Meyer A, Schloissnig S, Franchini P, Du K, Woltering JM, Irisarri I, Wong WY, Nowoshilow S, Kneitz S, Kawaguchi A, Fabrizius A, Xiong P, Dechaud C, Spaink HP, Volff JN, Simakov O, Burmester T, Tanaka EM, Schartl M.

Nature. 2021 Feb;590(7845):284-289. doi:10.1038/s41586-021-03198-8

Giant lungfish genome elucidates the conquest of land by vertebrates.

37-Gb assembly, 90% repetitive, with long introns. However, introns in developmental genes are proportionally smaller than other introns. The proportion of intronic sequences (~20%) is simlar to the one of human. Microchromosomes were retained.

“37-Gb assembly with an N50 contig size 1.86 Mb”

“The complete retention of microchromosomes [...] suggests that stabilizing selection maintains these ancestral units. In support of this, lungfish microchromosomes show—on average—higher gene densities and a lower density of long interspersed nuclear elements (LINEs), which are the major contributors to genome size”

“[We] identified 67.3% (24.65 Gb) as repetitive. To our knowledge, this is the highest repetitive DNA content in a genome found in the animal kingdom. [...] applying a second round of repeat annotation [...] revealed an additional 23.92% of repetitive DNA”

“All major categories of transposable elements (1,106 out of 1,821 (60.7%)) were expressed [in poly(A)-RNA-derived RNA-seq data].”

“The largest intron of the lungfish is 5.8 Mb (in the dmbt1 gene) and average intron size is 50 kb as in axolotl, compared to 1 kb in fugu and 6 kb in human. Introns in the N. forsteri genome comprise about 8 Gb (21% of genome)—a similar proportion to that in human (21%), but half that of fugu (40%).” ”Similar to axolotl, the introns in developmental genes in lungfish are smaller than in nondevelopmental genes”

“The 4 clusters of hox genes [...] comprise 43 genes; the presence of hoxb10 and hoxa14 in lungfish confirms their loss at the fish-to-tetrapod transition.”