scholarly journals Repeat Sequence Mapping Shows Different W Chromosome Evolutionary Pathways in Two Caprimulgiformes Families

Birds ◽  
2020 ◽  
Vol 1 (1) ◽  
pp. 19-34
Author(s):  
Marcelo Santos de Souza ◽  
Rafael Kretschmer ◽  
Suziane Alves Barcellos ◽  
Alice Lemos Costa ◽  
Marcelo de Bello Cioffi ◽  
...  
Keyword(s):  
Genomic Organization ◽  
Constitutive Heterochromatin ◽  
Repetitive Sequences ◽  
Repeat Sequence ◽  
Z Chromosome ◽  
W Chromosome ◽  
Variation Data ◽  
Extra Step ◽  
The Common ◽  
Consequent Increase

Although birds belonging to order Caprimulgiformes show extensive karyotype variation, data concerning their genomic organization is still scarce, as most studies have presented only results obtained from conventional staining analyses. Nevertheless, some interesting findings have been observed, such as the W chromosome of the Common Potoo, Nyctibius griseus (2n = 86), which has the same morphology and size of the Z chromosome, a rare feature in Neognathae birds. Hence, we aimed to investigate the process by which the W chromosome of this species was enlarged. For that, we analyzed comparatively the chromosome organization of the Common Potoo and the Scissor-tailed Nightjar, Hydropsalis torquata (2n = 74), which presents the regular differentiated sex chromosomes, by applying C-banding, G-banding and mapping of repetitive DNAs (microsatellite repeats and 18S rDNA). Our results showed an accumulation of constitutive heterochromatin in the W chromosome of both species. However, 9 out of 11 microsatellite sequences hybridized in the large W chromosome in the Common Potoo, while none of them hybridized in the W chromosome of the Scissor-tailed Nightjar. Therefore, we can conclude that the accumulation of microsatellite sequences, and consequent increase in constitutive heterochromatin, was responsible for the enlargement of the W chromosome in the Common Potoo. Based on these results, we conclude that even though these two species belong to the same order, their W chromosomes have gone through different evolutionary histories, with an extra step of accumulation of repetitive sequences in the Common Potoo.

Karyotype Evolution and Distinct Evolutionary History of the W Chromosomes in Swallows (Aves, Passeriformes)

2019 ◽  
Vol 158 (2) ◽  
pp. 98-105 ◽  
Author(s):  
Suziane A. Barcellos ◽  
Rafael Kretschmer ◽  
Marcelo S. de Souza ◽  
Alice L. Costa ◽  
Tiago M. Degrandi ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Evolutionary History ◽  
Karyotype Evolution ◽  
Sex Chromosome ◽  
Repetitive Sequences ◽  
Z Chromosome ◽  
W Chromosome ◽  
The Family ◽  
Agnor Staining ◽  
History Of

As in many other bird groups, data on karyotype organization and distribution of repetitive sequences are also lacking in species belonging to the family Hirundinidae. Thus, in the present study, we analyzed the karyotypes of 3 swallow species (Progne tapera, Progne chalybea, and Pygochelidon cyanoleuca) by Giemsa and AgNOR staining, C-banding, and FISH with 11 microsatellite sequences. The diploid chromosome number was 2n = 76 in all 3 species, and NORs were observed in 2 chromosome pairs each. The microsatellite distribution pattern was similar in both Progne species, whereas P. cyanoleuca presented a distinct organization. These repetitive DNA sequences were found in the centromeric, pericentromeric, and telomeric regions of the macrochromosomes, as well as in 2 interstitial blocks in the W chromosome. Most microchromosomes had mainly telomeric signals. The Z chromosome displayed 1 hybridization signal in P. tapera but none in the other species. In contrast, the W chromosome showed an accumulation of different microsatellite sequences. The swallow W chromosome is larger than that of most Passeriformes. The observed enlargement in chromosome size might be explained by these high amounts of repetitive sequences. In sum, our data highlight the significant role that microsatellite sequences may play in sex chromosome differentiation.

scholarly journals NOR- bearing as a plesiomorphic characteristic in Mimus saturninus (Passeriformes Mimidae)

2014 ◽  
Vol 5 (2) ◽  
pp. 140-147 ◽  
Author(s):  
Rafael Kretschmer ◽  
Vanusa Lilian Lima ◽  
Tiago Marafiga Degrandi ◽  
Lucia Vinadé ◽  
Adriano Luis Schünemann ◽  
...  
Keyword(s):  
Chromosome Banding ◽  
Diploid Number ◽  
Secondary Constriction ◽  
Constitutive Heterochromatin ◽  
Pericentromeric Region ◽  
Chromosome Morphology ◽  
Z Chromosome ◽  
Positive Staining ◽  
W Chromosome ◽  
Order Passeriformes

The order Passeriformes is the largest group of species karyotyped among birds, however little is known about the cytogenetic of the Mimidae family, registering only karyology basic data (giemsa staining). The aim of this study was to analyze the chromosomal complement from the species Mimus saturninus by conventional staining and differential chromosome banding. Diploid number and chromosome morphology were determined, as well as the distribution pattern of constitutive heterochromatin (CBG-banding), GTG-banding andAgNOR staining (NORs). The Chalk-browed Mockingbird has 2n=80. The first and fourth pairs are submetacentric and the second, third and fifth are acrocentric. The remaining chromosomes pairs of the complement have telocentric morphology. The Z chromosome is submetacentric and the W is metacentric. CBG-banding showed positive staining in the pericentromeric region of most macrochromosomes and microchromosomes and also at Z chromosome, differently from W chromosome which appeared totally heterochromatic. The GTG-banding was similar to Gallus gallus and in other species which have already been GTG-banded. The NORs were identified in a pair of microchromosomes characterized by presenting a remarkable secondary constriction. This can be considered as a plesiomorphic characteristic for M. saturninus once baseline groups (Paleognathae) also showed a pair of microchromosomes bearing NORs.

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

Animals ◽  
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.

scholarly journals Absence of W Chromosome in Psychidae Moths and Implications for the Theory of Sex Chromosome Evolution in Lepidoptera

Genes ◽  
2019 ◽  
Vol 10 (12) ◽  
pp. 1016
Author(s):  
Martina Hejníčková ◽  
Petr Koutecký ◽  
Pavel Potocký ◽  
Irena Provazníková ◽  
Anna Voleníková ◽  
...  
Keyword(s):  
Genome Size ◽  
Sex Chromosome ◽  
Phylogenetic Position ◽  
Z Chromosome ◽  
Comparative Genomic ◽  
W Chromosome ◽  
Sex Chromatin ◽  
Sex Chromosome System ◽  
The Common ◽  
Female Specific

Moths and butterflies (Lepidoptera) are the largest group with heterogametic females. Although the ancestral sex chromosome system is probably Z0/ZZ, most lepidopteran species have the W chromosome. When and how the W chromosome arose remains elusive. Existing hypotheses place the W origin either at the common ancestor of Ditrysia and Tischeriidae, or prefer independent origins of W chromosomes in these two groups. Due to their phylogenetic position at the base of Ditrysia, bagworms (Psychidae) play an important role in investigating the W chromosome origin. Therefore, we examined the W chromosome status in three Psychidae species, namely Proutia betulina, Taleporia tubulosa, and Diplodoma laichartingella, using both classical and molecular cytogenetic methods such as sex chromatin assay, comparative genomic hybridization (CGH), and male vs. female genome size comparison by flow cytometry. In females of all three species, no sex chromatin was found, no female-specific chromosome regions were revealed by CGH, and a Z-chromosome univalent was observed in pachytene oocytes. In addition, the genome size of females was significantly smaller than males. Overall, our study provides strong evidence for the absence of the W chromosome in Psychidae, thus supporting the hypothesis of two independent W chromosome origins in Tischeriidae and in advanced Ditrysia.

scholarly journals Symbol Grounding Association in Multimodal Sequences with Missing Elements

2018 ◽  
Vol 61 ◽  
pp. 787-806
Author(s):  
Federico Raue ◽  
Andreas Dengel ◽  
Thomas M. Breuel ◽  
Marcus Liwicki
Keyword(s):  
Dynamic Time Warping ◽  
Learning Rule ◽  
Abstract Concepts ◽  
Time Warping ◽  
Short Term ◽  
Recent Approach ◽  
Extra Step ◽  
The Common ◽  
Dynamic Time ◽  
General Scope

In this paper, we extend a symbolic association framework for being able to handle missing elements in multimodal sequences. The general scope of the work is the symbolic associations of object-word mappings as it happens in language development in infants. In other words, two different representations of the same abstract concepts can associate in both directions. This scenario has been long interested in Artificial Intelligence, Psychology, and Neuroscience. In this work, we extend a recent approach for multimodal sequences (visual and audio) to also cope with missing elements in one or both modalities. Our method uses two parallel Long Short-Term Memories (LSTMs) with a learning rule based on EM-algorithm. It aligns both LSTM outputs via Dynamic Time Warping (DTW). We propose to include an extra step for the combination with the max operation for exploiting the common elements between both sequences. The motivation behind is that the combination acts as a condition selector for choosing the best representation from both LSTMs. We evaluated the proposed extension in the following scenarios: missing elements in one modality (visual or audio) and missing elements in both modalities (visual and sound). The performance of our extension reaches better results than the original model and similar results to individual LSTM trained in each modality.

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

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.

scholarly journals Heterochromatin: Guardian of the Genome

2018 ◽  
Vol 34 (1) ◽  
pp. 265-288 ◽  
Author(s):  
Aniek Janssen ◽  
Serafin U. Colmenares ◽  
Gary H. Karpen
Keyword(s):  
Chromosome Segregation ◽  
Genome Stability ◽  
Constitutive Heterochromatin ◽  
Repetitive Sequences ◽  
Genome Integrity ◽  
Chromatin Domain ◽  
Cellular Processes ◽  
Eukaryotic Nucleus ◽  
And Function ◽  
Heterochromatin Structure

Constitutive heterochromatin is a major component of the eukaryotic nucleus and is essential for the maintenance of genome stability. Highly concentrated at pericentromeric and telomeric domains, heterochromatin is riddled with repetitive sequences and has evolved specific ways to compartmentalize, silence, and repair repeats. The delicate balance between heterochromatin epigenetic maintenance and cellular processes such as mitosis and DNA repair and replication reveals a highly dynamic and plastic chromatin domain that can be perturbed by multiple mechanisms, with far-reaching consequences for genome integrity. Indeed, heterochromatin dysfunction provokes genetic turmoil by inducing aberrant repeat repair, chromosome segregation errors, transposon activation, and replication stress and is strongly implicated in aging and tumorigenesis. Here, we summarize the general principles of heterochromatin structure and function, discuss the importance of its maintenance for genome integrity, and propose that more comprehensive analyses of heterochromatin roles in tumorigenesis will be integral to future innovations in cancer treatment.

scholarly journals Repeats as global DNA methylation marker in bovine preimplantation embryos

2017 ◽  
Vol 62 (No. 2) ◽  
pp. 43-50 ◽  
Author(s):  
W. Li ◽  
A. Van Soom ◽  
L. Peelman
Keyword(s):  
Dna Methylation ◽  
Mutation Rate ◽  
Methylation Level ◽  
Methylation Status ◽  
Repetitive Sequences ◽  
Cell Types ◽  
Blastocyst Stage ◽  
Repeat Sequence ◽  
Preimplantation Embryos ◽  
Global Dna Methylation

DNA methylation undergoes dynamic changes and is a crucial part of the epigenetic regulation during mammalian early development. To determine the DNA methylation levels in bovine embryos, we applied a bisulfite sequencing based method aimed at repetitive sequences including three retrotransposons (L1_BT, BovB, and ERV1-1-I_BT) and Satellite I. A more accurate estimate of the global DNA methylation level compared to previous methods using only one repeat sequence, like Alu, could be made by calculation of the weighted arithmetic mean of multiple repetitive sequences, considering the copy number of each repetitive sequence. Satellite I and L1_BT showed significant methylation reduction at the blastocyst stage, while BovB and ERV1-1-I_BT showed no difference. The mean methylation level of the repetitive sequences during preimplantation development was the lowest at the blastocyst stage. No methylation difference was found between embryos cultured in 5% and 20% O<sub>2</sub>. Because mutations of CpGs negatively influence the calculation accuracy, we checked the mutation rate of the sequenced CpG sites. Satellite I and L1_BT showed a relatively low mutation rate (1.92 and 3.72% respectively) while that of ERV1-1-I_BT and BovB was higher (11.95 and 24% respectively). Therefore we suggest using a combination of repeats with low mutation rate, taking into account the proportion of each sequence, as a relatively quick marker for the global DNA methylation status of preimplantation stages and possibly also for other cell types.

Sex identification of pigeons using polymerase chain reaction analysis with simple DNA extraction

2019 ◽  
Vol 12 (2) ◽  
pp. 45-48
Author(s):  
Shao-jie Liang ◽  
Ming-xia Chen ◽  
Chun-qi Gao ◽  
Hui-chao Yan ◽  
Guo-long Zhang ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Dna Extraction ◽  
Polymerase Chain Reaction Analysis ◽  
Sex Identification ◽  
Z Chromosome ◽  
W Chromosome ◽  
Chain Reaction ◽  
Assay Time ◽  
Polymerase Chain ◽  
The Cost

Sex identification plays an important role in avian production. Hitherto, it is difficult to distinguish the sexes of monomorphic birds based on their external features. The chromo-helicase-DNA-binding genes contain CHD-W gene and CHD-Z gene, which are located on the W chromosome and Z chromosome, respectively. Since CHD-W gene is unique to females, the polymerase chain reaction can be used for sex identification. However, extracting DNA procedures for verifying the sex is tedious and expensive. To address these disadvantages, the objective of this study was to develop a simple DNA extraction assay to efficiently process blood, liver, and feather samples. The results showed that 2% dimethylsulfoxide was suitable for processing blood, and phosphate-buffered saline was suitable for processing liver and feather samples. The specific primers were designed, and the length of the targets is 474 bp on Z chromosome and 319 bp on W chromosome. The pigeons were identified as females based on the presence of two bands on the gel, and as males based on the presence of one band. Taken together, our results suggested that feather samples were more appropriate than blood or liver for sex identification of pigeons. Compared to the traditional DNA extraction, this method shortened the assay time and reduced the cost.

scholarly journals Altered specificity of Hint-W123Q supports a role for Hint inhibition by ASW in avian sex determination

2004 ◽  
Vol 20 (1) ◽  
pp. 12-14 ◽  
Author(s):  
Kristen P. Parks ◽  
Heather Seidle ◽  
Nathan Wright ◽  
Jeffrey B. Sperry ◽  
Pawel Bieganowski ◽  
...  
Keyword(s):  
Enzyme Activity ◽  
Sex Determination ◽  
Dominant Negative ◽  
Z Chromosome ◽  
Enzyme Specificity ◽  
W Chromosome ◽  
Dominant Component ◽  
Lysine Modification ◽  
Female Specific

Hint is a universally conserved, dimeric AMP-lysine hydrolase encoded on the avian Z chromosome. Tandemly repeated on the female-specific W chromosome, Asw encodes a potentially sex-determining, dominant-negative Hint dimerization partner whose substrate-interacting residues were specifically altered in evolution. To test the hypothesis that Gln127 of Asw is responsible for depression and/or alteration of Hint enzyme activity, a corresponding mutant was created in the chicken Hint homodimer, and a novel substrate was developed that links reversal of AMP-lysine modification to aminomethylcoumarin release. Strikingly, the Hint-W123Q substitution reduced kcat/ Km for AMP-lysine hydrolysis 17-fold, while it increased specificity for AMP- para-nitroaniline hydrolysis by 160-fold. The resulting 2,700-fold switch in enzyme specificity suggests that Gln127 could be the dominant component of Asw dominant negativity in avian feminization.

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