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. 2024 Sep 3;16(9):evae182.
doi: 10.1093/gbe/evae182.

Tracing Homopolymers in Oikopleura dioica's Mitogenome

Nicolas Dierckxsens  1 , Kosei Watanabe  1   2 , Yongkai Tan  1 , Aki Masunaga  1 , Michael J Mansfield  1 , Jiashun Miao  1 , Nicholas M Luscombe  1 , Charles Plessy  1
Affiliations

Tracing Homopolymers in Oikopleura dioica's Mitogenome

Nicolas Dierckxsens et al. Genome Biol Evol. .

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.

Keywords: Appendicularia; Oikopleura dioica; homopolymers; larvacean; tunicate.

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Conflict of interest statement

No potential conflict of interest was reported by the authors.

Figures

Fig. 1.
Fig. 1.
Pie charts showing the proportion of the homopolymers of six successive bases or longer. C repeats do not exist and G repeats are slight in proportion, thus excluded from the charts.
Fig. 2.
Fig. 2.
Relation between cox1 sequenced this work and the other publicly available appendicularian sequences. Bootstrap values are displayed on each node.
Fig. 3.
Fig. 3.
Known protein-coding gene symbols are displayed on a green background for plus-strand genes and yellow for minus strand. Unknown proteins and transcript models are displayed in gray. The inner circle illustrates the repetitive regions; six or more successive A or T's are colored, respectively, red and blue.
See this image and copyright information in PMC

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