A cDNA resource for the cephalochordate amphioxus Branchiostoma floridae
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Cephalochordates are the basal invertebrate chordates within the phylum Chordata. They are widely used as a model system for research in evolutionary developmental biology (EvoDevo) to understand the basic patterning mechanisms for the chordate body plan and the origin of vertebrates. Recently, the genome of the cephalochordate Branchiostoma floridae was sequenced, which further brings this organism to the front for comparative genomic studies. In this paper, we report the generation of large-scale 5′- and 3′-expressed sequence tags (ESTs) from B. floridae and the complementary deoxyribonucleic acid (cDNA) resource for this species. Both 5′- and 3′-ESTs were sequenced for approximately 140,000 cDNA clones derived from five developmental stages, and the cDNA clones were subsequently grouped into independent clusters using 3′-EST sequences. We identified 21,229 cDNA clusters, and each corresponds to a unique transcript species from B. floridae. We then chose 24,020 cDNA clones representing all of these 21,229 clusters to generate the “Branchiostoma floridae Gene Collection Release 1.” We also constructed a database with a searchable interface for this EST dataset and the related information on “Branchiostoma floridae Gene Collection Release 1.” This set of cDNA clones along with our cDNA database will serve as an important resource for future research in this basal chordate. This Gene Collection and the original 140,000 individual cDNA clones are available to the research community upon request.
KeywordsCephalochordates Amphioxus cDNA EST Gene collection
We would like to thank Drs. John Lawrence, Susan Bell, Mr. Ray Martinez Jr., and Mr. James Swigart in University of South Florida, for providing laboratory facilities during the summer breeding season of Branchiostoma floridae. We would like to thank Joint Genome Institute for the Branchiostoma floridae genome sequence resources. Jr-Kai Yu is supported by the startup funding from Institute of Cellular and Organismic Biology, Academia Sinica, Taiwan, Republic of China. This work was supported by National Science Foundation grant IBN-04-16292 to Linda Z. Holland and by grants from MEXT, Japan and the 21th and Global COEs at Kyoto University to Noriyuki Satoh.
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