Limits...
De novo assembly and transcriptome analysis of contrasting sugarcane varieties.

Cardoso-Silva CB, Costa EA, Mancini MC, Balsalobre TW, Canesin LE, Pinto LR, Carneiro MS, Garcia AA, de Souza AP, Vicentini R - PLoS ONE (2014)

Bottom Line: Based on a similarity search, the unigenes showed significant similarity to more than 28,788 sorghum proteins, including a set of 5,272 unigenes that are not present in the public sugarcane EST databases; many of these unigenes are likely putative undescribed sugarcane genes.From this collection of unigenes, a large number of molecular markers were identified, including 5,106 simple sequence repeats (SSRs) and 708,125 single-nucleotide polymorphisms (SNPs).This new dataset will be a useful resource for future genetic and genomic studies in this species.

View Article: PubMed Central - PubMed

Affiliation: Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, SP, Brazil.

ABSTRACT
Sugarcane is an important crop and a major source of sugar and alcohol. In this study, we performed de novo assembly and transcriptome annotation for six sugarcane genotypes involved in bi-parental crosses. The de novo assembly of the sugarcane transcriptome was performed using short reads generated using the Illumina RNA-Seq platform. We produced more than 400 million reads, which were assembled into 72,269 unigenes. Based on a similarity search, the unigenes showed significant similarity to more than 28,788 sorghum proteins, including a set of 5,272 unigenes that are not present in the public sugarcane EST databases; many of these unigenes are likely putative undescribed sugarcane genes. From this collection of unigenes, a large number of molecular markers were identified, including 5,106 simple sequence repeats (SSRs) and 708,125 single-nucleotide polymorphisms (SNPs). This new dataset will be a useful resource for future genetic and genomic studies in this species.

Show MeSH

Related in: MedlinePlus

Histogram of the Clusters of Orthologous Groups (COG) classifications of the sugarcane transcripts and sorghum proteins.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3921171&req=5

pone-0088462-g002: Histogram of the Clusters of Orthologous Groups (COG) classifications of the sugarcane transcripts and sorghum proteins.

Mentions: COG classification was performed for the transcriptome data, and a total of 7,519 unigenes were identified (Figure 2). These unigenes were classified into 23 COG categories, with the largest number of unigenes being grouped in the ‘replication, recombination and repair’ cluster (20.49%), followed by the ‘general function prediction only’ cluster (17.05%) and the ‘posttranslational modification, protein turnover and chaperones’ cluster (7.39%). These three categories are the same categories that are highly represented in sorghum (Figure 2).


De novo assembly and transcriptome analysis of contrasting sugarcane varieties.

Cardoso-Silva CB, Costa EA, Mancini MC, Balsalobre TW, Canesin LE, Pinto LR, Carneiro MS, Garcia AA, de Souza AP, Vicentini R - PLoS ONE (2014)

Histogram of the Clusters of Orthologous Groups (COG) classifications of the sugarcane transcripts and sorghum proteins.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3921171&req=5

pone-0088462-g002: Histogram of the Clusters of Orthologous Groups (COG) classifications of the sugarcane transcripts and sorghum proteins.
Mentions: COG classification was performed for the transcriptome data, and a total of 7,519 unigenes were identified (Figure 2). These unigenes were classified into 23 COG categories, with the largest number of unigenes being grouped in the ‘replication, recombination and repair’ cluster (20.49%), followed by the ‘general function prediction only’ cluster (17.05%) and the ‘posttranslational modification, protein turnover and chaperones’ cluster (7.39%). These three categories are the same categories that are highly represented in sorghum (Figure 2).

Bottom Line: Based on a similarity search, the unigenes showed significant similarity to more than 28,788 sorghum proteins, including a set of 5,272 unigenes that are not present in the public sugarcane EST databases; many of these unigenes are likely putative undescribed sugarcane genes.From this collection of unigenes, a large number of molecular markers were identified, including 5,106 simple sequence repeats (SSRs) and 708,125 single-nucleotide polymorphisms (SNPs).This new dataset will be a useful resource for future genetic and genomic studies in this species.

View Article: PubMed Central - PubMed

Affiliation: Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, SP, Brazil.

ABSTRACT
Sugarcane is an important crop and a major source of sugar and alcohol. In this study, we performed de novo assembly and transcriptome annotation for six sugarcane genotypes involved in bi-parental crosses. The de novo assembly of the sugarcane transcriptome was performed using short reads generated using the Illumina RNA-Seq platform. We produced more than 400 million reads, which were assembled into 72,269 unigenes. Based on a similarity search, the unigenes showed significant similarity to more than 28,788 sorghum proteins, including a set of 5,272 unigenes that are not present in the public sugarcane EST databases; many of these unigenes are likely putative undescribed sugarcane genes. From this collection of unigenes, a large number of molecular markers were identified, including 5,106 simple sequence repeats (SSRs) and 708,125 single-nucleotide polymorphisms (SNPs). This new dataset will be a useful resource for future genetic and genomic studies in this species.

Show MeSH
Related in: MedlinePlus