Developing Germline Markers for a Species That Undergoes Programmed Genome Rearrangement

The sea lamprey (Petromyzon marinus) undergoes massive programmed genomic rearrangements (PGR) during early embryonic development, during the maternal to zygotic transition. These rearrangements result in the specific elimination of approximately 20% of the genome from somatic cells. Although it is known that adult germ cells contain ~500 megabases of additional sequence, little is known about the embryonic origin and development of the germline. In order to better track genomically-differentiated cell lineages in early embryogenesis, we sequenced and characterized the lamprey homolog of the classical germline marker vasa. Analyses of the germline locus have revealed that several successive introns have a repetitive structure with self-complementarity at the 5’ and 3’ intron boundaries. This unique intronic structure was not shared in the human homolog of the vasa gene, but is similar to sequence motifs (CA and GT dinucleotide repeats) that are enriched in regions that flank somatically-eliminated sequences. We speculate that this repetitive structure may be functionally related to the retention or expression of germline genes. Although it was anticipated that vasa should represent an ideal marker for lamprey germline, results of repeated in situ hybridizations suggested that a more robust embryogenesis marker was needed. To identify other candidate markers, we performed, RNA-seq analysis of testes, somatic tissues and developing embryos. Several candidate genes were identified that are highly expressed in germline and throughout embryogenesis. Ongoing in situ hybridization studies are being performed to validate and further characterize these markers.