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Background  Larval developmental patterns are extremely varied both between and within phyla, however the genetic mechanisms leading to this diversification are poorly understood. We assembled and compared the developmental transcriptomes for two sea biscuit species (Echinodermata: Echinoidea) with differing patterns of larval development, to provide a resource for investigating the evolution of alternate life cycles. One species ( Clypeaster subdepressus ) develops via an obligately feeding larva which metamorphoses 3–4 weeks after fertilization; the other ( Clypeaster rosaceus ) develops via a rare, intermediate larval type—facultative feeding— and can develop through metamorphosis entirely based on egg provisioning in under one week.    Results  Overall, the two transcriptomes are highly similar, containing largely orthologous contigs with similar functional annotation. However, we found distinct differences in gene expression patterns between the two species. Larvae from  C. rosaceus , the facultative planktotroph, turned genes on at earlier stages and had less differentiation in gene expression between larval stages, whereas,  C. subdepressus  showed a higher degree of stage-specific gene expression.    Conclusion  This study is the first genetic analysis of a species with facultatively feeding larvae. Our results are consistent with known developmental differences between the larval types and raise the question of whether earlier onset of developmental genes is a key step in the evolution of a reduced larval period. By publishing a transcriptome for this rare, intermediate, larval type, this study adds developmental breadth to the current genetic resources, which will provide a valuable tool for future research on echinoderm development as well as studies on the evolution of development in general.    Electronic supplementary material  The online version of this article (10.1186/s12864-018-4768-9) contains supplementary material, which is available to authorized users.

The developmental transcriptomes of two sea biscuit species with differing larval types