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

Abstract

Sequencing the mitochondrial genome of the tunicateOikopleura dioicais a challenging task because of the presence of long poly-T/A homopolymer stretches, which impair sequencing and assembly. Here, we report the sequencing and annotation of the majority of the mitochondrial genome ofO. dioicaby combining several DNA and amplicon reads obtained by Illumina and MinIon Oxford Nanopore Technologies (ONT) with public RNA sequences. We document extensive RNA editing, since all homopolymer stretches present in the mitochondrial DNA correspond to 6U-regions in the mitochondrial RNA. Out of the 13 canonical protein-coding genes, we were able to detect eight plus an unassigned ORF, which lacked sequence similarity to canonical mitochondrial protein-coding genes. We showed that thenad3gene has been transferred to the nucleus and acquired a mitochondria-targeting signal. In addition to two very short rRNAs, we could only identify a single tRNA (tRNA-Met), suggesting multiple losses of tRNA genes, supported by a corresponding loss of mitochondrial aminoacyl-tRNA synthetases in the nuclear genome. Based on the eight canonical protein-coding genes identified, we reconstructed maximum likelihood and Bayesian phylogenetic trees and inferred an extreme evolutionary rate of this mitochondrial genome. However, the phylogenetic position of appendicularians among tunicates could not be accurately determined.