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. 2024 May 21:9:286.
doi: 10.12688/wellcomeopenres.22286.1. eCollection 2024.

The genome sequence of the cut surfclam, Spisula subtruncata (da Costa, 1778)

Patrick Adkins  1 , Anna Holmes  2 , Andrew Mackie  2 , Teresa Darbyshire  2 ; Marine Biological Association Genome Acquisition Lab; Darwin Tree of Life Barcoding collective; 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; Tree of Life Core Informatics collective; Darwin Tree of Life Consortium
Affiliations

The genome sequence of the cut surfclam, Spisula subtruncata (da Costa, 1778)

Patrick Adkins et al. Wellcome Open Res. .

Abstract

We present a genome assembly from a specimen of Spisula subtruncata (the cut surfclam; Mollusca; Bivalvia; Venerida; Mactridae). The genome sequence is 930.8 megabases in span. Most of the assembly is scaffolded into 19 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 19.64 kilobases in length.

Keywords: Spisula subtruncata; Venerida; chromosomal; cut surfclam; genome sequence.

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Conflict of interest statement

No competing interests were disclosed.

Figures

Figure 1.
Figure 1.. Photograph of the Spisula subtruncata (xbSpiSubt1) specimen used for genome sequencing.
Figure 2.
Figure 2.. Genome assembly of Spisula subtruncata, xbSpiSubt1.1: 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 930,862,144 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 (75,865,956 bp, shown in red). Orange and pale-orange arcs show the N50 and N90 scaffold lengths (48,288,179 and 34,259,483 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/Spisula_subtruncata/dataset/GCA_963678985.1/snail.
Figure 3.
Figure 3.. Genome assembly of Spisula subtruncata, xbSpiSubt1.1: 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/Spisula_subtruncata/dataset/GCA_963678985.1/blob.
Figure 4.
Figure 4.. Genome assembly of Spisula subtruncata, xbSpiSubt1.1: 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/Spisula_subtruncata/dataset/GCA_963678985.1/cumulative.
Figure 5.
Figure 5.. Genome assembly of Spisula subtruncata, xbSpiSubt1.1: Hi-C contact map of the xbSpiSubt1.1 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=NB6vXH6NQ-m3FVQdho4_Xg.
See this image and copyright information in PMC

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