Phylogenetic analysis of forkhead transcription factors in the Panarthropoda

Abstract

Fox genes encode transcription factors that contain a DNA binding domain, the forkhead domain, and are known from diverse animal species. The exact homology of the Fox genes of different species is debated and this makes inferences about the evolution of the Fox genes, and their duplications and losses difficult. We have performed phylogenetic analyses of the Fox gene complements of 32 panarthropod species. Our results confirm an ancestral complement of FoxA, FoxB, FoxC, FoxD, FoxF, FoxG, FoxJ1, FoxJ2/3, FoxK, FoxL1, FoxL2, FoxN1/4, FoxN2/3, FoxO, FoxP, and FoxQ2 in the Arthropoda, and additionally FoxH and FoxQ1 in the Panarthropoda (including tardigrades and onychophorans). We identify a novel Fox gene sub-family, that we designate as FoxT that includes two genes in Drosophila melanogaster, Circadianly Regulated Gene (Crg-1) and forkhead domain 3F (fd3F). In a very recent paper, the same new Fox gene sub-family was identified in insects (Lin et al. 2021). Our analysis confirms the presence of FoxT and shows that its members are present throughout Panarthropoda. We show that the hitherto unclassified gene CG32006 from the fly Drosophila melanogaster belongs to FoxJ1. We also detect gene losses: FoxE and FoxM were lost already in the panarthropod ancestor, whereas the loss of FoxH occurred in the arthropod ancestor. Finally, we find an ortholog of FoxQ1 in the bark scorpion Centruroides sculpturatus, confirmed not only by phylogenetic analysis, but also by forming an evolutionarily conserved gene cluster with FoxF, FoxC, and FoxL1. This suggests that FoxQ1 belongs to the ancestral Fox gene complement in panarthropods and also in chelicerates, but has been lost at the base of the mandibulate arthropods.

A comprehensive study of arthropod and onychophoran Fox gene expression patterns

“…The phylogeny and gene content of panarthropod Fox genes have recently been discussed in [28]. According to this analysis, two classes of Fox genes appear to have been lost in panels G and H. Arrows in panels A, D, E and F point to expression in the interface between the embryo proper and the dorsal field.…”

“…CG32006), a gene that we and others believe is a FoxJ1 ortholog (cf. [62] with [27,28]). Gene expression analysis of CG32006/FoxJ1 genes supports this interpretation (discussed below).…”

“…Recently, yet another class of Fox genes, FoxT, has been identified that appears to be panarthropod specific [27,28].…”

The Fox gene repertoire in the annelid Owenia fusiformis reveals multiple expansions of the foxQ2 class in Spiralia

“…The copyright holder for this preprint this version posted March 2, 2022. ; https://doi.org/10.1101/2022.03.02.482670 doi: bioRxiv preprint Schomburg et al 2022;Mazet et al 2003;Wotton & Shimeld 2006;Tu et al 2006).…”

“…Since the discovery of the Forkhead domain in the fruit fly Drosophila melanogaster (Weigel et al 1989), Fox genes have been studied in a wide range of traditional developmental systems, mostly vertebrates (Mazet et al 2003; Hannenhalli & Kaestner 2009; Lee & Frasch 2004; Jackson et al 2010; Golson & Kaestner 2016). The initial description of 15 Fox gene classes in chordates, each identified by a letter (Kaestner et al 2000), and the establishment of a unified nomenclature facilitated phylogenetic analyses and comparisons with other major invertebrate clades, such as hemichordates (Fritzenwanker et al 2014), molluscs (Mei et al ., 2014; Wu et al ., 2020), platyhelminthes (Pascual-Carreras et al 2021), panarthropods (Schomburg et al 2022), cnidarians (Magie et al 2005), and sponges (Larroux et al 2006), as well as animal outgroups (Larroux et al 2008), ultimately uncovering a complex evolutionary history for this large family of transcription factors. Today, Fox genes are classified into 26 classes belonging to two major clades (Larroux et al 2008; Mazet et al 2003; Hannenhalli & Kaestner 2009; Benayoun et al 2011; Kaestner et al 2000; Pascual-Carreras et al 2021), where ancestral duplication events (e.g., the former class foxQ split into foxQ1 and foxQ2 , foxN into foxN1/4 and foxN2/3 , foxL into foxL1 and foxL2 , and foxJ into foxJ1 and foxJ2/3 ), gene innovations (e.g., foxR and foxS are unique of vertebrates, foxT is a novelty of panarthropods), expansions and losses (e.g., foxAB in vertebrates, foxQ2 in tetrapods, and foxAB , foxE , foxH , foxI in arthropods) are common (Paps et al 2012; Schomburg et al 2022; Mazet et al 2003; Wotton & Shimeld 2006; Tu et al 2006).…”