Abstract
Lungfishes belong to lobe-fined fish (Sarcopterygii) that, in the Devonian period, ‘conquered’ the land and ultimately gave rise to all land vertebrates, including humans1–3. Here we determine the chromosome-quality genome of the Australian lungfish (Neoceratodus forsteri), which is known to have the largest genome of any animal. The vast size of this genome, which is about 14× larger than that of humans, is attributable mostly to huge intergenic regions and introns with high repeat content (around 90%), the components of which resemble those of tetrapods (comprising mainly long interspersed nuclear elements) more than they do those of ray-finned fish. The lungfish genome continues to expand independently (its transposable elements are still active), through mechanisms different to those of the enormous genomes of salamanders. The 17 fully assembled lungfish macrochromosomes maintain synteny to other vertebrate chromosomes, and all microchromosomes maintain conserved ancient homology with the ancestral vertebrate karyotype. Our phylogenomic analyses confirm previous reports that lungfish occupy a key evolutionary position as the closest living relatives to tetrapods4,5, underscoring the importance of lungfish for understanding innovations associated with terrestrialization. Lungfish preadaptations to living on land include the gain of limb-like expression in developmental genes such as hoxc13 and sall1 in their lobed fins. Increased rates of evolution and the duplication of genes associated with obligate air-breathing, such as lung surfactants and the expansion of odorant receptor gene families (which encode proteins involved in detecting airborne odours), contribute to the tetrapod-like biology of lungfishes. These findings advance our understanding of this major transition during vertebrate evolution.
Highlights
Together with the coelacanths and tetrapods, lungfish are members of the Sarcopterygii; owing to the short branch that separates these three ancient lineages it has remained difficult to resolve their relationships
We ascertained the high completeness of the 37-Gb assembly by observing that 88.2% of the DNA and 84% of the RNA sequencing (RNA-seq) reads aligned to the genome, which gives an estimated total genome size of 43 Gb
We assessed the completeness of the genome assembly using the predicted gene set and the BUSCO pipeline, detecting 91.4% of core vertebrate genes (233 genes) and 90.9% of vertebrate conserved genes (2,586 genes) (Supplementary Table 2)
Summary
In lungfish and salamander lineages (Extended Data Fig. 3c), initially at similar rates in both lineages (161–165 Mb per million years) but subsequently at slower rates in the Australian lungfish (about 39 Mb per million years), but possibly not in the other lineages of extant lungfishes. Genome size increased in salamanders in two independent waves of DNA-repeat expansion All major categories of transposable elements (1,106 out of 1,821 (60.7%)) were expressed (Extended Data Fig. 6a). The repeat landscape (proportions of major classes of transposable element) of lungfish resembles tetrapods (including axolotl), whereas the third extant sarcopterygian lineage (the coelacanths) is more ‘fish’-like (Fig. 3b). Whereas long terminal repeat (LTR) elements are the most abundant class of transposable element (59%) in axolotl[8], LINEs (25.7%; mostly CR1 and L2 elements) dominate in lungfish Global repeat compositions differ between lungfish and axolotl, the same LTR class affects their genic regions (Extended Data Fig. 6, Supplementary Information). We found sall[1] strongly a
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