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8 Unraveling Genomic Regulatory Networks in the Simple Chordate, Ciona intestinalis

Weiyang Shi, Michael Levine, Brad Davidson


The ancestral chordate gave rise to three groups, i.e., the vertebrates, cephalochordates, and tunicates (which include the ascidians). While the vertebrates diversified into many familiar aquatic and terrestrial species, the cephalochordates and tunicates remained in the ocean and evolved into highly specialized filter feeders. In the tunicates, acquisition of an endoglucanase gene and cellulose tunic (possibly derived by lateral gene transfer from bacteria) (see Dehal et al. 2002; Matthysse et al. 2004; Nakashima et al. 2004) led to the evolution of a highly divergent adult body plan lacking almost all coelomic cavities. However, the morphogenesis of chordate structures (e.g., notochord and dorsal nerve cord) in tunicate tadpoles has been well conserved despite the “retrograde” evolution of adult anatomy.

The recent sequencing of two closely related ascidian species, Ciona intestinalis and Ciona savignyi, has revived the status of the ascidians as a major developmental model system (Dehal et al. 2002; Satoh 2003; Satoh et al. 2003). Research has confirmed that many aspects of ascidian and vertebrate embryogenesis rely on a conserved set of orthologous genes and cellular processes (Satoh 2003; Passamaneck and Di Gregorio 2005). This is clearly the case for development of the nervous system (Meinertzhagen et al. 2004), notochord (Passamaneck and Di Gregorio 2005), and heart (Satou et al. 2004) and may also be true for other tissues and organs, including the blood cells, pharyngeal gill slits, endostyle, and neural crest (Jeffery et al. 2004). However, ascidian embryos are extraordinarily simple, with low cell numbers, rapid development, and well-defined...

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