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. 2024 Jul 10:9:366.
doi: 10.12688/wellcomeopenres.22585.1. eCollection 2024.

The genome sequence of the heart cockle, Fragum sueziense (Issel, 1869)

Ruiqi Li  1 , Jingchun Li  1   2 , Sarah Lemer  3   4 , Jose Victor Lopez  5 , Graeme Oatley  6 , Elizabeth Sinclair  6 , Isabelle Ailish Clayton-Lucey  6 , Eerik Aunin  6 , Noah Gettle  6 , Camilla Santos  6 , Michael Paulini  6 , Haoyu Niu  6 , Victoria McKenna  6 , Rebecca O'Brien  6 ; Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory Team; Wellcome Sanger Institute Scientific Operations: Sequencing Operations; Wellcome Sanger Institute Tree of Life Core Informatics Team; EBI Aquatic Symbiosis Genomics Data Portal Team; Aquatic Symbiosis Genomics Project Leadership
Affiliations

The genome sequence of the heart cockle, Fragum sueziense (Issel, 1869)

Ruiqi Li et al. Wellcome Open Res. .

Abstract

We present a genome assembly from an individual Fragum sueziense (the heart cockle; Mollusca; Bivalvia; Cardiida; Cardiidae). The genome sequence is 1,206.1 megabases in span. Most of the assembly is scaffolded into 19 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 92.77 kilobases in length. Gene annotation of this assembly on Ensembl identified 70,309 protein-coding genes.

Keywords: Cardiida; Fraginae; Fragum sueziense; chromosomal; genome sequence; heart cockle.

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Conflict of interest statement

No competing interests were disclosed.

Figures

Figure 1.
Figure 1.. Photograph of the Fragum sueziense (xbFraSuez1) specimen used for genome sequencing.
Figure 2.
Figure 2.. Genome assembly of Fragum sueziense, xbFraSuez1.1: 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 1,206,214,559 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 (91,300,129 bp, shown in red). Orange and pale-orange arcs show the N50 and N90 scaffold lengths (59,593,990 and 40,995,196 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 mollusca_odb10 set is shown in the top right .An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/Fragum_sueziense/dataset/GCA_963680895.1/snail.
Figure 3.
Figure 3.. Genome assembly of Fragum sueziense, xbFraSuez1.1: BlobToolKit GC-coverage plot.
Scaffolds are coloured by phylum. Circles are sized in proportion to scaffold length. Histograms show the distribution of scaffold length sum along each axis. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/Fragum_sueziense/dataset/GCA_963680895.1/blob.
Figure 4.
Figure 4.. Genome assembly of Fragum sueziense, xbFraSuez1.1: BlobToolKit cumulative sequence plot.
The grey line shows cumulative length for all scaffolds. Coloured lines show cumulative lengths of scaffolds assigned to each phylum using the buscogenes taxrule. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/Fragum_sueziense/dataset/GCA_963680895.1/cumulative.
Figure 5.
Figure 5.. Genome assembly of Fragum sueziense, xbFraSuez1.1: Hi-C contact map of the xbFraSuez1.1 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=W-A293_JRHOE_RGQ7FQx7A.
See this image and copyright information in PMC

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