A Genome-Wide Hybrid Incompatibility Landscape between Caenorhabditis briggsae and C. nigoni

Abstract

Systematic characterization of ẖybrid incompatibility (HI) between related species remains the key to understanding speciation. The genetic basis of HI has been intensively studied in Drosophila species, but remains largely unknown in other species, including nematodes, which is mainly due to the lack of a sister species with which C. elegans can mate and produce viable progeny. The recent discovery of a C. briggsae sister species, C. nigoni, has opened up the possibility of dissecting the genetic basis of HI in nematode species. However, the paucity of dominant and visible marker prevents the efficient mapping of HI loci between the two species. To elucidate the genetic basis of speciation in nematode species, we first generated 96 chromosomally integrated GFP markers in the C. briggsae genome and mapped them into the defined locations by PCR and Next-Generation Sequencing (NGS). Aided by the marker, we backcrossed the GFP-associated C. briggsae genomic fragments into C. nigoni for at least 15 generations and produced 111 independent introgressions. The introgression fragments cover most of the C. briggsae genome. We finally dissected the patterns of HI by scoring the embryonic lethality, larval arrest, sex ratio and male sterility for each introgression line, through which we identified pervasive HI loci and produced a genome-wide landscape of HI between the two nematode species, the first of its type for any non-Drosophila species. The HI data not only provided insights into the genetic basis of speciation, but also established a framework for the possible cloning of HI loci between the two nematode species. Furthermore, the data on hybrids confirmed Haldane’s rule and suggested the presence of a large X effect in terms of fertility between the two species. Importantly, this work opens a new avenue for studying speciation genetics between nematode species and allows parallel comparison of the HI with that in Drosophila and other species.

Specific down-regulation of spermatogenesis genes targeted by 22G RNAs in hybrid sterile males associated with an X-Chromosome introgression

“…These observations support the hypothesis of X demasculinization or sexual antagonism and X inactivation (SAXI) (Wu and Xu 2003). Nevertheless, the X Chromosome is found to play a disproportionately larger role than autosomes in the development of hybrid male sterility (Masly and Presgraves 2007;Bi et al 2015). One possible explanation for this discrepancy is the presence of a genetic interaction between the X Chromosome and autosomes to maintain the correct expression ratios between the X Chromosome and the autosomes (hereafter termed as X:A imbalance), which is essential for spermatogenesis (Wu and Xu 2003).…”

“…Replacement of different fragments of the C. nigoni X Chromosome with homologous regions from C. briggsae results in defective spermatogenesis and sterility Our previous efforts in systematic introgression of GFP-linked C. briggsae genomic fragments into the C. nigoni background produced multiple independent introgression lines that demonstrate complete male sterility (Bi et al 2015). Here we focused on two male sterile lines, each of which carries an independent, nonoverlapping fragment from the C. briggsae X Chromosome (Fig.…”

“…The introgression was achieved by repeated backcrossing of the GFP-linked C. briggsae genomic fragment into C. nigoni for at least 15 generations ( Fig. 2D; Bi et al 2015), meaning the two male sterile lines essentially carry pure C. nigoni background except for the introgression region. To verify the introgression boundaries defined by singleworm PCR (Yan et al 2012), we performed NGS to determine the introgression boundaries as previously described (Bi et al 2015).…”

“…Results from the preliminary crossing between the two support Haldane's rule (Woodruff et al 2010;Kozlowska et al 2012). To facilitate the species pair as a model for isolation of HI loci, we have recently developed random labeling of C. briggsae chromosomes with GFP markers and mapped them into defined genomic regions (Bi et al 2015). Multiple independent introgressions from a C. briggsae X Chromosome produce sterile males in a C. nigoni background (Bi et al 2015), but the molecular mechanism underlying the observed sterilities remains unclear.…”

“…To facilitate the species pair as a model for isolation of HI loci, we have recently developed random labeling of C. briggsae chromosomes with GFP markers and mapped them into defined genomic regions (Bi et al 2015). Multiple independent introgressions from a C. briggsae X Chromosome produce sterile males in a C. nigoni background (Bi et al 2015), but the molecular mechanism underlying the observed sterilities remains unclear. Here we examined the molecular mechanisms of hybrid male sterility between C. briggsae and C. nigoni mainly through genomic approaches.…”