Evidence of widespread hemizygosity and gene presence/absence variation in invertebrate pangenomes: are we overlooking the impact of genomic structural variation in metazoans?

Invited talks

Marco Gerdol1*, Nicolò Fogal2, Carmen Federica Tucci2, Samuele Greco1, Marco Sollitto3, Amaro Saco4, Daniela Eugenia Nerelli1, Dona Kireta1, Magalì Rey-Campos4, Rui Faria5, Beatriz Novoa4, Antonio Figueras4, Umberto Rosani2, and Alberto Pallavicini1

1Department of Life Sciences, University of Trieste, Trieste, Italy

2Department of Biology, University of Padova, Padova, Italy

3Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Koper, Slovenia

4Instituto de Investigaciones Marinas (IIM), Consejo Superior de Investigaciones Científicas (CSIC), Vigo, Spain

5CIBIO, University of Porto, Porto, Portugal

mgerdol [at] units.it

Abstract

Recent advancements in genome sequencing technologies have unveiled unprecedented insights into the genomic makeup of non-model metazoans, whose distinct traits have been long overshadowed by the emphasis placed on monoploid reference assemblies. While the phenotypic effects of structural variation (SV) are well-documented in plants, their significance in the animal kingdom has only recently come to light. Bivalve mollusks, with their complex genomes, present an intriguing model for investigating these phenomena. Our research on the Mediterranean mussel and on the Pacific oyster uncovered an unexpected pangenomic organization, characterized by a plethora of dispensable genes exhibiting Presence/Absence Variation (PAV) and linked to hemizygous regions. Notably, these genes were disproportionately associated with immune response and survival functions, hinting at their role in local adaptation. Subsequent examinations revealed that widespread hemizygosity is a common feature among various bivalve species, indicating an underappreciated functional impact of SV and PAV in these organisms. Interestingly, preliminary analyses suggest that gene PAV is prevalent to varying degrees in aquatic environments, underscoring the necessity for a shift in genomic research focus in non-model metazoans, from monoploid reference assemblies to pan-genomes.

Keywords: presence/absence variation; local adaptation; pangenome assembly; whole genome resequencing