Gene Content Analysis of Sugarcane Public ESTs Reveals Thousands of Missing Coding-Genes and an Unexpected Pool of Grasses Conserved ncRNAs

@article{Vicentini2012GeneCA,
  title={Gene Content Analysis of Sugarcane Public ESTs Reveals Thousands of Missing Coding-Genes and an Unexpected Pool of Grasses Conserved ncRNAs},
  author={Renato Vicentini and Luiz Eduardo Vieira Del Bem and Marie-Anne Van Sluys and Fabio Tebaldi Silveira Nogueira and Michel Vincentz},
  journal={Tropical Plant Biology},
  year={2012},
  volume={5},
  pages={199-205}
}
Sugarcane is the most important crop for sugar industry and raw material for bioethanol. Here we present a quantitative analysis of the gene content from publicly available sugarcane ESTs. The current sugarcane EST collection sampled orthologs for ~58 % of the closely-related sorghum proteome, suggesting that more than 10,000 sugarcane coding-genes remain undiscovered. Moreover the existence of more than 2,000 ncRNAs conserved between sugarcane and sorghum was revealed, among which over 500 are… 
De Novo Assembly and Transcriptome Analysis of Contrasting Sugarcane Varieties
TLDR
De novo assembly and transcriptome annotation for six sugarcane genotypes involved in bi-parental crosses and a large number of molecular markers were identified, including 5,106 simple sequence repeats (SSRs) and 708,125 single-nucleotide polymorphisms (SNPs).
Building the sugarcane genome for biotechnology and identifying evolutionary trends
TLDR
The largest and most diverse set of sugarcane genome sequences to date is released, as part of an on-going initiative to provide a Sugarcane genomic information resource, with the ultimate goal of producing a gold standard genome.
A survey of the complex transcriptome from the highly polyploid sugarcane genome using full-length isoform sequencing and de novo assembly from short read sequencing
TLDR
The transcriptome dataset should contribute to improved Sugarcane gene models and sugarcane protein predictions; and will serve as a reference database for analysis of transcript expression in sugarcanes.
Functional analysis of sugarcane genes modulated by drought in roots : Análise funcional de genes de cana-de-açúcar modulados por seca em raízes
TLDR
This project aimed to identify genes modulated by drought by selecting 10 potentially relevant genes in root responses in drought conditions for functional studies using Arabidopsis thaliana and sugarcane transgenic plants.
Transcriptomic characterization and potential marker development of contrasting sugarcane cultivars
TLDR
Transcriptome sequencing for six contrasting sugarcane genotypes involved in leaf abscission, tolerance to pokkah boeng disease and drought stress identified a number of putative markers, including 8,630 simple sequence repeats (SSRs) and 442,152 single-nucleotide polymorphisms (SNPs).
Transcriptomic Analysis of Changes in Gene Expression During Flowering Induction in Sugarcane Under Controlled Photoperiodic Conditions
TLDR
This study investigates the transcriptome of +1 mature leaves of a sugarcane cultivar subjected to florally inductive and non-inductive photoperiodic treatments to identify gene expression patterns and molecular regulatory modules and reports a set of flowering-induced long non-coding RNAs and their level of conservation to other crops.
Impact of Agroclimatic Variables on Proteogenomics in Sugar Cane (Saccharum spp.) Plant Productivity
Sugar cane (Saccharum spp. hybrids) is a major crop for sugar and renewable bioenergy worldwide, grown in arid and semiarid regions. China, the world’s fourth-largest sugar producer after Brazil,
Overexpression of a Sugarcane BAHD Acyltransferase Alters Hydroxycinnamate Content in Maize Cell Wall
TLDR
It is shown that overexpression of ScAT10 in maize resulted in up to 75% increase in total pCA content, and a C4 plant that is promising for valorizing pCA production in biorefineries is generated.
Genome Editing in Sugarcane: Challenges Ahead
TLDR
TALEN mediated approach is reported for the first time to reduce lignin content in sugarcane to make it amenable for biofuel production and large genome size, polyploidy, low transformation efficiency, transgene silencing and lack of high throughput screening techniques are certainly great challenges.
...
...

References

SHOWING 1-10 OF 53 REFERENCES
An EST survey of the sugarcane transcriptome
TLDR
These EST sequences provide a foundation for many new studies to accelerate isolation of agronomically important genes from the cumbersome sugarcane genome and might be useful DNA markers for pan-angiosperm comparative mapping.
ESTs as a source for sequence polymorphism discovery in sugarcane: example of the Adh genes
TLDR
Results show that EST data constitute an invaluable source of sequence polymorphism for sugarcane that is worth carefully collecting for the future development of new marker tools.
Analysis and functional annotation of an expressed sequence tag collection for tropical crop sugarcane.
TLDR
A global analysis of the whole SUCEST data set indicated that 14,409 assembled sequences contained at least one cDNA clone with a full-length insert, which indicated that possibly 33,620 unique genes had been identified and indicated that >90% of the sugarcane expressed genes were tagged.
Identification and expression analysis of microRNAs and targets in the biofuel crop sugarcane
TLDR
Comparative analyses between sugarcane and sorghum suggest that these two species retain homologous miRNAs and targets in their genomes, and the findings support the notion that the regulation of SsCBP1 by miR528 is shared at least within graminaceous monocots, and this miRNA-based post-transcriptional regulation evolved exclusively within the monocot lineage after the divergence from eudicots.
Identification of a novel sugar transporter homologue strongly expressed in maturing stem vascular tissues of sugarcane by expressed sequence tag and microarray analysis
TLDR
The utility of genomic approaches using large-scale EST acquisition and microarray hybridization techniques for studies of the developmental regulation of metabolic enzymes and potential transporters in sugarcane is demonstrated.
Sugarcane Functional Genomics: Gene Discovery for Agronomic Trait Development
TLDR
Genome-based technology such as cDNA microarray data indicates genes associated with sugar content that may be used to develop new varieties improved for sucrose content or for traits that restrict the expansion of the cultivated land.
Genes expressed in sugarcane maturing internodal tissue
TLDR
A partial sequence analysis of random clones from maturing culm total and subtracted cDNA libraries provided a framework for functional gene analysis in sugarcane sucrose-accumulating tissues and identified genes that may be preferentially expressed during culm maturation.
Genetic and expression profiling in sugarcane
Commercial varieties of sugarcane accumulate up to 50-60% of the dry weight of stem tissues as sucrose. The accumulation of sucrose occurs in a developmentally programmed tissue-specific manner with
Orthologous comparison in a gene-rich region among grasses reveals stability in the sugarcane polyploid genome.
TLDR
This analysis of sugarcane haplotype organization at the sequence level suggests that the high ploidy in Sugarcane did not induce generalized reshaping of its genome, thus challenging the idea that polyploidy quickly induces generalized rearrangement of genomes.
A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. japonica)
TLDR
The genome of the japonica subspecies of rice, an important cereal and model monocot, was sequenced and assembled by whole-genome shotgun sequencing and suggests that the genome contains 32,000 to 50,000 genes.
...
...