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

Publication Overview
TitleSingle-molecule sequencing and optical mapping yields an improved genome of woodland strawberry (Fragaria vesca) with chromosome-scale contiguity
AuthorsEdger PP, VanBuren R, Colle M, Poorten TJ, Wai CM, Niederhuth CE, Alger EI, Ou S, Acharya CB, Wang J, Callow P, McKain MR, Shi J, Collier C, Xiong Z, Mower JP, Slovin JP, Hytönen T, Jiang N, Childs KL, Knapp SJ
TypeJournal Article
Journal NameGigaScience
Volume7
Issue2
Year2017
Page(s)1-7
CitationEdger PP, VanBuren R, Colle M, Poorten TJ, Wai CM, Niederhuth CE, Alger EI, Ou S, Acharya CB, Wang J, Callow P, McKain MR, Shi J, Collier C, Xiong Z, Mower JP, Slovin JP, Hytönen T, Jiang N, Childs KL, Knapp SJ. Single-molecule sequencing and optical mapping yields an improved genome of woodland strawberry (Fragaria vesca) with chromosome-scale contiguity. GigaScience. 2017 Dec 13; 7(2):1-7.

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 seven pseudomolecules using two 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 1,496 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.

Properties
Additional details for this publication include:
Property NameValue
DOI10.1093/gigascience/gix124
eISSN2047-217X
Elocation10.1093/gigascience/gix124
ISSN2047-217X
Journal AbbreviationGigascience
Journal CountryUnited States
LanguageEnglish
Language Abbreng
Publication Date2017 Dec 13
Publication ModelPrint-Electronic
Publication TypeJournal Article
Published Location1-7
Cross References
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DatabaseAccession
PMID: PubMedPMID:29253147