripts related with the phenylpropanoid pathway (Fig 2) shows transcripts of genes that encode the same enzyme and had different expression pattern between the two genotypes (higher or lower expression levels). However some gene families show a clear pattern. For instance, all transcripts of genes encoding ShPAL genes showed lower expression levels (or no differential expression) in the high lignin content genotype IACSP04-627 (Fig 1). ShHCT genes also showed strong divergent expression patterns between both genotypes, with some transcripts more expressed in the high-lignin genotype (in red) and others showed higher expression in the low-lignin genotype (in green).


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)

Simplified scheme of the phenylpropanoid biosynthesis pathway with genes identified in sugarcane transcriptome.Pair-wise comparisons were made between both genotypes. Each heatmap represent lignin transcript sequences identified in RNA-seq. The log2 (IACSP04-627 / IACSP04-065) expression ratio values were false color-coded using a scale of -1 to 1 and indicate the genotype that showed highest expression for each transcript. The intensity of green and red indicates the degree of down- and up-regulation of the corresponding lignin gene.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0134909.g002: Simplified scheme of the phenylpropanoid biosynthesis pathway with genes identified in sugarcane transcriptome.Pair-wise comparisons were made between both genotypes. Each heatmap represent lignin transcript sequences identified in RNA-seq. The log2 (IACSP04-627 / IACSP04-065) expression ratio values were false color-coded using a scale of -1 to 1 and indicate the genotype that showed highest expression for each transcript. The intensity of green and red indicates the degree of down- and up-regulation of the corresponding lignin gene.
Mentions: Despite of the orthology relationship previously showed, the use of high-throughput sequencing technology can also be useful to estimate the diversity of transcripts isoforms and gene families. As sugarcane is a polyploid species, polymorphisms can be generated from a different number of allelic copies present in each genotype [27]. Therefore, sugarcane cultivars are highly heterozygous, with several different alleles at each locus, and this high level of genetic complexity creates challenges during conventional and molecular breeding [67]. Some studies showed that a mutation in a single lignin biosynthesis gene can affect the expression of several other genes of the exact same biosynthetic pathway [16,68,69]. In this type of study with sugarcane it is possible to detect many transcripts that show high homology to functional genes. The MapMan analysis of sugarcane transcripts related with the phenylpropanoid pathway (Fig 2) shows transcripts of genes that encode the same enzyme and had different expression pattern between the two genotypes (higher or lower expression levels). However some gene families show a clear pattern. For instance, all transcripts of genes encoding ShPAL genes showed lower expression levels (or no differential expression) in the high lignin content genotype IACSP04-627 (Fig 1). ShHCT genes also showed strong divergent expression patterns between both genotypes, with some transcripts more expressed in the high-lignin genotype (in red) and others showed higher expression in the low-lignin genotype (in green).

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.