Dataset Information

Complex evolution of a Y-chromosomal double homeobox 4 (DUX4)-related gene family in hominoids.

ABSTRACT: The human Y chromosome carries four human Y-chromosomal euchromatin/heterochromatin transition regions, all of which are characterized by the presence of interchromosomal segmental duplications. The Yq11.1/Yq11.21 transition region harbours a peculiar segment composed of an imperfectly organized tandem-repeat structure encoding four members of the double homeobox (DUX) gene family. By comparative fluorescence in situ hybridization (FISH) analysis we have documented the primary appearance of Y-chromosomal DUX genes (DUXY) on the gibbon Y chromosome. The major amplification and dispersal of DUXY paralogs occurred after the gibbon and hominid lineages had diverged. Orthologous DUXY loci of human and chimpanzee show a highly similar structural organization. Sequence alignment survey, phylogenetic reconstruction and recombination detection analyses of human and chimpanzee DUXY genes revealed the existence of all copies in a common ancestor. Comparative analysis of the circumjacent beta-satellites indicated that DUXY genes and beta-satellites evolved in concert. However, evolutionary forces acting on DUXY genes may have induced amino acid sequence differences in the orthologous chimpanzee and human DUXY open reading frames (ORFs). The acquisition of complete ORFs in human copies might relate to evolutionary advantageous functions indicating neo-functionalization. We propose an evolutionary scenario in which an ancestral tandem array DUX gene cassette transposed to the hominoid Y chromosome followed by lineage-specific chromosomal rearrangements paved the way for a species-specific evolution of the Y-chromosomal members of a large highly diverged homeobox gene family.

SUBMITTER: Schmidt J

PROVIDER: S-EPMC2671837 | biostudies-literature | 2009

REPOSITORIES: biostudies-literature

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Complex evolution of a Y-chromosomal double homeobox 4 (DUX4)-related gene family in hominoids.

Schmidt Julia J Kirsch Stefan S Rappold Gudrun A GA Schempp Werner W

PloS one 20090430 4

The human Y chromosome carries four human Y-chromosomal euchromatin/heterochromatin transition regions, all of which are characterized by the presence of interchromosomal segmental duplications. The Yq11.1/Yq11.21 transition region harbours a peculiar segment composed of an imperfectly organized tandem-repeat structure encoding four members of the double homeobox (DUX) gene family. By comparative fluorescence in situ hybridization (FISH) analysis we have documented the primary appearance of Y-ch ...[more]

PMID: 19404400

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Project description:BackgroundLIM homeobox (Lhx) transcription factors are unique to the animal lineage and have patterning roles during embryonic development in flies, nematodes and vertebrates, with a conserved role in specifying neuronal identity. Though genes of this family have been reported in a sponge and a cnidarian, the expression patterns and functions of the Lhx family during development in non-bilaterian phyla are not known.ResultsWe identified Lhx genes in two cnidarians and a placozoan and report the expression of Lhx genes during embryonic development in Nematostella and the demosponge Amphimedon. Members of the six major LIM homeobox subfamilies are represented in the genomes of the starlet sea anemone, Nematostella vectensis, and the placozoan Trichoplax adhaerens. The hydrozoan cnidarian, Hydra magnipapillata, has retained four of the six Lhx subfamilies, but apparently lost two others. Only three subfamilies are represented in the haplosclerid demosponge Amphimedon queenslandica. A tandem cluster of three Lhx genes of different subfamilies and a gene containing two LIM domains in the genome of T. adhaerens (an animal without any neurons) indicates that Lhx subfamilies were generated by tandem duplication. This tandem cluster in Trichoplax is likely a remnant of the original chromosomal context in which Lhx subfamilies first appeared. Three of the six Trichoplax Lhx genes are expressed in animals in laboratory culture, as are all Lhx genes in Hydra. Expression patterns of Nematostella Lhx genes correlate with neural territories in larval and juvenile polyp stages. In the aneural demosponge, A. queenslandica, the three Lhx genes are expressed widely during development, including in cells that are associated with the larval photosensory ring.ConclusionsThe Lhx family expanded and diversified early in animal evolution, with all six subfamilies already diverged prior to the cnidarian-placozoan-bilaterian last common ancestor. In Nematostella, Lhx gene expression is correlated with neural territories in larval and juvenile polyp stages. This pattern is consistent with a possible role in patterning the Nematostella nervous system. We propose a scenario in which Lhx genes play a homologous role in neural patterning across eumetazoans.

Project description:Bamboos (Bambusoideae) are fast-growing species due to their rapid growth rate and ability to reproduce annually via cloned buds produced on the rhizome. WUSCHEL-related homeobox (WOX) genes have been reported to regulate shoot apical meristem organization, lateral organ formation, cambium and vascular proliferation, and so on, but have rarely been studied in bamboos. In this study, the WOXs of both herbaceous bamboo species (12 OlaWOXs and nine RguWOXs) and woody bamboo species (18 GanWOXs, 27 PheWOXs, and 26 BamWOXs) were identified and categorized into three clades based on their phylogenetic relationship-ancient, intermediate, or WUS clade. Polyploidy is the major driver of the expansion of the bamboo WOX family. Eight conserved domains, besides the homeodomain, were identified by comparatively analyzing the WOXs of dicot and monocot species. Intensive purifying selection pressure in the coding region of specific domains explained the functional similarity of WOXs between different species. For Bambusoideae WOXs, polyploidy is the major driver of the expansion of the WOX family. Stronger purifying selection was found in orthologous WOXs of Bambusoideae, especially for WOX4s and WOX5s, which are conserved not only at the translational levels, but also at the genome level. Several conserved cis-acting elements were discovered at similar position in the promoters of the orthologous WOXs. For example, AP2/ERF protein-binding elements and B3 protein-binding elements were found in the promoters of the bamboo WOX4, while MYB protein-binding elements and Dof protein-binding elements were found in the promoters of bamboo WOX5, and MADS protein-binding sites was found in the promoters of bamboo WUS, WOX3, and WOX9. These conserved positions may play an important role in regulating the expression of bamboo WOXs. Our work provides insight into the origin and evolution of bamboo WOXs, and will facilitate functional investigations of the clonal propagation of bamboos.

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Project description:BackgroundOver the past decades, extensive comparative mapping research has been performed in the plant family Solanaceae. The recent identification of a large set of single-copy conserved orthologous (COSII) markers has greatly accelerated comparative mapping studies among major solanaceous species including tomato, potato, eggplant, pepper and diploid Nicotiana species (as well as tetraploid tobacco). The large amount of comparative data now available for these species provides the opportunity to describe the overall patterns of chromosomal evolution in this important plant family. The results of this investigation are described herein.ResultsWe combined data from multiple COSII studies, and other comparative mapping studies performed in tomato, potato, eggplant, pepper and diploid Nicotiana species, to deduce the features and outcomes of chromosomal evolution in the Solanaceae over the past 30 million years. This includes estimating the rates and timing of chromosomal changes (inversions and translocations) as well as deducing the age of ancestral progenitor species and predicting their genome configurations.ConclusionsThe Solanaceae has experienced chromosomal changes at a modest rate compared with other families and the rates are likely conserved across different lineages of the family. Chromosomal inversions occur at a consistently higher rate than do translocations. Further, we find evidences for non-random positioning of the chromosomal rearrangement breakpoints. This finding is consistent with the similar finding in mammals, where hot spots for chromosomal breakages have apparently played a significant role in shaping genome evolution. Finally, by utilizing multiple genome comparisons we were able to reconstruct the most likely genome configuration for a number of now-extinct progenitor species that gave rise to the extant solanaceous species used in this research. The results from this study provide the first broad overview of chromosomal evolution in the family Solanaceae, and one of the most detailed thus far for any family of plants.

Dataset Information

Complex evolution of a Y-chromosomal double homeobox 4 (DUX4)-related gene family in hominoids.

Publications

Complex evolution of a Y-chromosomal double homeobox 4 (DUX4)-related gene family in hominoids.

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