TY  - JOUR
AU  - Schmidt, Maximilian HW
AU  - Vogel, Alexander
AU  - Denton, Alisandra K
AU  - Istace, Benjamin
AU  - Wormit, Alexandra
AU  - van de Geest, Henri
AU  - Bolger, Marie
AU  - Alseekh, Saleh
AU  - Maß, Janina
AU  - Pfaff, Christian
AU  - Schurr, Ulrich
AU  - Chetelat, Roger T.
AU  - Maumus, Florian
AU  - Aury, Jean-Marc
AU  - Koren, Sergey
AU  - Fernie, Alisdair R.
AU  - Zamir, Daniel
AU  - Bolger, Anthony
AU  - Usadel, Björn
TI  - De novo Assembly of a New Solanum pennellii Accession Using Nanopore Sequencing
JO  - The plant cell
VL  - 29
IS  - 10
SN  - 1040-4651
CY  - Rockville, Md.
PB  - Soc.
M1  - FZJ-2017-07018
SP  - 2336-2348
PY  - 2017
AB  - 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.
LB  - PUB:(DE-HGF)16
C6  - pmid:29025960
UR  - <Go to ISI:>//WOS:000414861100009
DO  - DOI:10.1105/tpc.17.00521
UR  - https://juser.fz-juelich.de/record/838406
ER  -