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

Dataset type: Genomic, Transcriptomic
Data released on February 06, 2018

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 JA; Engelen K; Cestaro A; Cavallini A; Sargent DJ (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

DOI10.5524/100407

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.

Additional details

Read the peer-reviewed publication(s):

Buti, M., Moretto, M., Barghini, E., Mascagni, F., Natali, L., Brilli, M., … Sargent, D. J. (2017). The genome sequence and transcriptome of Potentilla micrantha and their comparison to Fragaria vesca (the woodland strawberry). GigaScience, 7(4). doi:10.1093/gigascience/giy010

Accessions (data included in GigaDB):

PROJECT: PRJEB18433





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).




File NameSample IDData TypeFile FormatSizeRelease Date 
ReadmeTEXT3.64 KB2018-02-05
Phylogenetic treeUNKNOWN4.34 KB2018-02-05
Phylogenetic treeUNKNOWN7.67 KB2018-02-05
Coding sequenceFASTA11.71 KB2018-02-05
AlignmentsFASTA22.02 KB2018-02-05
annotationGFF125.8 KB2018-02-05
annotationUNKNOWN3.09 MB2018-02-05
Repeat sequenceFASTA3.72 MB2018-02-05
imageTIF4.25 MB2018-02-05
imageTIF5.24 MB2018-02-05
Displaying 1-10 of 14 File(s).
Funding body Awardee Award ID Comments
Fondazione Edmund Mach (FEM) from the Autonomous, Province of Trento grants office
Università di Pisa Andrea Cavellini Plantomics
Date Action
February 6, 2018 Dataset publish
March 7, 2018 Sample Attribute added : of Sample SAMPLE:SAMEA104136553
March 7, 2018 Sample Attribute added : of Sample SAMPLE:SAMEA104136553
March 7, 2018 Sample Attribute added : of Sample SAMPLE:SAMEA104136553
March 7, 2018 Sample Attribute added : of Sample SAMPLE:SAMEA104136553
March 7, 2018 Sample Attribute added : of Sample SAMPLE:SAMEA104136553
March 7, 2018 Sample Attribute added : of Sample SAMPLE:SAMEA104136553
March 7, 2018 Sample Attribute added : of Sample SAMPLE:SAMEA104136553
March 7, 2018 Sample Attribute added : of Sample SAMPLE:SAMEA104136553
March 7, 2018 Sample Attribute added : of Sample SAMPLE:SAMEA104136553
July 3, 2018 Manuscript Link added : 10.1093/gigascience/giy010