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Gigascience. 2018 Apr 1;7(4):1-14. doi: 10.1093/gigascience/giy010.

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

Author information

1
Department of Genomics and Biology of Fruit Crops, Research and Innovation Centre, Fondazione Edmund Mach (FEM) Via E. Mach 1, 38010 San Michele all'Adige, Italy.
2
Center for the Development and Improvement of Agri-Food Resources (BIOGEST-SITEIA) University of Modena and Reggio Emilia, P.le Europa 1, 42124 Reggio nell'Emilia (RE), Italy.
3
Unit of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach (FEM) Via E. Mach 1, 38010 San Michele all'Adige, Italy.
4
Department of Agricultural, Food, and Environmental Sciences, University of Pisa, Pisa I-56124, Italy.
5
Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova Agripolis, V.le dell'Università 16, 35020 Legnaro (PD), Italy.
6
Dipartimento di Bioscienze e Centro di Ricerca Pediatrica Romeo ed Enrica Invernizzi, Università degli Studi di Milano, Via Celoria 26, 20133 Milano.
7
Wallace H. Coulter Department of Biomedical Engineering, Georgia Tech, Atlanta, Georgia.
8
Driscoll's Strawberry Associates, Cassin Ranch, 121 Silliman Drive, Watsonville, California.
9
Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach (FEM) Via E. Mach 1, 38010 San Michele all'Adige, Italy.
10
Driscoll's Genetics Limited, East Malling Enterprise Centre, New Road, East Malling, Kent ME19 6BJ, UK.

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.

PMID:
29659812
PMCID:
PMC5893959
DOI:
10.1093/gigascience/giy010
[Indexed for MEDLINE]
Free PMC Article

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