Periodic Reporting for period 1 - HybridExpress (Hybridization derived novel patterns of gene expression)
Berichtszeitraum: 2022-09-01 bis 2025-02-28
Hybridization has been documented to the extent where its importance for generating evolutionary novelty can no longer be questioned. In spite of this, we lack an understanding of the evolution of regulation of gene expression in hybrids, and its role in hybridization derived novelty. Gene expression evolves in a stabilizing manner where cis(local)- and trans(distal) regulatory elements co-evolve. As hybridization breaks up co-inheritance of regulatory elements transgressive hybrid expression patterns, transcending the ranges of both parent species, may arise in spite of intermediate genome composition. Transgressive gene expression is very frequent in F1 hybrids but has hitherto not been studied in the context of hybrid novelty. In this project, we build on my findings of transgressive gene expression in a wild hybrid species, the Italian sparrow. The main objective of the project is to uncover the potential of altered hybrid regulation of gene expression to contribute novel variation that selection can act on. We address this by investigating gene expression and the factors that regulate it in three independently derived lineages of the homoploid hybrid Italian sparrow, Passer italiae, as well as the two parental species the house sparrow P. domesticus and the Spanish sparrow P. hispaniolensis.
Our specific aims include documenting the extent of transgression in gene expression across tissues and lineages of the Italian sparrow, determining general patterns, and uncovering if the regulatory network a gene belongs to, the function of a gene, or the regulatory basis of a gene, are predictive of transgressive expression (WP1). We aim to determine the contribution of novel structural variants, new insertions of transposable elements, and epigenetic regulatory factors on the level of expression in the hybrid species, increasing the general understanding of the intricate regulatory interactions resulting in novel patterns of gene expression (WP2). Finally, we will address whether aberrant gene expression contributes to sterility in early generation hybrids, and whether the expression phenotypes of early generation hybrids predict patterns of expression in stabilized hybrids (WP3).
Our specific aims include documenting the extent of transgression in gene expression across tissues and lineages of the Italian sparrow, determining general patterns, and uncovering if the regulatory network a gene belongs to, the function of a gene, or the regulatory basis of a gene, are predictive of transgressive expression (WP1). We aim to determine the contribution of novel structural variants, new insertions of transposable elements, and epigenetic regulatory factors on the level of expression in the hybrid species, increasing the general understanding of the intricate regulatory interactions resulting in novel patterns of gene expression (WP2). Finally, we will address whether aberrant gene expression contributes to sterility in early generation hybrids, and whether the expression phenotypes of early generation hybrids predict patterns of expression in stabilized hybrids (WP3).
We have produced a unique data set on gene expression in three lineages of the homoploid hybrid Italian sparrow and its parental species to uncover general patterns for how gene expression evolves following hybridization (WP1). To ensure that the gene expression, which is sensitive to life stage, phenology and environmental factors, is comparable among samples we have brought in the bird populations to the Lund University aviary facility and sampled birds in a common garden, the day after the first egg is laid. Samples are taken to ensure that both RNA (WP1), ATAC-seq, whole genome sequencing and methylation (WP2) can be investigated to uncover the genomic underpinnings of altered patterns of gene expression.
To disentangle contributions from differences in regulation from those in cell composition we have also produced Single Cell gene expression data for two individuals from each of both parent species and three independent lineages of Italian sparrow. This data will also provide insights into gene regulatory networks enabling us to address if gene expression changes at the network level (WP1).
We have assembled and are currently in the process of assembling PacBio and Hi-C data reference genomes, providing a first unique data set on the structural variants arising from homoploid hybridization (WP2). This will also provide a valuable resource for mapping RNA-seq data. We have also set up aviary populations for breeding of F1 hybrids between the parental species (WP3).
To disentangle contributions from differences in regulation from those in cell composition we have also produced Single Cell gene expression data for two individuals from each of both parent species and three independent lineages of Italian sparrow. This data will also provide insights into gene regulatory networks enabling us to address if gene expression changes at the network level (WP1).
We have assembled and are currently in the process of assembling PacBio and Hi-C data reference genomes, providing a first unique data set on the structural variants arising from homoploid hybridization (WP2). This will also provide a valuable resource for mapping RNA-seq data. We have also set up aviary populations for breeding of F1 hybrids between the parental species (WP3).
To address the overarching goal of the project, to integrate a gene expression perspective in the understanding of how novelty can arise from hybridization, we combine various lines of inquiry.
Theoretically, I have reviewed the evidence for novel transgressive patterns gene expression in both early generation hybrids and in established hybrid lineages, underscoring the high frequency of transgressive expression both in early generation hybrids and stabilized hybrid lineages or species.
Experimentally, we have produced a data set to uncover the genomic and epigenomic underpinnings of altered hybrid gene expression, comprising three independent lineages of the hybrid Italian sparrow and their parental species.
The combined approach, integrating the perspectives of adaptive novel variation from hybridization from the field of hybridization genomics with approaches enabling us to investigate changes to gene expression and the factors regulating it in hybrids holds great promise to change the way people are thinking about hybridization derived novelty.
Theoretically, I have reviewed the evidence for novel transgressive patterns gene expression in both early generation hybrids and in established hybrid lineages, underscoring the high frequency of transgressive expression both in early generation hybrids and stabilized hybrid lineages or species.
Experimentally, we have produced a data set to uncover the genomic and epigenomic underpinnings of altered hybrid gene expression, comprising three independent lineages of the hybrid Italian sparrow and their parental species.
The combined approach, integrating the perspectives of adaptive novel variation from hybridization from the field of hybridization genomics with approaches enabling us to investigate changes to gene expression and the factors regulating it in hybrids holds great promise to change the way people are thinking about hybridization derived novelty.