cDNA Sequences for Transcription Factors andSignaling Proteins of the Hemichordate Saccoglossuskowalevskii: Efficacy of the Expressed Sequence Tag(EST) Approach for Evolutionary and DevelopmentalStudies of a New Organism

摘要

We describe a collection of expressed se-quence tags (ESTs) for Saccoglossus kowalevskii, a direct-developing hemichordate valuable for evolutionary compar-isons with chordates. The 202,175 ESTs represent 163,633arrayed clones carrying cDNAs prepared from embryoniclibraries, and they assemble into 13,677 continuous se-quences (contigs), leaving 10,896 singletons (excluding mi-tochondrial sequences). Of the contigs, 53% had significantmatches when BLAST was used to query the NCBI data-bases (-10-10), as did 51% of the singletons. Contigs mostfrequently matched sequences from amphioxus (29%),chordates (67%), and deuterostomes (87%). From the clonearray, we isolated 400 full-length sequences for transcrip-tion factors and signaling proteins of use for evolutionaryand developmental studies. The set includes sequences forfox, pax, tbx, hox, and other homeobox-containing factors,and for ligands and receptors of the TGFp, Wnt, Hh, Delta/Notch, and RTK pathways. At least 80% of key sequenceshave been obtained, when judged against gene lists of modelReceived 29 October 2007; accepted 4 March 2008.* To whom correspondence should be addressed. E-mail: jgerhart@berkeley.eduAbbreviations: EST, expressed sequence tag; UTR, untranslated region.organisms. The median length of these cDNAs is 2.3 kb,including 1.05 kb of 3' untranslated region (UTR). Only30% are entirely matched by single contigs assembled fromESTs. We conclude that an EST collection based on150,000 clones is a rich source of sequences for moleculardevelopmental work, and that the EST approach is ani effi-cient way to initiate comparative studies of a new organism.