About the author
Emily Giles is a Phd Candidate at the Universidad Astral de Chile. Her work involves evaluating the contributions of evolutionary forces and genetic constraints to genomic divergence during speciation with gene flow. Specifically, she works with species and populations of the genus Scurria, true limpets common to the marine intertidal of the Southeastern Pacific.
Thanks to a scholarship from the AGA, I attended the fifth conference hosted by the Global Invertebrate Genomics Alliance (GIGA V) and the AGA in beautiful Cartagena, Colombia. There I presented my work, heard about exciting new research, and learned about ways others have overcome challenges in this field.
My research explores the interplay of gene flow, natural selection, genetic drift, and recombination in shaping complex patterns of genetic diversity within populations and among closely related species. A first step in evaluating genomic divergence is creating a genomic toolbox, ideally including a high-quality genome assembly and annotation. Then, multiple genomes can be compared to this reference to identify variants or regions that differ at close inter- and intraspecific scales. Thus, at GIGA V I presented the genome assemblies and annotations from three limpets of the genus Scurria. Upon comparing these genomes, I found substantial differences among species including deviations from synteny , i.e., chromosomal rearrangements, differences in gene and repeat content, genes unique to species, and additional duplicated genes in two of the species. These resources are useful in investigating variation within species at population levels.
At GIGA V, there were many interesting presentations spanning the themes of biodiversity genomics, comparative genomics, and metagenomics. The inspiring plenaries by Dr. Sara Lemer, Dr. JingChun Li, and Dr. Vanessa Yepes-Narváez discussed harnessing genomic resources to address broad questions in conservation and evolutionary biology. Other notable research that was presented included the effects of environment on invertebrate population structure and insights into hemizygosity, heterozygosity, and gene loss/gain in invertebrates. Additionally, the advances in sequencing technologies over the past few years have led to an explosion of available high quality genome assemblies for invertebrate taxa, and directed efforts by the Wellcome Sanger Institute and the Earth BioGenome Project are making these resources available to all. Next steps include producing phased assemblies, annotations, and pan genomes for the vast array of invertebrate taxa with available haploid genome assemblies.
Despite broad advances in invertebrate genomics, particularities of these taxa present unique challenges to researchers. At GIGA V, there was discussion about the shortcomings of BUSCOs as metrics for evaluating invertebrate genome assemblies. Furthermore, the small size and high microbial and algal symbiont load of many invertebrates makes seemingly straight-forward genome sequencing and assembly a real problem. Invertebrate genomics researchers are perseverant and deeply dedicated to unraveling the complexities of these taxa. This work includes developing techniques to create minimally biased assemblies from amplified genomes and developing a suit of both wet-lab and computational techniques to bring invertebrate genomes to the world.
Overall, attendance of the fifth conference of the Global Invertebrate Genomics Alliance was an unforgettable experience. Academic research can foster a professional climate that can be self-centered, non-inclusive, and highly competitive. Unfortunately, these are the negative consequences of resource limitation. The GIGA community is the antithesis to this behavior. GIGA is committed to promoting scientific genomics research on invertebrate species and makes every effort possible to support diversity in the field. Overall, I look forward to participating in GIGA in the future and encourage any researcher that is committed to invertebrates, genomics, and cooperative inclusion to also get involved. At the very least you will enjoy discussing invertebrate genomics while being wined and dined in exciting locations worldwide, all the while learning there is an alternative to how we do science. By working together, we can achieve more!