title: Overview of the transcriptome profiles identified in hagfish, shark, and bichir: current issues arising from some nonmodel vertebrate taxa.
abstract: Because of their crucial phylogenetic positions, hagfishes, sharks, and bichirs are recognized as key taxa in our understanding of vertebrate evolution. The expression patterns of the regulatory genes involved in developmental patterning have been analyzed in the context of evolutionary developmental studies. However, in a survey of public sequence databases, we found that the large-scale sequence data for these taxa are still limited. To address this deficit, we used conventional Sanger DNA sequencing and a next-generation sequencing technology based on 454 GS FLX sequencing to obtain expressed sequence tags (ESTs) of the Japanese inshore hagfish (Eptatretus burgeri; 161,482 ESTs), cloudy catshark (Scyliorhinus torazame; 165,819 ESTs), and gray bichir (Polypterus senegalus; 34,336 ESTs). We deposited the ESTs in a newly constructed database, designated the "Vertebrate TimeCapsule." The ESTs include sequences from genes that can be effectively used in evolutionary developmental studies; for instance, several encode cartilaginous extracellular matrix proteins, which are central to an understanding of the ways in which evolutionary processes affected the skeletal elements, whereas others encode regulatory genes involved in craniofacial development and early embryogenesis. Here, we discuss how hagfishes, sharks, and bichirs contribute to our understanding of vertebrate evolution, we review the current status of the publicly available sequence data for these three taxa, and we introduce our EST projects and newly developed database.
authors.affiliation: Laboratory for Evolutionary Morphology, Center for Developmental Biology, RIKEN, Kobe, Japan.
authors.forename: Masaki
authors.initials: M
authors.lastname: Takechi
authors.forename: Masaki
authors.initials: M
authors.lastname: Takeuchi
authors.forename: Kinya G
authors.initials: KG
authors.lastname: Ota
authors.forename: Osamu
authors.initials: O
authors.lastname: Nishimura
authors.forename: Makoto
authors.initials: M
authors.lastname: Mochii
authors.forename: Kazu
authors.initials: K
authors.lastname: Itomi
authors.forename: Noritaka
authors.initials: N
authors.lastname: Adachi
authors.forename: Maiko
authors.initials: M
authors.lastname: Takahashi
authors.forename: Satoko
authors.initials: S
authors.lastname: Fujimoto
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Tarui
authors.forename: Masataka
authors.initials: M
authors.lastname: Okabe
authors.forename: Shinichi
authors.initials: S
authors.lastname: Aizawa
authors.forename: Shigeru
authors.initials: S
authors.lastname: Kuratani
mesh_terms: D000818:Animals; D030561:Databases, Nucleic Acid; D019143:Evolution, Molecular; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D015723:Gene Library; D006196:Hagfishes / Q000145:classification* / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D010802:Phylogeny; D012754:Sharks / Q000145:classification* / Q000235:genetics; D059467:Transcriptome