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

Publication Overview
TitleThe genome sequence and transcriptome of Potentilla micrantha and their comparison to Fragaria vesca (the woodland strawberry)
AuthorsButi M, Moretto M, Barghini E, Mascagni F, Natali L, Brilli M, Lomsadze A, Sonego P, Giongo L, Alonge M, Velasco R, Varotto C, Šurbanovski N, Borodovsky M, Ward JA, Engelen K, Cavallini A, Cestaro A, Sargent DJ
TypeJournal Article
Journal NameGigaScience
Volume7
Issue4
Year2018
Page(s)1-14
CitationButi M, Moretto M, Barghini E, Mascagni F, Natali L, Brilli M, Lomsadze A, Sonego P, Giongo L, Alonge M, Velasco R, Varotto C, Šurbanovski N, Borodovsky M, Ward JA, Engelen K, Cavallini A, Cestaro A, Sargent DJ. The genome sequence and transcriptome of Potentilla micrantha and their comparison to Fragaria vesca (the woodland strawberry). GigaScience. 2018 Apr 01; 7(4):1-14.

Abstract

Background
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 Fragaria vesca. These similarities make P. micrantha an attractive choice for comparative genomics studies with F. vesca.

Findings
In this study, the P. 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 2674 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 micro-syntenic level with the genome of F. vesca, its closest sequenced relative. A total of 33,602 genes were predicted, and 95.1% of bench-marking universal single-copy orthologous genes were complete within the presented sequence. Thus, we argue that the majority of the gene-rich regions of the genome have been sequenced.

Conclusions
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.

Properties
Additional details for this publication include:
Property NameValue
Publication ModelPrint
ISSN2047-217X
eISSN2047-217X
Publication Date2018 Apr 01
Journal AbbreviationGigascience
DOI10.1093/gigascience/giy010
Elocation10.1093/gigascience/giy010
Journal CountryUnited States
LanguageEnglish
Language Abbreng
Publication TypeJournal Article
Cross References
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DatabaseAccession
PMID: PubMedPMID:29659812