The Fox Gene Repertoire in the Annelid Owenia fusiformis Reveals Multiple Expansions of the foxQ2 Class in Spiralia

Abstract

Fox genes are a large and conserved family of transcription factors involved in many key biological processes, including embryogenesis and body patterning. Although the role of Fox genes has been studied in an array of model systems, comprehensive comparative studies in Spiralia—a large clade of invertebrate animals including molluscs and annelids—are scarce but much needed to better understand the evolutionary history of this gene family. Here, we reconstruct and functionally characterise the Fox gene complement in the annelid Owenia fusiformis, a slow evolving species and member of the sister group to all remaining annelids. The genome of O. fusiformis contains at least a single ortholog for 20 of the 22 Fox gene classes that are ancestral to Bilateria, including an ortholog of the recently discovered foxT class. Temporal and spatial expression dynamics reveal a conserved role of Fox genes in gut formation, mesoderm patterning, and apical organ and cilia formation in Annelida and Spiralia. Moreover, we uncover an ancestral expansion of foxQ2 genes in Spiralia, represented by 11 paralogs in O. fusiformis. Notably, although all foxQ2 copies have apical expression in O. fusiformis, they show variable spatial domains and staggered temporal activation, which suggest cooperation and sub-functionalisation among foxQ2 genes for the development of apical fates in this annelid. Altogether, our study informs the evolution and developmental roles of Fox genes in Annelida and Spiralia generally, providing the basis to explore how regulatory changes in Fox gene expression might have contributed to developmental and morphological diversification in Spiralia.

Gene activation of metazoan Fox transcription factors at the onset of metamorphosis in the marine demosponge Amphimedon queenslandica

“…Analysis of the expression of Fox genes during A. queenslandica embryogenesis and metamorphosis, and in juveniles and adults – including in three cell types – reveals different expression profiles indicative of diverse roles in regulating sponge development and cell identity. A diversity of developmental roles for A. queenslandica Fox genes would be consistent with what has been observed in other animals (e.g., Golson & Kaestner, 2016 ; Leclère et al, 2019 ; Magie et al, 2005 ; Seudre et al, 2022 ; Shimeld, Boyle, et al, 2010a ; Tu et al, 2006 ).…”

“…The early embryonic expression of Fox genes suggests they contribute to early cell specification events. Independently evolved FoxN1 / 4 paralogs are maternally expressed and present in the cleaving embryo of the annelid Owenia fusiformis (Seudre et al, 2022 ). FoxN1 / 4 is also maternally expressed in an echinoderm (sea urchin) (Tu et al, 2006 ), raising the possibility of maternal expression being a conserved feature in bilaterians, and possibly metazoans.…”

“…For instance, bilaterian and cnidarian FoxO genes are developmentally expressed and involved in immunity, metabolism, and longevity (Arden, 2008;Boehm et al, 2012;Bosch, 2014;Carlsson & Mahlapuu, 2002;Hedrick et al, 2012;Martins et al, 2016;Tzivion et al, 2011), but it is unclear which of these are ancestral functions. Golson & Kaestner, 2016;Leclère et al, 2019;Magie et al, 2005;Seudre et al, 2022;Shimeld, Boyle, et al, 2010a;Tu et al, 2006).…”

“…As is the case with other metazoan transcription factor families, the specific functions of Fox genes have been elucidated largely from studies in Drosophila and vertebrate models (reviewed in Carlsson & Mahlapuu, 2002;Golson & Kaestner, 2016). Nonetheless, spatial and temporal expression in a range of eumetazoans are consistent with Fox genes regulating a wide range of developmentalincluding embryonic development, specification, and maintenance of cell state, cell proliferation, and differentiationand metabolic processes (Carlsson & Mahlapuu, 2002;Fritzenwanker et al, 2014;Golson & Kaestner, 2016;Hannenhalli & Kaestner, 2009;Leclère et al, 2019;Magie et al, 2005;Pascual-Carreras et al, 2021;Seudre et al, 2022;Tu et al, 2006). In some cases, specific Fox gene subfamilies appear to have a widely conserved function, such as FoxO that appears to regulate life spans from yeast to mammals (Finlay et al, 2019;Greer et al, 2007;Jiang et al, 2019).…”

Annelid functional genomics reveal the origins of bilaterian life cycles

“…In O. fusiformis , trunk (e.g., nkx6, msx paralogs 28 ) and posterior genes (e.g., evx 29 , wnt1 27 ) concentrate in a small ventral area and around the anal opening of the larva 27-29 and increase in spatial range and expression level as the trunk forms. On the other hand, anterior genes (e.g., foxQ2 genes 40 , gsc 29 , otx 29 ) pattern most of the mitraria and their expression remain fairly stable during development (Fig. 3d; Extended Data Fig.…”