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Table 1 Expression patterns and assumed function of the genes investigated in this study in annelid representatives from reported literature [9, 15, 16, 18, 23, 3336, 4042, 44, 70, 74, 75, 84]

From: Molecular regionalization in the compact brain of the meiofaunal annelid Dinophilus gyrociliatus (Dinophilidae)

Gene Species Expression pattern Proposed function References
Goosecoid (gsc) Platynereis dumerilii (trochophore larva) Around the stomodeum, in the anterior foregut, parts of the stomodeal nervous system Patterns roof of the foregut, marker for the anterior foregut and oral ectoderm [75]
  Capitella teleta or sp. 1 (late larval stages) Multiple cells at circumesophageal connectives (extend from each side of the brain in ventral–posterior direction laterally toward ventral nerve cord), bilateral pair in anterior ectoderm (several cells with distinctive elongate morphology) Marks subset of anterior neurons associated with stomodeum and foregut, maybe involved in development and differentiation of circumesophageal connectives and neuronal subtype identity [74]
Homeobrain (hbn) Capitella teleta or sp. 1 (late larval stages) Cells associated with epithelio–optic nerves and more medial cell clusters in the brain, in lateral epithelium clearly connected to eyes, between stages 6 and 8 medial brain cells expressing hbnl move closer together toward midline, later, two small clusters appear in anterior-most segment lateral to mouth. Expression levels appear to lower/in fewer cells/clusters in late stages and not present in juvenile stages Differentiates larval eye and brain, confers identity of neuronal subsets, more restricted to brain in Capitella than in Drosophila (there also in the VNC) [16]
Orthopedia (otp) Platynereis dumerilii (trochophore larva) Limited number of cells in the developing medial forebrain region comprising vasotocinergic neurons adjacent to large photoreceptor cilia and the RFamidergic neurons; peripherally, expression demarcates prototroch; also expressed in nerve cells in the apical organ Demarcates the neuropeptidergic sensory-neurosecretory cells in apical organ [18, 23]
Orthodenticle (otx) Platynereis dumerilii (trochophore larva) Most prominent in the oral region (stomodeum), along pre- and postoral ciliary bands, but also in cells of apical organ and few cells in the apical hemisphere, defining head region Patterning pre- and postoral ciliary bands/loops [75]
  Capitella teleta or sp. 1 (late larval stages) Expressed in bilateral lobes of the brain, developing foregut, within the posterior growth zone of the segmented trunk (lateral–posterior ectoderm), within a few cells of the ventral nerve cord along midline; later (stage 9) expressed in the brain, foregut, ventral nerve cord and posterior growth zone Involved in patterning/specifying oral ectoderm, endoderm, foregut and central nervous system in larval stages [74]
  Helobdella sp. At least three paralogs identified, limited to unsegmented head domain, expressed in central nervous system and foregut/surrounding the mouth opening at larval stage 8/9 and scattered cells in the epidermis, but not in the posterior trunk region   [41, 84]
  Pristina leidyi (regeneration) Two paralogs (similar expression region, stronger and/or broader in otx2), otx2 in single medial cell of the ventral ganglia of fully formed midbody segments, extensively expressed during anterior regeneration, in late stages of regeneration adjacent to cerebral ganglia and foregut/pharynx, during fission also detected in the VNC Definition of anterior structures during embryogenesis, involved in head development during regeneration and fission, involved in early processes of postembryonic head specification, possibly related to light-sensing organs [42]
  Hydroides elegans Early expression in the animal hemisphere, associated with ciliary bands in pre-metamorphic larvae (not in primary trochoblasts, but adjacent cells), also along midline (maybe as posterior sensory organ precursors) Specification of neuronal populations [36]
Paired box homeobox gene 6 (pax6) Platynereis dumerilii (trochophore larva) Bilateral patches of cells laterally around the prototroch in developing hemisphere and in ventral episphere; latter domains extend more dorsal than larval eyes—cells of the optic commissure, later also at the base of the differentiating eye; along the developing central nervous system of the body segments; neuroectoderm in trochophore larva Patterns ectopic eyes and ventral neurogenic domain [35, 40]
  Helobdella sp. Two paralogs, pax6A: N teloblast lineage and few cells of O teloblast lineage generating majority of segmentally arranged, ganglionic neurons, in the head closely related to developing supraesophageal ganglion and surrounding tissues; eyes at dorsal lip of rostral sucker; head signal maintained throughout development, segmental expression fades at later stages; dorsally three longitudinal rows of segmentally repeated cells symmetrical lateral to dorsal midline Widely conserved role in eye development, implication in CNS development [44]
Forkhead box gene G (foxg)—brain factor 1 (bf1) Platynereis dumerilii (trochophore larva) Horseshoe-shaped domain in the brain, more lateral part represents the eye anlage during early development, in the brain expression retained during larval development Coordinates activity of two opposing signaling centers patterning the telencephalon anlage: downstream of the ventral signal, Hh, to induce ventral (subpallial) identities and inhibits dorsal Wnt/b-catenin signaling through direct transcriptional repression of Wnt8 which induces dorsal (pallial) identities in vertebrates [9]
Six class gene 3/6 (six3/6) Platynereis dumerilii (trochophore larva) Almost the entire episphere, includes anlagen of antennae and palpae, surrounded by ring-like peristomial expression of Pdu-otx (covering equatorial/peristomial larval regions and overlapping with six3 in the periphery of the episphere) Covers the medial brain anlagen, includes a large part of the early differentiating neurosecretory cells [34]
NK homeobox gene 2.1 (nk2.1) Platynereis dumerilii (trochophore larva) Medioanterior expression of Pdu-nk2.1 laterally demarcated by Pdu-pax6 Subdividing the anterior body regions mediolaterally [9, 18, 34]
  Capitella teleta or sp. 1 (late larval stages) Two paralogs in stage 6/7: nk2.1a—subset of brain cells, dorsal–anterior foregut tissue, within the midgut and in rectum at posterior terminus of midgut; nk2.1b—two brain lobes, in subsurface cells of presumptive foregut, broad ventrolateral domain in trunk ectoderm and mesoderm, extending from posterior of the mouth to the telotroch Involved in endoderm patterning and differentiation; patterns anterior ectoderm [74]
NK homeobox gene 2.2 (nk2.2) Platynereis dumerilii (trochophore larva) Y-shaped pattern comprising slender domain of midline cells, demarcating medial edges of fusing neuroectoderm, strictly complementary to pax6 Patterns endoderm, together with other genes differentiating central nervous system [35]
Neurosecretory differentiation factor dimmed (dim) Platynereis dumerilii (trochophore larva) Colocalized broadly with otp in apical organ neurons Neuroendocrine transcription factor; differentiates neuroendocrine neurons; coexpressed with MIP in the median brain [70]
Membrane-trafficking protein synaptotagmin-1 (syt) Platynereis dumerilii (trochophore larva) Demarcating specific differentiating neurons; restricted to basal cells; neuroectoderm comprises a progenitor zone containing postmitotic, nondifferentiated neuronal precursors and differentiation zone Neuronal differentiation [35]
  Capitella teleta or sp. 1 (late larval stages) Most terminally differentiated neurons; expression pattern progresses from anterior to posterior and begins in the central nervous system; few cells on either side of the mouth; most, but not all of the forming ganglia in the ventral nerve cord; small number of cells along the dorsal midline; stomatogastric ganglia; single and small clusters of cells in the epidermis Exocytosis of synaptic vesicles, neuronal differentiation [33]
  Lamellibrachia satsuma Brain and in the ventral nerve cord, laterally and dorsally encapsulated neuropils of the brain, neural cell bodies located lateral to giant axon, distinct tubular structure in vestimentiferan nervous system Patterns nervous system [15]
  1. The majority of the genes tested in this study are located in the brain and/or the apical organ of adults and larval stages of the listed Annelida. The entire series of genes used in this study has not been assessed in any other annelid species