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

Abstract

Background The larvacean Oikopleura dioica is an abundant tunicate plankton with the smallest (65–70 Mbp) non-parasitic, non-extremophile animal genome identified to date. Currently, there are two genomes available for the Bergen (OdB3) and Osaka (OSKA2016) O. dioica laboratory strains. Both assemblies have full genome coverage and high sequence accuracy. However, a chromosome-scale assembly has not yet been achieved. Results Here, we present a chromosome-scale genome assembly (OKI2018_I69) of the Okinawan O. dioica produced using long-read Nanopore and short-read Illumina sequencing data from a single male, combined with Hi-C chromosomal conformation capture data for scaffolding. The OKI2018_I69 assembly has a total length of 64.3 Mbp distributed among 19 scaffolds. 99% of the assembly is contained within five megabase-scale scaffolds. We found telomeres on both ends of the two largest scaffolds, which represent assemblies of two fully contiguous autosomal chromosomes. Each of the other three large scaffolds have telomeres at one end only and we propose that they correspond to sex chromosomes split into a pseudo-autosomal region and X-specific or Y-specific regions. Indeed, these five scaffolds mostly correspond to equivalent linkage groups in OdB3, suggesting overall agreement in chromosomal organization between the two populations. At a more detailed level, the OKI2018_I69 assembly possesses similar genomic features in gene content and repetitive elements reported for OdB3. The Hi-C map suggests few reciprocal interactions between chromosome arms. At the sequence level, multiple genomic features such as GC content and repetitive elements are distributed differently along the short and long arms of the same chromosome. Conclusions We show that a hybrid approach of integrating multiple sequencing technologies with chromosome conformation information results in an accurate de novo chromosome-scale assembly of O. dioica’s highly polymorphic genome. This genome assembly opens up the possibility of cross-genome comparison between O. dioica populations, as well as of studies of chromosomal evolution in this lineage.

Improved Understanding of the Role of Gene and Genome Duplications in Chordate Evolution With New Genome and Transcriptome Sequences

“…several different tunicate lineages, including a chromosomal level assembly of O. dioica (Bliznina et al, 2021). Sequencing of two C. intestinalis Type B (i.e., C. intestinalis rather than C. robusta) genomes revealed that between and even within Ciona species, there have been many chromosomal inversions and there are high levels of polymorphism (Satou et al, 2021).…”

Modular Evolution and Population Variability of Oikopleura dioica Metallothioneins

“…The peculiar structural and evolutionary characteristics of OdiMTs together with the high evolutionary rate of O. dioica (Denoeud et al, 2010;Berna et al, 2012;Berna and Alvarez-Valin, 2014), and significant level of sequence variation detected between O. dioica populations (Wang et al, 2015(Wang et al, , 2020Bliznina et al, 2021), prompted us to investigate the OdiMT sequences in several O. dioica populations worldwide distributed. We analyzed the MT sequences from animals from Norway (NOR), Oregon (ORE), Japan (Japanese specimens were from two different localizations, Osaka (OSA) and Okinawa (OKI), and we have analyzed FIGURE 3 | Deconvoluted ESI-MS spectra recorded at pH 7.0 (A,B,E,F) and pH 2.4 (C,D,G,H) of OdiMT2 constructs 2.1 (A-D) and 2.2 (E-H) bioproduced with Zn (A,C,E,G) or Cd (B,D,F,H).…”

“…Second, we have shown a direct relationship between the number of the t-12C/12C domain repeats and the metal-binding capacity of OdiMTs. Finally, taking advantage of the high level of genetic variation among O. dioica populations (Wang et al, 2020;Bliznina et al, 2021), we have detected population variants of OdiMT2 with changes in their number of t-12C/12C domains. Our data expose a high structural plasticity of MTs in O. dioica that, as if it was a natural test-bench, seems to be exploring the chordate limits of MT modularity.…”

Diversity of Modes of Reproduction and Sex Determination Systems in Invertebrates, and the Putative Contribution of Genetic Conflict

“…Sex chromosomes are «heteromorphic» or differentiated when the X and the Y have different morphologies and genetic content, and «homomorphic» when they are morphologically indistinguishable. Sex chromosomes are present in many invertebrate species such as the sea urchin Paracentrotus lividus, the coral Corallium rubrum, the only non-bilaterian species for which GSD has been described so far [60,61], or Oikopleura dioica, the only gonochoric species among tunicates [62]. In other groups, such as Lepidoptera or parasitic flatworms from the genus Schistosoma, sex is determined by a ZW system, with ZZ individuals being males and ZW (or Z0) individuals being females.…”