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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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Diagram illustrating two alternative assembly pipelines. (A)De novo assembly and alignment pipeline using Trinity and PASA. (B) Reference guided assembly pipeline using TopHat and Cufflinks.
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Fig1: Diagram illustrating two alternative assembly pipelines. (A)De novo assembly and alignment pipeline using Trinity and PASA. (B) Reference guided assembly pipeline using TopHat and Cufflinks.

Mentions: The de novo assembly pipeline shown in (Figure 1A) was used to assemble the reads from 50 stage and tissue libraries, resulting in 754,400 transcripts. The average number of assembled transcripts across different samples is 30,176 (Table 1), with the minimum number of assembled transcripts found in the early stage embryo (Embryo3) and the maximum number found in the leaf (Leaf1). All de novo assembled transcripts were aligned to the F. vesca genome using GMAP [14] within PASA, with the aims of eliminating sequences not aligning to the genome and merging de novo assembled sequences to remove redundancy. An average of 88.32% of the de novo assembled transcripts from each sample aligned to the genome.Figure 1


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

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

Diagram illustrating two alternative assembly pipelines. (A)De novo assembly and alignment pipeline using Trinity and PASA. (B) Reference guided assembly pipeline using TopHat and Cufflinks.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig1: Diagram illustrating two alternative assembly pipelines. (A)De novo assembly and alignment pipeline using Trinity and PASA. (B) Reference guided assembly pipeline using TopHat and Cufflinks.
Mentions: The de novo assembly pipeline shown in (Figure 1A) was used to assemble the reads from 50 stage and tissue libraries, resulting in 754,400 transcripts. The average number of assembled transcripts across different samples is 30,176 (Table 1), with the minimum number of assembled transcripts found in the early stage embryo (Embryo3) and the maximum number found in the leaf (Leaf1). All de novo assembled transcripts were aligned to the F. vesca genome using GMAP [14] within PASA, with the aims of eliminating sequences not aligning to the genome and merging de novo assembled sequences to remove redundancy. An average of 88.32% of the de novo assembled transcripts from each sample aligned to the genome.Figure 1

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