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.

De novo assembly of a chromosome‐level reference genome of red‐spotted grouper (Epinephelus akaara) using nanopore sequencing and Hi‐C

“…Canu, a state‐of‐the‐art genome assembler known to support Oxford Nanopore sequencing technology (Schmidt et al, ), was used with the E. akaara ONT sequenced data. The initial assembly of these ONT data resulted in an assembly size of 1,124 Mb (Table ), which was close to the genome size estimated by the k‐mer distribution analysis (1,111 Mb), suggesting that the E. akaara genome size assembled by ONT reads is appropriate.…”

Computational aspects underlying genome to phenome analysis in plants

“…This trend continues as Oxford Nanopores, the latest long‐read technology, becomes more widely available. This technology (Jain et al ., ) has already successfully been used to reconstruct the Arabidopsis genome (Michael et al ., ) as well as the genome of a non‐model wild tomato species (Schmidt et al ., ) and has the added advantage of not requiring large capital investment. Long reads can not only reveal small‐scale variation and presence−absence dynamics in genes, but also large‐scale variation, including rearrangements from for example transposon activity, and can lead to potentially novel insights into a plant species.…”

“…In some cases, steps of different assemblers can be ‘mixed and matched’ for speed and efficiency. For instance, it can be beneficial to use the error correction steps of Canu coupled to SMART denovo (Schmidt et al ., ) or wtdbg (Koren: https://genomeinformatics.github.io/na12878update/).…”

Nanopore Sequencing Comes to Plant Genomes

“…The application of these new technologies to plant genomes has been challenging, in part because of the large size and highly repetitive nature of many plant genomes. New work from Schmidt et al (2017) reports on the state of the art, using long-read technology to sequence the genome of a wild tomato (Solanum pennellii) accession.…”