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Gigascience. 2018 Feb 1;7(2):1-7. doi: 10.1093/gigascience/gix124.

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

Author information

1
Department of Horticulture, Ecology, Evolutionary Biology, and Behavior, Department of Plant Biology, and Center for Genomics Enabled Plant Science, Michigan State University, East Lansing, Michigan, 48823.
2
Ecology, Evolutionary Biology, and Behavior, Department of Plant Biology, and Center for Genomics Enabled Plant Science, Michigan State University, East Lansing, Michigan, 48823.
3
Department of Plant Sciences, University of California - Davis, Davis, California, 95616.
4
Department of Genetics, University of Georgia, Athens, Georgia, 30602.
5
Department of Plant Biology, and Center for Genomics Enabled Plant Science, Michigan State University, East Lansing, Michigan, 48823.
6
Donald Danforth Plant Science Center, St. Louis, Missouri, 63132.
7
Bionano Genomics, San Diego, California, 92121.
8
Potato Engineering and Technology Research Center, Inner Mongolia University, Hohhot, 010021, China.
9
Center for Plant Science Innovation, University of Nebraska, Lincoln, Nebraska, 68588.
10
USDA/ARS, Genetic Improvement of Fruits and Vegetables Laboratory, Beltsville, Maryland, 20705.
11
Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, 00014, Finland.
12
Center for Genomics Enabled Plant Science, Michigan State University, East Lansing, Michigan, 48823.

Abstract

Background:

Although draft genomes are available for most agronomically important plant species, the majority are incomplete, highly fragmented, and often riddled with assembly and scaffolding errors. These assembly issues hinder advances in tool development for functional genomics and systems biology.

Findings:

Here we utilized a robust, cost-effective approach to produce high-quality reference genomes. 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 million base pairs (Mb), representing a ∼300-fold improvement of the previous version. The vast majority (>99.8%) of the assembly was anchored to 7 pseudomolecules using 2 sets of optical maps from Bionano Genomics. We obtained ∼24.96 Mb of sequence not present in the previous version of the F. vesca genome and produced an improved annotation that includes 1496 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.

Conclusions:

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.

KEYWORDS:

Fragaria vesca; optical map; rosaceae; strawberry; third-generation sequencing

PMID:
29253147
PMCID:
PMC5801600
DOI:
10.1093/gigascience/gix124
[Indexed for MEDLINE]
Free PMC Article

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