Biparental inheritance of germline-specific chromosomes in the sea lamprey and their roles in oocytes

Many eukaryotic species undergo programmed elimination of specific chromosomes during embryogenesis, typically retaining these chromosomes only in their germ cells. In some species, programmatic elimination of GRCs, or sex chromosomes, also occurs in a sex-specific manner, with specific chromosomes being transmitted or eliminated by only one sex. As such, these chromosomes provide a unique perspective on the evolution of gene functions that are advantageous to the germline and genetic tradeoffs between somatic vs germline or oocyte vs sperm biology. While GRCs have been extensively characterized in male sea lampreys (Petromyzon marinus), the status of GRCs in females has not yet been resolved, though it has been hypothesized that male-specific expression/transmission of these chromosomes might provide a solution to resolving the long-standing mystery of lamprey sex determining mechanisms. To gain insight into the roles of GRCs in female lampreys, we performed several karyological, transcriptomic, and genomic analyses, which demonstrate that GRCs are present in the female lamprey germline, transmitted by oocytes and somatically eliminated in both sexes. These analyses also show that GRCs play important roles in the maintenance and development of female germline but provide no evidence for sex-specific variation in the elimination and transmission of lamprey GRCs. These findings underscore the diversity of germline functions that are carried out by GRCs in both male and female lampreys and highlight the fact that sex-specific transmission/retention of GRCs likely follows no universal rules across the diverse lineages that have independently evolved to undergo developmentally programmed DNA elimination. Overall design: RNA was extracted from two pools of approximately 100 snap frozen oocytes via the standard Trizol extraction protocol, but supplementing the lysis reaction with 10mM dithiothreitol. Library preparation and sequencing was performed by NovoGene using the company's “Plant and Animal Eukaryotic mRNA” pipeline. Resulting RNAseq reads from this study and a previous studies targeting meiotic teste were aligned to the reference genome using HISAT2 v.2.2.1 and the resulting alignments were used to quantify the expression of annotated genes using Stringtie v.2.2.3. Differential gene expression was assessed using median of ratios normalization in R. For comparisons among paralogs, Orthofinder v2.5.4 was used to compare the complements of somatic vs germline genes and identify groups of paralogous genes that share a common ancestor with groups of one or more somatic gene. This study includes re-analysis of SRP009181.