Ordered expression pattern of Hox and ParaHox genes along the alimentary canal in the ascidian juvenile

Nakayama, Satoshi; Satou, Kunihiro; Orito, Wataru; Ogasawara, Michio

doi:10.1007/s00441-016-2360-7

Cited by 17 publications

(5 citation statements)

References 52 publications

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“…Interestingly, some coordination of Hox gene expression has been conserved in some tunicates, despite the extreme divergence of the Hox cluster ( Ikuta et al 2004 ; Seo et al. 2004 ; Nakayama et al 2016 ), calling into question the importance of tight clustering for proper embryonic development, at least for tunicates. Furthermore, knockdown experiments in Ci.…”

Section: Discussionmentioning

confidence: 99%

Inferring Tunicate Relationships and the Evolution of the Tunicate Hox Cluster with the Genome of Corella inflata

DeBiasse

Colgan

Harris

et al. 2020

Genome Biology and Evolution

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Abstract Tunicates, the closest living relatives of vertebrates, have served as a foundational model of early embryonic development for decades. Comparative studies of tunicate phylogeny and genome evolution provide a critical framework for analyzing chordate diversification and the emergence of vertebrates. Toward this goal, we sequenced the genome of Corella inflata (Ascidiacea, Phlebobranchia), so named for the capacity to brood self-fertilized embryos in a modified, “inflated” atrial chamber. Combining the new genome sequence for Co. inflata with publicly available tunicate data, we estimated a tunicate species phylogeny, reconstructed the ancestral Hox gene cluster at important nodes in the tunicate tree, and compared patterns of gene loss between Co. inflata and Ciona robusta, the prevailing tunicate model species. Our maximum-likelihood and Bayesian trees estimated from a concatenated 210-gene matrix were largely concordant and showed that Aplousobranchia was nested within a paraphyletic Phlebobranchia. We demonstrated that this relationship is not an artifact due to compositional heterogeneity, as had been suggested by previous studies. In addition, within Thaliacea, we recovered Doliolida as sister to the clade containing Salpida and Pyrosomatida. The Co. inflata genome provides increased resolution of the ancestral Hox clusters of key tunicate nodes, therefore expanding our understanding of the evolution of this cluster and its potential impact on tunicate morphological diversity. Our analyses of other gene families revealed that several cardiovascular associated genes (e.g., BMP10, SCL2A12, and PDE2a) absent from Ci. robusta, are present in Co. inflata. Taken together, our results help clarify tunicate relationships and the genomic content of key ancestral nodes within this phylogeny, providing critical insights into tunicate evolution.

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Section: Discussionmentioning

confidence: 99%

Inferring Tunicate Relationships and the Evolution of the Tunicate Hox Cluster with the Genome of Corella inflata

DeBiasse

Colgan

Harris

et al. 2020

Genome Biology and Evolution

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“…Nine Hox genes were identified in C. robusta and showed a regional expression pattern in the digestive system [ 13 , 31 , 32 ]. In this study, seven Hox genes were identified in intestine transcriptome data in C. savignyi .…”

Section: Discussionmentioning

confidence: 99%

Comparative Transcriptomic Analysis Reveals the Functionally Segmented Intestine in Tunicate Ascidian

Zhang

Jiang

et al. 2023

IJMS

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The vertebrate intestinal system consists of separate segments that remarkably differ in morphology and function. However, the origin of intestinal segmentation remains unclear. In this study, we investigated the segmentation of the intestine in a tunicate ascidian species, Ciona savignyi, by performing RNA sequencing. The gene expression profiles showed that the whole intestine was separated into three segments. Digestion, ion transport and signal transduction, and immune-related pathway genes were enriched in the proximal, middle, and distal parts of the intestine, respectively, implying that digestion, absorption, and immune function appear to be regional specializations in the ascidian intestine. We further performed a multi−species comparison analysis and found that the Ciona intestine showed a similar gene expression pattern to vertebrates, indicating tunicates and vertebrates might share the conserved intestinal functions. Intriguingly, vertebrate pancreatic homologous genes were expressed in the digestive segment of the Ciona intestine, suggesting that the proximal intestine might play the part of pancreatic functions in C. savignyi. Our results demonstrate that the tunicate intestine can be functionally separated into three distinct segments, which are comparable to the corresponding regions of the vertebrate intestinal system, offering insights into the functional evolution of the digestive system in chordates.

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“…Digoxigenin (DIG)-labeled RNA probes of Ci-AhR were synthesized using a DIG RNA labeling kit (Roche Applied Science, Indianapolis, IN, USA). WISH of juvenile Ciona specimens was performed as previously described [34][35][36].…”

Section: Whole-mount In Situ Hybridization Analysis Of Ci-ahrmentioning

confidence: 99%

Effect of Polycyclic Aromatic Hydrocarbons on Development of the Ascidian Ciona intestinalis Type A

Sekiguchi

Akitaya

Nakayama

et al. 2020

IJERPH

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Polycyclic aromatic hydrocarbons (PAHs) are pollutants that exert harmful effects on marine invertebrates; however, the molecular mechanism underlying PAH action remains unclear. We investigated the effect of PAHs on the ascidian Ciona intestinalis type A (Ciona robusta). First, the influence of PAHs on early Ciona development was evaluated. PAHs such as dibenzothiophene, fluorene, and phenanthrene resulted in formation of abnormal larvae. PAH treatment of swimming larva induced malformation in the form of tail regression. Additionally, we observed the Ciona aryl hydrocarbon receptor (Ci-AhR) mRNA expression in swimming larva, mid body axis rotation, and early juvenile stages. The time correlation between PAH action and AhR mRNA expression suggested that Ci-AhR could be associated with PAH metabolism. Lastly, we analyzed Ci-AhR mRNA localization in Ciona juveniles. Ci-AhR mRNA was localized in the digestive tract, dorsal tubercle, ganglion, and papillae of the branchial sac, suggesting that Ci-AhR is a candidate for an environmental pollutant sensor and performs a neural function. Our results provide basic knowledge on the biological function of Ci-AhR and PAH activity in marine invertebrates.

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Ordered expression pattern of Hox and ParaHox genes along the alimentary canal in the ascidian juvenile

Cited by 17 publications

References 52 publications

Inferring Tunicate Relationships and the Evolution of the Tunicate Hox Cluster with the Genome of Corella inflata

Inferring Tunicate Relationships and the Evolution of the Tunicate Hox Cluster with the Genome of Corella inflata

Comparative Transcriptomic Analysis Reveals the Functionally Segmented Intestine in Tunicate Ascidian

Effect of Polycyclic Aromatic Hydrocarbons on Development of the Ascidian Ciona intestinalis Type A

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