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.
Original language | English (US) |
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Article number | gix124 |
Journal | GigaScience |
Volume | 7 |
Issue number | 2 |
DOIs |
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State | Published - Feb 1 2018 |
Funding
We thank the reviewers and Editor for their helpful comments during the review of this manuscript. This work was supported by Michigan State University AgBioResearch to P.P.E., USDA-NIFA HATCH 1009804 to P.P.E., NSF MCB-1121650 to N.J., USDA-NIFA SCRI 2017-51181-26833 to S.J.K., California Strawberry Commission to S.J.K., and University of California to S.J.K
Keywords
- Fragaria vesca
- Optical map
- Rosaceae
- Strawberry
- Third-generation sequencing
ASJC Scopus subject areas
- General Medicine