A New Genome Assembly to Support Analysis of Rare Sexual Chimeras in Butterflies

Abstract

Biology research is becoming increasingly computerized and increasingly team based. These trends are occurring against a backdrop of questions about research reproducibility and faltering public support for science in the United States. I spent my time as PhD candidate in Genetics and Genomics striving to develop computational skills with an emphasis on rigor, reproducibility, and re-usability, while also focusing on building competency working with teams, collaborators, and the broader societal implications of my work. I pursued these goals in the context of studying a gyanandromorphic individual of the neotropical butterfly species Heliconius melpomene. Gynandromorphs and Heliconius butterflies have both had an outsized impact on the history of biology and both are captivating to a broader audience. These features made the heliconius gynandromorph characterization project a particularly exciting one to undertake with my team of four undergraduate mentees. Together we examined the genetic and developmental mechanisms of lepidopteran gynandromorphs, which had not previously been undertaken using modern sequencing technologies. To facilitate this work, I developed the HiFi-helper snakemake workflow for genome assembly and used it to generate a new Heliconius melpomene rosina (HMR) reference genome. Critically, this new HMR assembly includes the previously unidentified W sex chromosome. Through work on HiFi-helper I conclude that reproducible workflows benefit from streamlined package management, containerization, and extensive user testing. Workflow outputs show that assemblies from HiFi reads alone suffer from low contiguity, but offer a compelling level of BUSCO completeness, benefit from assembly parameter optimization, and can fulfill a valuable niche for cost-effective analysis and improvement of existing assemblies. From my experience on the gynandromorph project I learned that team based science requires a higher level of structure and organization but is effective and highly rewarding. My team and I discovered that the Heliconius melpomene gynandromorph we examined is a sexual chimera, composed of two separate genomes with differing sex chromosome complements. As a whole, my PhD experience deepened my conviction that public and political support for science is critical, as is the engagement of scientists with the moral and social dimensions of science.