Supporting data for "Single-molecule sequencing and optical mapping yields an improved genome of woodland strawberry (Fragaria vesca) with chromosome-scale contiguity"

Dataset type: Genomic, Genome-Mapping
Data released on November 28, 2017

Edger P; VanBuren R; Colle M; Poorten TJ; Wai CM; Niederhuth CE; Alger EI; Ou S; Acharya CB; Wang J; Callow P; McKain MR; Shi J; Collier C; Xiong Z; Mower JP; Slovin JP; Hytonen T; Jiang N; Childs KL; Knapp SJ (2017): Supporting data for "Single-molecule sequencing and optical mapping yields an improved genome of woodland strawberry (Fragaria vesca) with chromosome-scale contiguity" GigaScience Database. http://dx.doi.org/10.5524/100372

DOI10.5524/100372

We report a near-complete genome of diploid woodland strawberry (Fragaria vesca) using single-molecule real-time sequencing from Pacific Biosciences (PacBio). This assembly has a contig N50 length of ~7.9 Mb, representing a ~300 fold improvement of the previous version. The vast majority (>99.8%) of the assembly was anchored to seven pseudomolecules using two sets of optical maps from Bionano Genomics. We obtained ~24.96 million base pairs (Mb) of sequence not present in the previous version of the F. vesca genome and produced an improved annotation that includes 1,496 new genes. Comparative syntenic analyses uncovered numerous, large-scale scaffolding errors present in each chromosome in the previously published version of the F. vesca genome. Our results highlight the need to improve existing short-read based reference genomes. Furthermore, we demonstrate how genome quality impacts commonly used analyses for addressing both fundamental and applied biological questions.

Keywords:

Additional details

Read the peer-reviewed publication(s):

Edger, P. P., VanBuren, R., Colle, M., Poorten, T. J., Wai, C. M., Niederhuth, C. E., … Knapp, S. J. (2017). Single-molecule sequencing and optical mapping yields an improved genome of woodland strawberry (Fragaria vesca) with chromosome-scale contiguity. GigaScience, 7(2). doi:10.1093/gigascience/gix124

Accessions (data included in GigaDB):

BioProject: PRJNA383733





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
Anther_10_A57918European strawberrywild strawberryFragaria vesca Alternative names:wild strawberry
Description:Anthers from stage 10 flowers; replica...
Analyte type:RNA
...
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Anther_10_B57918European strawberrywild strawberryFragaria vesca Alternative names:wild strawberry
Description:Anthers from stage 10 flowers; replica...
Analyte type:RNA
...
+
Anther_11_A57918European strawberrywild strawberryFragaria vesca Alternative names:wild strawberry
Description:Anthers from stage 11 flowers; replica...
Analyte type:RNA
...
+
Anther_11_B57918European strawberrywild strawberryFragaria vesca Alternative names:wild strawberry
Description:Anthers from stage 11 flowers; replica...
Analyte type:RNA
...
+
Anther_12_A57918European strawberrywild strawberryFragaria vesca Alternative names:wild strawberry
Description:Anthers from stage 12 flowers; replica...
Analyte type:RNA
...
+
Anther_12_B57918European strawberrywild strawberryFragaria vesca Alternative names:wild strawberry
Description:Anthers from stage 12 flowers; replica...
Analyte type:RNA
...
+
Anther_6-7_A57918European strawberrywild strawberryFragaria vesca Alternative names:wild strawberry
Description:Anthers from stage 6 or 7 flowers; rep...
Analyte type:RNA
...
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Anther_6-7_A57918European strawberrywild strawberryFragaria vesca Alternative names:wild strawberry
Description:Anthers from stage 6 or 7 flowers; rep...
Analyte type:RNA
...
+
Anther_7-8_A57918European strawberrywild strawberryFragaria vesca Alternative names:wild strawberry
Description:Anthers from stage 7 or 8 flowers; rep...
Analyte type:RNA
...
+
Anther_7-8_B57918European strawberrywild strawberryFragaria vesca Alternative names:wild strawberry
Description:Anthers from stage 7 or 8 flowers; rep...
Analyte type:RNA
...
+
Displaying 1-10 of 81 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
otherTAR15.3 MB2017-11-07
Sequence assemblyFASTA213 MB2017-11-07
annotationGFF34.1 MB2017-11-07
otherTEXT6.7 MB2017-11-07
Expression dataUNKNOWN7.6 MB2017-11-07
Coding SequenceFASTA47.3 MB2017-11-07
protein sequenceFASTA12.8 MB2017-11-07
Repeat sequenceFASTA4.8 MB2017-11-07
Optical mapTAR349 MB2017-11-07
Optical mapTAR343 MB2017-11-07
Displaying 1-10 of 11 File(s).
Funding body Awardee Award ID Comments
AgBioResearch Patrick Edger
U.S. Department of Agriculture Steven J Knapp 2017-51181-26833
California Strawberry Commission Steven J Knapp
University of California Steven J Knapp
National Science Foundation Ning Jiang 1121650
Date Action
November 28, 2017 Dataset publish
November 28, 2017 Title updated from : Supporting data for single-molecule sequencing and optical mapping yields an improved genome of woodland strawberry (Fragaria vesca) with chromosome-scale contiguity
November 29, 2017 File F_vesca_v4_makerStandard_proteins.fasta updated
November 29, 2017 File F_vesca_v2nv4_CoGe_Synteny.txt updated
November 29, 2017 File BUSCO_Fvescav4.1.6.tar.gz updated
November 29, 2017 File F_vesca_new_gene_ids_finalAnnot.gff updated
November 29, 2017 File F_vesca_v4_gene_expression.csv updated
November 29, 2017 File F_vesca_v4_makerStandard_CDS.fasta updated
November 29, 2017 File F_vesca_V4_TE_Library.fasta updated
November 29, 2017 File F_vesca_H4_V4.1.fasta updated
November 29, 2017 File HS_aggressive_BspQI.tar.bz2 updated
November 29, 2017 File HS_aggressive_BssSI.tar.bz2 updated
November 29, 2017 File readme.txt updated
November 30, 2017 File readme.txt updated
January 9, 2018 Manuscript Link added : 10.1093/gigascience/gix124