A genome database for a Japanese population of the larvacean Oikopleura dioica

Abstract

The larvacean Oikopleura dioica is a planktonic chordate and is a tunicate that belongs to the closest relatives to vertebrates. Its simple and transparent body, invariant embryonic cell lineages, and short life cycle of 5 days make it a promising model organism for the study of developmental biology. The genome browser OikoBase was established in 2013 using Norwegian O. dioica. However, genome information for other populations is not available, even though many researchers have studied local populations. In the present study, we sequenced using Illumina and PacBio RSII technologies the genome of O. dioica from a southwestern Japanese population that was cultured in our laboratory for 3 years. The genome of Japanese O. dioica was assembled into 576 scaffold sequences with a total length and N50 length of 56.6 and 1.5 Mb, respectively. A total of 18,743 gene models (transcript models) were predicted in the genome assembly, named OSKA2016. In addition, 19,277 non‐redundant transcripts were assembled using RNA‐seq data. The OSKA2016 has global sequence similarity of only 86.5% when compared with the OikoBase, highlighting the sequence difference between the two far distant O. dioica populations on the globe. The genome assembly, transcript assembly, and transcript models were incorporated into ANISEED (https://www.aniseed.cnrs.fr/) for genome browsing and BLAST searches. Mapping of reads obtained from male‐ or female‐specific genome libraries yielded male‐specific scaffolds in the OSKA2016 and revealed that over 2.6 Mb of sequence were included in the male‐specific Y‐region. The genome and transcriptome resources from two distinct populations will be useful datasets for developmental biology, evolutionary biology, and molecular ecology using this model organism.

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

“…Annotation of the genome yielded 18,794 transcript isoforms distributed among 17,260 protein-coding genes. The number of predicted genes for the OKI2018_I69 is slightly lower than what was reported for OdB3 (18,020) [ 9 ] and OSKA2016 (18,743) [ 13 ] (Table 2 ). The rest of the genes are either lost from the Okinawan O. dioica genome or were not assembled and/or annotated with our pipeline.…”

“…Due to limitations in sequencing technologies at the time, it is highly fragmented, comprising 1260 scaffolds with an N50 of 0.4 Mbp. The recently released OSKA2016 assembly was generated from long-read PacBio data and, therefore, has a larger N50 and fewer scaffolds (Table 1 ) [ 13 ]. Both assemblies have high sequence quality and nearly full genome coverage, but neither of them contains resolved chromosomes.…”

“…However, the short life span of O. dioica combined with limited mobility and high mutation rate contribute to an accelerated genome evolution that might have led to multiple speciation events. Sequence polymorphism was previously noted when comparing the OdB3 genome to genomic libraries of a laboratory strain collected on the North American Pacific coast [ 9 ], and more recently when comparing OdB3 to OSKA2016 [ 12 , 13 ]. The chromosome-scale OKI2018_I69 assembly opens up the possibility for further work on cross-comparison among O. dioica populations that will elucidate the relation of the Okinawan populations to the North Atlantic and North Pacific ones.…”

“…The OdB3 assembly was scaffolded with a physical map produced from BAC-end sequences, which revealed two autosomal linkage groups and a sex chromosome with a long pseudo-autosomal region (PAR) [ 9 ]. Recently, a genome assembly for a mainland Japanese population of O. dioica (OSKA2016, OSKA denotes Osaka) was published, which displayed a high level of coding sequence divergence compared with the OdB3 reference [ 12 , 13 ]. Although OSKA2016 was sequenced with single-molecule long reads produced with the PacBio RSII technology, it does not have chromosomal resolution.…”

Telomere-to-telomere assembly of the genome of an individualOikopleura dioicafrom Okinawa using Nanopore-based sequencing

“…To predict alternative isoforms and update the models, we ran the PASA annotation pipeline that yielded 18,485 transcript isoforms distributed among 16,936 protein-coding genes. The number of predicted genes for the OKI2018_I69 is lower than what was reported for OdB3(18,020;Denoeud et al, 2010) and OSKA2016(18,743;Wang et al, 2020). The rest of the genes are either lost from the Okinawan O. dioica genome or were not assembled and/or annotated with our pipeline.…”