Genomic structural variation in Barramundi Perch Lates calcarifer and potential roles in speciation and adaptation.

Abstract

Advances in genome sequencing and assembly techniques have increased the documentation of structural variants in wild organisms. Of these variants, chromosomal inversions are especially prominent due to their large size and active recombination suppression between alternative homokaryotypes. This suppression enables the two forms of the inversion to be maintained and allows preservation of locally adapted alleles. The Barramundi Perch (Lates calcarifer) is a widespread species complex with three main genetic lineages located in the biogeographic regions of Australia and New Guinea (AUS+NG), Southeast Asia (SEA), and the Indian Subcontinent (IND). Barramundi Perch are typically considered to be a protandrous sequential hermaphrodite species that exhibits catadromy. Freshwater occupancy and intraspecific variation in life history (e.g., partially migratory populations) exist and provide opportunities for strongly divergent selection associated with, for example, salinity tolerance, swimming ability, and marine dispersal. Herein, we utilize genomic data generated from all three genetic lineages to identify and describe three polymorphic candidate chromosomal inversions. These candidate chromosomal inversions appear to be fixed for ancestral variants in the IND lineage, fixed for inverted versions in the AUS+NG lineage, and exhibit variation in all three inversions in the SEA lineage. Barramundi Perch have a diverse portfolio of life history options that includes migratory strategy as well as sexual system (i.e., hermaphroditism and gonochorism). We propose that the some of the life history variability observed in Barramundi Perch may be linked to inversions and, in so doing, we present genetic data that might be useful in enhancing aquaculture production and population management.