The cosmopolitan appendicularian Oikopleura dioica reveals hidden genetic diversity around the globe

Abstract

Appendicularian tunicates are some of the most abundant mesozooplankton organisms with key roles in marine trophic webs and global carbon flux. Like most appendicularians with cosmopolitan distributions, Oikopleura dioica Fol, 1872 is considered a single species worldwide based on morphological features that distinguish them from other appendicularians. Despite their abundance, however, there are still only ~ 70 described appendicularian species, compared to over 2800 ascidian tunicates. Here we perform a molecular phylogenetic, morphological, and reproductive assessment of O. dioica specimens collected from the Ryukyu Archipelago, mainland Japan, and Europe. The specimens are morphologically very similar, with only detailed examination of the oikoplastic epithelium and quantitative measurements revealing minor distinguishing characteristics. Phylogenetic analyses of the ribosomal gene loci and mitochondrial cytochrome oxidase I (COI) gene strongly indicate that they form three separate genetic clades despite their morphological similarities. Finally, in vitro crosses between the Ryukyu and mainland Japanese specimens show total prezygotic reproductive isolation. Our results reveal that the current taxonomic O. dioica classification likely hides multiple cryptic species, highlighting the genetic diversity and complexity of their population structures. Cryptic organisms are often hidden under a single species name because their morphological similarities make them difficult to distinguish and their correct identification is fundamental to understanding Earth’s biodiversity. O. dioica is an attractive model to understand how morphological conservation can be maintained despite pronounced genetic divergence.

Extreme genome scrambling in crypticOikopleura dioicaspecies

“…Multi-chromosome line plots comparing O. dioica from different locations further revealed that the genome scrambling phenomenon was not restricted to the comparison of Osaka and Okinawa, but instead common amongst all compared genomes (Figure 1B). In general, the extent of genome scrambling increased with increasing genetic distance, as measured by previous analyses of marker genes (Masunaga et al 2022). Comparisons of O. dioica originating from the same geographic region, such as the comparison of two individuals from the subtropical North Pacific population in Okinawa and Kume, showed little scrambling, with large, intact collinear segments of DNA visible.…”

“…Considering the remarkable similarity of morphology and ecology of the O. dioica cryptic species studied here (Masunaga et al 2022), the extent of scrambling that we have observed in the chromosomal assemblies appears to be unprecedented. In order to relate the rate of scrambling to evolutionary distance, we estimated a species tree and divergence times for O. dioica using orthologues common to chordates (Figure 6, Supplementary Table 2).…”

“…We report extensive scrambling of gene order in three species of Oikopleura dioica that are so morphologically similar to each other that they are classified as a single species (Masunaga et al 2022). Our study design utilising 6 genome assemblies ensures that our findings are supported by at least two inter-population comparisons, and each of these comparisons are consistent with the comparison to a second genome from the same species.…”

“…Populations sampled from the Japanese Seto inland sea (Osaka University laboratory strain) and from the sub-tropical island of Okinawa, Japan (OIST laboratory strain), were shown to be reproductively isolated and exhibited remarkably high genetic distance despite their overall phenotypic similarity (Masunaga et al 2022). The process of generating a telomere-to-telomere assembly and gene annotation of O. dioica from Okinawa (Bliznina et al 2021) further prompted important differences in gene organisation through comparison with the assemblies of individuals from Osaka (Denoeud et al 2010;K.…”

Evolutionary Insights from the Mitochondrial Genome ofOikopleura dioica: Sequencing Challenges, RNA Editing, Gene Transfers to the Nucleus, and tRNA Loss

“…These differences suggest that the poly-T/A stretches loci may not be conserved in the mitochondrial genomes of different populations or species. Of note, it was recently suggested that O. dioica from Japan and Norway represent different species (Masunaga, et al 2022). The birth and death dynamics of these poly-T/A stretches will be better clarified when genomic and transcriptomic data from a larger appendicularian taxonomic sampling becomes available.…”