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Data released on November 28, 2017

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

Edger, P; VanBuren, R; Colle, M; Poorten, T, J; Wai, C, M; Niederhuth, C, E; Alger, E, I; Ou, S; Acharya, C, B; Wang, J; Callow, P; McKain, M, R; Shi, J; Collier, C; Xiong, Z; Mower, J, P; Slovin, J, P; Hytonen, T; Jiang, N; Childs, K, L; Knapp, S, J (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 RIS BibTeX Text

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.

Contact Submitter

Accessions (data included in GigaDB):

BioProject: PRJNA383733

Keywords:

Genomic, Genome-Mapping

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Funding:

  • Funding body - AgBioResearch
  • Awardee - Patrick Edger
  • Funding body - U.S. Department of Agriculture
  • Award ID - 2017-51181-26833
  • Awardee - Steven J Knapp
  • Funding body - California Strawberry Commission
  • Awardee - Steven J Knapp
  • Funding body - University of California
  • Awardee - Steven J Knapp
  • Funding body - National Science Foundation
  • Award ID - 1121650
  • Awardee - Ning Jiang

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
Cortex1_157918European strawberrywild strawberryFragaria vesca Alternative names: wild strawberry
Description: Stage 1 cortex replicate 1: cortex ti...
Analyte type: RNA
...
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Cortex1_257918European strawberrywild strawberryFragaria vesca Alternative names: wild strawberry
Description: Stage 1 cortex replicate 2: cortex ti...
Analyte type: RNA
...
+
Cortex2_157918European strawberrywild strawberryFragaria vesca Alternative names: wild strawberry
Description: Stage 2 cortex replicate 1: cortex ti...
Analyte type: RNA
...
+
Cortex2_257918European strawberrywild strawberryFragaria vesca Alternative names: wild strawberry
Description: Stage 2 cortex replicate 2: cortex ti...
Analyte type: RNA
...
+
Cortex3_157918European strawberrywild strawberryFragaria vesca Alternative names: wild strawberry
Description: Stage 3 cortex replicate 1: cortex ti...
Analyte type: RNA
...
+
Cortex3_257918European strawberrywild strawberryFragaria vesca Alternative names: wild strawberry
Description: Stage 3 cortex replicate 2: cortex ti...
Analyte type: RNA
...
+
Cortex4_157918European strawberrywild strawberryFragaria vesca Alternative names: wild strawberry
Description: Stage 4 cortex replicate 1: cortex ti...
Analyte type: RNA
...
+
Cortex4_257918European strawberrywild strawberryFragaria vesca Alternative names: wild strawberry
Description: Stage 4 cortex replicate 2: cortex ti...
Analyte type: RNA
...
+
Cortex5_157918European strawberrywild strawberryFragaria vesca Alternative names: wild strawberry
Description: Stage 5 cortex replicate 1: cortex ti...
Analyte type: RNA
...
+
Cortex5_257918European strawberrywild strawberryFragaria vesca Alternative names: wild strawberry
Description: Stage 5 cortex replicate 2: cortex ti...
Analyte type: RNA
...
+
Displaying 21-30 of 81 Sample(s).

Files: (FTP site) Table Settings

Columns:

File Description
Sample ID
File Type
File Format
Size
Release Date
Download Link
File Attributes

File NameSample IDFile 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).

History:

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