Gene duplications and losses within the cyclooxygenase family of teleosts and other chordates

Cyclooxygenase (COX) produces prostaglandins in animals via the oxidation and reduction of arachidonic acid. Different types and numbers of COX genes have been found in corals, sea squirts, fishes, and tetrapods, but no study has used a comparative phylogenetic approach to investigate the evolutionary history of this complex gene family. Therefore, to examine COX evolution in the teleosts and chordates, 9 novel COX sequences (possessing residues and domains critical to COX function) were acquired from the euryhaline killifish, longhorn sculpin, sea lamprey, Atlantic hagfish, and amphioxus using standard polymerase chain reaction (PCR) and cloning methods. Phylogenetic analyses of these and other COX sequences show a complicated history of COX duplications and losses. There are three main lineages of COX in the chordates corresponding to the three subphyla in the phylum Chordata, with each lineage representing an independent COX duplication. Hagfish and lamprey most likely have traditional COX-1/2 genes, suggesting that these genes originated with the first round of genome duplication in the vertebrates according to the 2R hypothesis and are not exclusively present in the gnathostomes. All teleosts examined have three COX genes due to a teleost-specific genome duplication followed by variable loss of a COX-1 (in the zebrafish and rainbow trout) or COX-2 gene (in the derived teleosts). Future studies should examine the functional ramifications of these differential gene losses.     

On a possible evolutionary link of the stomochord of hemichordates to pharyngeal organs of chordates

As a group closely related to chordates, hemichordate acorn worms are in a key phylogenic position for addressing hypotheses of chordate origins. The stomochord of acorn worms is an anterior outgrowth of the pharynx endoderm into the proboscis. In 1886 Bateson proposed homology of this organ to the chordate notochord, crowning this animal group “hemichordates.” Although this proposal has been debated for over a century, the question still remains unresolved. Here we review recent progress related to this question. First, the developmental mode of the stomochord completely differs from that of the notochord. Second, comparison of expression profiles of genes including Brachyury, a key regulator of notochord formation in chordates, does not support the stomochord/notochord homology. Third, FoxE that is expressed in the stomochord‐forming region in acorn worm juveniles is expressed in the club‐shaped gland and in the endostyle of amphioxus, in the endostyle of ascidians, and in the thyroid gland of vertebrates. Based on these findings, together with the anterior endodermal location of the stomochord, we propose that the stomochord has evolutionary relatedness to chordate organs deriving from the anterior pharynx rather than to the notochord. genesis 52:925–934, 2014. © 2014 Wiley Periodicals, Inc.     

A conserved role for the nodal signaling pathway in the establishment of dorso-ventral and left-right axes in deuterostomes

Nodal factors play crucial roles during embryogenesis of chordates. They have been implicated in a number of developmental processes, including mesoderm and endoderm formation and patterning of the embryo along the anterior-posterior and left-right axes. We have analyzed the function of the Nodal signaling pathway during the embryogenesis of the sea urchin, a non-chordate organism. We found that Nodal signaling plays a central role in axis specification in the sea urchin, but surprisingly, its first main role appears to be in ectoderm patterning and not in specification of the endoderm and mesoderm germ layers as in vertebrates. Starting at the early blastula stage, sea urchin nodal is expressed in the presumptive oral ectoderm where it controls the formation of the oral-aboral axis. A second conserved role for nodal signaling during vertebrate evolution is its involvement in the establishment of left-right asymmetries. Sea urchin larvae exhibit profound left-right asymmetry with the formation of the adult rudiment occurring only on the left side. We found that a nodal/lefty/pitx2 gene cassette regulates left-right asymmetry in the sea urchin but that intriguingly, the expression of these genes is reversed compared to vertebrates. We have shown that Nodal signals emitted from the right ectoderm of the larva regulate the asymmetrical morphogenesis of the coelomic pouches by inhibiting rudiment formation on the right side of the larva. This result shows that the mechanisms responsible for patterning the left-right axis are conserved in echinoderms and that this role for nodal is conserved among the deuterostomes. We will discuss the implications regarding the reference axes of the sea urchin and the ancestral function of the nodal gene in the last section of this review.     

Evolution of the globin gene family in deuterostomes: lineage-specific patterns of diversification and attrition

In the Metazoa, globin proteins display an underlying unity in tertiary structure that belies an extraordinary diversity in primary structures, biochemical properties, and physiological functions. Phylogenetic reconstructions can reveal which of these functions represent novel, lineage-specific innovations, and which represent ancestral functions that are shared with homologous globin proteins in other eukaryotes and even prokaryotes. To date, our understanding of globin diversity in deuterostomes has been hindered by a dearth of genomic sequence data from the Ambulacraria (echinoderms + hemichordates), the sister group of chordates, and the phylum Xenacoelomorpha, which includes xenoturbellids, acoelomorphs, and nemertodermatids. Here, we report the results of a phylogenetic and comparative genomic analysis of the globin gene repertoire of deuterostomes. We first characterized the globin genes of the acorn worm, Saccoglossus kowalevskii, a representative of the phylum Hemichordata. We then integrated genomic sequence data from the acorn worm into a comprehensive analysis of conserved synteny and phylogenetic relationships among globin genes from representatives of the eight lineages that comprise the superphylum Deuterostomia. The primary aims were 1) to unravel the evolutionary history of the globin gene superfamily in deuterostomes and 2) to use the estimated phylogeny to gain insights into the functional evolution of deuterostome globins. Results of our analyses indicate that the deuterostome common ancestor possessed a repertoire of at least four distinct globin paralogs and that different subsets of these ancestral genes have been retained in each of the descendant organismal lineages. In each major deuterostome group, a different subset of ancestral precursor genes underwent lineage-specific expansions of functional diversity through repeated rounds of gene duplication and divergence. By integrating results of the phylogenetic analysis with available functional data, we discovered that circulating oxygen-transport hemoglobins evolved independently in several deuterostome lineages and that intracellular nerve globins evolved independently in chordates and acoelomorph worms.     

BMP2/4 and BMP5-8 in jellyfish development and transdifferentiation

Bone morphogenetic proteins (BMPs) have key roles in gastrulation, mesoderm induction and axial patterning. The multitude of bilaterian BMPs employed in these morphogenetic processes contrasts starkly with the scarcity of BMPs in Cnidaria, the most basal eumetazoan phylum. In coral, sea anemone and hydra species, BMPs have been found to be associated with larval and polyp axial patterning. In the hydrozoan jellyfish Podocoryne (Hydractinia) carnea the BMP2/4 and BMP5-8 genes are expressed unilaterally in the larva, corroborating a possible role in larval axial development. With the focal area of BMP expression in the anterior region, however, the jellyfish larva may have a developmental reversal of spatial polarity compared to the anthozoan larva. In medusa development, BMP genes are expressed in divergent expression territories within the presumptive radial canals and in various parts of the endoderm, indicative of an involvement in mesoderm patterning and gastrovascular system formation reminiscent of bilaterian BMP functions. In addition, the BMP2/4 and BMP5-8 genes may play roles in wound response and dedifferentiation or S-phase re-entry, respectively, as the former is expressed in striated muscle cells immediately after excision from the bell and the latter in the initial phase of muscle cell transdifferentiation.     

Group B sox genes that contribute to specification of the vertebrate brain are expressed in the apical organ and ciliary bands of hemichordate larvae

We have identified and characterized the sequence and expression of two Group B Sox genes in the acorn worm, Ptychodera flava. One sequence represents a Group B1 Sox gene and is designated Pf-SoxB1; the other is a Group B2 Sox gene and is designated Pf-SoxB2. Both genes encode polypeptides with an HMG domain in the N-terminal half. Whole-mount in situ hybridization to embryonic and larval stages of P. flava shows that the two genes are expressed in rather similar patterns at these stages. Expression is first detected in the cells of the blastula and subsequently localizes to the ectoderm during gastrulation. As the mouth forms, expression becomes concentrated in the stomodeum region. During morphogenesis of the tornaria larva, expression in the stomodeal ectoderm remains prominent around the mouth and under the oral hood. Later the genes are prominently upregulated in the ciliary bands and the apical organ. These results provide additional evidence that genes playing essential roles in the formation of the chordate dorsal central nervous system function in the development of the ciliary bands and apical organ, neural structures of this non-chordate deuterostome larva.     

Development of the nervous system in the acorn worm Balanoglossus simodensis: insights into nervous system evolution

SUMMARY To examine the evolutionary origin of the chordate nervous system, an outgroup comparison with hemichordates is needed. When the nervous systems of chordates and hemichordates are compared, two possibilities have been proposed, one of which is that the chordate nervous system has evolved from the nervous system of hemichordate‐like larva and the other that it is comparable to the adult nervous system of hemichordates. To address this issue, we investigated the entire developmental process of the nervous system in the acorn worm Balanoglossus simodensis. In tornaria larvae, the nervous system developed along the longitudinal ciliary band and the telotroch, but no neurons were observed in the ventral band or the perianal ciliary ring throughout the developmental stages. The adult nervous system began to develop at the dorsal midline at the Krohn stage, considerably earlier than metamorphosis. During metamorphosis, the larval nervous system was not incorporated into the adult nervous system. These observations strongly suggest that the hemichordate larval nervous system contributes little to the newly formed adult nervous system.     

Dorsoventral axis inversion: Enteropneust anatomy links invertebrates to chordates turned upside down

The relationships between chordates with their dorsal nerve cord and other animal groups remain unclear. The hemichordata, specifically the enteropneusta (acorn worms), have been considered a sister group to the chordata. Enteropneusts combine various chordate features (e.g. lateral gill openings, dorsal nerve cord) with features that are usually associated with gastroneuralian invertebrates (e.g. dorsal heart, circumenteric nerve ring, ventral nerve cord). Here we analyse various morphological and functional characteristics that enteropneusts share with either invertebrates or chordates in the light of our recent proposal that the chordata may derive – by bodily dorsoventral inversion – from a gastroneuralian ancestor. We show that many seemingly non-chordate features of enteropneusts will align with similar features in the chordates – provided that we compare the ventral side of an enteropneust to the dorsal side of a chordate. This inversion proposes several interesting and new putative homologies between enteropneusts and acranian chordates, such as between their epibranchial ridge/endostyle (later thyroid gland), their postanal tails, atrial walls, and also between the chordates' dorsal notochord and the enteropneusts' posteroventral pygochord. Significantly, positional homology between notochord and pygochord is also supported by the expression domains of Brachyury orthologs in vertebrates and invertebrates: a Brachyury ortholog is active in the postero ventral mesoderm in Drosophila and in the dorsal mesoderm in chordates. In conclusion, we propose that the anatomy of enteropneusts may serve as a conceptual 'missing link' between gastroneuralian invertebrates and notoneuralian chordates. We discuss whether the enteropneust's dorsoanterior nervous centre plus their ventral trunk cord then corresponds to brain and dorsal nerve cord in the chordata.     

Metaphylogeny of 82 gene families sheds a new light on chordate evolution

Achieving a better comprehension of the evolution of species has always been an important matter for evolutionary biologists. The deuterostome phylogeny has been described for many years, and three phyla are distinguishable: Echinodermata (including sea stars, sea urchins, etc...), Hemichordata (including acorn worms and pterobranchs), and Chordata (including urochordates, cephalochordates and extant vertebrates). Inside the Chordata phylum, the position of vertebrate species is quite unanimously accepted. Nonetheless, the position of urochordates in regard with vertebrates is still the subject of debate, and has even been suggested by some authors to be a separate phylum from cephalochordates and vertebrates. It was also the case for agnathans species -myxines and hagfish- for which phylogenetic evidence was recently given for a controversial monophyly. This raises the following question: which one of the cephalochordata or urochordata is the sister group of vertebrates and what are their relationships? In the present work, we analyzed 82 protein families presenting homologs between urochordata and other deuterostomes and focused on two points: 1) testing accurately the position of urochordata and cephalochordata phyla in regard with vertebrates as well as chordates monophyly, 2) performing an estimation of the rate of gene loss in the Ciona intestinalis genome. We showed that the urochordate phyla is the vertebrate sister group and that gene loss played a major role in structuring the urochordate genome.     

TOTAL CELL NUMBER AND NUMBER OF THE PRIMARY MESENCHYME CELLS IN WHOLE, 1/2 AND 1/4 LARVAE OF CLYPEASTER JAPONICUS*

Total cell number and number of the primary mesenchyme cells of 1/2 and 1/4 larvae were counted at several developmental stages after hatching in comparison with those of a whole larva, using Clypeaster japonicus as material. To obtain partial larvae, blastomeres were isolated at the 2- or 4-cell stage in Ca-free sea water and cultured in natural sea water at around 23°C. Isolated blastomeres cleaved as in situ, namely, as a part of an embryo. Although each partial embryo tended to spread into a plate, it acquired spherical shape prior to hatching of control whole embryo and developed normally in terms of both developmental rate and morphogenesis. Total cell number of a whole larva was about 620 just after hatching and increased almost linearly until i t reached 1850 at the pluteus stage. A half and quarter larvae contained roughly 1/2 and 1/4, respectively, of the number of cells of whole larva through all stages counted. Numbers of the primary mesenchyme cells in the partial larvae, however, tended to be slightly larger than a half or a fourth of that in whole larva. In whole larva, 35, 50, 56 and 58 was counted at the mesenchyme blastula, early gastrula, late gastrula and pluteus stage, respectively.     

Chordate evolution in a new light

Gene expression studies in embryos often provide insights into evolutionary relationships across phyla. In this issue of Cell, Lowe et al. examine the patterning of the bilaterian nervous system by studying gene expression in a hemichordate, the acorn worm. Although these animals have an unstructured nervous system, they show surprisingly conserved gene expression domains, shedding new light on the evolution of the central nervous system and the phylogenetic placement of chordates.