Data from: Calcisponges have a ParaHox gene and dynamic expression of dispersed NK homeobox genes

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.海绵动物是细胞类型较少的简单动物，但其基因组却反常地包含多种发育转录因子1,2,3,4，其中包括属于触角足（Antennapedia, ANTP）类的同源框基因5,6；在两侧对称动物中，该类基因涵盖Hox基因、ParaHox基因与NK基因。在寻常海绵纲动物*Amphimedon queenslandica*的基因组中，并未发现Hox或ParaHox基因，但NK基因以紧密簇集的形式存在，其结构与两侧对称动物的NK基因簇类似5。此前有研究提出，在海绵动物从刺胞动物与两侧对称动物的祖先谱系分化后，Hox与ParaHox基因由NK簇基因演化而来5,7。另一方面，同线性（synteny）分析为“*Amphimedon queenslandica*中缺失Hox与ParaHox基因是次生丢失所致（幽灵基因座假说）8”这一观点提供了支持。本研究对两种钙质海绵——毛壶*Sycon ciliatum*与复杂白枝海绵*Leucosolenia complicata*的全套ANTP类同源框基因进行了分析。系统发育分析结果显示，这些钙质海绵拥有两侧对称动物NK基因（Hex、Hmx与Msx）的直系同源基因、数量不等的其他NK基因，以及1个ParaHox基因Cdx。尽管我们获得了跨越多个基因的基因组支架序列（scaffold），但未发现毛壶NK基因存在簇集的证据。所有毛壶的ANTP类基因均呈现发育表达模式，其表达模式提示这些基因参与胚胎与成体的细胞类型特化、变态发育以及体模式构建。本研究结果表明，ParaHox基因的起源早于海绵动物的分化，从而验证了幽灵基因座假说8，同时也凸显了分析多海绵类群基因组的必要性，以完整解析最原始动物基因组的祖先组成。