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. 2024 Mar 19:9:145.
doi: 10.12688/wellcomeopenres.21136.1. eCollection 2024.

The genome sequence of the giant clam, Tridacna gigas (Linnaeus, 1758)

Ruiqi Li  1 , Jingchun Li  1   2 , Jose Victor Lopez  3 , Graeme Oatley  4 , Isabelle Ailish Clayton-Lucey  4 , Elizabeth Sinclair  4 , Eerik Aunin  4 , Noah Gettle  4 , Camilla Santos  4 , Michael Paulini  4 , Haoyu Niu  4 , Victoria McKenna  4 , Rebecca O'Brien  4 ; 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 giant clam, Tridacna gigas (Linnaeus, 1758)

Ruiqi Li et al. Wellcome Open Res. .

Abstract

We present a chromosomal-level genome assembly from an individual Tridacna gigas (the giant clam; Mollusca; Bivalvia; Veneroida; Cardiidae). The genome sequence is 1,175.9 megabases in span. Most of the assembly is scaffolded into 17 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 25.34 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,177 protein coding genes.

Keywords: Tridacna gigas; Veneroida; chromosomal; genome sequence; giant clam.

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Conflict of interest statement

No competing interests were disclosed.

Figures

Figure 1.
Figure 1.. Photograph of the Tridacna gigas (xbTriGiga4) specimen used for genome sequencing.
Figure 2.
Figure 2.. Genome assembly of Tridacna gigas, xbTriGiga4.2: 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 1,175,968,439 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 (117,261,666 bp, shown in red). Orange and pale-orange arcs show the N50 and N90 scaffold lengths (68,447,427 and 54,827,388 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/CAMAOV02/dataset/CAMAOV02/snail.
Figure 3.
Figure 3.. Genome assembly of Tridacna gigas, xbTriGiga4.2: 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/CAMAOV02/dataset/CAMAOV02/blob.
Figure 4.
Figure 4.. Genome assembly of Tridacna gigas, xbTriGiga4.2: 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/CAMAOV02/dataset/CAMAOV02/cumulative.
Figure 5.
Figure 5.. Genome assembly of Tridacna gigas, xbTriGiga4.2: Hi-C contact map of the xbTriGiga4.2 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=BscNBFj0TFu9wH4hMpdhvw.
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. Bernt M, Donath A, Jühling F, et al. : MITOS: Improved de novo metazoan mitochondrial genome annotation. Mol Phylogenet Evol. 2013;69(2):313–319. 10.1016/j.ympev.2012.08.023 - DOI - PubMed
    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

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