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22 results for “chordates”
Data from: Tunicate mitogenomics and phylogenetics: peculiarities of the Herdmania momus mitochondrial genome and support for the new chordate phylogeny
BACKGROUND: Tunicates represent a key metazoan group as the sister-group of vertebrates within chordates. The six complete mitochondrial genomes available so far for tunicates have revealed distinctive features. Extensive gene rearrangements and particularly high evolutionary rates have been evidenced with regard to other chordates. This peculiar evolutionary dynamics has hampered the reconstruction of tunicate phylogenetic relationships within chordates based on mitogenomic data. RESULTS: In order to further understand the atypical evolutionary dynamics of the mitochondrial genome of tunicates, we determined the complete sequence of the solitary ascidian Herdmania momus. This genome from a stolidobranch ascidian presents the typical tunicate gene content with 13 protein-coding genes, 2 rRNAs and 24 tRNAs which are all encoded on the same strand. However, it also presents a novel gene arrangement, highlighting the extreme plasticity of gene order observed in tunicate mitochondrial genomes. Probabilistic phylogenetic inferences were conducted on the concatenation of the 13 mitochondrial protein-coding genes from representatives of major metazoan phyla. We show that whereas standard homogeneous amino acid models support an artefactual sister position of tunicates relative to all other bilaterians, the CAT and CAT+BP site- and time-heterogeneous mixture models place tunicates as the sister-group of vertebrates within monophyletic chordates. Moreover, the reference phylogeny indicates that tunicate mitochondrial genomes have experienced a drastic acceleration in their evolutionary rate that equally affects protein-coding and ribosomal-RNA genes. CONCLUSION: This is the first mitogenomic study supporting the new chordate phylogeny revealed by recent phylogenomic analyses. It illustrates the beneficial effects of an increased taxon sampling coupled with the use of more realistic amino acid substitution models for the reconstruction of animal phylogeny.
Data for: Three amphioxus reference genomes reveal gene and chromosome evolution of chordates
<p><span>The slow-evolving invertebrate amphioxus has an irreplaceable role in advancing our understanding into vertebrate origin and innovations. Here we resolve the nearly complete chromosomal genomes of three amphioxus species, one of which best recapitulates the 17 chordate ancestor linkage groups. We reconstruct the fusions, retention, or rearrangements between descendants of whole genome duplications (WGDs), which gave rise to the extant microchromosomes that likely existed in the vertebrate ancestor. Similar to vertebrates, the amphioxus genome gradually establishes its 3D chromatin architecture at the onset of zygotic activation and forms two topologically associated domains at the <em>Hox</em> gene cluster. We find that all three amphioxus species have ZW sex chromosomes with little sequence differentiation, and their putative sex-determining regions are nonhomologous to each other. Our results illuminate the unappreciated interspecific diversity and developmental dynamics of amphioxus genomes and provide high-quality references for understanding the mechanisms of chordate functional genome evolution.</span></p>
Data from: Tunicate mitogenomics and phylogenetics: peculiarities of the Herdmania momus mitochondrial genome and support for the new chordate phylogeny
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Data for: Three amphioxus reference genomes reveal gene and chromosome evolution of chordates
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Data from: Additional molecular support for the new chordate phylogeny
Recent phylogenomic analyses have suggested tunicates instead of cephalochordates as the closest living relatives of vertebrates. In direct contradiction with the long accepted view of Euchordates, this new phylogenetic hypothesis for chordate evolution has been the object of some skepticism. We assembled an expanded phylogenomic dataset focused on deuterostomes. Maximum-likelihood using standard models and Bayesian phylogenetic analyses using the CAT site-heterogeneous mixture model of amino-acid replacement both provided unequivocal support for the sister-group relationship between tunicates and vertebrates (Olfactores). Chordates were recovered as monophyletic with cephalochordates as the most basal lineage. These results were robust to both gene sampling and missing data. New analyses of ribosomal rRNA also recovered Olfactores when compositional bias was alleviated. Despite the inclusion of 25 taxa representing all major lineages, the monophyly of deuterostomes remained poorly supported. The implications of these phylogenetic results for interpreting chordate evolution are discussed in light of recent advances from evolutionary developmental biology and genomics.
Chordate System Prophylactic Migraine Clinical Investigation
ClinicalTrials.gov study NCT02243865. IPD Sharing: NO. Countries: 1. Publications: 0.
Data from: Additional molecular support for the new chordate phylogeny
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Transcriptome Analysis of the Basal Chordate Botryllus schlosseri Reveals a Set of Genes Associated with Fertility
GEO Series GSE62112. Botryllus schlosseri. 42 samples. Type: Expression profiling by high throughput sequencing.
A single cell analysis of the molecular lineage of chordate embryogenesis
GEO Series GSE113788. Ciona savignyi. 56 samples. Type: Expression profiling by high throughput sequencing.
A distinct class of small RNAs arises from pre-miRNA-proximal regions in a simple chordate
GEO Series GSE13625. Ciona intestinalis; Drosophila melanogaster. 6 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Cis-regulatory architecture of a brain-signaling center predates the origin of chordates
GEO Series GSE78005. Mus musculus. 1 samples. Type: Expression profiling by high throughput sequencing.
Immune cell type divergence in a basal chordate
GEO Series GSE296253. Ciona robusta. 2 samples. Type: Expression profiling by high throughput sequencing.
Quantitative proteome dynamics across embryogenesis in a model chordate
GEO Series GSE237005. Ciona robusta. 16 samples. Type: Expression profiling by high throughput sequencing.
Exceptional diversity of allorecognition receptors in a nonvertebrate chordate reveals principles of innate allelic discrimination
GEO Series GSE295655. Botryllus schlosseri. 78 samples. Type: Expression profiling by high throughput sequencing.
Acquisition of neural crest promoted thyroid evolution from chordate endostyle
GEO Series GSE294220. Petromyzon marinus. 12 samples. Type: Expression profiling by high throughput sequencing.
Chordate System S020 Acute Migraine Clinical Investigation
ClinicalTrials.gov study NCT02185703. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Investigation of Kinetic Oscillation Stimulation by the Chordate System S101 in the Treatment of Non Allergic Rhinitis
ClinicalTrials.gov study NCT03399721. IPD Sharing: Not stated. Countries: 6. Publications: 0.
Vascular Aging in the Invertebrate Chordate, Botryllus schlosseri
GEO Series GSE115267. Botryllus schlosseri. 27 samples. Type: Expression profiling by high throughput sequencing.
Single-cell analysis of cell fate bifurcation in the chordate Ciona
GEO Series GSE160701. Ciona robusta. 6 samples. Type: Expression profiling by high throughput sequencing.
An ancient gene regulatory network sets the position of the forebrain in chordates
GEO Series GSE239838. Branchiostoma lanceolatum. 12 samples. Type: Expression profiling by high throughput sequencing.
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