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. 2025 Apr 25:10:222.
doi: 10.12688/wellcomeopenres.23988.1. eCollection 2025.

The chromosome-level genome sequences of the freshwater sponge, Spongilla lacustris (Linnaeus, 1759) and the chlorophyte cobiont Choricystis sp., and the associated microbial metagenome sequences

Sally P Leys  1 , Ute Hentschel  2 , Graeme Oatley  3 , Elizabeth Sinclair  3 , Eerik Aunin  3 , Noah Gettle  3 , Camilla Santos  3 , Michael Paulini  3 , Dirk Erpenbeck  3 , Haoyu Niu  3 , Victoria McKenna  3 ; 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 chromosome-level genome sequences of the freshwater sponge, Spongilla lacustris (Linnaeus, 1759) and the chlorophyte cobiont Choricystis sp., and the associated microbial metagenome sequences

Sally P Leys et al. Wellcome Open Res. .

Abstract

We present a genome assembly from an individual Spongilla lacustris (freshwater sponge; Porifera; Demospongiae; Spongillida; Spongillidae). The genome sequence is 248.7 megabases in span. Most of the assembly is scaffolded into 23 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 28.04 kilobases in length. A 14.6-megabase genome assembly of the green algal cobiont Choricystis sp. (Chlorophyta; Trebouxiophyceae) was scaffolded into 16 chromosomal pseudomolecules. Additionally, three bacterial metagenome bins were recovered from the same sample. Gene annotation of this assembly at Ensembl identified 30,435 protein coding genes.

Keywords: Spongilla lacustris; Spongillida; microbial metagenome assembly; chromosomal; freshwater sponge; genome sequence.

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Conflict of interest statement

No competing interests were disclosed.

Figures

Figure 1.
Figure 1.. Image of a representative Spongilla lacustris (odSpoLacu1) specimen, similar to the one used for genome sequencing.
Photograph by Sally Leys.
Figure 2.
Figure 2.
A. Snail plot summary of assembly statistics for assembly odSpoLacu1.1: An interactive version of this figure is available here. B. Snail plot summary of assembly statistics for assembly ucChoSpea1.1: An interactive version of this figure is available here. The BlobToolKit snail plots show N50 metrics and BUSCO gene completeness. The main plot is divided into 1,000 bins around the circumference with each bin representing 0.1% of the assembly. The distribution of scaffold lengths is shown in dark grey with the plot radius scaled to the longest scaffold present in the assembly (shown in red). Orange and pale-orange arcs show the N50 and N90 scaffold lengths 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 is shown in the top right.
Figure 3.
Figure 3.. BlobToolKit GC-coverage plots.
Scaffolds are coloured by phylum. Circles are sized in proportion to scaffold length. Histograms show the distribution of scaffold length sum along each axis. A. Genome assembly of Spongilla lacustris, odSpoLacu1.1: An interactive version of this figure is available here. B. Genome assembly of Choricystis sp. odSpoLacu1, ucChoSpea1.1: An interactive version of this figure is available here.
Figure 4.
Figure 4.. BlobToolKit cumulative sequence plots.
The grey line shows cumulative length for all scaffolds. Coloured lines show cumulative lengths of scaffolds assigned to each phylum using the buscogenes taxrule. A. Cumulative sequence length for assembly odSpoLacu1.1: An interactive version of this figure is available here. B. Cumulative sequence length for assembly ucChoSpea1.1: An interactive version of this figure is available here.
Figure 5.
Figure 5.. Hi-C contact maps visualised using HiGlass.
Chromosomes are shown in order of size from left to right and top to bottom. A. Genome assembly of Spongilla lacustris, odSpoLacu1.1: An interactive version of this figure may be viewed here. B. Genome assembly of Choricystis sp., ucChoSpea1.1: An interactive version of this figure may be viewed here.
Figure 6.
Figure 6.. Blob plot of base coverage in mapped against GC proportion for sequences in the Spongilla lacustris metagenome.
Binned contigs are coloured by family. Circles are sized in proportion to sequence length on a square-root scale, ranging from 2,309 to 6,234,830. Histograms show the distribution of sequence length sum along each axis. An interactive version of this figure may be viewed here.
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. Adams EDM: Physiology and morphology of epithelia in the freshwater demosponge.Spongilla lacustris (MSc Thesis). University of Alberta, Edmonton,2010.
    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. Benoit G, Raguideau S, James R, et al. : High-quality metagenome assembly from long accurate reads with metaMDBG. Nat Biotechnol. 2024;42(9):1378–1383. 10.1038/s41587-023-01983-6 - DOI - PMC - PubMed

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