Abstract
Gene expression by mRNA-Seq
In silico gene prediction in eukaryotic genomes is a complicated and error prone process. Nonetheless, a high-quality gene annotation is very important for the usefulness of a genome sequence to the scientific community.
In the potato genome sequencing consortium, we have employed a large mRNA-seq data set to improve and validate ab initio predicted gene models. This direct experimental evidence also provides reliable determinations of UTR regions and polyadenylation sites, which are not easily predicted in plants.
Furthermore, once an annotated genome sequence is available, gene expression by mRNA-Seq enables acquisition of a more complete overview of gene isoform usage in complex enzymatic pathways enabling the identification of key genes.
Metabolism in potatoes
This information is useful e.g. for crop improvement based on manipulation of agronomically important metabolic pathways like starch metabolism in potato. This metabolism is highly redundant both in terms of gene isoform usage, enzymatic reactions, and location since starch synthesis takes place both in tubers and leaves. Using mRNA-Seq sequencing of a double monoploid, DM, and the diploid breeding hybrid, RH, the expression of individual isoforms has been analyzed.
Interestingly a high degree of tissue specificity is observed, indicating that to a great extent contrasting isoforms and metabolic routes are utilized in tubers and leaves, respectively.
Furthermore, while the hydrolytic starch catabolic pathway is transcriptionally active in DM, this is virtually non-existing in RH, possible reflecting the selection for high yield in European breeding programs.
In silico gene prediction in eukaryotic genomes is a complicated and error prone process. Nonetheless, a high-quality gene annotation is very important for the usefulness of a genome sequence to the scientific community.
In the potato genome sequencing consortium, we have employed a large mRNA-seq data set to improve and validate ab initio predicted gene models. This direct experimental evidence also provides reliable determinations of UTR regions and polyadenylation sites, which are not easily predicted in plants.
Furthermore, once an annotated genome sequence is available, gene expression by mRNA-Seq enables acquisition of a more complete overview of gene isoform usage in complex enzymatic pathways enabling the identification of key genes.
Metabolism in potatoes
This information is useful e.g. for crop improvement based on manipulation of agronomically important metabolic pathways like starch metabolism in potato. This metabolism is highly redundant both in terms of gene isoform usage, enzymatic reactions, and location since starch synthesis takes place both in tubers and leaves. Using mRNA-Seq sequencing of a double monoploid, DM, and the diploid breeding hybrid, RH, the expression of individual isoforms has been analyzed.
Interestingly a high degree of tissue specificity is observed, indicating that to a great extent contrasting isoforms and metabolic routes are utilized in tubers and leaves, respectively.
Furthermore, while the hydrolytic starch catabolic pathway is transcriptionally active in DM, this is virtually non-existing in RH, possible reflecting the selection for high yield in European breeding programs.
| Original language | English |
|---|---|
| Publication date | 9 Jun 2011 |
| Publication status | Published - 9 Jun 2011 |