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Molecular mechanisms of embryonic tail development in the self-fertilizing mangrove killifish Kryptolebias

ABSTRACT: Molecular mechanisms of embryonic tail development in the self-fertilizing mangrove killifish Kryptolebias

PROVIDER: PRJNA767883 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR16155233_1.fastq.gz	Fastqsanger.gz
	SRR16155233_2.fastq.gz	Fastqsanger.gz
	SRR16155234_1.fastq.gz	Fastqsanger.gz
	SRR16155234_2.fastq.gz	Fastqsanger.gz
	SRR16155235_1.fastq.gz	Fastqsanger.gz

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Molecular mechanisms of embryonic tail development in the self-fertilizing mangrove killifish Kryptolebias

Project description:Molecular mechanisms of embryonic tail development in the self-fertilizing mangrove killifish Kryptolebias

| PRJNA767883 | ENA

Developmental defects in ectodermal appendages caused by missense mutation in edaradd gene in the nfr mangrove killifish, Kryptolebias marmoratus

Project description:The mangrove killifish, Kryptolebias marmoratus, can reproduce with self-fertilisation, offering a unique and useful genetic tool for generation of genetic mutants and quick identification of mutated genes. From an ENU-mutated mangrove killifish line R228, we have isolated a novel mutant line, no-fin-ray/nfr in which homozygous mutant of adult fish fin ray development is largely reduced. Besides the reduction of the fin, the nfr mutant also exhibited other phenotype associated with ectodermal cell lineages including loss of scales, deformation in the gill structure such as decreasing the number of gill filaments, the reduction in the number of jaw teeth, pharyngeal teeth and gill rakers. Illumina RNAseq with 3 embryos each from mutants, siblings and the parental WT strain Hon9 (only 9 embryos as total) identified a mutation in the edaradd in a highly conserved C-terminal death domain. Edaradd is known as a cytoplasmic accessory protein for the Ectodysplasin A (EDA) signalling pathway. To confirm the crucial role of edaradd during fin development, CRISPR RNAs were designed to knock out the gene in another killifish species, Arabian killifish. Indeed, Arabian killifish edaradd crispants showed a potent reduction of the fin development with 100% frequency. Furthermore, EDA crispants also showed identical phenotypes to that of edaradd crispants, confirming the fin defect in the mutants/crispants is caused by the signalling pathway of the EDA in the killifish species. These data demonstrate a powerful genetic approach using isogenic self-fertilising mangrove killifish as a tool for identifying mutants and their mutation, and revealed the crucial role of edaradd for the first time in the fish fin development and other ectoderm derived epithelial tissues.

2024-07-29 | GSE273026 | GEO

Molecular mechanisms of embryonic tail development in the self-fertilizing mangrove killifish Kryptolebias marmoratus.

Project description:Using the self-fertilizing mangrove killifish, we characterized two mutants, shorttail (stl) and balltail (btl). These mutants showed abnormalities in the posterior notochord and muscle development. Taking advantage of a highly inbred isogenic strain of the species, we rapidly identified the mutated genes, noto and msgn1 in the stl and btl mutants, respectively, using a single lane of RNA sequencing without the need of a reference genome or genetic mapping techniques. Next, we confirmed a conserved morphant phenotype in medaka and demonstrate a crucial role of noto and msgn1 in cell sorting between the axial and paraxial part of the tail mesoderm. This novel system could substantially accelerate future small-scale forward-genetic screening and identification of mutations. Therefore, the mangrove killifish could be used as a complementary system alongside existing models for future molecular genetic studies.

| S-EPMC8722387 | biostudies-literature

Molecular mechanisms of embryonic tail development in the self-fertilizing mangrove killifish Kryptolebias

Project description:We report the application of single-molecule-based sequencing technology for high-throughput profiling of histone modifications in mammalian cells. By obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of mouse embryonic stem cells, neural progenitor cells and embryonic fibroblasts. We find that lysine 4 and lysine 27 trimethylation effectively discriminates genes that are expressed, poised for expression, or stably repressed, and therefore reflect cell state and lineage potential. Lysine 36 trimethylation marks primary coding and non-coding transcripts, facilitating gene annotation. Trimethylation of lysine 9 and lysine 20 is detected at satellite, telomeric and active long-terminal repeats, and can spread into proximal unique sequences. Lysine 4 and lysine 9 trimethylation marks imprinting control regions. Finally, we show that chromatin state can be read in an allele-specific manner by using single nucleotide polymorphisms. This study provides a framework for the application of comprehensive chromatin profiling towards characterization of diverse mammalian cell populations.

2021-10-04 | GSE185186 | GEO

Developmental defects in ectodermal appendages caused by missense mutation in edaradd gene in the nfr mangrove killifish, Kryptolebias marmoratus

Project description:Developmental defects in ectodermal appendages caused by missense mutation in edaradd gene in the nfr mangrove killifish, Kryptolebias marmoratus

| PRJNA1139807 | ENA

Complete mitochondrial genome of the mangrove killifish <i>Kryptolebias hermaphroditus</i> (Cyprinodontiformes, Rivulidae).

Project description:The complete mitochondrial genome was sequenced from the mangrove killifish (Kryptolebias hermaphroditus). The genome sequence was 17,487?bp in size, and the gene order and contents were identical with those of the congeneric species (K. marmoratus) in the genus Kryptolebias with emphasis on the second control region (795?bp). Of 13 protein-coding genes (PGCs), 5 genes (ND2, CO2, CO3, ND3, and Cytb) had incomplete stop codons as shown in K. marmoratus. Furthermore, the stop codon of ND6 gene was AGG, while the start codon of CO1 gene was GTG. The base composition of K. hermaphroditus mitogenome showed an anti-G bias (13.45% and 8.19%) on the second and third position of the protein-coding genes (PCGs), respectively.

| S-EPMC7800439 | biostudies-literature

Correlation between microbiota and growth in Mangrove Killifish (Kryptolebias marmoratus) and Atlantic cod (Gadus morhua).

Project description:The vertebrate gut is host to large communities of bacteria, and one of the beneficial contributions of this commensal gut microbiota is the increased nutritional gain from feed components that the host cannot degrade on its own. Fish larvae of similar age and under the same rearing conditions often diverge with regards to growth. The underlying reasons for this could be differences in genetic background, feeding behavior or digestive capacity. Both feeding behavior and digestion can be influenced by differences in the microbiota. To investigate possible correlations between the size of fish larvae and their gut microbiota, we analyzed the microbiota small and large genetically homogenous killifish and genetically heterogeneous cod larvae by Bray-Curtis Similarity measures of 16S DNA DGGE patterns. A significant difference in richness (p = 0.037) was observed in the gut microbiota of small and large killifish, but the overall gut microbiota was not found to be significantly different (p = 0.13), indicating strong genetic host selection on microbiota composition at the time of sampling. The microbiota of small and large cod larvae was significantly different with regards to evenness and diversity (p = 0.0001), and a strong correlation between microbiota and growth was observed.

| S-EPMC4753419 | biostudies-literature

Effect of water emersion on the gill proteome of Mangrove killifish

Project description:Gill proteome of Mangrove killifish was compared by LC-MS/MS using 6 biological replicates of fish exposed to emersion stress versus 6 biological replicates kept under water that served as controls. PI: Experiments and fish exposures were performed in the laboratory of Prof. Patricia Wright at the University of Guelph (Canada). Proteomics contact: Proteomics sample preparation and biological mass spectrometry were performed in the laboratory of Prof. Dietmar Kueltz laboratory at UC Davis (CA).

2017-03-15 | MSV000080634 | MassIVE

Kryptolebias ocellatus

Project description:Kryptolebias ocellatus

| PRJNA802258 | ENA

Kryptolebias brasiliensis

Project description:Kryptolebias brasiliensis

| PRJNA783653 | ENA