Tracing Homopolymers inOikopleura dioica’s mitogenome

Abstract

Oikopleura dioica is a planktonic tunicate (Appendicularia class) found extensively across the marine waters of the globe. The genome of a single male individual collected from Okinawa, Japan was sequenced using the single-molecule PacBio Hi-Fi method and assembled with NOVOLoci. The mitogenome is 39,268 bp long, featuring a large control region of around 22,000 bp. We annotated the proteins atp6, cob, cox1, cox2, cox3, nad1, nad4 and nad5, and found one more open reading frame that did not match any known gene. This study marks the first complete mitogenome assembly for an appendicularian, and reveals that A and T homopolymers cumulatively account for nearly half of its length. This reference sequence will be an asset for environmental DNA and phylogenetic studies.

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

“…The sequence PP146516 from Okinawa (Dierckxsens et al 2024) not only greatly differed from the Norway sequences, (above 111 bp difference in the barcoding region and K2P distance of above 0.198 substitutions per site) but also greatly differed from the Japanese contig we had assembled from mainland Japan (94 bp difference in the barcoding region and K2P distance of 0.163 substitutions per site), supporting the view that PP146516 belongs to a third Oikopleura lineage (Masunaga et al 2022;Plessy et al 2024).…”

“…dioica from Okinawa (Japan) (accession number PP146516) was reported in a preprint (Dierckxsens et al 2024). While numerous substitutions differentiate the two genomic sequences (113 bp difference in the barcoding region corresponding to a K2P distance of 20.3%), the gene order was identical.…”

“…One difference is that of the presence of a region containing several tandem repeats between the cox1 and the gene we have labeled ODI_mt_ORF196. Remarkably, Dierckxsens et al (2024) succeeded in assembling a circular molecule. The region in the Okinawa sample that is homologous to the part that we failed to sequence, is a large non-coding region of ~28,000 bp composed of numerous repetitive elements.…”

The complete mitogenome of an unidentifiedOikopleuraspecies

“…Appendicularian mitochondrial genomes use the ascidian mitochondrial genetic code [4,5,6,7,8], which differs from the invertebrate one by the reassignment of AGR codons from serine to glycine. In one clade within appendicularians containing O. dioica, homopolymers interrupt coding sequences and are resolved to hexamers by an unknown editing process [4,6,7].…”

“…Appendicularian mitochondrial genomes use the ascidian mitochondrial genetic code [4,5,6,7,8], which differs from the invertebrate one by the reassignment of AGR codons from serine to glycine. In one clade within appendicularians containing O. dioica, homopolymers interrupt coding sequences and are resolved to hexamers by an unknown editing process [4,6,7]. In this study, we sequenced the mitochondrial genome of an unknown appendicularian species sampled from the Amami Oshima island, Japan, in order to increase the taxonomic power of eDNA studies based on the sequence of mitochondrial genes.…”