Evidence map›Paper›PMID 39162185›Full record

ArticleGenome biology and evolution2024

Tracing Homopolymers in Oikopleura dioica's Mitogenome.

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

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genome biology and evolution, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

3 citing papers in PubMed.

  1. Article
  2. Article
  3. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

8 authors.

Nicolas DierckxsensGenomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.ORCID 0000-0001-8051-6602
Kosei WatanabeGenomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.
Yongkai TanGenomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.ORCID 0000-0002-1413-3424
Aki MasunagaGenomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.ORCID 0000-0002-6913-8417
Michael J MansfieldGenomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.ORCID 0000-0003-4717-4721
Jiashun MiaoGenomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.ORCID 0000-0002-5227-5431
Nicholas M LuscombeGenomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.ORCID 0000-0001-5293-4778
Charles PlessyGenomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.ORCID 0000-0001-7410-6295

Funding

Japan Society for the Promotion of ScienceJSPS International Research FellowLuscombe UnitOISTOIST x KEIO Long-term Research Internship Program
6 · The paper itself

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.

Indexed as

Genome, MitochondrialUrochordataAnimalsMalePhylogenyAppendiculariahomopolymerslarvaceanOikopleura dioicatunicate

Identifiers

PMID39162185
PMCPMC11384890

What OpenQuestion holds

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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.