Rapid Gene Family Evolution of a Nematode Sperm Protein Despite Sequence Hyper-conservation

Abstract

Reproductive proteins are often observed to be the most rapidly evolving elements within eukaryotic genomes. The major sperm protein (MSP) is unique to the phylum Nematoda and is required for proper sperm locomotion and fertilization. Here, we annotate the MSP gene family and analyze their molecular evolution in 10 representative species across Nematoda. We show that MSPs are hyper-conserved across the phylum, having maintained an amino acid sequence identity of 83.5–97.7% for over 500 million years. This extremely slow rate of evolution makes MSPs some of the most highly conserved genes yet identified. However, at the gene family level, we show hyper-variability in both gene copy number and genomic position within species, suggesting rapid, lineage-specific gene family evolution. Additionally, we find evidence that extensive gene conversion contributes to the maintenance of sequence identity within chromosome-level clusters of MSP genes. Thus, while not conforming to the standard expectation for the evolution of reproductive proteins, our analysis of the molecular evolution of the MSP gene family is nonetheless consistent with the widely repeatable observation that reproductive proteins evolve rapidly, in this case in terms of the genomic properties of gene structure, copy number, and genomic organization. This unusual evolutionary pattern is likely generated by strong pleiotropic constraints acting on these genes at the sequence level, balanced against expansion at the level of the whole gene family.

Proteomic and evolutionary analyses of sperm activation identify uncharacterized genes in Caenorhabditis nematodes

“…However, not all regions of the gene appear to be under the same constraint, as evidenced by the short species-specific repeating motif, although the functional relevance of this motif remains unknown. The pattern of seemingly independent gene copy number expansion and genomic organization despite sequence constraint observed here is strikingly similar to the evolutionary pattern we previously observed in the MSP gene family [ 20 ], and suggests lineage-specific gene family evolution rather than preservation of an ancestral gene family structure.…”

“…From an evolutionary perspective, then, patterns of evolution in secreted membranous organelle proteins do not match expectations for typical seminal fluid proteins. However, this pattern of sequence conservation coupled with lineage-specific gene family evolution observed here has also been previously identified for the MSP gene family [ 20 ]. There thus appears to be a “nematode sperm protein evolution syndrome” in which structural rearrangements and copy number variants are a more prevalent mechanism of genetic evolution than sequence divergence per se.…”

“…3 ). Interestingly, our data reveal three previously unannotated genes (Y59E9AR.7, Y59H11AM.1, and ZK1248.4) as MSPs based on high nucleotide sequence identity and presence of the MSP domain [ 20 ]. Overall, 62% of the proteins identified in the un-activated spermatid proteome were also identified in either the membranous organelle or activated sperm proteome.…”

“…Since MSP proteins are important not only for motility, but also for oocyte signaling [ 28 ], identifying them as an abundant membranous organelle component implicates membranous organelle fusion as an additional method by which free-floating MSP is added to the seminal fluid (see [ 29 ]). There are 31 annotated MSP gene copies in C. elegans , with potentially more uncharacterized copies as seen here, and as of yet we do not know if some of them might be subfunctionally located within different parts of the sperm [ 20 ]. We also found that sperm proteome composition was largely conserved between C. elegans and C. remanei , particularly within the activated sperm itself.…”

Genetic basis to hybrid inviability is more complex than hybrid male sterility in Caenorhabditis nematodes

“…One possibility is that incompatibilities localize to only particular loci in Caenorhabditis associated with a disruption of gonad morphogenesis. In Caenorhabditis, sperm-related genes have a faster rate of evolution than either oocyte or somatic genes (Cutter and Ward 2005;Artieri et al 2008;Kasimatis and Phillips 2018). We, however, analyzed defects in the development of the somatic gonad and C. elegans genes expressed throughout male tissues have especially slow rates of protein evolution (Cutter and Ward 2005), suggesting that "faster male" theory might not apply in this case in a simple way (Wu and Davis 1993).…”