Telomere-to-telomere assembly of the genome of an individual Oikopleura dioica from Okinawa using Nanopore-based sequencing

Genome and transcriptome reads generated with various sequencing technologies for individuals of Oikopleura dioica, a globally distributed tunicate zooplankton. These data were used to generate OKI2018_I69_1.0 reference genome assembly. All O. dioica specimens for this study were collected from on-going laboratory culture deriving from the wild population in Ishikawa Harbor (Okinawa; 26°25'39.3"N 127°49'56.6"E). A fully matured male called I69 was collected at generation 47. Genomic DNA (~200 ng) isolated from I69 was sequenced with Oxford Nanopore MinION technology. The raw Nanopore reads submitted here were basecalled with the Guppy software version 2.3.5 (model “template_r9.4.1_450bps_large_flipflop”), and are also provided in raw FAST5 format to support re-basecalling with improved algorithms. The Nanopore reads were assembled into contigs with Canu pipeline v1.8 (correctedErrorRate=0.105, minReadLength=1000). In addition, around 5 ng of the I69 genomic DNA was whole-genome amplified and sequenced with Illumina MiSeq platform. The Illumina data from this run was used for polishing and error correction of the I69 contig assembly. The Hi-C libraries were prepared from 50 mature males following manufacturer's protocol (Dovetail, 21004) and sequenced on Illumina MiSeq platform. Resulting reads were used to order and orient the contigs into scaffolds (OKI2018_I69_1.0 assembly). Mixed stage embryos, immature adults (3 days after hatching) and adults (4 days after hatching) were collected separately from the laboratory culture for RNA-Seq analysis. Total RNA was extracted and isolated with RNeasy Micro Kit. Each cDNA library was sequenced paired-end with Illumina MiSeq platform. The RNA-Seq data was used to assemble transcriptome with Trinity software and to predict gene model in the OKI2018_I69_1.0 assembly. Another O. dioica male called I28 was collected at generation 44. The DNA extracted from I28 individual was sequenced with Nanopore technology. The reads basecalled with Guppy were assembled with Canu pipeline. The reads were assembled into OKI2018_I28 contig assembly that was used to validate the OKI2018_I69_1.0 genome assembly.