While adaptive radiations significantly contribute to the world's biodiversity, much is unknown about the genetic and ecological factors underlying these rapid successions of speciation. It has been suggested that hybridisation can facilitate the speciation process by generating genetic diversity on which diversifying selection can act. Sailfin silverside fishes (Telmatherinidae) in the Malili Lakes system in Sulawesi have diversified within the last 2 million years. To establish a phylogenetic framework and investigate the presence of hybridisation in this radiation, we assembled and annotated a chromosome-scale reference genome of the riverine sailfin silverside Telmatherina bonti and generated whole genome sequences of all species of Telmatherina in Lake Matano, South Sulawesi, Indonesia, one of the world's oldest and deepest lakes. We reconstructed the phylogenetic relationships and inferred past and ongoing introgression patterns. Genome-wide tests confirmed two monophyletic clades, sharpfins and roundfins. However, within clades, we found mismatches between morphology-based taxonomic assignments and genome-wide genetic relationships. We found signs of both old and ongoing introgression between river-dwelling T. bonti and the lacustrine sharpfin group, as shown in elevated D-statistic, f4-ratio and f-branch statistic. Levels of excess allele sharing between riverine species and the three most common lacustrine species declined with increasing distance from the river-inlet, indicating ongoing introgression at the lake-river interface. This combination of past and ongoing hybridisation in a radiating species flock makes Lake Matano Telmatherina a particularly valuable system to study fundamental mechanisms driving rapid speciation under genomic exchange. The phylogenomic framework elaborated in this study provides the foundation for studies of the processes shaping this charismatic radiation.

We present a genome assembly from an individual Lycopodina hypogea (carnivorous sponge; Porifera; Demospongiae; Poecilosclerida; Cladorhizidae). The genome sequence has a total length of 235.10 megabases. Most of the assembly (98.85%) is scaffolded into 15 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 31.1 kilobases. Gene annotation of this assembly by Ensembl identified 16 317 protein-coding genes. From the metagenome data we recovered 39 bins, of which 27 were high-quality MAGs, including four fully circularised genomes. The MAGs included archaea and bacteria involved in nitrification and sulfate-reduction as well as known sponge symbionts affiliated with Gammaproteobacteria ( Candidatus Spongiihabitans, Porisulfidus) and Acidimicrobiales ( Candidatus Poriferisodalaceae), among others.

We present a genome assembly from a Muricea muricata specimen (spiny sea fan; Cnidaria; Anthozoa; Malacalcyonacea; Plexauridae). The genome sequence has a total length of 453.40 megabases. Most of the assembly (98.45%) is scaffolded into 16 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 19.29 kilobases. Gene annotation of this assembly by Ensembl identified 52 164 protein-coding genes. From the metagenome data, we recovered five bins, of which three were high-quality MAGs.

We present a genome assembly from a specimen of Phakellia ventilabrum (Porifera; Demospongiae; Bubarida; Bubaridae). The genome sequence has a total length of 211.92 megabases. Most of the assembly (99.97%) is scaffolded into 25 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 24.36 kilobases in length. Gene annotation of this assembly by Ensembl identified 21 622 protein-coding genes. Thirty-three binned genomes were generated from the metagenome assembly, of which eight were classified as high-quality metagenome assembled genomes (MAGs) and of which four of the MAGs are fully circular. The MAGs were taxonomically assigned to Pseudomonadota (i.e. Candidatus Poriferihabitaceae), Nitrospirota, Nitrospinota, and the archaeal Nitrosopumilus clade.

We present a genome assembly from an individual Rhopaloeides odorabile (Porifera; Demospongiae; Dictyoceratida; Spongiidae). The genome sequence has a total length of 291.63 megabases. Most of the assembly (98.17%) is scaffolded into 17 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 16.42 kilobases. From the metagenome data, we recovered 162 bins, of which 96 were high-quality MAGs. R. odorabile displays a characteristic high microbial abundance sponge profile, with MAGs representing diverse phyla (i.e., Acidobacteriota, Pseudomonadota, and Chloroflexota) and candidate phyla (i.e., Ca. Latescibacteria, Ca. Poribacteria, and Ca. Tectomicrobia).

We present a genome assembly from an individual Sabellastarte sp. h YS-2021 (feather duster worm; Annelida; Polychaeta; Sabellida; Sabellidae). The genome sequence has a total length of 1 786.39 megabases. Most of the assembly (97.94%) is scaffolded into 14 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 15.35 kilobases. From the metagenome data, we recovered 5 bins, of which one was a high-quality MAG.

We present a genome assembly from an individual Eumandya parva (spotty bobtail squid; Mollusca; Cephalopoda; Sepiida; Sepiolidae). The assembly contains two haplotypes with total lengths of 4 425.89 megabases and 4 365.42 megabases. Most of haplotype 1 (92.07%) is scaffolded into 47 chromosomal pseudomolecules. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 19.24 kilobases. Gene annotation of this assembly by Ensembl identified 15 797 protein-coding genes. This assembly was generated as part of the Aquatic Symbiosis Genomics Project.

We present a genome assembly from a specimen of Siderastrea radians (lesser starlet coral; Cnidaria; Anthozoa; Scleractinia; Rhizangiidae). The genome sequence has a total length of 807.19 megabases. Most of the assembly (94.17%) is scaffolded into 14 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 19.38 kilobases. Gene annotation of this assembly by Ensembl identified 47 051 protein-coding genes. From the metagenome data, we recovered two binned metagenomes assigned to the bacterial phylum Bacteroidota and class Bacteroidia.

We present a genome assembly from an individual Lamellibrachia columna (tubeworm; Annelida; Polychaeta; Sabellida; Siboglinidae). The genome sequence has a total length of 879.73 megabases. Most of the assembly (99.96%) is scaffolded into 15 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 16.78 kilobases. Gene annotation of this assembly by Ensembl identified 21 983 protein-coding genes.

We present a genome assembly from an individual Lamellibrachia columna (tubeworm; Annelida; Polychaeta; Sabellida; Siboglinidae). The genome sequence has a total length of 879.73 megabases. Most of the assembly (99.96%) is scaffolded into 15 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 16.78 kilobases. Gene annotation of this assembly by Ensembl identified 21 983 protein-coding genes.

We present a genome assembly from from a specimen of the clarki ecotype of an individual specimen of the lettuce sea slug Elysia crispata (lettuce sea slug; Mollusca; Gastropoda; Plakobranchidae). The genome sequence has a total length of 542.56 megabases. Most of the assembly (87.52%) is scaffolded into 15 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 14.17 kilobases. Additionally, we sequenced the chloroplast genomes of two dietary algae, Penicillus capitatus and P. lamourouxii , from plastids sequestered inside of slug cells where they remain photosynthetically active. Gene annotation of this assembly by Ensembl identified 18 436 protein-coding genes. From the metagenome data, we recovered six bins, of which four were high-quality MAGs.

We present a genome assembly from an individual Rhopaloeides odorabile (Porifera; Demospongiae; Dictyoceratida; Spongiidae). The genome sequence has a total length of 291.63 megabases. Most of the assembly (98.17%) is scaffolded into 17 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 16.42 kilobases. From the metagenome data, we recovered 162 bins, of which 96 were high-quality MAGs. R. odorabile displays a characteristic high microbial abundance sponge profile, with MAGs representing diverse phyla (i.e., Acidobacteriota, Pseudomonadota, and Chloroflexota) and candidate phyla (i.e., Ca. Latescibacteria, Ca. Poribacteria, and Ca. Tectomicrobia).

We present a genome assembly from a specimen of Meandrina meandrites (maze coral; Cnidaria; Anthozoa; Scleractinia; Meandrinidae). The genome sequence has a total length of 551.16 megabases. Most of the assembly (99.25%) is scaffolded into 14 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 17.2 kilobases. Gene annotation of this assembly by Ensembl identified 30 464 protein-coding genes. We recovered two bins from the metagenome data.

We present a genome assembly from an individual Hermodice carunculata (bearded fireworm; Annelida; Polychaeta; Eunicida; Amphinomidae). The genome sequence has a total length of 2 103.51 megabases. Most of the assembly (90.04%) is scaffolded into 19 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 15.87 kilobases. This genome was generated as part of the Aquatic Symbiosis Genomics Project.

We present a genome assembly from an individual Aurelia sp. 4 Dawson et al ., 2005 (moon jellyfish; Cnidaria; Scyphozoa; Semaeostomeae; Ulmaridae). The genome sequence has a total length of 462.10 megabases. Most of the assembly (99.99%) is scaffolded into 21 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 16.88 kilobases. From the metagenome data, we recovered 3 bins, of which 2 were high-quality MAGs.

We present a genome assembly from a specimen of Maea johnstoni (Fiege, Licher & Mackie, 2000) (shovel-head worm; Annelida; Polychaeta; Spionida; Magelonidae). The genome sequence has a total length of 881.61 megabases. Most of the assembly (97.37%) is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 15.47 kilobases. From the metagenome data, we recovered two Spirochaetota bins, one of which was a MAG.

We present a genome assembly from an individual Geodia parva (sponge; Porifera; Demospongiae; Tetractinellida; Geodiidae). The genome sequence has a total length of 113.34 megabases. Most of the assembly (99.89%) is scaffolded into 21 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 18.04 kilobases. Gene annotation of this assembly by Ensembl identified 20 464 protein-coding genes. From the metagenome data, we recovered 241 bins, of which 69 were high-quality MAGs. The microbial profile was characteristic of high microbial abundance (HMA) sponges with bins representing 17 different phyla and candidate phyla. Most MAGs were affiliated with the phyla Pseudomonadota, Acidobacteriota and Chloroflexota as well as several candidate phyla ( Ca. Latescibacteria, Ca. Poribacteria and Ca. Binatota).

We present a genome assembly from a Micromussa lordhowensis specimen (starry cup coral; Cnidaria; Anthozoa; Scleractinia; Lobophylliidae). The genome sequence has a total length of 582.08 megabases. Most of the assembly (89.67%) is scaffolded into 15 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 18.25 kilobases. Gene annotation of this assembly by Ensembl identified 32 953 protein-coding genes. From the metagenome data, we recovered 11 bins, of which four were high-quality MAGs.

We present a genome assembly from an individual Diacarnus erythraeanus (sponge; Porifera; Demospongiae; Poecilosclerida; Podospongiidae). The genome sequence has a total length of 140.86 megabases. Most of the assembly (98.57%) is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 19.34 kilobases in length. Sixty-four binned genomes were generated from the metagenome assembly, of which 46 were classified as high-quality metagenome assembled genomes (MAGs). The microbial signature is typical of HMA sponges, including the Pseudomonadota, Chloroflexota and Acidobacteriota as dominant phyla and several candidate phyla (Poribacteria, Binatota, Latescibacterota) as well as the archaeal clade Nitrosopumilaceae in lower abundance.

We present a genome assembly from an individual Ricordea florida (Florida corallimorph; Cnidaria; Anthozoa; Corallimorpharia; Ricordeidae). The genome sequence has a total length of 537.84 megabases. Most of the assembly (99.81%) is scaffolded into 16 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 21.38 kilobases.