Skip to Main content Skip to Navigation
Journal articles

De novo assembly of a new Solanum pennellii accession using nanopore sequencing

Abstract : Updates in nanopore technology have made it possible to obtain gigabases of sequence data. Prior to this, nanopore sequencing technology was mainly used to analyze microbial samples. Here, we describe the generation of a comprehensive nanopore sequencing data set with a median read length of 11,979 bp for a self-compatible accession of the wild tomato species Solanum pennellii. We describe the assembly of its genome to a contig N50 of 2.5 MB. The assembly pipeline comprised initial read correction with Canu and assembly with SMARTdenovo. The resulting raw nanopore-based de novo genome is structurally highly similar to that of the reference S. pennellii LA716 accession but has a high error rate and was rich in homopolymer deletions. After polishing the assembly with Illumina reads, we obtained an error rate of <0.02% when assessed versus the same Illumina data. We obtained a gene completeness of 96.53%, slightly surpassing that of the reference S. pennellii. Taken together, our data indicate that such long read sequencing data can be used to affordably sequence and assemble gigabase-sized plant genomes.
Document type :
Journal articles
Complete list of metadata

Cited literature [72 references]  Display  Hide  Download

https://hal.inrae.fr/hal-02625700
Contributor : Migration Prodinra Connect in order to contact the contributor
Submitted on : Tuesday, May 26, 2020 - 3:20:19 PM
Last modification on : Wednesday, November 3, 2021 - 4:21:59 AM

File

2017_Schmidt_Plant Cell_1.pdf
Publisher files allowed on an open archive

Licence


Distributed under a Creative Commons Attribution 4.0 International License

Identifiers

Collections

Citation

Maximilian H.-W. Schmidt, Alexander Vogel, Alisandra K. Denton, Benjamin Istace, Alexandra Wormit, et al.. De novo assembly of a new Solanum pennellii accession using nanopore sequencing. The Plant cell, American Society of Plant Biologists (ASPB), 2017, 29, pp.2336-2348. ⟨10.1105/tpc.17.00521⟩. ⟨hal-02625700⟩

Share

Metrics

Record views

69

Files downloads

140