Extended Data Fig. 9: Comparison of Neoceratodus and mouse hox clusters.
From: Giant lungfish genome elucidates the conquest of land by vertebrates
Four hox clusters are present in the Neoceratodus genome (hoxa, hoxb, hoxc and hoxd), comprising 43 genes and 6 conserved miRNA genes (miR10 and miR196). Neoceratodus preserves a copy of hoxb10 and hoxa14, which are lost in tetrapods. The 3′ hoxc cluster contains the hoxc1 and hoxc3 genes, which are lost in several tetrapod lineages but have been shown to be part of the original tetrapod hox complement96. Consistent with the overall expansion of the Neoceratodus genome, its hox clusters are larger than their mouse counterparts. Expansion has occurred unevenly across the clusters and intergenic regions of highest expansion are indicated with yellow mark up (hoxa11 to hoxa13; hoxb10 to hoxb13; hoxc1 to hoxc3; hoxc3 to hoxc4; hoxc11 to hoxc12; and hoxd12 to hoxd13). Furthermore, the introns of hoxa3 and hoxd3 are enlarged. All clusters shown (both mouse and Neoceratodus) are drawn to scale with the respective sizes indicated, except for the 11 Mb between hoxb10 and hoxb13, which is drawn about 20-fold reduced. The Neoceratodus hoxb13 and hoxd13 are present on separate contigs and the exact genomic distance to their nearest neighbouring hox gene has not been determined. The sizes for the hoxb and hoxd clusters therefore represent a lower limit. The mouse has lost hoxa14 and the indicated synteny for hoxa runs from hoxa1 through hoxa13. Similarly, the mouse hoxc cluster lacks hoxc1 and hoxc3 and the comparative hoxc synteny runs from hoxc4 through hoxc13. Gene labels are included for the Neoceratodus cluster, whereas in the mouse clusters genes are indicated only using red boxes. miRNAs are indicated only for the Neoceratodus clusters. Silhouettes are from ref. 36.
