Clustered Organization of Reproductive Genes in the C. elegans Genome Michael A. Miller, Asher D. Cutter, Ikuko Yamamoto, Samuel Ward, David Greenstein  Current Biology  Volume 14, Issue 14, Pages 1284-1290 (July 2004) DOI: 10.1016/j.cub.2004.07.025

Figure 1 Sperm-Enriched Genes Are Nonrandomly Distributed across the Genome The probability that the observed number of sperm-enriched genes lies in a given 0.5 cM interval is plotted as a function of recombination distance (centimorgans) for each chromosome. Similar results were observed with 250 kb chromosome intervals. An M marks the positions of msp genes. Black bars represent chromosomal windows analyzed in Figure 2. Current Biology 2004 14, 1284-1290DOI: (10.1016/j.cub.2004.07.025)

Figure 2 Observed versus Expected Distribution of Genes within SGC Regions that Have Common mRNA Expression Patterns DNA microarrays comprising either 63% or 92% of total loci in the genome were used to identify genes with common transcriptional profiles [10, 15–17]. The ratio of the number of observed to the number expected by chance is plotted for each microarray dataset. Chromosomal windows containing clusters II (–3.2 to –0.5 cM), IV-A (+1.0 to +2.3 cM), and IV-B (+3.9 to +5.0) are plotted separately. *P < 0.001. Current Biology 2004 14, 1284-1290DOI: (10.1016/j.cub.2004.07.025)

Figure 3 Differences in Reproductive Gene Clustering in C. elegans and C. briggsae Correlate with Differences in Regulation (A) Genes in clustered regions of the C. elegans genome are distributed differently in C. briggsae. Colors represent distinct C. briggsae supercontigs mapped onto C. elegans genomic regions by using the positions of homologous genes. If multiple C. briggsae homologs of a C. elegans gene exist on different supercontigs, then sequence breaks were minimized, if possible. msp genes were not included because sequence analyses suggest that they are paralogous (see Figure S2). C. elegans chromosome positions are shown below in Mb (cM). The positions of selected C. elegans reproductive genes are shown above each chromosome region. Asterisks indicate the relative positions of C. briggsae msp genes. (B) C. briggsae supercontigs that exhibit synteny with clustered chromosome IV regions lack most reproductive genes, including the msps. Red arrowheads mark the relative positions of C. elegans msp genes in these C. briggsae supercontigs. The positions of black genes are conserved in both species, whereas red genes have different locations. Black arrows represent C. elegans sperm-enriched genes whose positions are conserved in the two genomes. (C) DAPI staining indicates that C. briggsae (Cb) oocytes progress through pachytene and diplotene meiotic stages more gradually (arrows) than C. elegans (Ce). MAPK activation, assayed by using the MAPK-YT antibody [12], is downregulated in C. elegans as oocytes exit pachytene (arrowhead). By contrast, this does not occur in C. briggsae. Other differences include brood size variability, reproductive efficiency, and the rate of sheath cell contraction. Current Biology 2004 14, 1284-1290DOI: (10.1016/j.cub.2004.07.025)