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

RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are.BACKGROUND: Lbx/ladybird genes originated as part of the metazoan cluster of Nk homeobox genes. In all animals investigated so far, both the protostome genes and the vertebrate Lbx1 genes were found to play crucial roles in neural and muscle development. Recently however, additional Lbx genes with divergent expression patterns were discovered in amniotes. Early in the evolution of vertebrates, two rounds of whole genome duplication are thought to have occurred, during which 4 Lbx genes were generated. Which of these genes were maintained in extant vertebrates, and how these genes and their functions evolved, is not known. RESULTS: Here we searched vertebrate genomes for Lbx genes and discovered novel members of this gene family. We also identified signature genes linked to particular Lbx loci and traced the remnants of 4 Lbx paralogons (two of which retain Lbx genes) in amniotes. In teleosts, that have undergone an additional genome duplication, 8 Lbx paralogons (three of which retain Lbx genes) were found. Phylogenetic analyses of Lbx and Lbx-associated genes show that in extant, bony vertebrates only Lbx1- and Lbx2-type genes are maintained. Of these, some Lbx2 sequences evolved faster and were probably subject to neofunctionalisation, while Lbx1 genes may have retained more features of the ancestral Lbx gene. Genes at Lbx1 and former Lbx4 loci are more closely related, as are genes at Lbx2 and former Lbx3 loci. This suggests that during the second vertebrate genome duplication, Lbx1/4 and Lbx2/3 paralogons were generated from the duplicated Lbx loci created during the first duplication event. CONCLUSION: Our study establishes for the first time the evolutionary history of Lbx genes in bony vertebrates, including the order of gene duplication events, gene loss and phylogenetic relationships. Moreover, we identified genetic hallmarks for each of the Lbx paralogons that can be used to trace Lbx genes as other vertebrate genomes become available. Significantly, we show that bony vertebrates only retained copies of Lbx1 and Lbx2 genes, with some Lbx2 genes being highly divergent. Thus, we have established a base on which the evolution of Lbx gene function in vertebrate development can be evaluated

The efficiency of Xenopus primordial germ cell migration depends on the germplasm mRNA encoding the PDZ domain protein Grip2

A microarray analysis of vegetal pole sequences in the egg and early Xenopus laevis embryo identified Unigene Xl.14891 as a vegetally localized RNA. Analysis of the Xenopus tropicalis genome showed this Unigene to be localized near the 3' end of the Grip2 (glutamate receptor interacting protein 2) transcription unit. RACE showed that the Unigene represented the 3' UTR of Grip2 mRNA. Grip2 mRNA is present in the mitochondrial cloud of late pre-vitellogenic oocytes and then in the germplasm through oogenesis and early development until tailbud tadpole stages. Interference with Grip2 mRNA translation using two antisense morpholino oligos (MOs) impairs primordial germ cell (PGC) migration to the germinal ridges. Both MOs also inhibit swimming movements of the tailbud tadpole, known to involve glutamate receptors. We conclude that Grip2 has several functions in the embryo, including enabling efficient PGC migration

Comparative genomics of Lbx loci reveals conservation of identical Lbx ohnologs in bony vertebrates-0

Ologous groups while light grey boxes indicate gene linkage. Bootstrap values below 70 have been removed. Only two Lbx proteins are included as the third sequence (found on scaffold 8483) is incomplete. Note that the Lbx sequences separate into two clear groups, Lbx1 and Lbx2, which are supported by bootstrap values of 79 and 83 (boxed), respectively. The chicken protein previously denoted as Lbx3 [18], the zebrafish protein previously denoted as Lbx1 [14] and one of the fugu, , stickleback and medaka sequences group with mammalian Lbx2 sequences. The two novel zebrafish Lbx sequences and the remaining teleost sequences group with mammalian, chicken and frog Lbx1. The tree shows significantly longer branch lengths for the Lbx2 proteins indicating that these sequences may be evolving at a quicker rate than the Lbx1 proteins. For common names of species see additional file .<p><b>Copyright information:</b></p><p>Taken from "Comparative genomics of Lbx loci reveals conservation of identical Lbx ohnologs in bony vertebrates"</p><p>http://www.biomedcentral.com/1471-2148/8/171</p><p>BMC Evolutionary Biology 2008;8():171-171.</p><p>Published online 9 Jun 2008</p><p>PMCID:PMC2446394.</p><p></p

Comparative genomics of Lbx loci reveals conservation of identical Lbx ohnologs in bony vertebrates-1

Deduced from analysis of the human genome using NCBI map viewer Build 36.2 (September 2006). Genes are represented by boxes with gene names appearing above and gene subfamilies indicated by numbers inside. Letters on the far left indicate paralogon designation, while chromosomal locations are indicated on the far right. Numbers between genes are approximate intergenic distances in Kb. Background shading indicates paralogous genes. Blue and red dots indicate sites of inversions. Note that and genes appear only at the locus and and appear only at the locus. and genes are linked with and genes at more than one locus, suggesting that these genes were acquired by the cluster during or before the two rounds of vertebrate genome duplication. Also note that a and a gene are associated with on chromosome 4. A gene is located on the long arm of chromosome2, however at a distance to , suggesting that it is not an original component of the paralogon.<p><b>Copyright information:</b></p><p>Taken from "Comparative genomics of Lbx loci reveals conservation of identical Lbx ohnologs in bony vertebrates"</p><p>http://www.biomedcentral.com/1471-2148/8/171</p><p>BMC Evolutionary Biology 2008;8():171-171.</p><p>Published online 9 Jun 2008</p><p>PMCID:PMC2446394.</p><p></p