Identification of loci/genes responsible for hybrid incompatibilities between Caenorhabditis briggsae and C. Nigoni

Abstract

Identification of genetic basis of Hybrid Incompatibility (HI) in hybrids between closely related species leads to a comprehensive understanding of speciation. Although model organism C. elegans is well-established in laboratory, it has performed little contribution to this research area, because C. elegans failed to mate with other sister species and produce viable progeny. As a sister species of C. briggsae, which is close to C. elegans, newly discovered C. nigoni made it possible to identify the genetic basis of HI in nematode species. In this study, a new species pair including C. nigoni and C. briggsae was used to study the genetic and molecular bases of HI. 96 GFP markers were randomly integrated into the genome of C. briggsae by biolistic bombardment. Next-Generation Sequencing (NGS) combined with single worm PCR were performed to identify the location of GFP markers. By tracking those markers, the genomic fragments of C. briggsae linked to GFP were backcrossed into C. nigoni. Such process was repeated for at least 15 generations and total 111 strains carrying independent introgressions were generated. Widespread HI loci were identified on a genome-wide scale for the first time in nematode species, which also supported Haldane's Rule and large X-effect theory between the two species. In this study, C. nigoni genome "cn1" was de novo assembled by using a hybrid approach, which combined Illumina synthetic long-read technology and massive parallel sequencing of Fosmid mate-pair library. Two lines of hybrid sterile males each carrying an independent introgression fragment from C. briggsae X chromosome in an otherwise C. nigoni background, demonstrate similar defects in spermatogenesis. A similar pattern of downregulated genes that are specific for spermatogenesis between the two hybrids and wild type control was observed. Importantly, the downregulated genes caused by the X chromosome introgressions are significantly enriched on autosomes, suggesting an epistatic interaction between the X chromosome and autosomes. By measuring small RNAs, the results shows that a subset of 22G RNAs specifically targeting the downregulated spermatogenesis genes are significantly upregulated in hybrids, indicating that perturbation of small RNA-mediated regulation may contribute to the X-autosome interaction.