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000838406 1001_ $$0P:(DE-HGF)0$$aSchmidt, Maximilian HW$$b0
000838406 245__ $$aDe novo Assembly of a New Solanum pennellii Accession Using Nanopore Sequencing
000838406 260__ $$aRockville, Md.$$bSoc.$$c2017
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000838406 520__ $$aUpdates 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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000838406 7001_ $$0P:(DE-HGF)0$$aVogel, Alexander$$b1
000838406 7001_ $$0P:(DE-HGF)0$$aDenton, Alisandra K$$b2
000838406 7001_ $$0P:(DE-HGF)0$$aIstace, Benjamin$$b3
000838406 7001_ $$0P:(DE-HGF)0$$aWormit, Alexandra$$b4
000838406 7001_ $$0P:(DE-HGF)0$$avan de Geest, Henri$$b5
000838406 7001_ $$0P:(DE-Juel1)162335$$aBolger, Marie$$b6$$ufzj
000838406 7001_ $$0P:(DE-HGF)0$$aAlseekh, Saleh$$b7
000838406 7001_ $$0P:(DE-HGF)0$$aMaß, Janina$$b8
000838406 7001_ $$0P:(DE-Juel1)164481$$aPfaff, Christian$$b9$$ufzj
000838406 7001_ $$0P:(DE-Juel1)129402$$aSchurr, Ulrich$$b10$$ufzj
000838406 7001_ $$0P:(DE-HGF)0$$aChetelat, Roger T.$$b11
000838406 7001_ $$0P:(DE-HGF)0$$aMaumus, Florian$$b12
000838406 7001_ $$0P:(DE-HGF)0$$aAury, Jean-Marc$$b13
000838406 7001_ $$0P:(DE-HGF)0$$aKoren, Sergey$$b14
000838406 7001_ $$0P:(DE-HGF)0$$aFernie, Alisdair R.$$b15
000838406 7001_ $$0P:(DE-HGF)0$$aZamir, Daniel$$b16
000838406 7001_ $$0P:(DE-HGF)0$$aBolger, Anthony$$b17
000838406 7001_ $$0P:(DE-Juel1)145719$$aUsadel, Björn$$b18$$eCorresponding author
000838406 773__ $$0PERI:(DE-600)2004373-9$$a10.1105/tpc.17.00521$$gp. tpc.00521.2017 -$$n10$$p2336-2348$$tThe plant cell$$v29$$x1040-4651$$y2017
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