Comparative genomics of Lbx loci reveals conservation of identical Lbx ohnologs in bony vertebrates

Table 1 Distribution of paralogous genes at the four Lbx-Tlx loci.

	Lbx1/Tlx1 locus	Former Lbx4/Tlx4 locus	(Former Lbx3)/Tlx3 locus	Lbx2/Tlx2 locus	Lbx-less Nkx3.2 locus	Lbx2/Tlx2 loci
				amniotes	tetrapods	teleosts
Msx			Msx2
Nkx2/tin	Nkx2.3	Nkx2.6	Nkx2.5
Nkx3/bap		Nkx3.1			Nkx3.2	Nkx3.2
		(chicken: Nkx2.8 only)
Nkx6		Nkx6.3
Lbx	Lbx1			Lbx2		Lbx2
Tlx	Tlx1		Tlx3	Tlx2		Tlx2
Pol	Poll	Polb
Dpcd	Dpcd
Fbxw4	Fbxw4
Fbxw7					Fbxw7	Fbxw7
Slc2a15	Slc2a15				Slc2a9 (tetrapods)
Aup				Aup1		Aup1
Pcgf1				Pcgf1		Pcgf1
Fbxw11/Btrc	Btrc		Fbxw11/Btrc2
Mgea	Mgea5			Mgea2 (chicken)		Mgea2
Kazald	Kazald1 (tetrapods)	Kazald3 (fish)		Kazald2 (zebrafish)
Ldb	Ldb1				Ldb2	Ldb2
Prom	Prom3 (fish)	Prom2 (tetrapods)*			Prom1	Prom1
Loxl	Loxl4	Loxl2		Loxl3		Loxl3
Slit	Slit1		Slit3		Slit2	Slit2
Dok		Dok2	Dok3	Dok1		Dok1
Fgf	Fgf8	Fgf17	Fgf18			Fgf24
Npm	Npm3	Npm2	Npm1			Npm4
Kcnip	Kcnip2	Kcnip3*	Kcnip1		Kcnip4	Kcnip4

* in human, cattle, dog, Prom2-Kcnip3 are on the same chromosome but at a distance to Lbx2.
Note, genes occurring at single Lbx/Tlx loci form monophyletic trees, i.e. the loci in fish and tetrapods are related (see additional file 2). Genes at more than one locus: gene phylogeny matches genomic localisation and environment (exception: Dok2 genes which are distinct from Dok1 but do not group well; see additional file 2). Genes at the putative Lbx4-Tlx4 locus, characterised amongst others by Fgf17-Npm2, match between fish and tetrapods. Genes found associated with Lbx2 loci in fish match genes in amniotes distributed between the Lbx2 locus and the Lbx-free Nkx3.2 locus, suggesting that the amniote Lbx2 locus once belonged to the Nkx3.2 containing Nk cluster. Genes in bold: genes that supported by high bootstrap values are more related to each other than to other paralogues, suggesting that the Lbx1 and Lbx4 loci evolved from one and the Lbx2 and Lbx3 from the other of the paralogons generated during the first round of vertebrate genome duplication.

ISSN: 2730-7182