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Apoptosis and autophagy are fundamental mechanisms of programed cell death activated during protostome and deuterostome embryonic development, contributing to the creation and remodeling of different anatomical structures. Programed cell death has been investigated at morphological and biochemical levels, but there is a lack of information concerning gene expression of death factors during deuterostome embryonic development. In this study, we analyze the expression patterns of 13 genes involved in autophagy, extrinsic and intrinsic apoptosis during blastula, gastrula, and pluteus stages of the sea urchin Paracentrotus lividus embryonic development. Results suggested the occurrence of all death mechanisms investigated, highlighting the simultaneous involvement of apoptosis and autophagy during embryonic development. In particular, gastrula was the developmental stage where the majority of death genes were highly expressed. During gastrulation apoptotic processes are fundamental for tissue remodeling, such as cavity formation and removal of inner ectodermal cells. This is the first report that identifies a panel of cell death genes in the P. lividus genome and analyzes their expression variations during ontogenesis. [ABSTRACT FROM AUTHOR]