Amphioxus and ascidian Dmbx homeobox genes give clues to the vertebrate origins of midbrain development

Unraveling genomic regulatory networks in the simple chordate, Ciona intestinalis

The draft genome of the primitive chordate, Ciona intestinalis, was published three years ago. Since then, significant progress has been made in utilizing Ciona's genomic and morphological simplicity to better understand conserved chordate developmental processes. Extensive annotation and sequencing of staged EST libraries make the Ciona genome one of the best annotated among those that are publicly available. The formation of the Ciona tadpole depends on simple, well-defined cellular lineages, and it is possible to trace the lineages of key chordate tissues such as the notochord and neural tube to the fertilized egg. Electroporation methods permit the targeted expression of regulatory genes and signaling molecules in defined cell lineages, as well as the rapid identification of regulatory DNAs underlying cell-specific gene expression. The recent sequencing of a second Ciona genome (C. savignyi) permits the use of simple alignment algorithms for the identification of conserved noncoding sequences, including microRNA genes and enhancers. Detailed expression profiles are now available for almost every gene that encodes a regulatory protein or cell-signaling molecule. The combination of gene-expression profiles, comparative genome analysis, and gene-disruption assays should permit the determination of high-resolution genomic regulatory networks underlying the specification of basic chordate tissues such as the heart, blood, notochord, and neural tube.

Cataloging transcription factor and major signaling molecule genes for functional genomic studies in Ciona intestinalis

The ascidian Ciona intestinalis provides an excellent experimental system for functional genomic studies because (1) its genome has been sequenced, (2) the transcription factor genes and genes for major signal transduction molecules have been extensively screened and annotated on a genome-wide scale using the molecular phylogenetical method, and (3) their embryonic expression profiles have been almost completely determined. However, the entire genetic structure, including the 5' and 3' untranslated regions and the protein-coding regions, of most gene models used in these prior studies is not always supported by cDNA evidence, and thus, these gene models are potentially imprecise. To facilitate functional genomic studies based on precise gene structures, our present study determined 406 cDNA sequences for 357 transcription factor genes and 112 cDNA sequences for 107 signal transduction molecule genes, greatly improving the previous gene models and revealing transcript variants for 44 genes. Considering these data alongside those of previously characterized genes deposited in the DNA Data Bank of Japan/European Molecular Biology Laboratory/GENBANK databases, 95.6% of the catalogued transcription factor genes (373/390) and 98.3% of the catalogued signal transduction molecule genes (117/119) have now been verified by cDNA sequences. Thus, the present study greatly improves the resources available for functional genomic studies in C. intestinalis.

Genes and homology in nervous system evolution: comparing gene functions, expression patterns, and cell type molecular fingerprints

The evolution of the nervous system is one of the most fascinating, but also most nebulous fields of homology research. We do not know for example whether the last common ancestors of human, squid, and fly already possessed an elaborate brain and eyes, or rather had a simple, diffuse nervous system. Nevertheless, in the past decade molecular data has greatly advanced our understanding of bilaterian nervous system evolution. In this methodological review, I explain the four levels on which molecular genetic studies advance the quest for homologies between animal nervous systems. (I) Bioinformatic homology research elucidates the evolutionary history of gene families relevant for nervous system evolution such as the opsin superfamily. It tells us when and in what order genes and their functions have emerged. Based on this, we can (II) infer the organismal complexity of some remote ancestor from the functional diversity of its reconstructed proteome. (III) Most common in molecular homology research has been the comparison of expression patterns of developmental control genes. This approach matches and aligns embryonic regions along the body axes, between remote bilaterians. It does not tell us much, however, about the complexity of structures that developed from these regions in Urbilateria. (IV) This is overcome by a novel variant of molecular homology research, the comparison of cell types. Here, a similar "molecular fingerprint" of cells is taken as indication of cross-bilaterian homology. This approach makes it possible to reconstruct the cell-type repertoire of the urbilaterian nervous system.

Development of the central nervous system in the larvacean Oikopleura dioica and the evolution of the chordate brain

In non-vertebrate chordates, central nervous system (CNS) development has been studied in only two taxa, the Cephalochordata and a single Class (Ascidiacea) of the morphologically diverse Urochordata. To understand development and molecular regionalization of the brain in a different deeply diverging chordate clade, we isolated and determined the expression patterns of orthologs of vertebrate CNS markers (otxa, otxb, otxc, pax6, pax2/5/8a, pax2/5/8b, engrailed, and hox1) in Oikopleura dioica (Subphylum Urochordata, Class Larvacea). The three Oikopleura otx genes are expressed similarly to vertebrate Otx paralogs, demonstrating that trans-homologs converged on similar evolutionary outcomes by independent neo- or subfunctionalization processes during the evolution of the two taxa. This work revealed that the Oikopleura CNS possesses homologs of the vertebrate forebrain, hindbrain, and spinal cord, but not the midbrain. Comparing larvacean gene expression patterns to published results in ascidians disclosed important developmental differences and similarities that suggest mechanisms of development likely present in their last common ancestor. In contrast to ascidians, the lack of a radical reorganization of the CNS as larvaceans become adults allows us to relate embryonic gene expression patterns to three subdivisions of the adult anterior brain. Our study of the Oikopleura brain provides new insights into chordate CNS evolution: first, the absence of midbrain is a urochordate synapomorphy and not a peculiarity of ascidians, perhaps resulting from their drastic CNS metamorphosis; second, there is no convincing evidence for a homolog of a midbrain-hindbrain boundary (MHB) organizer in urochordates; and third, the expression pattern of "MHB-genes" in the urochordate hindbrain suggests that they function in the development of specific neurons rather than in an MHB organizer.

Ciona intestinalis: chordate development made simple

Thanks to their transparent and rapidly developing mosaic embryos, ascidians (or sea squirts) have been a model system for embryological studies for over a century. Recently, ascidians have entered the postgenomic era, with the sequencing of the Ciona intestinalis genome and the accumulation of molecular resources that rival those available for fruit flies and mice. One strength of ascidians as a model system is their close similarity to vertebrates. Literature reporting molecular homologies between vertebrate and ascidian tissues has flourished over the past 15 years, since the first ascidian genes were cloned. However, it should not be forgotten that ascidians diverged from the lineage leading to vertebrates over 500 million years ago. Here, we review the main similarities and differences so far identified, at the molecular level, between ascidian and vertebrate tissues and discuss the evolution of the compact ascidian genome.

Insights into the urbilaterian brain: conserved genetic patterning mechanisms in insect and vertebrate brain development

Recent molecular genetic analyses of Drosophila melanogaster and mouse central nervous system (CNS) development revealed strikingly similar genetic patterning mechanisms in the formation of the insect and vertebrate brain. Thus, in both insects and vertebrates, the correct regionalization and neuronal identity of the anterior brain anlage is controlled by the cephalic gap genes otd/Otx and ems/Emx, whereas members of the Hox genes are involved in patterning of the posterior brain. A third intermediate domain on the anteroposterior axis of the vertebrate and insect brain is characterized by the expression of the Pax2/5/8 orthologues, suggesting that the tripartite ground plans of the protostome and deuterostome brains share a common evolutionary origin. Furthermore, cross-phylum rescue experiments demonstrate that insect and mammalian members of the otd/Otx and ems/Emx gene families can functionally replace each other in embryonic brain patterning. Homologous genes involved in dorsoventral regionalization of the CNS in vertebrates and insects show remarkably similar patterning and orientation with respect to the neurogenic region (ventral in insects and dorsal in vertebrates). This supports the notion that a dorsoventral body axis inversion occurred after the separation of protostome and deuterostome lineages in evolution. Taken together, these findings demonstrate conserved genetic patterning mechanisms in insect and vertebrate brain development and suggest a monophyletic origin of the brain in protostome and deuterostome bilaterians.

The evolutionary origins of vertebrate midbrain and MHB: insights from mouse, amphioxus and ascidian Dmbx homeobox genes

Comparative studies on developmental gene expression suggest that the ancestral chordate central nervous system comprised anterior, midbrain-hindbrain boundary (MHB) and posterior regions. The most anterior region consists of both forebrain and midbrain in vertebrates. It remains, however, unresolved when or how the vertebrate midbrain was established from this anterior zone. I previously reported a mouse PRD-class homeobox gene, Dmbx1, expressed in the presumptive midbrain at early developmental stages, and in the hindbrain at later stages, with exclusion from the MHB. To investigate the evolution of midbrain development, I have cloned Dmbx genes from amphioxus and from Ciona, representing the two most closely related lineages to the vertebrates, and examined embryonic Dmbx expression in these species. In amphioxus, no Dmbx expression is observed in the neural tube, supporting previous arguments that the MHB equivalent region has been secondarily lost in evolution. In Ciona, the CiDmbx gene is detected in neural cells posterior to Pax-2/5/8-positive cells (MHB homologue), but not in any cells anterior to them. These results support the lack of a midbrain homologue in Ciona, and suggest that midbrain development is a vertebrate innovation. Here, I report the full sequences of these genes and discuss the evolution of midbrain development in relation to the tripartite neural ground plan and the origin of the MHB organizer.

Outlining the nascent nervous system of Branchiostoma floridae (amphioxus) by the pan-neural marker AmphiElav

The cephalochordate amphioxus is the closest living relative of the vertebrates. The anatomy and development of the amphioxus nervous system is giving insights into the basic chordate neural organisation, prior to the increase in neural complexity that characterised the origin of vertebrates. We have analysed the expression of the pan-neural marker AmphiElav in the Florida lancelet (Branchiostoma floridae) through development and up to larval stages. AmphiElav is expressed in the developing neural tube with particular temporal and spatial dynamics that correlate with neuronal differentiation. In addition, AmphiElav is expressed in isolated epidermal cells from mid-neurula embryos. This epidermal expression probably corresponds to precursors of sensory neurons. Together with data from other neural markers, we discuss the evolutionary relevance of these neural precursors to the origin of some of the most dramatic vertebrate inventions, neural crests and placodes.