Metagenomic data for Halichondria panicea from Illumina and nanopore sequencing and preliminary genome assemblies for the sponge and two microbial symbionts

Objectives

These data were collected to generate a novel reference metagenome for the sponge Halichondria panicea and its microbiome for subsequent differential expression analyses.

Data description

These data include raw sequences from four separate sequencing runs of the metagenome of a single individual of Halichondria panicea—one Illumina MiSeq (2 × 300 bp, paired-end) run and three Oxford Nanopore Technologies (ONT) long-read sequencing runs, generating 53.8 and 7.42 Gbp respectively. Comparing assemblies of Illumina, ONT and an Illumina-ONT hybrid revealed the hybrid to be the ‘best’ assembly, comprising 163 Mbp in 63,555 scaffolds (N50: 3084). This assembly, however, was still highly fragmented and only contained 52% of core metazoan genes (with 77.9% partial genes), so it was also not complete. However, this sponge is an emerging model species for field and laboratory work, and there is considerable interest in genomic sequencing of this species. Although the resultant assemblies from the data presented here are suboptimal, this data note can inform future studies by providing an estimated genome size and coverage requirements for future sequencing, sharing additional data to potentially improve other suboptimal assemblies of this species, and outlining potential limitations and pitfalls of the combined Illumina and ONT approach to novel genome sequencing.

Conservative and Atypical Ferritins of Sponges

Ferritins comprise a conservative family of proteins found in all species and play an essential role in resistance to redox stress, immune response, and cell differentiation. Sponges (Porifera) are the oldest Metazoa that show unique plasticity and regenerative potential. Here, we characterize the ferritins of two cold-water sponges using proteomics, spectral microscopy, and bioinformatic analysis. The recently duplicated conservative HdF1a/b and atypical HdF2 genes were found in the Halisarca dujardini genome. Multiple related transcripts of HpF1 were identified in the Halichondria panicea transcriptome. Expression of HdF1a/b was much higher than that of HdF2 in all annual seasons and regulated differently during the sponge dissociation/reaggregation. The presence of the MRE and HRE motifs in the HdF1 and HdF2 promotor regions and the IRE motif in mRNAs of HdF1 and HpF indicates that sponge ferritins expression depends on the cellular iron and oxygen levels. The gel electrophoresis combined with specific staining and mass spectrometry confirmed the presence of ferric ions and ferritins in multi-subunit complexes. The 3D modeling predicts the iron-binding capacity of HdF1 and HpF1 at the ferroxidase center and the absence of iron-binding in atypical HdF2. Interestingly, atypical ferritins lacking iron-binding capacity were found in genomes of many invertebrate species. Their function deserves further research.

Tissue sloughing in the sponge Halichondria panicea: a fouling organism prevents being fouled

Specimens of the sponge Halichondria panicea Pallas kept in running sea-water aquaria at 15° C slough off their complete outer tissue layer in regular intervals of three weeks. Sloughing starts at the rim of the oscula and extends over the whole surface within two weeks. Microscopic inspection of the tissue flakes shows them to harbour large numbers of different live organisms, as well as biogenic debris such as pieces of copepod carapaces and diatom frustules. No such community is found on freshly sloughed sponge tissue. After sloughing, the surface skeletal structure of H. panicea is markedly altered, as the characteristic halichondroid reticulum has been replaced by the irregular spicule array typical for the inner sponge tissue. When H. panicea is kept in closed aquaria filled with 0.2 μm filtered sea-water, no sloughing occurs during 3 months of maintenance. As those sponges shedding their outer tissue grow steadily at the same time, the tissue sloughing can be regarded as a reaction to sedimentation of organic material and settlement of small organisms on the sponge surface. The sponge thus counteracts clogging of its ostia and prevents the establishment of a micro fouling community on its surface, inhibiting further fouling processes.