Dataset (multifasta) of DNA contig sequences assembled from Illumina metagenomic reads of Haliclona fulva hologenome. The sequences analyses are described in the peer-reviewed article at https://doi.org/10.3389/fmars.2021.736817 entitled: "The Hologenome of Haliclona fulva (Porifera, Demospongiae) Reveals an Abundant and Diverse Viral Community" by Erika García-Bonilla1,2†, Diego Chaves-Moreno3†, Diego Riaño-Pachón4, Wilson Terán5, Alberto Acosta1 and Howard Junca2* 1Laboratorio Ecosistemas Marinos Estratégicos, Unidad de Ecología y Sistemática - UNESIS, Facultad de Ciencias - Departamento de Biología, Pontificia Universidad Javeriana, Bogotá, Colombia 2RG Microbial Ecology: Metabolism, Genomics & Evolution, Division of Ecogenomics & Holobionts, Microbiomas Foundation, Chía, Colombia 3Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany 4Laboratório de Biologia Computacional, Evolutiva e de Sistemas, Centro de Energía Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, Brazil 5Biología de Plantas y Sistemas Productivos, Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia "Sample Collection Three specimens of H. fulva (HF1, HF2, and HF3) were collected by SCUBA diving in the Mediterranean Sea at the Grotte du Lido, in the bay of Villefranche-sur-Mer, France (latitude: 43° 41′ 31.49″ N; longitude: 7° 19′ 12.19″ E) at 35 m depth. After collection, all individual samples were placed in independent plastic bags. They were preserved in ethanol 70% (v/v) and stored at −20°C until further analysis. The samples were selected based on the findings of our previous study (García-Bonilla et al., 2019) and are coming from exactly the same spots and colonies/specimens analyzed regarding microbiome content by 16S amplicons, showing a stable and consistent microbial composition of low microbial abundance and diversity. DNA Extraction and Sequencing Metagenomic DNA was extracted from 15 g sponge wet weight using a MagAttract® HMW DNA kit (Qiagen, Germany) following the manufacturer’s instructions. Tissue lysis was made for 16 h according to protocol. Extracted DNA was eluted with 50 μl water, and its concentration determined by fluorescence using the Qubit® dsDNA BR assay kit (Thermo Fisher Scientific). Nucleic acid integrity was verified by 0.8% agarose gel electrophoresis. Sponge DNA extracts were used as template to perform isothermal multiple displacement hologenome amplification with a phi29 polymerase of high processivity and fidelity in order to increase total DNA concentrations (Lasken, 2007) and to avoid the effect of coextracted enzymatic inhibitors detected in H. fulva, improving further downstream processes (library construction and sequencing). The amplification process was made using REPLI-g Mini kit (Qiagen, Germany), according to manufacturer’s recommendations. Briefly, samples were incubated at 30°C for 11 h followed by 3 min at 65°C for polymerase inactivation. For all assays, a negative control was run to evaluate the presence of contaminants during amplification. Quantity and quality of DNA was measured as described previously. Genomic libraries were constructed using TruSeq DNA PCR free kit (Illumina, United States). Shotgun hologenome sequencing was performed using paired-end Illumina technology (Macrogen, South Korea). The complete raw sequencing data obtained is publicly accessible at NCBI GenBank SRA under Bioproject PRJNA741981. Raw Data Processing and Assembly An initial filtering of the sequencing reads was done after visual evaluation using FastQC (v.0.11.8) consisting of a quality and length-based filtering performed with Trimmomatic (v.0.31). Filtered and processed reads were assembled using Megahit (v.1.0) (Li et al., 2014) and IDBA-UD (Peng et al., 2012) with default parameters. To compare, identify and join overlaps between reads from each assembly, we used minimus2 from the AMOS suite with default parameters (Treangen et al., 2011). Obtained contigs were filtered and those <500 bp were removed."