Fig. 2.

Germ1. (A) Sequence analysis: Germ1 was isolated by screening a size-selected (9–10 kb) HindIII library (from sperm DNA) for presence of the rpt200 probe. Sequencing of this fragment revealed that this particular germline-enriched element is internally composed of several different repetitive elements. Analysis of somatic depth of coverage reveals that much of the sequence is abundantly represented by somatic whole genome shotgun reads, similar to the functional rDNAs. Notably though, the 5′ region (not homologous to 28S RNA) is relatively rarer. Labels show the position of sequence elements and molecular probes: FISH, the FISH probe corresponding to the somatically rare region (see Fig. S3); RT, the real-time probe for Germ1 (note that this probe overlaps the boundary between somatically-rare and 28S rDNA-like regions); RT (control), the real-time probe for 28S rDNA (note that the forward primer matches only rDNA, and the reverse primer matched both sequences) (see Fig. 4). (B) Structural differences between germline and soma are widespread and reproducible. To test whether fragments that were identified as sperm specific in our initial screen are truly unique to germline, rpt200 was used to probe Southern blots of respective genomic DNAs that were isolated from testes and several somatic tissues of two animals. Fragment sizes were estimated on the basis of electrophoretic migration of molecular mass markers (Low Range PFG Marker; New England Biolabs) that were run in adjacent lanes. T, testes; B, blood; L, liver; K, kidney; F, fin; M, muscle.