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

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.


Background
Giant clams (subfamily Tridacninae) are the largest extant bivalves (Soo & Todd, 2014).All species within the subfamily form a photosymbiotic partnership with Symbiodiniaceae dinoflagellates (Ip & Chew, 2021).In addition to their reef building capacity, giant clams serve as reservoirs of Symbiodiniaceae, offer substrates for epibionts to colonise, and enhance coral reefs' topographic heterogeneity (Neo et al., 2015).Among the twelve currently recognised extant species, Tridacna gigas is a true gigantic species, with the largest individual measuring an impressive 137 cm in length and weighing a remarkable 500 kg (Neo, 2023).
T. gigas naturally distribute in shallow tropical habitats in the central Indo-Pacific, ranging from Myanmar to Kiribati, and Ryukyus to Queensland (Neo et al., 2017).Due to its enormous size, it faces extensive exploitation from over-fishing for both its flesh and shells, and increasing demands from the aquarium trade, despite CITES regulations (Tan et al., 2022).Coupled with the effects of global warming and ocean acidification, T. gigas populations have been declining rapidly in the wild, and many failed to recover (Gomez, 2015).
Examining the chromosome-level genome assembly of T. gigas allows us to gain deeper insights into its population demographics, and the genetic framework that underlies the symbiotic relationship with Symbiodiniaceae, which may lead to practical conservation strategies during this era of climate change.Conducting comparative genomics analyses among various giant clam species may also uncover genetic mechanisms responsible for the remarkable size of T. gigas.Being part of the broader Aquatic Symbiosis Genomics project (McKenna et al., 2021), which includes sequencing diverse photosymbiotic hosts, we have the opportunity to explore both shared and novel molecular pathways in different species and gain comprehensive understanding of the evolution of photosymbiosis.

Genome sequence report
The genome was sequenced from a specimen of Tridacna gigas (Figure 1) collected from Marshall Islands Mariculture Farm, Majuro, Marshall Islands.A total of 36-fold coverage in Pacific Biosciences single-molecule HiFi long reads was generated.Primary assembly contigs were scaffolded with chromosome conformation Hi-C data.Manual assembly curation corrected 29 missing joins or mis-joins and removed 23 haplotypic duplications, reducing the assembly length by 0.71% and the scaffold number by 55.32.
The final assembly has a total length of 1175.9Mb in 20 sequence scaffolds with a scaffold N50 of 68.4 Mb (Table 1).
The snail plot in Figure 2 provides a summary of the assembly statistics, while the distribution of assembly scaffolds on GC proportion and coverage is shown in Figure 3.The cumulative assembly plot in Figure 4 shows curves for subsets of scaffolds assigned to different phyla.Most (99.98%) of the assembly sequence was assigned to 17 chromosomallevel scaffolds.Chromosome-scale scaffolds confirmed by the Hi-C data are named in order of size (Figure 5; Table 2).While not fully phased, the assembly deposited is of one haplotype.Contigs corresponding to the second haplotype have also been deposited.The mitochondrial genome was also assembled and can be found as a contig within the multifasta file of the genome submission.
The resulting annotation includes 37,598 transcribed mRNAs from 18,177 protein-coding and 6,818 non-coding genes.

Sample acquisition and nucleic acid extraction
A Tridacna gigas (specimen ID NSU0010103, ToLID xbTri-Giga4) was purchased from Oceans, Reefs & Aquariums (ORA) in Marshall Islands Mariculture Farm, Majuro, Marshall     Hi-C data were also generated from tissue of xbTriGiga4 using the Arima2 kit and sequenced on the Illumina NovaSeq 6000 instrument.

Genome annotation
The Ensembl Genebuild annotation system (Aken et al., 2016) at the EBI was used to generate annotation for the Tridacna gigas assembly (GCA_945859785.2).Annotation was created primarily through alignment of transcriptomic data to the genome, with gap filling via protein-togenome alignments of a select set of proteins from UniProt (UniProt Consortium, 2019).

Wellcome Sanger Institute -Legal and Governance
The materials that have contributed to this genome note have been supplied by a Tree of Life collaborator.The Wellcome Sanger Institute employs a process whereby due diligence is carried out proportionate to the nature of the materials themselves, and the circumstances under which they have been/are to be collected and provided for use.The purpose of this is to address and mitigate any potential legal and/or ethical implications of receipt and use of the materials as part of the research project, and to ensure that in doing so we align with best practice wherever possible.The overarching areas of consideration are: • Ethical review of provenance and sourcing of the material The number of missing BUSCOs appears to be high (16%), but is comparable to the other Tridacninae chromosomal assemblies already reported in this journal.This said, it may be useful to rule out incompleteness of the assembly by also searching for BUSCOs in the transcriptome and showing that the missing ones are the same.Alternatively, it could be checked if most missing BUSCOs are absent from both haplotypes, or also absent in other Tridacninae chromosomal assemblies.
Is the rationale for creating the dataset(s) clearly described?

Daniel Garcia-Souto
University of Santiago de Compostela, Santiago de Compostela, Galicia, Spain The authors present a much-needed genome assembly of the giant clam Tridacna gigas.This assembly was achieved at chromosome level, displaying top-tier annotation and completeness stats.All data is freely available well ahead of publication.This represents a significant addition for future genomics and comparative analysis.
As a side note, from a pure taxonomical perspective, it would be beneficial to supplement these (and other) reports with more detailed views or photographs of the specimen.In addition to the general view of the animal, including the typical shell features used for species identification (such as hinge or pallial lines) would be highly valuable.This is especially important as bivalves can involve cryptic species or subspecies that may complicate identification.

Is the rationale for creating the dataset(s) clearly described? Yes
Are the protocols appropriate and is the work technically sound?Yes

Are sufficient details of methods and materials provided to allow replication by others? Yes
Are the datasets clearly presented in a useable and accessible format?Yes Competing Interests: No competing interests were disclosed.
I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.

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 xbTriGiga4.2assembly, 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.

Table 3
contains a list of relevant software tool versions and sources.

Yes Are the protocols appropriate and is the work technically sound? Yes Are sufficient details of methods and materials provided to allow replication by others? Yes Are the datasets clearly presented in a useable and accessible format? Yes
Reviewer Expertise: Pairwise genome comparisonsI confirm that I

have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.
This is an open access peer review report distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.