期刊
PLANT CELL
卷 29, 期 10, 页码 2336-2348出版社
OXFORD UNIV PRESS INC
DOI: 10.1105/tpc.17.00521
关键词
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资金
- Federal Ministry of Education and Research [0315961, 031A053, 031A536C]
- Ministry of Innovation, Science, and Research [313/323-400-002 13]
- Deutsche Forschungsgemeinschaft within ERACAPS Regulatome [US98/7-1, FE552/29-1]
- Deutsche Forschungsgemeinschaft (Grossgerate NextSeq LC-MS)
- France Genomique [ANR-10-INBS-09]
- Horizon-2020 Grant G2P-SOL [677379]
- Intramural Research Program of the National Human Genome Research Institute, National Institutes of Health
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.
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