Genome assembly and annotation of understudied algae

Genomic data is critical for uncovering evolutionary relationships and the genetic basis of key traits, especially in seed-free plants and their green algal relatives, which exhibit unique biological features. Although 4604 plant genomes from 1482 plant species have been published to date, most of these efforts have focused on seed plants, leaving a significant gap in our understanding of seed-free plant lineages. This project aimed to bridge the genomic gap in a clade of deeply understudied green algae, comprising the orders Oedogoniales, Chaetophorales and Chaetopeltidales (OCC) by generating high quality nuclear genome assemblies. One representative from each order was sequenced using Oxford Nanopore long-read technology: Gormaniella terricola (Chaetopeltidales), Stigeoclonum aestivale (Chaetophorales), and Oedogonium obesium (Oedogonium obesum). A genome assembly pipeline was implemented, including read trimming and filtering, contig-level assembly, polishing with Illumina short reads, Hi-C-based scaffolding, and gene prediction using RNA-seq data. As a result, scaffolded and annotated nuclear genomes were obtained for G. terricola and S. aestivale. Although O. obesium ONT reads did not support a complete nuclear assembly, they were successfully used to assemble and annotate its chloroplast genome. These genomic resources lay a foundation for future studies on evolutionary, developmental, and functional biology in the OCC clade. They will enable comparative genomics across green algae and land plants, deepen our understanding of multicellularity, reproduction, and chloroplast evolution, and provide new insights into early events that shaped the transition to terrestrial life.

This summer at BTI was one of the most rewarding experiences of my life. I experienced tremendous growth as a scientist, developing hard skills such as wet lab sequencing techniques, data analysis, and Linux-based bioinformatics, as well as soft skills like science communication, conflict management and troubleshooting. The experience also gave me a broad understanding of what a scientific career in research entails—from the character and skills required to the inner workings of academia. Most importantly, I had the chance to exchange ideas and experiences with incredible people, from whom I learned far more than I had anticipated and with whom I hope to stay in touch.