Comparative mapping of a new repetitive DNA sequence and chromosome region-specific probes unveiling rearrangements in an Amazonian frog complex

The frog species Physalaemus ephippifer exists in the Amazonian region and harbors heteromorphic Z and W chromosomes. A genetic lineage closely related to this species was recognized based on its mitochondrial DNA and RADseq-style markers, but its taxonomic status is still unclear and has been referred to as Lineage 1 of “P. cuvieri”. The heteromorphic sex chromosomes found in P. ephippifer are not present in this lineage and which of its chromosome pairs is homologous to the sex chromosomes of P. ephippifer remain to be elucidated as well as the role of such a karyotypic divergence in the evolution of these frogs. Here, we described a new family of repetitive DNA and used its chromosomal sites along with the markers detected by a probe constructed from the microdissected segment of the Z chromosome of P. ephippifer to infer chromosomal homology. We also analyzed an unnamed species that is considered to be the sister group of the clade composed of Lineage 1 of “P. cuvieri” and P. ephippifer. Our results suggest that complex rearrangements involving the chromosomes that were inferred to be homeologous to the sex chromosomes of P. ephippifer have occurred during the divergence of this group of frogs.

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Genetic sex determination and sex-specific lifespan in tetrapods – evidence of a toxic Y effect

10.1101/2020.03.09.983700 ◽

2020 ◽

Author(s):

Zahida Sultanova ◽

Philip A. Downing ◽

Pau Carazo

Keyword(s):

Sex Chromosomes ◽

Alternative Hypothesis ◽

Z Chromosome ◽

W Chromosome ◽

Deleterious Mutations ◽

Recessive Mutations ◽

Y Chromosomes ◽

Heterogametic Sex ◽

Taxonomic Patterns

ABSTRACTSex-specific lifespans are ubiquitous across the tree of life and exhibit broad taxonomic patterns that remain a puzzle, such as males living longer than females in birds and vice versa in mammals. The prevailing “unguarded-X” hypothesis (UXh) explains this by differential expression of recessive mutations in the X/Z chromosome of the heterogametic sex (e.g., females in birds and males in mammals), but has only received indirect support to date. An alternative hypothesis is that the accumulation of deleterious mutations and repetitive elements on the Y/W chromosome might lower the survival of the heterogametic sex (“toxic Y” hypothesis). Here, we report lower survival of the heterogametic relative to the homogametic sex across 138 species of birds, mammals, reptiles and amphibians, as expected if sex chromosomes shape sex-specific lifespans. We then analysed bird and mammal karyotypes and found that the relative sizes of the X and Z chromosomes are not associated with sex-specific lifespans, contrary to UXh predictions. In contrast, we found that Y size correlates negatively with male survival in mammals, where toxic Y effects are expected to be particularly strong. This suggests that small Y chromosomes benefit male lifespans. Our results confirm the role of sex chromosomes in explaining sex differences in lifespan, but indicate that, at least in mammals, this is better explained by “toxic Y” rather than UXh effects.

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Chromosomal Spreading of Microsatellites and (TTAGGG)n Sequences in the Characidium zebra and C. gomesi Genomes (Characiformes: Crenuchidae)

Cytogenetic and Genome Research ◽

10.1159/000447959 ◽

2016 ◽

Vol 149 (3) ◽

pp. 182-190 ◽

Cited By ~ 12

Author(s):

Marcela B. Pucci ◽

Patricia Barbosa ◽

Viviane Nogaroto ◽

Mara C. Almeida ◽

Roberto F. Artoni ◽

...

Keyword(s):

Repetitive Dna ◽

Sex Chromosomes ◽

Dna Sequences ◽

Tandem Repeats ◽

Additional Data ◽

Sex Chromosome ◽

Binding Motif ◽

W Chromosome ◽

Repeat Sequences ◽

Heteromorphic Sex Chromosomes

Sex chromosome evolution involves the accumulation of repeat sequences such as multigenic families, noncoding repetitive DNA (satellite, minisatellite, and microsatellite), and mobile elements such as transposons and retrotransposons. Most species of Characidium exhibit heteromorphic ZZ/ZW sex chromosomes; the W is characterized by an intense accumulation of repetitive DNA including dispersed satellite DNA sequences and transposable elements. The aim of this study was to analyze the distribution pattern of 18 different tandem repeats, including (GATA)n and (TTAGGG)n, in the genomes of C. zebra and C. gomesi, especially in the C. gomesi W chromosome. In the C. gomesi W chromosome, weak signals were seen for (CAA)10, (CAC)10, (CAT)10, (CGG)10, (GAC)10, and (CA)15 probes. (GA)15 and (TA)15 hybridized to the autosomes but not to the W chromosome. The (GATA)n probe hybridized to the short arms of the W chromosome as well as the (CG)15 probe. The (GATA)n repeat is known to be a protein-binding motif. GATA-binding proteins are necessary for the decondensation of heterochromatic regions that hold coding genes, especially in some heteromorphic sex chromosomes that may keep genes related to oocyte development. The (TAA)10 repeat is accumulated in the entire W chromosome, and this microsatellite accumulation is probably involved in the sex chromosome differentiation process and crossover suppression in C. gomesi. These additional data on the W chromosome DNA composition help to explain the evolution of sex chromosomes in Characidium.

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Repetitive Sequence and Sex Chromosome Evolution in Vertebrates

Advances in Evolutionary Biology ◽

10.1155/2014/104683 ◽

2014 ◽

Vol 2014 ◽

pp. 1-9 ◽

Cited By ~ 25

Author(s):

Tariq Ezaz ◽

Janine E. Deakin

Keyword(s):

Repetitive Dna ◽

Sex Chromosomes ◽

Repetitive Sequence ◽

Chromosome Evolution ◽

Sex Chromosome ◽

Repetitive Sequences ◽

Sex Chromosome Evolution ◽

Genomic Changes ◽

Heteromorphic Sex Chromosomes ◽

Simple Repetitive Sequences

Sex chromosomes are the most dynamic entity in any genome having unique morphology, gene content, and evolution. They have evolved multiple times and independently throughout vertebrate evolution. One of the major genomic changes that pertain to sex chromosomes involves the amplification of common repeats. It is hypothesized that such amplification of repeats facilitates the suppression of recombination, leading to the evolution of heteromorphic sex chromosomes through genetic degradation of Y or W chromosomes. Although contrasting evidence is available, it is clear that amplification of simple repetitive sequences played a major role in the evolution of Y and W chromosomes in vertebrates. In this review, we present a brief overview of the repetitive DNA classes that accumulated during sex chromosome evolution, mainly focusing on vertebrates, and discuss their possible role and potential function in this process.

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Karyotype Evolution and Genomic Organization of Repetitive DNAs in the Saffron Finch, Sicalis flaveola (Passeriformes, Aves)

Animals ◽

10.3390/ani11051456 ◽

2021 ◽

Vol 11 (5) ◽

pp. 1456

Author(s):

Rafael Kretschmer ◽

Benilson Silva Rodrigues ◽

Suziane Alves Barcellos ◽

Alice Lemos Costa ◽

Marcelo de Bello Cioffi ◽

...

Keyword(s):

Biological Diversity ◽

Genomic Organization ◽

Repetitive Sequences ◽

Artificial Chromosome ◽

Sister Group ◽

Z Chromosome ◽

Domestic Species ◽

Dna Mapping ◽

Evolution Of Birds

The Saffron finch (Sicalis flaveola), a semi-domestic species, is tolerant of human proximity and nesting in roof spaces. Considering the importance of cytogenomic approaches in revealing different aspects of genomic organization and evolution, we provide detailed cytogenetic data for S. flaveola, including the standard Giemsa karyotype, C- and G-banding, repetitive DNA mapping, and bacterial artificial chromosome (BAC) FISH. We also compared our results with the sister groups, Passeriformes and Psittaciformes, bringing new insights into the chromosome and genome evolution of birds. The results revealed contrasting rates of intrachromosomal changes, highlighting the role of SSR (simple short repetition probes) accumulation in the karyotype reorganization. The SSRs showed scattered hybridization, but brighter signals were observed in the microchromosomes and the short arms of Z chromosome in S. flaveola. BACs probes showed conservation of ancestral syntenies of macrochromosomes (except GGA1), as well as the tested microchromosomes. The comparison of our results with previous studies indicates that the great biological diversity observed in Passeriformes was not likely accompanied by interchromosomal changes. In addition, although repetitive sequences often act as hotspots of genome rearrangements, Passeriformes species showed a higher number of signals when compared with the sister group Psittaciformes, indicating that these sequences were not involved in the extensive karyotype reorganization seen in the latter.

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Heteromorphic sex chromosomes in the Australian frog Crinia bilingua (Anura: Myobatrachidae)

Genome ◽

10.1139/g91-055 ◽

1991 ◽

Vol 34 (3) ◽

pp. 334-337 ◽

Cited By ~ 11

Author(s):

M. J. Mahony

Keyword(s):

Sex Chromosomes ◽

Early Stage ◽

Proximal Region ◽

Z Chromosome ◽

W Chromosome ◽

Cytological Evidence ◽

Nucleolar Organiser ◽

Organiser Region ◽

Nucleolar Organiser Region ◽

Heteromorphic Sex Chromosomes

The karyotype of Crinia bilingua was examined and analysed with standard staining, C-banding, and silver-staining. Heteromorphic sex chromosomes of the ZW ♂/ZZ ♀ type were observed. The larger W chromosome is submetacentric and the smaller Z chromosome is acrocentric. The centromere and proximal region of the short arm of the W chromosome consist of constitutive heterochromatin (C-band region), and beyond this is a small euchromatic terminal region. The centromere of the Z chromosome did not C-band. The long arms of the Z and W chromosomes are euchromatic and equal in length. The nucleolar organiser region occurs terminally on the long arm of both the Z and W chromosomes, and there is no cytological evidence for inactivity of the nucleolar organiser region on the W chromosome. These features indicate an early stage in the evolution of heteromorphic sex chromosomes.Key words: heteromorphic sex chromosomes, frog, Crinia bilingua.

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The role of repetitive DNA in structure and evolution of sex chromosomes in plants

Heredity ◽

10.1038/hdy.2009.17 ◽

2009 ◽

Vol 102 (6) ◽

pp. 533-541 ◽

Cited By ~ 76

Author(s):

E Kejnovsky ◽

R Hobza ◽

T Cermak ◽

Z Kubat ◽

B Vyskot

Keyword(s):

Repetitive Dna ◽

Sex Chromosomes ◽

Evolution Of Sex

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Chromosome analysis in Saccodon wagneri (Characiformes) and insights into the karyotype evolution of Parodontidae

Neotropical Ichthyology ◽

10.1590/1982-0224-2020-0103 ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Mauro Nirchio ◽

Maria Cecilia Masache ◽

Fabilene Gomes Paim ◽

Marcelo de Bello Cioffi ◽

Orlando Moreira Filho ◽

...

Keyword(s):

Sex Chromosomes ◽

5S Rdna ◽

Chromosome Analysis ◽

Valid Species ◽

Z Chromosome ◽

Rdna Genes ◽

Heteromorphic Sex Chromosomes ◽

Karyotype Structure ◽

Interstitial Telomeric Sites

ABSTRACT Parodontidae is a relatively small group of Neotropical characiform fishes consisting of three genera (Apareiodon, Parodon, and Saccodon) with 32 valid species. A vast cytogenetic literature is available on Apareiodon and Parodon, but to date, there is no cytogenetic data about Saccodon, a genus that contains only three species with a trans-Andean distribution. In the present study the karyotype of S. wagneri was described, based on both conventional (Giemsa staining, Ag-NOR, C-bands) and molecular (repetitive DNA mapping by fluorescent in situ hybridization) methods. A diploid chromosome number of 2n = 54 was observed in both sexes, and the presence of heteromorphic sex chromosomes of the ZZ/ZW type was detected. The W chromosome has a terminal heterochromatin band that occupies approximately half of the long arm, being this band approximately half the size of the Z chromosome. The FISH assay showed a synteny of the 18S-rDNA and 5S-rDNA genes in the chromosome pair 14, and the absence of interstitial telomeric sites. Our data reinforce the hypothesis of a conservative karyotype structure in Parodontidae and suggest an ancient origin of the sex chromosomes in the fishes of this family.

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DNA methylation in satellite repeats disorders

Essays in Biochemistry ◽

10.1042/ebc20190028 ◽

2019 ◽

Vol 63 (6) ◽

pp. 757-771 ◽

Cited By ~ 4

Author(s):

Claire Francastel ◽

Frédérique Magdinier

Keyword(s):

Dna Methylation ◽

Human Genome ◽

Repetitive Dna ◽

Dna Sequences ◽

Satellite Repeats ◽

Tremendous Progress ◽

Genes Encoding ◽

Dna Elements ◽

Near Future

Abstract Despite the tremendous progress made in recent years in assembling the human genome, tandemly repeated DNA elements remain poorly characterized. These sequences account for the vast majority of methylated sites in the human genome and their methylated state is necessary for this repetitive DNA to function properly and to maintain genome integrity. Furthermore, recent advances highlight the emerging role of these sequences in regulating the functions of the human genome and its variability during evolution, among individuals, or in disease susceptibility. In addition, a number of inherited rare diseases are directly linked to the alteration of some of these repetitive DNA sequences, either through changes in the organization or size of the tandem repeat arrays or through mutations in genes encoding chromatin modifiers involved in the epigenetic regulation of these elements. Although largely overlooked so far in the functional annotation of the human genome, satellite elements play key roles in its architectural and topological organization. This includes functions as boundary elements delimitating functional domains or assembly of repressive nuclear compartments, with local or distal impact on gene expression. Thus, the consideration of satellite repeats organization and their associated epigenetic landmarks, including DNA methylation (DNAme), will become unavoidable in the near future to fully decipher human phenotypes and associated diseases.

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The Role of Global Appearance of Omnidirectional Images in Relative Distance and Orientation Retrieval

Sensors ◽

10.3390/s21103327 ◽

2021 ◽

Vol 21 (10) ◽

pp. 3327

Author(s):

Vicente Román ◽

Luis Payá ◽

Adrián Peidró ◽

Mónica Ballesta ◽

Oscar Reinoso

Keyword(s):

Mobile Robotics ◽

A Priori ◽

Computational Cost ◽

Relevant Information ◽

Local Features ◽

New Family ◽

Lighting Conditions ◽

Omnidirectional Images ◽

Great Development

Over the last few years, mobile robotics has experienced a great development thanks to the wide variety of problems that can be solved with this technology. An autonomous mobile robot must be able to operate in a priori unknown environments, planning its trajectory and navigating to the required target points. With this aim, it is crucial solving the mapping and localization problems with accuracy and acceptable computational cost. The use of omnidirectional vision systems has emerged as a robust choice thanks to the big quantity of information they can extract from the environment. The images must be processed to obtain relevant information that permits solving robustly the mapping and localization problems. The classical frameworks to address this problem are based on the extraction, description and tracking of local features or landmarks. However, more recently, a new family of methods has emerged as a robust alternative in mobile robotics. It consists of describing each image as a whole, what leads to conceptually simpler algorithms. While methods based on local features have been extensively studied and compared in the literature, those based on global appearance still merit a deep study to uncover their performance. In this work, a comparative evaluation of six global-appearance description techniques in localization tasks is carried out, both in terms of accuracy and computational cost. Some sets of images captured in a real environment are used with this aim, including some typical phenomena such as changes in lighting conditions, visual aliasing, partial occlusions and noise.

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The Diversity and Evolution of Sex Chromosomes in Frogs

Genes ◽

10.3390/genes12040483 ◽

2021 ◽

Vol 12 (4) ◽

pp. 483

Author(s):

Wen-Juan Ma ◽

Paris Veltsos

Keyword(s):

Sex Determination ◽

Sex Chromosomes ◽

Chromosome Evolution ◽

Sex Chromosome ◽

Comparative Genomic ◽

Ancestral State ◽

Heteromorphic Sex Chromosomes ◽

Genomic Studies ◽

Evolutionary Trajectories ◽

Heterogametic Sex

Frogs are ideal organisms for studying sex chromosome evolution because of their diversity in sex chromosome differentiation and sex-determination systems. We review 222 anuran frogs, spanning ~220 Myr of divergence, with characterized sex chromosomes, and discuss their evolution, phylogenetic distribution and transitions between homomorphic and heteromorphic states, as well as between sex-determination systems. Most (~75%) anurans have homomorphic sex chromosomes, with XY systems being three times more common than ZW systems. Most remaining anurans (~25%) have heteromorphic sex chromosomes, with XY and ZW systems almost equally represented. There are Y-autosome fusions in 11 species, and no W-/Z-/X-autosome fusions are known. The phylogeny represents at least 19 transitions between sex-determination systems and at least 16 cases of independent evolution of heteromorphic sex chromosomes from homomorphy, the likely ancestral state. Five lineages mostly have heteromorphic sex chromosomes, which might have evolved due to demographic and sexual selection attributes of those lineages. Males do not recombine over most of their genome, regardless of which is the heterogametic sex. Nevertheless, telomere-restricted recombination between ZW chromosomes has evolved at least once. More comparative genomic studies are needed to understand the evolutionary trajectories of sex chromosomes among frog lineages, especially in the ZW systems.

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