Table 1 Literature summary

Gene name

Observed expression in S. kowalevskii

Related gene expression domain in other organisms

foxA

Late blastula:

Protostomes:

Vegetal plate.

Endoderm specification [103, 114–116].

48 hpf:

Hemichordates:

Anterior collar groove ectoderm; entire endoderm.

Vegetal plate, endoderm/foregut [117].

Juvenile stage:

Echinoderms:

Entire endoderm with the exception of the dorsolateral outpocketing gill pores; most anterior collar ectoderm with a gap in expression on the dorsal midline

Presumptive ventral ectoderm [118]; Endomesoderm specification [44, 46].

Vertebrates:

Gastrulation, endoderm patterning, notochord formation [18, 119].

Urochordates:

Gastrulation, axis formation [120].

Cnidarians:

Preendodermal plate, pharynx [62, 121].

foxAB

24 hpf:

Protostomes:

Circumferential ectodermal ring which localizes to the anterior collar groove during later development.

In the bryozoans larval ciliated cleft and apical ectodermal territory [103].

Juvenile stage:

FoxAB orthologues are further identified in echinoderms [20], cephalochordates [21], cnidarians [19] but expression is unknown.

The developing mouth of the embryo breaks through at the ventral side of the embryo inside the foxAB expression domain

foxB

Late blastula:

Sea urchins:

Ring pattern surrounding the vegetal plate.

Ingressing primary mesenchyme cells; asymmetrically expressed along the oral-aboral axis in the oral ectoderm and endoderm [122–124].

48 hpf:

Cnidarians:

Ventral ectoderm anterior and posterior to the ciliated band.

Around the site of gastrulation, larval endoderm region, in the statocyst, gonad and tentacle bulb of the medusa [19, 63].

Juvenile stage:

Chordates:

Ventral ectoderm and ventral pharyngeal endoderm.

Dorsal ectoderm, mesoderm, brain: Xenopus[125–127], ascidians [59], B. floridae[128].

Protostomes:

Ventral ectoderm [40, 129]; ventral nervous system [35].

foxC

Late blastula:

Chordates:

Vegetal plate.

Pharyngeal mesoderm patterning [31, 32, 34, 130–132]. Pharyngeal endoderm [34].

24 hpf:

Vertebrates:

Anterior endomesoderm.

Ventral and lateral mesoderm, lateral border of neuroectoderm, eye, pronephros [133, 134] (Xenopus, reviewed in [122])

48 hpf:

Cnidarians:

Circumferential ectodermal expression in the anterior and posterior collar groove; endomesodermally at the positions of mesoderm formation.

Presumptive endoderm and mesenteries [63].

Juvenile stage:

Endodermal expression in the pharyngeal endoderm associated with gill pouch formation.

foxD

24 hpf:

Chordates:

Anterior ectodermal circumferential ring.

Notochord [52, 57]

36 hpf:

Diencephalon: reviewed in [61]

Neural crest [52, 76, 135–142] (Reviewed in [52, 122]). Maintenance of dorsolateral mesoderm (Xenopus)[130, 143] (reviewed in [122]). Hindgut [135, 144].

Urochordates:

Anterior ectodermal circumferential ring.

Dorsal anterior ectoderm [57].

Posterior endomesoderm.

48 hpf:

Cephalochordates:

Anterior ectodermal circumferential ring.

Anterior neural plate, the anterior somites, the neural tube, and later in the cerebral vesicle, hindgut [52, 122, 145–149].

Ectodermal single cells throughout the proboscis.

Juvenile stage:

Sea urchins:

Posterior-most endoderm forming the hindgut; ventrolateral mesoderm.

Hindgut [20].

Protostomes:

Dorso-ventral circumferential cell migration and axon projection; ventral mediolateral muscles, intestinal precursor cells (C. elegans)[150–153]. Ventral nervous system (Drosophila) [19].

Cnidarians:

Aboral third of the embryo, tentacle buds [63].

Interaction with BMP/TGF-beta pathway:

[36, 40, 55, 130, 143, 150, 151, 154],[155].

foxE

12 hpf:

Vertebrates:

Ectodermal ring around the animal pole.

Thyroid (Endoderm) [156]

48 hpf:

Urochordates:

Ectodermal circumferential ring localized at the base of the prosome (48 hpf).

Endostyle (Endoderm) [58] Reviewed in [157].

Juvenile stage:

Cephalochordates:

Anterior-dorsal pharynx endoderm including the stomochord.

Club shaped gland (Endoderm) [51, 158].

foxF

24 hpf:

Chordates:

Anterior endomesoderm.

Mesoderm patterning [19, 31, 32, 34, 159–161].

36 hpf:

Gill slit formation in chordates: reviewed in [34].

Developing lateral and posterior mesoderm.

Neural plate border, cephalic neural crest, pronephros: Xenopus, reviewed in [122].

48 hpf:

Protostomes:

Posterior, central, and anterior mesoderm.

Mesoderm [36].

Juvenile stage:

Mesoderm surrounding the pharynx; mesoderm around the posterior gut; a mesodermal spot underneath the site of apical organ formation; heart-kidney complex; the pharyngeal mesoderm with accumulation of foxF expressing cells anterior and posterior to the forming gill pores. (Expression is absent at the position where the evaginating gill pore endoderm connects to the ectoderm.)

foxG

24 hpf:

Vertebrates:

Few single cells in the ectoderm.

Telencephalon (reviewed [50]) [162–164].

36 hpf:

Cephalochordates:

Strong ectodermal circumferential ring in the anterior third of the embryo.

Scattered cells surrounding the cerebral vesicle and inside the cerebral vesicle [50]

48 hpf:

Two ectodermal rings with a gap of expression on the dorsal midline; single cell expression throughout the proboscis with a density of single cells at the proboscis tip.

Juvenile stage:

Additionally to 48 hpf expression: dorsal mesoderm overlaying the pharynx and gut.

foxH

Not present in the S. kowalevskii genome

foxI

48 hpf:

Vertebrates:

Most posterior endoderm; weak ectodermal circumferential ring of anterior to the ciliated band.

Craniofacial development [122, 127, 165].

Juvenile stage:

Sea urchins:

Small domain in the center of the outpocketing gill pouch endoderm; posterior gut.

Larval hindgut with high expression levels on the aboral side [20].

foxJ1

24 hpf:

Vertebrates:

Ectodermal in the ciliated band domain.

Master regulator in the formation of motile cilia [60, 166–172].

Mediates left-right asymmetry [166, 173–177].

Juvenile stage:

Echinoderms:

Ectodermal in the ciliated band, anterior proboscis ectoderm including the apical organ; gill pores; posterior collar.

Oral side of the apical plate [20]; Larval ciliary band [48].

Protostomes:

Ampullary cells, crescent cells, and prototroch (Platynereis) [113]

Cnidarians:

[17, 178]

Yeast:[178]

(Hcm1p) is involved in spindle pole body formation [179].

FoxJ1 orthologues are further identified in Choanoflagellates [180], sponges [66], other deuterostomes and protostomes [33], but expression and function is not known.

foxJ2/3

Not determined.

foxK

>12 hpf:

Vertebrates:

Ubiquitous throughout the ectoderm with the exception of the ciliated band.

Dorsal midline, lateral cephalic neural crest, brain, eye, lateral muscle precursors (Xenopus) [122, 168].

Juvenile stage:

Collar ectoderm.

foxL1

48 hpf:

Chordates:

Circumferential ectodermal band in the anterior collar groove and in the endoderm of the outpocketing gill pores. This expression persists until the one gill slit stage.

Pharyngeal mesoderm patterning [31, 32, 34].

Gill slit endoderm (Scyliorhinus canicula)[34].

foxL2

Not determined.

foxM

Not determined.

foxN1/4

12 hpf:

Mammals:

Ubiquitous expression in the ectoderm.

foxN1 is essential for proper immune response in mice [181]. Downstream target of the Wnt-pathway [182].

foxN4 is involved in specifying amacrine and horizontal cells in the retina and is upstream of the bHLH gene Math3, NeuroD1, and Prox1 [113, 183, 184] (reviewed in [185]).

It is necessary for the development of V2a and V2b interneurons in the spinal cord using lateral inhibition via the Delta-Notch pathway by activating the transcription of Delta4 and the bHLH gene Mash-1 [186, 187].

24 hpf:

Ubiquitous ectodermal expression with the exception of the ciliated band.

48 hpf:

Entire ectoderm with the exception of the central and posterior collar region and the ciliated band. Nested inside these expression domains are single cells that show a high levels of expression.

Juvenile stage:

Proboscis and collar region; thin row of cells posterior to the ciliated band.

foxN2/3

Not determined

foxO

Not determined

foxP

24 hpf:

Vertebrates:

Entire ectoderm with the exception of the ciliated band.

Basal ganglia, cerebral cortex, cerebellum, and thalamus, hippocampus [127, 188–190]. In Medaka foxP1 expression indicates a role during striatum projection neuron development [191] and basal ganglia development of the developing and central nervous system [192].

>36 hpf:

Mutations in human foxP2 gene lead to severe language disorders [193–195] (reviewed in [127, 196]).

High levels of expression in single cells in the anterior ectoderm of the embryo; weak endodermal expression.

Urochordate:

Developing brain [59].

Echinoderms:

Fore- and mid-gut of the larva [20].

Protostomes:

In Drosophila the two splice variants of foxP (fd85Ea and fd85Eb) are expressed in the developing CNS [37, 197].

A FoxP ortholog is also found in other ecdysozoans, cnidarians, and sponges [33, 66], but expression patterns are not yet reported.

foxQ1

48 hpf:

Vertebrates:

Anterior endoderm at the position where the gill pores are forming; faint circumferential ectodermal ring at the position where the gill pores are forming.

Prospective pharynx, pharyngeal pouches [60],

Juvenile stage:

Cephalochordates:

Anterior pharynx.

Endostyle [54].

Urochordates:

Pharyngeal gills, endostyle [58].

Protostomes:

Pharyngeal endoderm [32].

foxQ2-1

12 hpf:

Deuterostomes:

Animal hemisphere.

Apical ectoderm [20, 21, 53, 198].

>24 hpf:

In protostomes:

During the development from gastrula to juvenile, the ectodermal expression becomes refined to cells forming the apical organ.

Anterior tip of the embryo at the blastoderm stage, pharyngeal structures and the brain hemispheres (Drosophila) [37]. Apical ectoderm (Platynereis) [113]

Cnidarians:

Apical tuft [19, 178].

Linke to Wnt/β-catenin signaling:

[19, 45, 64, 73].

foxQ2-2

foxQ2-2 expression resembles the expression of foxQ2-1 with additional ubiquitous expression throughout the embryo ectoderm.

foxQ2-3

24 hpf:

Apical ectodermal territory.

36 hpf:

Ectodermal stripe along the dorsal axis of the embryo starting from the most apical part of the embryo and extending posterior, covering approximately two-thirds of the embryo.

Juvenile stage:

Ectodermal stripe along the dorsal proboscis midline.