Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

The genome sequence of the blonde ray, Raja brachyura Lafont, 1871

Patrick Adkins et al. Wellcome Open Res. .

Abstract

We present a genome assembly from an individual female Raja brachyura (Blonde Ray; Chordata; Chondrichthyes; Rajiformes; Rajidae). The genome sequence spans 2,700.50 megabases. Most of the assembly is scaffolded into 49 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 17.12 kilobases in length. Gene annotation of this assembly on Ensembl identified 24,252 protein-coding genes.

Keywords: Raja brachyura; Rajiformes; blonde ray; chromosomal; genome sequence.

PubMed Disclaimer

Conflict of interest statement

No competing interests were disclosed.

Figures

Figure 1.
Figure 1.
Photograph of the Raja brachyura (sRajBra1) specimen used for genome sequencing: A. Dorsal view, B. Ventral view.
Figure 2.
Figure 2.. Genome assembly of Raja brachyura, sRajBra1.1: metrics.
The BlobToolKit snail plot shows N50 metrics and BUSCO gene completeness. The main plot is divided into 1,000 size-ordered bins around the circumference with each bin representing 0.1% of the 2,700,467,673 bp assembly. The distribution of scaffold lengths is shown in dark grey with the plot radius scaled to the longest scaffold present in the assembly (187,439,314 bp, shown in red). Orange and pale-orange arcs show the N50 and N90 scaffold lengths (68,366,687 and 26,303,439 bp), respectively. The pale grey spiral shows the cumulative scaffold count on a log scale with white scale lines showing successive orders of magnitude. The blue and pale-blue area around the outside of the plot shows the distribution of GC, AT and N percentages in the same bins as the inner plot. A summary of complete, fragmented, duplicated and missing BUSCO genes in the vertebrata_odb10 set is shown in the top right. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/Raja%20brachyura/dataset/CAUPSL01/snail.
Figure 3.
Figure 3.. Genome assembly of Raja brachyura, sRajBra1.1: BlobToolKit GC-coverage plot.
Sequences are coloured by phylum. Circles are sized in proportion to sequence length. Histograms show the distribution of sequence length sum along each axis. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/Raja%20brachyura/dataset/CAUPSL01/blob.
Figure 4.
Figure 4.. Genome assembly of Raja brachyura sRajBra1.1: BlobToolKit cumulative sequence plot.
The grey line shows cumulative length for all sequences. Coloured lines show cumulative lengths of sequences assigned to each phylum using the buscogenes taxrule. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/Raja%20brachyura/dataset/CAUPSL01/cumulative.
Figure 5.
Figure 5.. Genome assembly of Raja brachyura sRajBra1.1: Hi-C contact map of the sRajBra1.1 assembly, visualised using HiGlass.
Chromosomes are shown in order of size from left to right and top to bottom. An interactive version of this figure may be viewed at https://genome-note-higlass.tol.sanger.ac.uk/l/?d=DS9CH9xQRVC81LrwHEfXaQ.
See this image and copyright information in PMC

References

    1. Abdennur N, Mirny LA: Cooler: scalable storage for Hi-C data and other genomically labeled arrays. Bioinformatics. 2020;36(1):311–316. 10.1093/bioinformatics/btz540 - DOI - PMC - PubMed
    1. Aken BL, Ayling S, Barrell D, et al. : The ensembl gene annotation system. Database (Oxford). 2016;2016: baw093. 10.1093/database/baw093 - DOI - PMC - PubMed
    1. Allio R, Schomaker-Bastos A, Romiguier J, et al. : MitoFinder: efficient automated large-scale extraction of mitogenomic data in target enrichment phylogenomics. Mol Ecol Resour. 2020;20(4):892–905. 10.1111/1755-0998.13160 - DOI - PMC - PubMed
    1. Beasley J, Uhl R, Forrest LL, et al. : DNA barcoding SOPs for the Darwin Tree of Life Project. protocols.io. 2023; [Accessed 25 June 2024]. 10.17504/protocols.io.261ged91jv47/v1 - DOI
    1. Challis R, Richards E, Rajan J, et al. : BlobToolKit – interactive quality assessment of genome assemblies. G3 (Bethesda). 2020;10(4):1361–1374. 10.1534/g3.119.400908 - DOI - PMC - PubMed

LinkOut - more resources