Expansion, diversification, and expression of T-box family genes in Porifera

Abstract

Sponges are among the earliest diverging lineage within the metazoan phyla. Although their adult morphology is distinctive, at several stages of development, they possess characteristics found in more complex animals. The T-box family of transcription factors is an evolutionarily ancient gene family known to be involved in the development of structures derived from all germ layers in the bilaterian animals. There is an incomplete understanding of the role that T-box transcription factors play in normal sponge development or whether developmental pathways using the T-box family share similarities between parazoan and eumetazoan animals. To address these questions, we present data that identify several important T-box genes in marine and freshwater sponges, place these genes in a phylogenetic context, and reveal patterns in how these genes are expressed in developing sponges. Phylogenetic analyses demonstrate that sponges have members of at least two of the five T-box subfamilies (Brachyury and Tbx2/3/4/5) and that the T-box genes expanded and diverged in the poriferan lineage. Our analysis of signature residues in the sponge T-box genes calls into question whether "true" Brachyury genes are found in the Porifera. Expression for a subset of the T-box genes was elucidated in larvae from the marine demosponge, Halichondria bowerbanki. Our results show that sponges regulate the timing and specificity of gene expression for T-box orthologs across larval developmental stages. In situ hybridization reveals distinct, yet sometimes overlapping expression of particular T-box genes in free-swimming larvae. Our results provide a comparative framework from which we can gain insights into the evolution of developmentally important pathways.

Early evolution of the T-box transcription factor family

“…1). No T-box genes were found in higher fungi (Dikarya), in agreement with previous surveys (13,14,16). This confirms that T-box transcription factors were lost during fungal evolution (16).…”

“…Both groups appear to have been lost in some lineages during metazoan evolution. As in previous studies (7,14), our data do not support the monophyly of Tbx6 class, but no putative orthologs were identified in early-branching metazoans. Thus, this class likely evolved later during metazoan evolution.…”

“…S2). The presumed Tbx1/15/20 homologs identified in the demosponges A. queenslandica and Axinella verrucosa (13) were previously thought to comprise a new demosponge-specific T-box class (14). We also recover this group, but surprisingly it also includes a sequence from the deuterostome Saccoglossus kowalevski.…”

“…Previous studies have identified T-box genes in nonbilaterian metazoans (11)(12)(13)(14). This knowledge has enabled a reconstruction of the Urmetazoan T-box complement, which putatively included three classes (Tbx4/5, Brachyury, and a putative Tbx1/15/20), with other classes being added in a stepwise manner through the evolution of metazoans.…”

“…With only a few exceptions (8), all classes of T-box genes are widespread among bilaterian animals, with a handful being identified and studied in nonbilaterian metazoans, such as cnidarians (5,9), ctenophores (7,10), and sponges (11)(12)(13)(14). T-box genes were initially thought to be specific to metazoans (13,15), but two recent studies revealed the presence of T-box genes in nonmetazoan lineages (14,16), including the unicellular filose amoeba Capsaspora owczarzaki, a close relative of animals, and the chytrid fungus Spizellomyces punctatus. T-box genes were not identified in any other sequenced eukaryote, suggesting that T-box genes were secondarily lost in choanoflagellates (both in unicellular and colonial species) and most fungi.…”