Spatio-temporal regulation of Rx and mitotic patterns shape the eye-cup of the photoreceptor cells in Ciona

Oonuma, Kouhei; Kusakabe, Takehiro

doi:10.1016/j.ydbio.2018.11.011

Cited by 8 publications

(12 citation statements)

References 60 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…2019; Mizutani et al. 2019; Oonuma and Kusakabe 2019). For the sake of clarity, the genome that was further explored in this study was from C. intestinalis type A ( C. robusta ).…”

Section: Introductionmentioning

confidence: 99%

A Nearly Complete Genome of Ciona intestinalis Type A (C. robusta) Reveals the Contribution of Inversion to Chromosomal Evolution in the Genus Ciona

Satou

Nakamura

et al. 2019

Genome Biology and Evolution

105

View full text Add to dashboard Cite

Since its initial publication in 2002, the genome of Ciona intestinalis type A (Ciona robusta), the first genome sequence of an invertebrate chordate, has provided a valuable resource for a wide range of biological studies, including developmental biology, evolutionary biology, and neuroscience. The genome assembly was updated in 2008, and it included 68% of the sequence information in 14 pairs of chromosomes. However, a more contiguous genome is required for analyses of higher order genomic structure and of chromosomal evolution. Here, we provide a new genome assembly for an inbred line of this animal, constructed with short and long sequencing reads and Hi-C data. In this latest assembly, over 95% of the 123 Mb of sequence data was included in the chromosomes. Short sequencing reads predicted a genome size of 114–120 Mb; therefore, it is likely that the current assembly contains almost the entire genome, although this estimate of genome size was smaller than previous estimates. Remapping of the Hi-C data onto the new assembly revealed a large inversion in the genome of the inbred line. Moreover, a comparison of this genome assembly with that of Ciona savignyi, a different species in the same genus, revealed many chromosomal inversions between these two Ciona species, suggesting that such inversions have occurred frequently and have contributed to chromosomal evolution of Ciona species. Thus, the present assembly greatly improves an essential resource for genome-wide studies of ascidians.

show abstract

“…2019; Mizutani et al. 2019; Oonuma and Kusakabe 2019). For the sake of clarity, the genome that was further explored in this study was from C. intestinalis type A ( C. robusta ).…”

Section: Introductionmentioning

confidence: 99%

A Nearly Complete Genome of Ciona intestinalis Type A (C. robusta) Reveals the Contribution of Inversion to Chromosomal Evolution in the Genus Ciona

Satou

Nakamura

et al. 2019

Genome Biology and Evolution

105

View full text Add to dashboard Cite

show abstract

“…The 2.8-kb upstream region of tagln-r.b was amplified from the genomic DNA by PCR using a pair of nucleotide primers (5′-AAACTCGAGTCACACGAATTAAGCAAAGC-3′ and 5′-TTTTTCTCGTTGCGCCAT-3′). To generate mutant constructs, tagln-r.b ΔBS1-3 > kaede and tagln-r.b ΔBS1-8 > kaede , putative Fox binding sites (RYAAAYA; Chen et al, 2016 ) were mutagenized by the PCR-based method as previously described ( Oonuma and Kusakabe, 2019 ). Oligonucleotide primers used for the mutagenesis of fox binding sites (BS1-8) were: 5′-GGTACGgcccaAAGCAGGAATTTTAATAGCAGT-3′ and 5′ -CTGCTTtgggcCGTACCTTTACCTTACTGGGTGG-3′ for BS1; 5′-GCTTCTcgggtTCTTGCCAAATAAGGCGA-3′ and 5′-GCAA GAacccgAGAAGCACGAAGCAAATTC-3′ for BS2; 5′-AACT GTTtgggtTCTTGGGCGAGCTAAGC-3′ and 5′-CCCAAGAac ccaAACAGTTTCATTGAAAGAGCC-3′ for BS3; 5′-GCAAA AGacccgATTCGTGCGACGGATTC-3′ and 5′-CACGAATcgggt CTTTTGCTCTCCCATGCA-3′ for BS4; 5′-CCTAGATcgggcTC GTACAACAGTTTGACGTAAGTTC-3′ and 5′-TGTACGAgc ccgATCTAGGCGTATTTCCACACG-3′ for BS5; 5′-TGTTATG gcccgACTCCATTCGTTCAACTTTCTAGA-3′ and 5′-GGAGT cgggcCATAACACCATACCTGTCGCGCG-3′ for BS6; 5′-GCGTTTtgggcCGTTTGATTGATAAATGTACGTAAGAGA-3′ and 5′-CAAACGgcccaAAACGCATTTAAAAGCCAGTT-3′ for BS7; 5′-CCTCATAGacccaAGCGAATCCATTGTCAAGTC-3′ and 5′-ATTCGCTtgggtCTATGAGGAGTATAGGCGAGGTG-3′ for BS8.…”

Section: Methodsmentioning

confidence: 99%

“…Antisense RNA probes were synthesized with T7 RNA polymerase by using a DIG RNA Labeling Kit (Sigma-Aldrich, St. Louis, MI, United States). Ciona intestinalis type A embryos were fixed at the early tailbud stage in 4% paraformaldehyde in 0.1 M MOPS (pH 7.5) and 0.5 M NaCl at 4 • C for 16 h, prior to storage in 80% ethanol at −30 • C. Whole-mount in situ hybridization was carried out as described (Oonuma and Kusakabe, 2019).…”

Section: Whole-mount In Situ Hybridizationmentioning

confidence: 99%

Evolution of Developmental Programs for the Midline Structures in Chordates: Insights From Gene Regulation in the Floor Plate and Hypochord Homologues of Ciona Embryos

Oonuma

Yamamoto

Moritsugu

et al. 2021

Front. Cell Dev. Biol.

Self Cite

View full text Add to dashboard Cite

In vertebrate embryos, dorsal midline tissues, including the notochord, the prechordal plate, and the floor plate, play important roles in patterning of the central nervous system, somites, and endodermal tissues by producing extracellular signaling molecules, such as Sonic hedgehog (Shh). In Ciona, hedgehog.b, one of the two hedgehog genes, is expressed in the floor plate of the embryonic neural tube, while none of the hedgehog genes are expressed in the notochord. We have identified a cis-regulatory region of hedgehog.b that was sufficient to drive a reporter gene expression in the floor plate. The hedgehog.b cis-regulatory region also drove ectopic expression of the reporter gene in the endodermal strand, suggesting that the floor plate and the endodermal strand share a part of their gene regulatory programs. The endodermal strand occupies the same topographic position of the embryo as does the vertebrate hypochord, which consists of a row of single cells lined up immediately ventral to the notochord. The hypochord shares expression of several genes with the floor plate, including Shh and FoxA, and play a role in dorsal aorta development. Whole-embryo single-cell transcriptome analysis identified a number of genes specifically expressed in both the floor plate and the endodermal strand in Ciona tailbud embryos. A Ciona FoxA ortholog FoxA.a is shown to be a candidate transcriptional activator for the midline gene battery. The present findings suggest an ancient evolutionary origin of a common developmental program for the midline structures in Olfactores.

show abstract

“…More recently, a larval nervous system connectome has been revealed [28] and collections of single cell transcriptomics generated [29][30][31][32][33]. Emerging studies are now aiming to annotate each neuron identified in the connectome with the gene expression patterns, including neurotransmitter types, described from in situ hybridization/immunostaining analysis or single cell transcriptomics datasets, as well as to the cell lineage history and ultimately to neuronal function and larval behavior [29,[34][35][36][37][38][39].…”

Section: The Ascidian Larval Cnsmentioning

confidence: 99%

“…Ascidian embryos develop with a fixed cell cleavage pattern and lineage, allowing the exact lineage relationships between different cell types to be known as long as the cells can be traced and identified [3,8,13,26,37,38,50,58]. The embryos are bilaterally symmetrical so each cell name refers to a pair of cells [72].…”

Section: A Large Part Of the Ascidian Cns Is Derived From Bi-fated Neuromesodermal Precursorsmentioning

confidence: 99%

Neuromesodermal Lineage Contribution to CNS Development in Invertebrate and Vertebrate Chordates

Hudson

Yasuo

2021

Genes

View full text Add to dashboard Cite

Ascidians are invertebrate chordates and the closest living relative to vertebrates. In ascidian embryos a large part of the central nervous system arises from cells associated with mesoderm rather than ectoderm lineages. This seems at odds with the traditional view of vertebrate nervous system development which was thought to be induced from ectoderm cells, initially with anterior character and later transformed by posteriorizing signals, to generate the entire anterior-posterior axis of the central nervous system. Recent advances in vertebrate developmental biology, however, show that much of the posterior central nervous system, or spinal cord, in fact arises from cells that share a common origin with mesoderm. This indicates a conserved role for bi-potential neuromesoderm precursors in chordate CNS formation. However, the boundary between neural tissue arising from these distinct neural lineages does not appear to be fixed, which leads to the notion that anterior-posterior patterning and neural fate formation can evolve independently.

show abstract

Spatio-temporal regulation of Rx and mitotic patterns shape the eye-cup of the photoreceptor cells in Ciona

Cited by 8 publications

References 60 publications

A Nearly Complete Genome of Ciona intestinalis Type A (C. robusta) Reveals the Contribution of Inversion to Chromosomal Evolution in the Genus Ciona

A Nearly Complete Genome of Ciona intestinalis Type A (C. robusta) Reveals the Contribution of Inversion to Chromosomal Evolution in the Genus Ciona

Evolution of Developmental Programs for the Midline Structures in Chordates: Insights From Gene Regulation in the Floor Plate and Hypochord Homologues of Ciona Embryos

Neuromesodermal Lineage Contribution to CNS Development in Invertebrate and Vertebrate Chordates

Contact Info

Product

Resources

About