Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2025 May 29:10:283.
doi: 10.12688/wellcomeopenres.24166.1. eCollection 2025.

The chromosomal genome sequence of the kidney sponge, Chondrosia reniformis Nardo, 1847, and its associated microbial metagenome sequences

Lucia Pita  1   2 , Manuel Maldonado  3 , Vassiliki Koutsouveli  4 , Ana Riesgo  5 , Ute Hentschel  6 , Graeme Oatley  7 , Elizabeth Sinclair  7 , Eerik Aunin  7 , Noah Gettle  7 , Camilla Santos  7 , Michael Paulini  7 , Haoyu Niu  7 , Victoria McKenna  7 , Rebecca O'Brien  7 ; 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 chromosomal genome sequence of the kidney sponge, Chondrosia reniformis Nardo, 1847, and its associated microbial metagenome sequences

Lucia Pita et al. Wellcome Open Res. .

Abstract

We present a genome assembly from a specimen of Chondrosia reniformis (kidney sponge; Porifera; Demospongiae; Chondrillida; Chondrillidae). The genome sequence has a total length of 117.37 megabases. Most of the assembly (99.98%) is scaffolded into 14 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 17.45 kilobases in length. Several symbiotic bacterial genomes were assembled as MAGs. Gene annotation of the host organism assembly on Ensembl identified 17,340 protein-coding genes. The metagenome of the specimen was also assembled and 53 binned bacterial genomes were identified, including 40 high-quality MAGs that were representative of a typical high microbial abundance sponge and included three candiate phyla (Poribacteria, Latescibacteria, Binatota).

Keywords: Chondrillida; microbial metagenome; Chondrosia reniformis; chromosomal; genome sequence; kidney sponge.

PubMed Disclaimer

Conflict of interest statement

No competing interests were disclosed.

Figures

Figure 1.
Figure 1.. Specimen of Chondrosia reniformis (odChoReni1) used for genome sequencing, pictured in the CEAB wet laboratory three hours after its collection and immediately prior to tissue dissection.
Figure 2.
Figure 2.. Genome assembly of Chondrosia reniformis, odChoReni1.1: metrics.
The BlobToolKit Snailplot shows 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 117,390,217 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 (10,413,042 bp, shown in red). Orange and pale-orange arcs show the N50 and N90 scaffold lengths (8,459,200 and 6,903,244 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 metazoa_odb10 set is shown in the top right. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/odChoReni1_1/dataset/odChoReni1_1/snail.
Figure 3.
Figure 3.. Genome assembly of Chondrosia reniformis, odChoReni1.1: 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/odChoReni1_1/dataset/odChoReni1_1/blob.
Figure 4.
Figure 4.. Genome assembly of Chondrosia reniformis, odChoReni1.1: 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/odChoReni1_1/dataset/odChoReni1_1/cumulative.
Figure 5.
Figure 5.. Genome assembly of Chondrosia reniformis: Hi-C contact map of the odChoReni1.1 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=A60qQ7saS1qCspApxo8K0g.
Figure 6.
Figure 6.. Blob plot of base coverage in mapped against GC proportion for sequences in the Chondrosia reniformis metagenome.
Binned contigs are coloured by phylum. Circles are sized in proportion to sequence length on a square root scale, ranging from 1,831 to 10,530,910. Histograms show the distribution of sequence length sum along each axis. An interactive version may be viewed here.
Figure 7.
Figure 7.. Cladogram showing the taxonomic placement of metagenome bins, constructed using NCBI taxonomic identifiers with taxonomizr and annotated in iTOL.
Colours indicate phylum-level taxonomy. Additional tracks show sequencing coverage (log 10), genome size (Mbp), and completeness. Bins that meet the criteria for MAGs are marked with a grey circle and fully circularised MAGs are marked in black.
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. Bateman A, Martin MJ, Orchard S, et al. : UniProt: the universal protein knowledgebase in 2023. Nucleic Acids Res. 2023;51(D1):D523–D531. 10.1093/nar/gkac1052 - DOI - PMC - PubMed
    1. Bayer K, Kamke J, Hentschel U: Quantification of bacterial and archaeal symbionts in high and low microbial abundance sponges using real-time PCR. FEMS Microbiol Ecol. 2014;89(3):679–90. 10.1111/1574-6941.12369 - DOI - PubMed

LinkOut - more resources