cDNA Sequences for Transcription Factors and Signaling Proteins of the HemichordateSaccoglossus kowalevskii: Efficacy of the Expressed Sequence Tag (EST) Approach for Evolutionary and Developmental Studies of a New Organism

Abstract

Abstract.We describe a collection of expressed sequence tags (ESTs) for Saccoglossus kowalevskii, a directdeveloping hemichordate valuable for evolutionary comparisons with chordates. The 202,175 ESTs represent 163,633 arrayed clones carrying cDNAs prepared from embryonic libraries, and they assemble into 13,677 continuous sequences (contigs), leaving 10,896 singletons (excluding mitochondrial sequences). Of the contigs, 53% had significant matches when BLAST was used to query the NCBI databases (Յ10 Ϫ10 ), as did 51% of the singletons. Contigs most frequently matched sequences from amphioxus (29%), chordates (67%), and deuterostomes (87%). From the clone array, we isolated 400 full-length sequences for transcription factors and signaling proteins of use for evolutionary and developmental studies. The set includes sequences for fox, pax, tbx, hox, and other homeobox-containing factors, and for ligands and receptors of the TGF␤, Wnt, Hh, Delta/ Notch, and RTK pathways. At least 80% of key sequences have been obtained, when judged against gene lists of model organisms. The median length of these cDNAs is 2.3 kb, including 1.05 kb of 3Ј untranslated region (UTR). Only 30% are entirely matched by single contigs assembled from ESTs. We conclude that an EST collection based on 150,000 clones is a rich source of sequences for molecular developmental work, and that the EST approach is an efficient way to initiate comparative studies of a new organism.

β-Catenin specifies the endomesoderm and defines the posterior organizer of the hemichordate Saccoglossus kowalevskii

“…The availability of a large collection of ESTs (Freeman et al, 2008) and extensive expression data allowed us to select a collection of markers of different regions of the ectoderm and endomesoderm. Some examples are shown in Fig.…”

Evolutionary crossroads in developmental biology: hemichordates

“…Development and refinement of new functional approaches, together with the availability of new genomic datasets, provide the essential resources with which to address a wide range of key questions in developmental and evolutionary biology. The genomics resources for S. kowalevskii are well developed and include an extensive EST collection for a range of developmental stages and adult tissues (Freeman et al, 2008), and an EST resource is currently being developed for P. flava (Röttinger and Martindale, 2011). In addition, the genomes for both species have been sequenced and are currently in the process of being assembled and annotated.…”

Man is but a worm: Chordate origins

“…However, homology of these large cells to giant cells found in other invertebrates or chordates is still uncertain. Genomic resources, such as EST projects (Freeman et al, 2008) and/or monoclonal antibodies, will be instrumental in isolating and characterizing specific genes expressed in these cells. This information may, in turn, be informative as far as the homology of these cells to large neuronal cells in nervous systems of other animal species.…”

“…Developmental gene expression data and morphological analyses suggest that hemichordates share the pharyngeal gill slits and postanal tail with chordates, but homologies of the other features are currently being investigated (reviewed in Gerhart et al, 2005;Satoh, 2008;Swalla, 2007). Hemichordates are the last major deuterostome phyla to have their complete genome sequenced, but a large number of ESTs are currently available for the direct developing hemichordate worm, Saccoglossus kowalevskii (Freeman et al, 2008). In this article, we compare the anterior sensory organs, the dorsal neural tube, the A-P and D-V axes between ptychoderid hemichordates and lancelets, and suggest where studies will be most fruitful to evaluate further homologies.…”