Hybrid Genome Assembly and Annotation of Danionella Translucida

Overview

Journal Sci Data

Specialty Science

Date 2019 Aug 28

PMID 31451709

Citations 16

Authors

Mykola Kadobianskyi

Lisanne Schulze

Markus Schuelke

Benjamin Judkewitz

Affiliations

Soon will be listed here.

Abstract

Studying neuronal circuits at cellular resolution is very challenging in vertebrates due to the size and optical turbidity of their brains. Danionella translucida, a close relative of zebrafish, was recently introduced as a model organism for investigating neural network interactions in adult individuals. Danionella remains transparent throughout its life, has the smallest known vertebrate brain and possesses a rich repertoire of complex behaviours. Here we sequenced, assembled and annotated the Danionella translucida genome employing a hybrid Illumina/Nanopore read library as well as RNA-seq of embryonic, larval and adult mRNA. We achieved high assembly continuity using low-coverage long-read data and annotated a large fraction of the transcriptome. This dataset will pave the way for molecular research and targeted genetic manipulation of this novel model organism.

Citing Articles

Danionella fishes.

Bass A, Perelmuter J Nat Methods. 2024; 21(10):1767-1769.

PMID: 39384984 DOI: 10.1038/s41592-024-02433-0.

The genome sequence of the Dracula fish, (Britz, Conway & Rüber, 2009).

Ruber L, Britz R, Conway K, Bista I, McCarthy S, Wood J Wellcome Open Res. 2024; 9:194.

PMID: 39224769 PMC: 11367074. DOI: 10.12688/wellcomeopenres.21117.1.

Blazed oblique plane microscopy reveals scale-invariant inference of brain-wide population activity.

Hoffmann M, Henninger J, Veith J, Richter L, Judkewitz B Nat Commun. 2023; 14(1):8019.

PMID: 38049412 PMC: 10695970. DOI: 10.1038/s41467-023-43741-x.

Genome assembly and isoform analysis of a highly heterozygous New Zealand fisheries species, the tarakihi (Nemadactylus macropterus).

Papa Y, Wellenreuther M, Morrison M, Ritchie P G3 (Bethesda). 2022; 13(2).

PMID: 36477875 PMC: 9911067. DOI: 10.1093/g3journal/jkac315.

Longitudinal in vivo imaging of adult Danionella cerebrum using standard confocal microscopy.

Lam P Dis Model Mech. 2022; 15(12).

PMID: 36398624 PMC: 9844135. DOI: 10.1242/dmm.049753.

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