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Data released on February 06, 2018

Supporting data for "The genome sequence and transcriptome of Potentilla micrantha and their comparison to Fragaria vesca (the woodland strawberry)"

Buti, M; Moretto, M; Barghini, E; Mascagni, F; Natali, L; Brilli, M; Lomsadze, A; Sonego, P; Giongo, L; Alonge, M; Velasco, R; Varotto, C; Surbanovski, N; Borodovsky, M; Ward, J, A; Engelen, K; Cestaro, A; Cavallini, A; Sargent, D, J (2018): Supporting data for "The genome sequence and transcriptome of Potentilla micrantha and their comparison to Fragaria vesca (the woodland strawberry)" GigaScience Database. http://dx.doi.org/10.5524/100407 RIS BibTeX Text

The genus Potentilla is closely related to that of Fragaria, the economically important strawberry genus. Potentilla micrantha is a species that does not develop berries, but shares numerous morphological and ecological characteristics with F. vesca. These similarities make P. micrantha an attractive choice for comparative genomics studies with F. vesca.
In this study, the Potentilla micrantha genome was sequenced and annotated, and RNA-Seq data from the different developmental stages of flowering and fruiting were used to develop a set of gene predictions. A 327 Mbp sequence and annotation of the genome of P. micrantha, spanning 2,674 sequence contigs, with an N50 size of 335,712, estimated to cover 80% of the total genome size of the species was developed.
The genus Potentilla has a characteristically larger genome size than Fragaria, but the recovered sequence scaffolds were remarkably collinear at the microsyntenic level with the genome of F. vesca, its closest sequenced relative. A total of 33,602 genes were predicted, and 95.1% of BUSCO genes were complete within the presented sequence. Thus, we argue that the majority, of the gene-rich regions of the genome have been sequenced. Comparisons of RNA-Seq data from the stages of floral and fruit development revealed genes differentially expressed between P. micrantha and F. vesca. The data presented are a valuable resource for future studies of berry development in Fragaria and the Rosaceae and they also shed light on the evolution of genome size and organization in this family.

Contact Submitter

Accessions (data included in GigaDB):

PROJECT: PRJEB18433

Keywords:

long-read sequencing evolutionary development angiosperms genome sequence transcriptomics 

Genomic, Transcriptomic

http://gigadb.org/images/data/cropped/100407.jpg

Funding:

  • Funding body - Fondazione Edmund Mach (FEM)
  • Location - Italy
  • Comment - from the Autonomous, Province of Trento grants office
  • Funding body - Università di Pisa
  • Comment - Plantomics
  • Awardee - Andrea Cavellini

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
SAMEA10411770457941  Potentilla micrantha Description:DNA extract from juvenile vascular lea...
Analyte type:DNA
Alternative accession-SRA Sample:ERS1781597
...
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SAMEA10411905957941  Potentilla micrantha Description:DNA extract from juvenile vascular lea...
Analyte type:DNA
Alternative accession-SRA Sample:ERS1782952
...
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SAMEA10413655357941  Potentilla micrantha Description:DNA extract from adult vascular leaf (...
Analyte type:DNA
Alternative accession-SRA Sample:ERS1795571
...
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Displaying 1-3 of 3 Sample(s).

Files: (FTP site) Table Settings

Columns:

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

File NameSample IDData TypeFile FormatSizeRelease Date 
Expression dataEXCEL6.3 MB2018-02-05
Coding sequenceFASTA11.71 KB2018-02-05
AlignmentsFASTA22.02 KB2018-02-05
Repeat sequenceFASTA3.72 MB2018-02-05
protein sequenceFASTA7.74 MB2018-02-05
Genome sequenceFASTA86.09 MB2018-02-05
annotationGFF125.8 KB2018-02-05
ReadmeTEXT3.64 KB2018-02-05
imageTIF5.24 MB2018-02-05
imageTIF4.25 MB2018-02-05
Displaying 1-10 of 14 File(s).

History:

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