Periodic Reporting for period 1 - SEXY (Selfish Genome Exclusion under Hybridogenesis)
Periodo di rendicontazione: 2021-12-01 al 2023-11-30
The existence of genetic elements which enhance their own inheritance at the expense of others, the infamous “selfish genes”, has fascinated scientists and laymen alike for decades. One extreme case of selfish transmission, called hybridogenesis, can be observed in some hybrid species. Here, one entire haploid genome is transmitted clonally while the other haploid genome is eliminated prior to or during gamete formation. It gets renewed each generation through mating with the corresponding parental species which results in maintaining a first generation hybrid state over time. Unlike the evolutionary dynamics that underlie the spread and maintenance of selfish transmission strategies, the molecular innovations that enable the selfish transmission of one complete genome at the expense of another in hybridogenetic animals still remain elusive. Here, we took advantage of Bacillus stick insects as a model to elucidate the phylogenomic origin of hybridogenesis (and parthenogenesis) and identify the molecular foundation of selfish transmission and genome exclusion. Our phylogenomic analyses suggest that sex was lost in favor of hybridogenesis after a single hybridization event followed by at least one secondary reproductive mode diversification, most likely a transition from hybridogenesis to parthenogenesis. These findings indicate transitions between unorthodox modes of reproduction that were previously not known to occur, suggesting that the loss of sex per se can be a driver of reproductive mode diversification. This conclusion is supported by crossing experiments aimed at revealing the genomic foundation of hybridogenesis, which display an unexpected transition from hybridogenesis to an effectively clonal transmission of both parental genomes.
We generated reduced representation genome sequencing (RADseq) data for more than 500 individuals sampled during several field trips to the mediterranean with a focus on sicily. Based on the data we first described all parental lineages and their hybrids and tested for losses of heterozygosity which revealed the absence of large scale losses. Further, we have generated genomic resources of eight (sub)species of Bacillus stick insects using long read and short read sequencing, and chromosome conformation capture. We utilized the whole-genome data to phase the genomes of all hybrid Bacillus lineages, i.e. separate sequences derived from the mother and the father, and reconstruct a genome-wide phylogenetic tree including the phased haplosets of the hybrids and the parental species. Further, we phased the RADseq data and reconstructed a maternal and a paternal phylogeny including all maternal and paternal haplosets, respectively. Both trees comprise > 350 individual haplosets. The results indicate a single, common origin of all hybrid lineages and showcase a scenario in which a transition to hybridogenesis was likely followed by a host switch and a transition to parthenogenesis. Such a transition between alternative reproductive strategies in the absence of sex has not been previously described.
Further, we conducted a series of crosses aimed at revealing associations between hybridogenesis and genomic regions. We first crossed hybridogenetic females with males of the maternal ancestral species. We backcrossed the resulting offspring (F1; here the hybridogenetic genome and the “sexual” maternal genome undergo meiosis) with males of the paternal species to reestablish the hybrid state (F2). This has resulted in rearing ~100 F2 individuals. In order to narrow down the genomic regions associated with hybridogenesis, we continued the crossing experiments by mating the obtained F2 females again with males of the maternal species (F3) and their offspring again with males of the paternal species (F4). We determined the reproductive mode of the F2 generation by genotyping their unfertilised eggs. We successfully detected the two expected reproductive phenotypes among the F2 generation: hyridogenesis was characterized by complete absence of the paternal genome in unfertilized eggs while meiotic production of eggs was characterized by presence of both parental haplotypes with distinct recombination break points visible in genotyping data. Surprisingly, we also detected a transition to an effectively clonal transmission of both parental haplosets that was characterized by presence of maternal and paternal haplotypes along the entire length of the genome. In addition to the whole genome sequencing data of the maternal haploset of the hybridogenetic lineages (see above) we generated whole genome sequencing data of the males of the maternal species that were used to initiate the crossing experiment. Presence of both datasets enables us to test for recombination between the hybridogenetic and the paternal haploset and ultimately identify the regions associated with hybridogenesis. These analyses are in progress.
We have engaged in several activities designated to disseminate our results including publication in eminent journals, several presentations at international conferences, presentations at (invited) seminars, dissemination via social media, a personal homepage and at workshops. The results of the project have stimulated several ongoing collaborative actions and grant applications.
Further, we conducted a series of crosses aimed at revealing associations between hybridogenesis and genomic regions. We first crossed hybridogenetic females with males of the maternal ancestral species. We backcrossed the resulting offspring (F1; here the hybridogenetic genome and the “sexual” maternal genome undergo meiosis) with males of the paternal species to reestablish the hybrid state (F2). This has resulted in rearing ~100 F2 individuals. In order to narrow down the genomic regions associated with hybridogenesis, we continued the crossing experiments by mating the obtained F2 females again with males of the maternal species (F3) and their offspring again with males of the paternal species (F4). We determined the reproductive mode of the F2 generation by genotyping their unfertilised eggs. We successfully detected the two expected reproductive phenotypes among the F2 generation: hyridogenesis was characterized by complete absence of the paternal genome in unfertilized eggs while meiotic production of eggs was characterized by presence of both parental haplotypes with distinct recombination break points visible in genotyping data. Surprisingly, we also detected a transition to an effectively clonal transmission of both parental haplosets that was characterized by presence of maternal and paternal haplotypes along the entire length of the genome. In addition to the whole genome sequencing data of the maternal haploset of the hybridogenetic lineages (see above) we generated whole genome sequencing data of the males of the maternal species that were used to initiate the crossing experiment. Presence of both datasets enables us to test for recombination between the hybridogenetic and the paternal haploset and ultimately identify the regions associated with hybridogenesis. These analyses are in progress.
We have engaged in several activities designated to disseminate our results including publication in eminent journals, several presentations at international conferences, presentations at (invited) seminars, dissemination via social media, a personal homepage and at workshops. The results of the project have stimulated several ongoing collaborative actions and grant applications.
Our findings indicate the occurrence of transitions between different transmission strategies (hybridogenesis and parthenogenesis) that were previously unknown to occur. They suggest that a loss of sex per se can be a driver of reproductive mode diversification and that parthenogenesis may evolve via transitional steps in asexual species of hybrid origin. Further, findings of genomic regions associated with hybridogenesis, which is expected as a result of our ongoing crossing experiments, may reveal novel molecular underpinnings of genome exclusion with applicable potential in fields like medicine and agriculture. Overall, the project has contributed to a solidified understanding of the origin of selfish transmission strategies and alternative reproductive strategies, one of the most fundamental questions in evolutionary biology.