A chromosome-scale assembly of the Oikopleura dioica genome from Okinawa, Japan. The contig assembly was generated with long-read Nanopore data using Canu pipeline v1.8, and polished with short Illumina MiSeq reads using Pilon v1.22. Both Nanopore and Illumina data were generated from DNA of a single O. dioica male. Hi-C chromosomal conformation capture data was used to order and orient the contigs into scaffolds using Juicer v1.6 and 3D de novo assembly (3D-DNA) pipelines. The OKI2018_I69_1.0 assembly comprises 19 scaffolds with an N50 of 16.2 Mbp (OKI2018_I69_1.0.fa). The total assembly length is 64.3 Mbp. The five longest scaffolds represent autosomal chromosomes (chr 1 and chr 2), and sex chromosomes split into pseudo-autosomal region (PAR) and X-specific (XSR) or Y-specific (YSR) regions. One of the smaller scaffolds represent a draft assembly of mitochondrial genome (chrUn_12). The rest of scaffolds are highly repetitive and were marked as unplaced. The OKI2018_I69_1.0 assembly was annotated with AUGUSTUS v3.3 and MAKER v3.01.03 pipelines. Gene predictions from these software were refined and merged using EvidenceModeler v1.1.1. To predict UTRs and alternative isoforms, the EVM models were updated using two round of PASA pipeline, resulting in 18,485 transcript models distributed among 16,936 protein-coding genes (OKI2018_I69_1.0.gene_models.gff3).

The genome is now published in BMC genomics (Bliznina et al., 2021) and deposited to ENA (BioProject ID PRJEB40135) .