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32 results for “fish chromosomes”
Fig. 2 in Chromosome evolution in fishes: a new challenging proposal from Neotropical species
Fig. 2. Scatter-plot of (a, c) diploid number (2n), and (b, d) pg of DNA per haploid nucleus (C-Value), against the phylogenetic position of Actinopterygii families presented by Nelson (2006). Data include all available species (a, b) or exclude possible polyploidy species (c, d). Ellipses with 95% confidence are used as a correlation indicator.
Fig. 1 in Chromosome evolution in fishes: a new challenging proposal from Neotropical species
Fig. 1. Scatter-plot of (a) diploid number (2n) and (b) fundamental number (FN), against the phylogenetic position of Actinopterygii families presented by Nelson (2006) for 103 fish species. Ellipses with 95% confidence are used as a correlation indicator.
Fig. 3 in Chromosome polymorphism of heterochromatin and nucleolar regions in two populations of the fish Astyanax bockmanni (Teleostei: Characiformes)
Fig. 3. Inter-individual polymorphisms of the heterochromatic blocks in Astyanax bockmanni from the Campo Novo River population. Each letter (a-d) represents a single individual.
Fig. 4. Sequential C in Chromosome polymorphism of heterochromatin and nucleolar regions in two populations of the fish Astyanax bockmanni (Teleostei: Characiformes)
Fig. 4. Sequential C-banding (a1 and b1) and Ag-NOR staining (a2 and b2) in a specimen from the Campo Novo River, demonstrating the association between heterochromatin and NOR. In (a2) and (b2), arrows indicate the presence of heterochromatin/NOR association, and arrowheads show NORs not associated with heterochromatin.
Fig. 1 in Chromosome polymorphism of heterochromatin and nucleolar regions in two populations of the fish Astyanax bockmanni (Teleostei: Characiformes)
Fig. 1. Karyotypes of Astyanax bockmanni arranged from Giemsa-stained chromosomes. Specimens from Barra Seca Stream (2n = 50) (a) and Campo Novo River (2n = 50) (b).
Lacustrine speciation associated with chromosomal inversion in a lineage of riverine fishes
<p>Geographic isolation is the primary driver of speciation in many vertebrate lineages. This trend is exemplified by North American darters, a clade of freshwater fishes where nearly all sister species pairs are allopatric and separated by millions of years of divergence. One of the only exceptions is the Lake Waccamaw endemic <em>Etheostoma perlongum</em> and its riverine sister species <em>E. maculaticeps</em>, which have no physical barriers to gene flow. Here we show that lacustrine speciation of <em>E. perlongum</em> is characterized by morphological and ecological divergence likely facilitated by a large chromosomal inversion. While <em>Etheostoma perlongum</em> is phylogenetically nested within the geographically widespread <em>E. maculaticeps</em>, there is a sharp genetic and morphological break coinciding with the lake-river boundary in the Waccamaw River system. Despite recent divergence, an active hybrid zone, and ongoing gene flow, analyses using a de novo reference genome reveal a 9 Mb chromosomal inversion with elevated divergence between <em>E. perlongum</em> and <em>E. maculaticeps</em>. This region exhibits striking synteny with known inversion supergenes in two distantly related fish lineages, suggesting deep evolutionary convergence of genomic architecture. Our results illustrate that rapid, ecological speciation with gene flow is possible even in lineages where geographic isolation is the dominant mechanism of speciation.</p>
Lacustrine speciation associated with chromosomal inversion in a lineage of riverine fishes
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Data from: Chromosome-level genome assembly of a cyprinid fish Onychostoma macrolepis by integration of Nanopore Sequencing, Bionano and Hi-C technology
<p><i>Onychostoma macrolepis</i> is an emerging commercial cyprinid fish species. It is a model system for studies of sexual dimorphism and genome evolution. Here, we report the chromosome-level assembly of the<i> O.macrolepis</i> genome obtained from the integration of Nanopore long-read sequencing with physical maps produced using Bionano and Hi-C technology. A total of 87.9 Gb of Nanopore sequence provided approximately 100-fold coverage of the genome. The preliminary genome assembly was 883.2 Mb in size with a contig N50 size of 11.2 Mb. The 969 corrected contigs obtained from Bionano optical mapping were assembled into 853 scaffolds and produced an assembly of 886.5 Mb with a scaffold N50 of 16.5 Mb. Finally, using the Hi-C data, 881.3 Mb (99.4% of genome) in 526 scaffolds were anchored and oriented in 25 chromosomes ranging in size from 25.27 to 56.49 Mb. In total, 24,770 protein-coding genes were predicted in the genome, and ~96.85% of the genes were functionally annotated. The annotated assembly contains 93.3% complete genes from the BUSCO reference set. In addition, we identified 409 Mb (46.23% of the genome) of repetitive sequence, and 11,213 non-coding RNAs, in the genome. Evolutionary analysis revealed that <i>O.macrolepis</i> diverged from common carp approximately 24.25 million years ago. The chromosomes of <i>O.macrolepis</i> showed an unambiguous correspondence to the chromosomes of zebrafish. The high-quality genome assembled in this work provides a valuable genomic resource for further biological and evolutionary studies of <i>O. macrolepis</i>.</p>
Data from: Study of regional differences in GC content values in chromosomes of the guppy and related fish species
<p><span><span><span><span><span><span><span><span><span><span><span>Genetic and physical mapping of the guppy (<i>P. reticulata</i>) have shown that recombination patterns differ greatly between males and females. Crossover events occur evenly across the chromosomes in females, but in male meiosis they are restricted to the tip furthest from the centromere of each chromosome, creating very high recombination rates per megabase, similar to the high rates in of pseudo-autosomal regions (PARs) of mammalian sex chromosomes. We here used the intronic GC content to indirectly infer the recombination patterns on guppy chromosomes. This is based on evidence that recombination is associated with GC-biased gene conversion, so that genome regions with high recombination rates should be detectable by high GC content. We used intron sequences and 3<sup>rd</sup> positions of codons, in order to make comparisons between sequences that are matched, as far as possible, with respect to selective constraints. Both these types of sites are likely to be under weak selection. Almost all guppy chromosomes, including the sex chromosome (LG12), prove to have very high GC values near their assembly ends, suggesting high recombination rates due to strong crossover localisation in male meiosis. Our test does not suggest that the guppy XY pair has stronger crossover localisation than the autosomes, or than the homologous chromosome in a closely related fish, the platyfish (<i>Xiphophorus maculatus</i>). We therefore conclude that the guppy XY pair has not recently undergone an evolutionary change to a different recombination pattern, or reduced its crossover rate, but that the guppy evolved Y-linkage due to acquiring a male-determining factor that also conferred the male crossover pattern. The results also identify the centromere ends of guppy chromosomes, which were not determined in the guppy genome assembly. </span></span></span></span></span></span></span></span></span></span></span></p>
Shared, modular chromosome rearrangements enable parallel adaptation in a marine fish
Genomic architecture and standing variation can play a key role in ecological adaptation, and contribute to the predictability of evolution. In Atlantic cod (Gadus morhua), four large chromosomal rearrangements have been associated with ecological gradients and migratory behaviour in regional analyses. However, the degree of parallelism , the extent of independent inheritance, and functional distinctiveness of these rearrangements remains poorly understood. Here, we use a 12K single nucleotide polymorphism (SNP) array to demonstrate extensive individual variation in rearrangement genotype within populations across the species range, suggesting that local adaptation to fine-scale ecological variation is enabled by rearrangements with independent inheritance. Our results demonstrate significant association of rearrangement with migration phenotype and environmental gradients across the species range. Individual rearrangements exhibit functional modularity, but also contain loci showing multiple environmental associations. Clustering in genetic distance trees and reduced differentiation within rearrangements across the species range are consistent with shared variation as a source of contemporary adaptive diversity in Atlantic cod. Conversely, we also find that haplotypes in the LG12 and LG1 rearranged region have diverged across the Atlantic, despite consistent environmental associations. Exchange of these structurally variable genomic regions, as well as local selective pressures have likely facilitated individual diversity within Atlantic cod stocks. Our results highlight the importance of genomic architecture and standing variation in enabling fine-scale adaptation in marine species.
Identification of a novel sex determining chromosome in cichlid fishes that acts as XY or ZW in different lineages
<p>Sex determination systems are highly conserved among most vertebrates with genetic sex determination, but can be variable and evolve rapidly in some. Here, we study sex determination in a clade with exceptionally high sex chromosome turnover rates. We identify the sex determining chromosomes in three interspecific crosses of haplochromine cichlid fishes from Lakes Victoria and Malawi. We find evidence for different sex determiners in each cross. In the Malawi cross and one Victoria cross the same chromosome is sex-linked but while females are the heterogametic sex in the Malawi species, males are the heterogametic sex in the Victoria species. This chromosome has not previously been reported to be sex determining in cichlids, increasing the number of different chromosomes shown to be sex determining in cichlids to 12. All Lake Victoria species of our crosses are less than 15,000 years divergent, and we identified different sex determiners among them. Our study provides further evidence for the diversity and evolutionary flexibility of sex determination in cichlids, factors which might contribute to their rapid adaptive radiations.</p>
Diversity of sex chromosomes in Sulawesian medaka fishes
<p><span>Recent genetic and genomic studies have revealed tremendous diversity in sex chromosomes across diverse taxa. Closely related species with different sex chromosomes provide us with excellent opportunities to investigate the driving forces and the consequences of sex chromosome turnover. In the present study, we investigated the diversity of sex chromosomes of 13 <em>Oryzias</em> species from Sulawesi, Indonesia, which diversified during the last 4.86 million years. Using pooled sequencing we found sex chromosomes in 9 species that all had XY systems, with a species being possibly modified by multiple loci. Seven species (<em>O. woworae</em>, <em>O</em>. <em>asinua</em>, <em>O</em>. <em>wolasi</em>, <em>O</em>. <em>matanensis</em>, <em>O</em>. <em>celebensis</em>, <em>O</em>. <em>hadiatyae</em>, and <em>O</em>. <em>dopingdopingensis</em>) share linkage group (LG) 24 as sex chromosomes; however, they differed in the length and magnitude of sequence divergence between the X and Y chromosomes. The sex chromosome of <em>O</em>. <em>eversi</em> was LG4, which has not been reported as a sex chromosome in any other medaka species. In <em>O</em>. <em>sarasinorum</em>, LG16 and LG22 are associated with sex. Although LG16 was found to be sex-linked in another medaka species previously examined, the sex-determining regions did not overlap. No significant signatures for sex chromosomes were identified in the other 4 species (<em>O</em>. <em>marmoratus</em>, <em>O</em>. <em>nigrimas</em>, <em>O</em>. <em>nebulosus</em>, and <em>O</em>. <em>orthognathus</em>). Frequent turnovers and the great diversity of the sex chromosomes will make Sulawesian medaka species a model system for investigating the driving forces and consequences of sex chromosome turnover.</span></p>
FIGURE. Results of FISH physical mapping on metaphase chromosomes of hyacinth 1. The distribution of 45S rDNA (red arrow) and 5S rDNA (green arrow) signals on the chromosomes; 2. The distribution of telomeric repeats signals on the chromosomes; 3. Chromosome karyotype with 45S rDNA and 5S rDNA; 4. Chromosome karyotype with telomeric repeats. A. 'Gypsy Queen' B.'Purple sensation' C.'Pink pearl' D.'Gypsy princess' E.'Blue pearl' F.'Odysseus' G.'Yellow stone' H.'Red pearl' in Physical mapping of 45S and 5S rDNA and telomeric repeat loci in eight diploid hyacinth cultivars
FIGURE. Results of FISH physical mapping on metaphase chromosomes of hyacinth 1. The distribution of 45S rDNA (red arrow) and 5S rDNA (green arrow) signals on the chromosomes; 2. The distribution of telomeric repeats signals on the chromosomes; 3. Chromosome karyotype with 45S rDNA and 5S rDNA; 4. Chromosome karyotype with telomeric repeats. A. 'Gypsy Queen' B.'Purple sensation' C.'Pink pearl' D.'Gypsy princess' E.'Blue pearl' F.'Odysseus' G.'Yellow stone' H.'Red pearl'
FIGURE 3. FISH showing the chromosomes with 35S in Does Solidago litoralis (Asteraceae) merit specific rank? Insights from cytogenetic, molecular and ecological data
FIGURE 3. FISH showing the chromosomes with 35S (red) and 5S (green) signals. A. Partial metaphase of S. litoralis; B. Partial metaphase of S. virgaurea (Livorno); C. S. virgaurea (Monte Pisano); D. S. virgaurea (Tre Potenze). Scale bar: 10 μm.
Identification of a novel sex determining chromosome in cichlid fishes that acts as XY or ZW in different lineages
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Modular chromosome rearrangements reveal parallel and nonparallel adaptation in a marine fish
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Data from: Study of regional differences in GC content values in chromosomes of the guppy and related fish species
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Data from: A FISH-based chromosome map for the European corn borer yields insights into ancient chromosomal fusions in the silkworm
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Data from: Chromosome-level genome assembly of a cyprinid fish Onychostoma macrolepis by integration of Nanopore Sequencing, Bionano and Hi-C technology
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Diversity of sex chromosomes in Sulawesian medaka fishes
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