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Re-annotation of the woodland strawberry (Fragaria vesca) genome.

Darwish O, Shahan R, Liu Z, Slovin JP, Alkharouf NW - BMC Genomics (2015)

Bottom Line: The total number of gene predictions that do not overlap with the previous annotations is 2286, most of which were found to be homologous to other plant genes.We have experimentally verified one of the new gene model predictions to validate our results.This complete genome re-annotation will significantly benefit functional genomic studies of the strawberry and other members of the Rosaceae.

View Article: PubMed Central - PubMed

Affiliation: Department of Computer and Information Sciences, Towson University, 7800 York Road, Towson, Maryland, 21252, USA. ODARWISH@TOWSON.EDU.

ABSTRACT

Background: Fragaria vesca is a low-growing, small-fruited diploid strawberry species commonly called woodland strawberry. It is native to temperate regions of Eurasia and North America and while it produces edible fruits, it is most highly useful as an experimental perennial plant system that can serve as a model for the agriculturally important Rosaceae family. A draft of the F. vesca genome sequence was published in 2011 [Nat Genet 43:223,2011]. The first generation annotation (version 1.1) were developed using GeneMark-ES+[Nuc Acids Res 33:6494,2005]which is a self-training gene prediction tool that relies primarily on the combination of ab initio predictions with mapping high confidence ESTs in addition to mapping gene deserts from transposable elements. Based on over 25 different tissue transcriptomes, we have revised the F. vesca genome annotation, thereby providing several improvements over version 1.1.

Results: The new annotation, which was achieved using Maker, describes many more predicted protein coding genes compared to the GeneMark generated annotation that is currently hosted at the Genome Database for Rosaceae ( http://www.rosaceae.org/ ). Our new annotation also results in an increase in the overall total coding length, and the number of coding regions found. The total number of gene predictions that do not overlap with the previous annotations is 2286, most of which were found to be homologous to other plant genes. We have experimentally verified one of the new gene model predictions to validate our results.

Conclusions: Using the RNA-Seq transcriptome sequences from 25 diverse tissue types, the re-annotation pipeline improved existing annotations by increasing the annotation accuracy based on extensive transcriptome data. It uncovered new genes, added exons to current genes, and extended or merged exons. This complete genome re-annotation will significantly benefit functional genomic studies of the strawberry and other members of the Rosaceae.

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Summary of overall bioinformatics pipeline forF. vescagenome re-annotation. Evidence data including de novo assembled transcripts from all 50 samples, reference-guided assembled transcripts from all 50 samples, gene models generated using ab initio algorithm based tools (Augustus, SNAP and GeneMark), the first generation F. vesca gene predictions and plant reference proteins were passed to the MAKER pipeline to generate TowU_Fve annotation.
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Fig2: Summary of overall bioinformatics pipeline forF. vescagenome re-annotation. Evidence data including de novo assembled transcripts from all 50 samples, reference-guided assembled transcripts from all 50 samples, gene models generated using ab initio algorithm based tools (Augustus, SNAP and GeneMark), the first generation F. vesca gene predictions and plant reference proteins were passed to the MAKER pipeline to generate TowU_Fve annotation.

Mentions: We then used the MAKER annotation pipeline (Figure 2) to generate the revised F. vesca annotation. MAKER is able to generate ab initio gene prediction using several tools within its pipeline; it identifies repeats, aligns proteins and ESTs to a genome, and automatically combines all classes of evidence data into gene annotations. Data analyzed in the MAKER pipeline included: 1) 754,400 de novo assembled transcripts from 25 samples (Table 1), each with two biological replicates; 2) trained ab initio predictions from the SNAP gene prediction tool; 3) Augustus trained datasets of Arabidopsis thaliana and Solanum lycopersicum (tomato) transcriptomes; 4) first generation F. vesca gene predictions obtained from the Genome Database for Rosaceae; 5) reference-based assemblies (1,302,739) obtained by aligning all RNA-Seq samples to the F. vesca genome version 1.1 using Cufflinks; and 6) plant reference proteins downloaded from the Universal Protein Resource (UNIPROT) database. This second-generation annotation for F. vesca is named TowU_Fve and is available at GDR (http://www.rosaceae.org).Figure 2


Re-annotation of the woodland strawberry (Fragaria vesca) genome.

Darwish O, Shahan R, Liu Z, Slovin JP, Alkharouf NW - BMC Genomics (2015)

Summary of overall bioinformatics pipeline forF. vescagenome re-annotation. Evidence data including de novo assembled transcripts from all 50 samples, reference-guided assembled transcripts from all 50 samples, gene models generated using ab initio algorithm based tools (Augustus, SNAP and GeneMark), the first generation F. vesca gene predictions and plant reference proteins were passed to the MAKER pipeline to generate TowU_Fve annotation.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4318131&req=5

Fig2: Summary of overall bioinformatics pipeline forF. vescagenome re-annotation. Evidence data including de novo assembled transcripts from all 50 samples, reference-guided assembled transcripts from all 50 samples, gene models generated using ab initio algorithm based tools (Augustus, SNAP and GeneMark), the first generation F. vesca gene predictions and plant reference proteins were passed to the MAKER pipeline to generate TowU_Fve annotation.
Mentions: We then used the MAKER annotation pipeline (Figure 2) to generate the revised F. vesca annotation. MAKER is able to generate ab initio gene prediction using several tools within its pipeline; it identifies repeats, aligns proteins and ESTs to a genome, and automatically combines all classes of evidence data into gene annotations. Data analyzed in the MAKER pipeline included: 1) 754,400 de novo assembled transcripts from 25 samples (Table 1), each with two biological replicates; 2) trained ab initio predictions from the SNAP gene prediction tool; 3) Augustus trained datasets of Arabidopsis thaliana and Solanum lycopersicum (tomato) transcriptomes; 4) first generation F. vesca gene predictions obtained from the Genome Database for Rosaceae; 5) reference-based assemblies (1,302,739) obtained by aligning all RNA-Seq samples to the F. vesca genome version 1.1 using Cufflinks; and 6) plant reference proteins downloaded from the Universal Protein Resource (UNIPROT) database. This second-generation annotation for F. vesca is named TowU_Fve and is available at GDR (http://www.rosaceae.org).Figure 2

Bottom Line: The total number of gene predictions that do not overlap with the previous annotations is 2286, most of which were found to be homologous to other plant genes.We have experimentally verified one of the new gene model predictions to validate our results.This complete genome re-annotation will significantly benefit functional genomic studies of the strawberry and other members of the Rosaceae.

View Article: PubMed Central - PubMed

Affiliation: Department of Computer and Information Sciences, Towson University, 7800 York Road, Towson, Maryland, 21252, USA. ODARWISH@TOWSON.EDU.

ABSTRACT

Background: Fragaria vesca is a low-growing, small-fruited diploid strawberry species commonly called woodland strawberry. It is native to temperate regions of Eurasia and North America and while it produces edible fruits, it is most highly useful as an experimental perennial plant system that can serve as a model for the agriculturally important Rosaceae family. A draft of the F. vesca genome sequence was published in 2011 [Nat Genet 43:223,2011]. The first generation annotation (version 1.1) were developed using GeneMark-ES+[Nuc Acids Res 33:6494,2005]which is a self-training gene prediction tool that relies primarily on the combination of ab initio predictions with mapping high confidence ESTs in addition to mapping gene deserts from transposable elements. Based on over 25 different tissue transcriptomes, we have revised the F. vesca genome annotation, thereby providing several improvements over version 1.1.

Results: The new annotation, which was achieved using Maker, describes many more predicted protein coding genes compared to the GeneMark generated annotation that is currently hosted at the Genome Database for Rosaceae ( http://www.rosaceae.org/ ). Our new annotation also results in an increase in the overall total coding length, and the number of coding regions found. The total number of gene predictions that do not overlap with the previous annotations is 2286, most of which were found to be homologous to other plant genes. We have experimentally verified one of the new gene model predictions to validate our results.

Conclusions: Using the RNA-Seq transcriptome sequences from 25 diverse tissue types, the re-annotation pipeline improved existing annotations by increasing the annotation accuracy based on extensive transcriptome data. It uncovered new genes, added exons to current genes, and extended or merged exons. This complete genome re-annotation will significantly benefit functional genomic studies of the strawberry and other members of the Rosaceae.

Show MeSH