Dispersal of NK homeobox gene clusters in amphioxus and humans

Abstract

The Drosophila melanogaster genome has six physically clustered NK-related homeobox genes in just 180 kb. Here we show that the NK homeobox gene cluster was an ancient feature of bilaterian animal genomes, but has been secondarily split in chordate ancestry. The NK homeobox gene clusters of amphioxus and vertebrates are each split and dispersed at two equivalent intergenic positions. From the ancestral NK gene cluster, only the Tlx-Lbx and NK3-NK4 linkages have been retained in chordates. This evolutionary pattern is in marked contrast to the Hox and ParaHox gene clusters, which are compact in amphioxus and vertebrates, but have been disrupted in Drosophila.

Figure 1

Deduced homeodomain amino acid sequences of amphioxus NK-related homeobox genes aligned to orthologues from D. melanogaster and human. Dashes indicate identical residues.

Figure 2

Contigs containing amphioxus NK-related homeobox genes. Only cosmid clones are shown, showing RZPD clone ID numbers; phage clones are not shown. Red bars are fully sequenced clones; black bars are partially sequenced clones. Green boxes are homeobox gene exons; yellow circles and ovals are nonhomeobox genes identified; arrows denote transcriptional orientation. G, related to germ cell-less genes; P, catalytic subunit of ser/thr protein phosphatase; S, synaptojanin-related; S18, syntaxin 18-related; Tm, gene for putative transmembrane protein.

Figure 3

Fluorescent in situ hybridization to amphioxus metaphase chromosomes. Cosmid probes used were from: (a) contig 1 (red) and contig 2 (green); (b) contig 3 (red) and contig 2 (green); and (c) contig 1 (red, arrowhead), contig 3 (red, arrow), and contig 2 (green). (Bars, 1 μm.)

Figure 4

Comparison of NK homeobox gene clusters between Anopheles, Drosophila, amphioxus, and human chromosomes. Boxes indicate homeobox genes, color coding denotes orthologous relationships. Cluster breaks are denoted by double-parallel marks (when intergenic distance >1 Mb), triple parallel marks (very large distances), or zigzag (transposition between chromosomes). Angular double arrows denote a large chromosomal inversion in amphioxus; curved double arrows denote a local inversion of a gene pair (relative to the Drosophila gene order). Genomic location is shown for human.