Retroviral-like elements (RL elements) include retroviruses and long terminal repeat (LTR)-containing retrotransposons. We report the presence of sea urchin RL elements (termed SURL) in eight species of sea urchins and find that these RL elements belong to several subfamilies. The complete DNA sequence of one SURL element in Tripneustes grailla is 5266 base pairs long, including 254-nucleotide-long identical long terminal repeats (LTRs) (RT), and DNA copies of transcripts are inserted into the host genome. Together, LTR-containing retrotransposons and retroviruses are conveniently termed "retroviral-like elements" (RL elements) (2).RL elements are known in a wide variety of organisms, including yeast (3-5), dipterans (6), lepidopterans (7), gymnosperms (8), angiosperms (9-11), and vertebrates, where they are recognized as retroviruses or endogenous retroviruses and sometimes as retrotransposons (12). RL elements are apparently widely distributed among echinoids. We have observed the RT gene coding region of RL elements in the DNA of all sea urchin species that we have examined, including one cidaroid (Eucidaris tribuloides) and seven euechinoids (Strongylocentrotus purpuratus, Strongylocentrotusfranciscanus, Strongylocentrotus drobachiensis, Tripneustes gratilla, Lytechinus pictus, Lytechinus variegatus, and Arbacia punctulata).In early work on long, interspersed, repeated DNA of sea urchins, electron micrographic examination of reassociated DNA heteroduplexes revealed elements (called cs2108) that were about 5.2 kilobases (kb) long and had an interesting family and subfamily pattern (13). The elements are now named sea urchin RL elements (SURL elements). There are -400 copies of the RT gene coding region interspersed in the genome ofS. purpuratus (13,14). Cloned elements are named as in the example SURL1-21 (Sp), where the number 1 defines the SURL subfamily, 21 is an arbitrary label for the individual clone, and the letters in parentheses are the acronym of the species from which it was derived.Earlier data (13, 14) and our recent work (unpublished data) indicate that the SURL element family consists of subfamilies. Each subfamily contains from a few to 50 members (13). The subfamilies have been distinguished by the DNA sequence divergence of a conserved segment of the RT gene coding region. Members of each subfamily have closely similar sequences (1-10% divergent), whereas this DNA sequence region of each subfamily is greatly divergent from that of other subfamilies (30-45%). Interestingly, examples of intermediate divergence (10-30%) are rare or nonexistent. The implication is that copies of the RL elements that have been inserted into the genome drift in sequence, and the observation of stop codons in required coding regions suggests that many pseudogenes or "pseudocopies" are present. A similar pattern (termed superfamily and families) has been observed for the Ta elements of Arabidopsis (10) that are similar to copia of Drosophila (15). However, these elements are less similar to retroviruses tha...