@article{harry_zakas_2023, title={Maternal patterns of inheritance alter transcript expression in eggs}, volume={24}, ISSN={["1471-2164"]}, DOI={10.1186/s12864-023-09291-8}, abstractNote={Abstract Background Modifications to early development can lead to evolutionary diversification. The early stages of development are under maternal control, as mothers produce eggs loaded with nutrients, proteins and mRNAs that direct early embryogenesis. Maternally provided mRNAs are the only expressed genes in initial stages of development and are tightly regulated. Differences in maternal mRNA provisioning could lead to phenotypic changes in embryogenesis and ultimately evolutionary changes in development. However, the extent that maternal mRNA expression in eggs can vary is unknown for most developmental models. Here, we use a species with dimorphic development— where females make eggs and larvae of different sizes and life-history modes—to investigate the extent of variation in maternal mRNA provisioning to the egg. Results We find that there is significant variation in gene expression across eggs of different development modes, and that there are both qualitative and quantitative differences in mRNA expression. We separate parental effects from allelic effects, and find that both mechanisms contribute to mRNA expression differences. We also find that offspring of intraspecific crosses differentially provision their eggs based on the parental cross direction (a parental effect ) , which has not been previously demonstrated in reproductive traits like oogenesis. Conclusion We find that maternally controlled initiation of development is functionally distinct between eggs of different sizes and maternal genotypes. Both allele-specific effects and parent-of-origin effects contribute to gene expression differences in eggs. The latter indicates an intergenerational effect where a parent’s genotype can affect gene expression in an egg made by the next generation.}, number={1}, journal={BMC GENOMICS}, author={Harry, Nathan D. D. and Zakas, Christina}, year={2023}, month={Apr} }
 @article{zakas_harry_scholl_rockman_2022, title={The Genome of the Poecilogonous Annelid Streblospio benedicti}, volume={14}, ISSN={["1759-6653"]}, url={https://doi.org/10.1093/gbe/evac008}, DOI={10.1093/gbe/evac008}, abstractNote={Abstract Streblospio benedicti is a common marine annelid that has become an important model for developmental evolution. It is the only known example of poecilogony (where two distinct developmental modes occur within a single species) that is due to a heritable difference in egg size. The dimorphic developmental programs and life-histories exhibited in this species depend on differences within the genome, making it an optimal model for understanding the genomic basis of developmental divergence. Studies using S. benedicti have begun to uncover the genetic and genomic principles that underlie developmental uncoupling, but until now they have been limited by the lack of availability of genomic tools. Here, we present an annotated chromosomal-level genome assembly of S. benedicti generated from a combination of Illumina reads, Nanopore long reads, Chicago and Hi-C chromatin interaction sequencing, and a genetic map from experimental crosses. At 701.4 Mb, the S. benedicti genome is the largest annelid genome to date that has been assembled to chromosomal scaffolds. The complete genome of S. benedicti is valuable for functional genomic analyses of development and evolution, as well as phylogenetic comparison within the annelida and the Lophotrochozoa. Despite having two developmental modes, there is no evidence of genome duplication or substantial gene number expansions. Instead, lineage-specific repeats account for much of the expansion of this genome compared with other annelids.}, number={2}, journal={GENOME BIOLOGY AND EVOLUTION}, author={Zakas, Christina and Harry, Nathan D. and Scholl, Elizabeth H. and Rockman, Matthew V}, editor={Lavrov, DennisEditor}, year={2022}, month={Feb} }