Tunicates are invertebrate chordates and are the sister group to the vertebrates. Although tunicates share little morphological resemblance to vertebrates in their adult stage, they do share several features in their larval stage: a hollow dorsal neural tube, gill slits, and a post-anal tail, containing a notochord--a group of cells organized in a rod shaped structure - the key features that classify the phyla. Within the tunicates, several ascidians have undergone tail-loss, and many of them are Molgulidae. Hybrids have been produced through the cross fertilization of two Molgula species (Molgula occulta and Molgula oculata), and no other solitary Molgula species have been known to hybridize. Here we have sequenced the transcriptomes of several developmental stages of both M. occulta and M. oculata-- two closely related, free-spawning ascidian species, and their hybrid, in order to study the mechanisms behind tail lost in M. occulta. We were first presented with the problem of identifying the best pipeline for the de novo assembly of our transcriptomes. Here we determined that processing reads through digital normalization, a redundancy reduction step, had less of an effect on assemblies than the assembler used. We then sequenced and assembled the genomes of M. occulta, M. oculata and a more distant species, M. occidentalis. This allowed us to characterize the genomes, discovering that the species are more divergent then they appear phenotypically, and also building better gene models. Through differential expression analysis we determined that M. oculata and the hybrid appear to have overlapping transcripts that are up-regulated during the formation of the ascidian tail, and that the genes are primarily overexpressed by the tailed species and hybrid in relation to the tail-less species.
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