DOI: 10.5061/dryad.tn0f3
title: Data from: Calcisponges have a ParaHox gene and dynamic expression of dispersed NK homeobox genes

description: 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.
description: 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