Evolution of cis-regulatory modules for the head organizer gene goosecoid in chordates: comparisons between Branchiostoma and Xenopus

Background: In cephalochordates (amphioxus), the notochord runs along the dorsal to the anterior tip of the body. In contrast, the vertebrate head is formed anterior to the notochord, as a result of head organizer formation in anterior mesoderm during early development. A key gene for the vertebrate head organizer, goosecoid (gsc), is broadly expressed in the dorsal mesoderm of amphioxus gastrula. Amphioxus gsc expression subsequently becomes restricted to the posterior notochord from the early neurula. This has prompted the hypothesis that a change in expression patterns of gsc led to development of the vertebrate head during chordate evolution. However, molecular mechanisms of head organizer evolution involving gsc have never been elucidated.Results: To address this question, we compared cis-regulatory modules of vertebrate organizer genes between amphioxus, Branchiostoma japonicum, and frogs, Xenopus laevis and Xenopus tropicalis. Here we show conservation and diversification of gene regulatory mechanisms through cis-regulatory modules for gsc, lim1/lhx1, and chordin in Branchiostoma and Xenopus. Reporter analysis using Xenopus embryos demonstrates that activation of gsc by Nodal/FoxH1 signal through the 5′ upstream region, that of lim1 by Nodal/FoxH1 signal through the first intron, and that of chordin by Lim1 through the second intron, are conserved between amphioxus and Xenopus. However, activation of gsc by Lim1 and Otx through the 5′ upstream region in Xenopus are not conserved in amphioxus. Furthermore, the 5′ region of amphioxus gsc recapitulated the amphioxus-like posterior mesoderm expression of the reporter gene in transgenic Xenopus embryos.Conclusions: On the basis of this study, we propose a model, in which the gsc gene acquired the cis-regulatory module bound with Lim1 and Otx at its 5′ upstream region to be activated persistently in anterior mesoderm, in the vertebrate lineage. Because Gsc globally represses trunk (notochord) genes in the vertebrate head organizer, this cooption of gsc in vertebrates appears to have resulted in inhibition of trunk genes and acquisition of the head organizer and its derivative prechordal plate

The Realisation of Violating Cooperative Principles in Sundanese Humour

To relieve tense, people usually use humour which is a verbal or nonverbal impulse to create a smile or even laugh. Humour can be easily found in our daily lives. It can be used to communicate and create intimacy.This research is focused on analyzing the realisation of violating the cooperative principles and what type of maxims that is usually viloted to create humour. The data were taken fromhumour column in Sundanese magazine Mangle. The humour is analyzed based on Grice\u27s maxim principles.The results show that maxim of quantity is the most violated maxims employed by the speakers even the hearers to create humourous effect.This is considered the easiest way to create and understand humour

The chordate ancestor possessed a single copy of the Brachyury gene for notochord acquisition

Background: The T-box family transcription-factor gene, Brachyury, has two expression domains with discretefunctions during animal embryogenesis. The primary domain, associated with the blastopore, is shared by mostmetazoans, while the secondary domain, involved in the notochord, is specific to chordates. In most animals,Brachyury is present in a single copy, but in cephalochordates, the most basal of the chordates, the gene is presentin two copies, suggesting allotment of the two domains to each of the duplicates.Results: In order to clarify whether Brachyury duplication occurred in the common ancestor of chordates afterwhich one of duplicates was lost in the urochordate and vertebrate lineages, we estimated phylogeneticrelationships of Brachyury genes and examined the synteny of a Brachyury-containing genomic region ofdeuterostomes with decoded genomes. The monophyletic origin of tandemly arranged Brachyury genes ofcephalochordates indicates that the tandem duplication occurred in the cephalochordate lineage, but not in thechordate ancestor.Conclusions: Our results thus suggest that, in the common ancestor of chordates, a single copy of Brachyuryacquired two expression domains and that the duplication was not involved in the acquisition of the notochord.However, in relation to regulatory mechanisms, both possibilities—namely a single copy with two domains andtwo copies with different domains—should be considered in future studies of Brachyury

High variability of expression profiles of homeologous genes for Wnt, Hh, Notch, and Hippo signaling pathways in Xenopus laevis

Cell signaling pathways, such as Wnt, Hedgehog (Hh), Notch, and Hippo, are essential for embryogenesis, organogenesis, and tissue homeostasis. In this study, we analyzed 415 genes involved in these pathways in the allotetraploid frog, Xenopus laevis. Most genes are retained in two subgenomes called L and S (193 homeologous gene pairs and 29 singletons). This conservation rate of homeologs is much higher than that of all genes in the X. laevis genome (86.9% vs 60.2%). Among singletons, 24 genes are retained in the L subgenome, a rate similar to the average for all genes (82.8% vs 74.6%). In addition, as general components of signal transduction, we also analyzed 32 heparan sulfate proteoglycan (HSPG)-related genes and eight TLE/Groucho transcriptional corepressors-related genes. In these gene sets, all homeologous pairs have been retained. Transcriptome analysis using RNA-seq data from developmental stages and adult tissues demonstrated that most homeologous pairs of signaling components have variable expression patterns, in contrast to the conservative expression profiles of homeologs for transcription factors. Our results indicate that homeologous gene pairs for cell signaling regulation have tended to become subfunctionalized after allotetraploidization. Diversification of signaling pathways by subfunctionalization of homeologs may enhance environmental adaptability. These results provide insights into the evolution of signaling pathways after polyploidization

Genome evolution in the allotetraploid frog Xenopus laevis

To explore the origins and consequences of tetraploidy in the African clawed frog, we sequenced the Xenopus laevis genome and compared it to the related diploid X. tropicalis genome. We characterize the allotetraploid origin of X. laevis by partitioning its genome into two homoeologous subgenomes, marked by distinct families of ???fossil??? transposable elements. On the basis of the activity of these elements and the age of hundreds of unitary pseudogenes, we estimate that the two diploid progenitor species diverged around 34 million years ago (Ma) and combined to form an allotetraploid around 17-18 Ma. More than 56% of all genes were retained in two homoeologous copies. Protein function, gene expression, and the amount of conserved flanking sequence all correlate with retention rates. The subgenomes have evolved asymmetrically, with one chromosome set more often preserving the ancestral state and the other experiencing more gene loss, deletion, rearrangement, and reduced gene expression.ope

De novo transcription of multiple Hox cluster genes takes place simultaneously in early Xenopus tropicalis embryos

hox genes are found as clusters in the genome in most bilaterians. The order of genes in the cluster is supposed to be correlated with the site of expression along the anterior-posterior body axis and the timing of expression during development, and these correlations are called spatial and temporal collinearity, respectively. Here we studied the expression dynamics of all hox genes of the diploid species Xenopus tropicalis in four Hox clusters (A–D) by analyzing high-temporal-resolution RNA-seq databases and the results showed that temporal collinearity is not supported, which is consistent with our previous data from allotetraploid Xenopus laevis. Because the temporal collinearity hypothesis implicitly assumes the collinear order of gene activation, not mRNA accumulation, we determined for the first time the timing of when new transcripts of hox genes are produced, by detecting pre-spliced RNA in whole embryos with reverse transcription and quantitative PCR (RT-qPCR) for all hoxa genes as well as several selected hoxb, hoxc and hoxd genes. Our analyses showed that, coinciding with the RNA-seq results, hoxa genes started to be transcribed in a non-sequential order, and found that multiple genes start expression almost simultaneously or more posterior genes could be expressed earlier than anterior ones. This tendency was also found in hoxb and hoxc genes. These results suggest that temporal collinearity of hox genes is not held during early development of Xenopus

Additional file 4: of The chordate ancestor possessed a single copy of the Brachyury gene for notochord acquisition

Molecular phylogeny of Brachyury family members based on an amino acid dataset comprising 436 unambiguously aligned sites. Arrowheads indicate topological incongruities with the tree obtained from comparisons of nucleotides (Fig. 2). Probably due to the short length of the analyzed sequence, the Botryllus schlosseri (urochordate) gene was placed as a sister lineage of a clade comprising cephalochordate and vertebrate genes. (PDF 150 kb