Sycon ciliatum genomeSycon ciliatum genome assembly freeze 02.08.2013. The assembly was generated using two (360bp and 530bp) paired-end libraries and several mate-pair libraries ranging from 2.0 to 9.0 kb. Assembly was performed using SOAPdenovo2 and scaffolding using SSPACE v2.2. Genomic scaffolds of sponge origin (as opposed to those derived from associated organisms) were identified by aligning the resulting assembly to reads from an Illumina sequenced library obtained from laboratory grown, eukaryotic- contamination free juveniles.sycon.genome.fa.gzSycon ciliatum coding sequencesSycon ciliatum coding sequences. De-novo assembly of transcriptome and identification of coding sequences was performed with Trinity pipeline using an extensive collection of RNA-Seq libraries derived from larvae, juveniles, non-reproductive adults, adults containing oocytes and embryos, and regenerating adult tissue. The coding sequences were aligned on the Sycon ciliatum genome to identify genes and sort out sequences of non-sponge origin.sycon.cds.fa.gzSycon ciliatum proteinsSycon ciliatum proteins, translations of Sycon ciliatum coding sequences.sycon.pep.fa.gzLeucosolenia complicata coding sequencesLeucosolenia complicata coding sequences. De-novo assembly of transcriptome and identification of coding sequences was performed with Trinity pipeline using RNA-Seq libraries derived from adult tissues containing oocytes and a variety of embryonic stages. Leucosolenia 'genes' were artificially created without use of a genome, by clustering of coding sequences sharing identical fragments.leucosolenia.cds.fa.gzLeucosolenia complicata proteinsLeucosolenia complicata proteins, translations of Leucosolenia complicata coding sequences.leucosolenia.pep.fa.gz

Sponges are simple animals with few cell types, but their genomes paradoxically contain a wide variety of developmental transcription factors1, 2, 3, 4, including homeobox genes belonging to the Antennapedia (ANTP) class5, 6, which in bilaterians encompass Hox, ParaHox and NK genes. In the genome of the demosponge Amphimedon queenslandica, no Hox or ParaHox genes are present, but NK genes are linked in a tight cluster similar to the NK clusters of bilaterians5. It has been proposed that Hox and ParaHox genes originated from NK cluster genes after divergence of sponges from the lineage leading to cnidarians and bilaterians5, 7. On the other hand, synteny analysis lends support to the notion that the absence of Hox and ParaHox genes in Amphimedon is a result of secondary loss (the ghost locus hypothesis)8. Here we analysed complete suites of ANTP-class homeoboxes in two calcareous sponges, Sycon ciliatum and Leucosolenia complicata. Our phylogenetic analyses demonstrate that these calcisponges possess orthologues of bilaterian NK genes (Hex, Hmx and Msx), a varying number of additional NK genes and one ParaHox gene, Cdx. Despite the generation of scaffolds spanning multiple genes, we find no evidence of clustering of Sycon NK genes. All Sycon ANTP-class genes are developmentally expressed, with patterns suggesting their involvement in cell type specification in embryos and adults, metamorphosis and body plan patterning. These results demonstrate that ParaHox genes predate the origin of sponges, thus confirming the ghost locus hypothesis8, and highlight the need to analyse the genomes of multiple sponge lineages to obtain a complete picture of the ancestral composition of the first animal genome.