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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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cDNA sequences support the re-annotation of gene11268. (A)F. vesca gene11268 annotation predicted by the first generation annotation at GDR. Colored boxes denote exons and gray lines denote introns. (B) Re-annotation of F. vesca gene11268 revealed the presence of additional exons. RNA-Seq reads from stage 7_8 anther are represented as red rectangles. Gray peaks below the red rectangles represent the abundance of additional reads beyond those shown. (C) The TowU_Fve predicted structure of F. vesca gene11268 after splicing is supported by the sequence of cDNA clones from YW5AF7 anther mRNA. Sequences of two such cDNA clones were identical and yielded the TowU_Fve predicted gene structure as shown.
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Fig4: cDNA sequences support the re-annotation of gene11268. (A)F. vesca gene11268 annotation predicted by the first generation annotation at GDR. Colored boxes denote exons and gray lines denote introns. (B) Re-annotation of F. vesca gene11268 revealed the presence of additional exons. RNA-Seq reads from stage 7_8 anther are represented as red rectangles. Gray peaks below the red rectangles represent the abundance of additional reads beyond those shown. (C) The TowU_Fve predicted structure of F. vesca gene11268 after splicing is supported by the sequence of cDNA clones from YW5AF7 anther mRNA. Sequences of two such cDNA clones were identical and yielded the TowU_Fve predicted gene structure as shown.

Mentions: We PCR amplified, cloned and sequenced the cDNA of gene11268 encoding a MADS box protein to confirm experimentally the TowU_Fve annotation. TowU_Fve predicts additional exons in the second intron based on the RNA-seq data (Figure 4A,B). Figure 4C illustrates the amplified coding region found by sequencing two independent cDNA clones, which contained the additional TowU_Fve predicted exons.Figure 4


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

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

cDNA sequences support the re-annotation of gene11268. (A)F. vesca gene11268 annotation predicted by the first generation annotation at GDR. Colored boxes denote exons and gray lines denote introns. (B) Re-annotation of F. vesca gene11268 revealed the presence of additional exons. RNA-Seq reads from stage 7_8 anther are represented as red rectangles. Gray peaks below the red rectangles represent the abundance of additional reads beyond those shown. (C) The TowU_Fve predicted structure of F. vesca gene11268 after splicing is supported by the sequence of cDNA clones from YW5AF7 anther mRNA. Sequences of two such cDNA clones were identical and yielded the TowU_Fve predicted gene structure as shown.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig4: cDNA sequences support the re-annotation of gene11268. (A)F. vesca gene11268 annotation predicted by the first generation annotation at GDR. Colored boxes denote exons and gray lines denote introns. (B) Re-annotation of F. vesca gene11268 revealed the presence of additional exons. RNA-Seq reads from stage 7_8 anther are represented as red rectangles. Gray peaks below the red rectangles represent the abundance of additional reads beyond those shown. (C) The TowU_Fve predicted structure of F. vesca gene11268 after splicing is supported by the sequence of cDNA clones from YW5AF7 anther mRNA. Sequences of two such cDNA clones were identical and yielded the TowU_Fve predicted gene structure as shown.
Mentions: We PCR amplified, cloned and sequenced the cDNA of gene11268 encoding a MADS box protein to confirm experimentally the TowU_Fve annotation. TowU_Fve predicts additional exons in the second intron based on the RNA-seq data (Figure 4A,B). Figure 4C illustrates the amplified coding region found by sequencing two independent cDNA clones, which contained the additional TowU_Fve predicted exons.Figure 4

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