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

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Edger , P P , VanBuren , R , Colle , M , Poorten , T J , Wai , C M , Niederhuth , C E , Alger , E I , Ou , S , Acharya , C B , Wang , J , Callow , P , McKain , M R , Shi , J , Collier , C , Xiong , Z , Mower , J P , Slovin , J P , Hytonen , T , Jiang , N , Childs , K L & Knapp , S J 2017 , ' Single-molecule sequencing and optical mapping yields an improved genome of woodland strawberry (Fragaria vesca) with chromosome-scale contiguity ' , GigaScience , vol. 7 , no. 2 , pp. 1-7 . https://doi.org/10.1093/gigascience/gix124

Title: Single-molecule sequencing and optical mapping yields an improved genome of woodland strawberry (Fragaria vesca) with chromosome-scale contiguity
Author: Edger, Patrick P.; VanBuren, Robert; Colle, Marivi; Poorten, Thomas J.; Wai, Ching Man; Niederhuth, Chad E.; Alger, Elizabeth I.; Ou, Shujun; Acharya, Charlotte B.; Wang, Jie; Callow, Pete; McKain, Michael R.; Shi, Jinghua; Collier, Chad; Xiong, Zhiyong; Mower, Jeffrey P.; Slovin, Janet P.; Hytonen, Timo; Jiang, Ning; Childs, Kevin L.; Knapp, Steven J.
Contributor organization: Strawberry research group
Viikki Plant Science Centre (ViPS)
Department of Agricultural Sciences
Plant Production Sciences
Date: 2017-12-13
Language: eng
Number of pages: 7
Belongs to series: GigaScience
ISSN: 2047-217X
DOI: https://doi.org/10.1093/gigascience/gix124
URI: http://hdl.handle.net/10138/233558
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 similar to 7.9 million base pairs (Mb), representing a similar to 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 similar to 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.
Subject: Fragaria vesca
strawberry
rosaceae
third-generation sequencing
optical map
WILD STRAWBERRY
PHYLOGENETIC ANALYSIS
GENE
DUPLICATIONS
ANNOTATION
EXPRESSION
BRACTEATA
ROSACEAE
INSIGHTS
REGION
414 Agricultural biotechnology
1184 Genetics, developmental biology, physiology
Peer reviewed: Yes
Rights: cc_by
Usage restriction: openAccess
Self-archived version: publishedVersion


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