Lungfish Mega-Genomes: Analysis of the Largest Vertebrate Genomes and the Evolution of Tetrapod Adaptations

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Lungfish are the closest living relatives to all land vertebrates among the "fishes". Their phylogenetic position is crucial for the investigation of both tetrapod evolution and innovations associated with the terrestrialization of vertebrates and its required adaptations. The project aims to better understand the transition from fish to tetrapod adaptations to a terrestrial environment. Lungfish also show remarkable physiological adaptations, such as hypoxia tolerance, aestivation, longevity, and the ability of regeneration of entire limbs. Lungfish also have the largest genomes (40-130 GB) known in the animal kingdom that prohibited their sequencing and assembly technically (and financially) so far. The structure of these megagenomes and the mechanisms that have led to their size are still poorly understood - highlighting the need for a better understanding, both to study tetrapod innovations and the evolution and maintenance of huge genomes. Only through the recent advent of long-read sequencing (PacBio, Oxford Nanopore, etc.) and mapping (Hi-C, BioNano) technologies, is it now possible to sequence, assemble and analyze the lungfish genome. We will obtain a high-quality genomic sequence of the Australian lungfish (Neoceratodus forsteri) through a combination of short-read and long-read technologies and mapping methods (e.g. Bionano), which will provide information on the structure, composition, and origin of megagenomes. Tissue-specific transcriptomes from all six lungfish species (1 Australian, 1 South American and 4 African) will aid in the assembly, annotation and analysis of gene and gene family evolution (gains, losses, selection, etc.) and provide functional data for comparative studies. The genomic and transcriptomic data will provide information on tetrapod innovations as well as on lungfish-specific adaptations.