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42 results for “Nothobranchius furzeri”
Data from: Strong population genetic structuring in an annual fish, Nothobranchius furzeri, suggests multiple savannah refugia in southern Mozambique
Background: Intraspecific genetic variation of African fauna has been signific antly affected by pronounced climatic fluctuations in Plio-Pleistocene, but, with the exception of large mammals, very limited empirical data on diversity of natural populations are available for savanna-dwelling animals. Nothobranchius furzeri is an annual fish from south-eastern Africa, inhabiting discrete temporary savannah pools outside main river alluvia. Their dispersal is limited and population processes affecting its genetic structure are likely a combination of those affecting terrestrial and aquatic taxa. N. furzeri is a model taxon in ageing research and several populations of known geographical origin are used in laboratory studies. Here, we analysed the genetic structure, diversity, historical demography and temporal patterns of divergence in natural populations of N. furzeri across its entire distribution range. Results: Genetic structure and historical demography of N. furzeri were analysed using a combination of mitochondrial (partial cytochrome b sequences, 687 bp) and nuclear (13 microsatellites) markers in 693 fish from 36 populations. Genetic markers consistently demonstrated strong population structuring and suggested two main genetic groups associated with river basins. The split was dated to the Pliocene (>2 Mya). The northern group inhabits savannah pools across the basin of the intermittent river Chefu in south-western Mozambique and eastern Zimbabwe. The southern group (from southernmost Mozambique) is subdivided, with the River Limpopo forming a barrier (maximum divergence time 1 Mya). A strong habitat fragmentation (isolated temporary pools) is reflected in significant genetic structuring even between adjacent pools, with a major influence of genetic drift and significant isolation-by-distance. Analysis of historical demography revealed that the expansion of both groups is ongoing, supported by frequent founder effects in marginal parts of the range and evidence of secondary contact between Chefu and Limpopo populations. Conclusions: We demonstrated: (1) ancient (pre-Pleistocene) divergence between the two main N. furzeri lineages, their recent secondary contact and lack of reproductive isolation; (2) important genetic structuring attributed to the fragmented nature of their environment and isolation-by-distance, suggesting that dispersal is limited, occurs over short distances and is not directly associated with river routes; (3) an apparent role of the River Limpopo as a barrier to dispersal and gene flow.
Data from: Strong population genetic structuring in an annual fish, Nothobranchius furzeri, suggests multiple savannah refugia in southern Mozambique
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Sex chromosome differentiation via changes in the Y chromosome repeat landscape in African annual killifishes Nothobranchius furzeri and N. kadleci
<p><span>Repetitive DNA represents an important driver of sex chromosome differentiation. Yet repetitive sequences tend to be misrepresented or overlooked in genomic studies. We analysed repetitive landscape of sex chromosomes in several populations of a turquoise killifish <em>Nothobranchius</em> <em>furzeri</em> and its sister species <em>N</em>. <em>kadleci</em> (Teleostei: Nothobranchiidae), representatives of African annual killifishes with high rate of karyotype and sex chromosome evolution. We combined bioinformatic analyses of repeatome with molecular cytogenetic techniques such as comparative genomic hybridization, fluorescence in situ hybridization with satellite sequences, genes for ribosomal RNAs (rDNA) and bacterial artificial chromosomes (BACs) and immunostaining of </span><span>SYCP3 and MLH1 proteins, which marked lateral elements of synaptonemal complexes and recombination sites, respectively</span><span>. We revealed that <em>N</em>. <em>furzeri</em> and <em>N</em>. <em>kadleci</em> share the XY sex chromosome system, which is thus much older than previously assumed. Sex chromosomes are mostly heteromorphic as evidenced by distinct distribution of satellite DNAs and major rDNA. Yet, the heteromorphic X and Y sex chromosomes pair almost exclusively regularly in meiosis, which implies synaptic adjustment. Physical mapping of BACs identified inversions on Y chromosomes of the <em>N</em>. <em>kadleci</em> populations, similar to the pattern previously reported in <em>N</em>. <em>furzeri</em>. Yet, the repetitive DNA landscape of X and Y sex chromosomes either diverged in parallel in populations of both species, or it evolved in their common ancestor and thus predates the inversions. The observed differentiation via repeat repatterning thus cannot be explained by the classical sexual antagonistic model. Rather, we hypothesized that relaxed meiotic drive and recombination reduced by neutral processes could drive changes in repeatome and secondary inversions could be maintained </span><span>by sexually antagonistic regulatory effects resulting from evolution of dosage compensation. </span><span><br></span></p>
Sex chromosome differentiation via changes in the Y chromosome repeat landscape in African annual killifishes Nothobranchius furzeri and N. kadleci
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A cross-sectional study of gene expression in different strains of Nothobranchius furzeri
GEO Series GSE207748. Nothobranchius furzeri. 168 samples. Type: Expression profiling by high throughput sequencing.
Sequencing of Nothobranchius furzeri brain in two age groups
GEO Series GSE124638. Nothobranchius furzeri. 16 samples. Type: Expression profiling by high throughput sequencing; Other.
small RNA-seq of three tissues (brain, liver, skin) of Nothobranchius furzeri (at different ages), embryonic samples of N. furzeri and 6 other killifish species
GEO Series GSE92854. Nothobranchius rachovii; Iconisemion striatum; Nothobranchius furzeri; Nothobranchius kuhntae; Nothobranchius pienaari; Nothobranchius korthausae; Nothobranchius kadleci. 169 samples. Type: Non-coding RNA profiling by high throughput sequencing.
RNA-seq of the brain of Nothobranchius furzeri at different time points and strains (smallRNA)
GEO Series GSE150149. Nothobranchius furzeri. 16 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Aging triggers H3K27 trimethylation hoarding in the chromatin of Nothobranchius furzeri skeletal muscle.
GEO Series GSE135032. Nothobranchius furzeri. 9 samples. Type: Expression profiling by high throughput sequencing.
RNA-seq of the brain of Nothobranchius furzeri at different time points and strains
GEO Series GSE125373. Nothobranchius furzeri. 16 samples. Type: Expression profiling by high throughput sequencing.
small RNA-seq of three tissues (brain, liver, skin) of Nothobranchius furzeri (at different ages) and Brain samples of 6 other killifish species
GEO Series GSE104321. Nothobranchius rachovii; Nothobranchius kadleci; Nothobranchius kuhntae; Nothobranchius korthausae; Iconisemion striatum; Nothobranchius furzeri; Nothobranchius pienaari. 162 samples. Type: Non-coding RNA profiling by high throughput sequencing.
RNA sequencing of gonad tissue of Nothobranchius furzeri at different age in males and females
GEO Series GSE263626. Nothobranchius furzeri. 19 samples. Type: Expression profiling by high throughput sequencing.
RNA-seq of Nothobranchius furzeri (Nfu) brain after miR29 knock-down
GEO Series GSE79825. Nothobranchius furzeri. 8 samples. Type: Expression profiling by high throughput sequencing.
RNA-seq of the killifish Nothobranchius furzeri strain MZM-0410
GEO Series GSE72584. Nothobranchius furzeri. 12 samples. Type: Expression profiling by high throughput sequencing.
Longitudinal RNA-Seq study of Nothobranchius furzeri fin biopsies
GEO Series GSE150318. Nothobranchius furzeri. 228 samples. Type: Expression profiling by high throughput sequencing.
RNA-seq of the brain of Nothobranchius furzeri at different time points
GEO Series GSE52462. Nothobranchius furzeri. 25 samples. Type: Expression profiling by high throughput sequencing.
Aging triggers H3K27 trimethylation hoarding in the chromatin of Nothobranchius furzeri skeletal muscle
GEO Series GSE135129. Nothobranchius furzeri. 4 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
RNA-seq of three tissues (brain, liver, skin) of Nothobranchius furzeri (at age of 12 weeks)
GEO Series GSE69122. Nothobranchius furzeri. 15 samples. Type: Expression profiling by high throughput sequencing.
RNA-Seq of Nothobranchius furzeri brain of male fishes of two strains (MZM_A41 and MZM-0410) of age 39/35 dph (days post hatch)
GEO Series GSE183037. Nothobranchius furzeri. 8 samples. Type: Expression profiling by high throughput sequencing.
RNA-Seq of Nothobranchius furzeri brain of male and female with an age of 39-108 days post hatch (dph).
GEO Series GSE183039. Nothobranchius furzeri. 24 samples. Type: Expression profiling by high throughput sequencing.
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