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y chromosome evolution

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https://www.readbyqxmd.com/read/29329524/uncovering-the-evolutionary-history-of-neo-xy-sex-chromosomes-in-the-grasshopper-ronderosia-bergii-orthoptera-melanoplinae-through-satellite-dna-analysis
#1
Octavio M Palacios-Gimenez, Diogo Milani, Bernardo Lemos, Elio R Castillo, Dardo A Martí, Erica Ramos, Cesar Martins, Diogo C Cabral-de-Mello
BACKGROUND: Neo-sex chromosome systems arose independently multiple times in evolution, presenting the remarkable characteristic of repetitive DNAs accumulation. Among grasshoppers, occurrence of neo-XY was repeatedly noticed in Melanoplinae. Here we analyzed the most abundant tandem repeats of R. bergii (2n = 22, neo-XY♂) using deep Illumina sequencing and graph-based clustering in order to address the neo-sex chromosomes evolution. RESULTS: The analyses revealed ten families of satDNAs comprising about ~1% of the male genome, which occupied mainly C-positive regions of autosomes...
January 8, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29284187/sex-antagonistic-genes-xy-recombination-and-feminized-y-chromosomes
#2
Elisa Cavoto, Samuel Neuenschwander, Jérôme Goudet, Nicolas Perrin
The canonical model of sex-chromosome evolution predicts that sex-antagonistic (SA) genes play an instrumental role in the arrest of XY recombination and ensuing Y-chromosome degeneration. Although this model might account for the highly differentiated sex chromosomes of birds and mammals, it does not fit the situation of many lineages of fish, amphibians or non-avian reptiles, where sex chromosomes are maintained homomorphic through occasional XY recombination and/or high turnover rates. Such situations call for alternative explanatory frameworks...
December 28, 2017: Journal of Evolutionary Biology
https://www.readbyqxmd.com/read/29251591/free-living-human-cells-reconfigure-their-chromosomes-in-the-evolution-back-to-uni-cellularity
#3
Jin Xu, Xinxin Peng, Yuxin Chen, Yuezheng Zhang, Qin Ma, Liang Liang, Ava C Carter, Xuemei Lu, Chung-I Wu
Cells of multi-cellular organisms evolve toward uni-cellularity in the form of cancer and, if humans intervene, continue to evolve in cell culture. During this process, gene dosage relationships may evolve in novel ways to cope with the new environment and may regress back to the ancestral uni-cellular state. In this context, the evolution of sex chromosomes vis-a-vis autosomes is of particular interest. Here, we report the chromosomal evolution in ~ 600 cancer cell lines. Many of them jettisoned either Y or the inactive X; thus, free-living male and female cells converge by becoming 'de-sexualized'...
December 18, 2017: ELife
https://www.readbyqxmd.com/read/29222702/molecular-insights-into-the-non-recombining-nature-of-the-spinach-male-determining-region
#4
Tomohiro Kudoh, Mitsuhiko Takahashi, Takayuki Osabe, Atsushi Toyoda, Hideki Hirakawa, Yutaka Suzuki, Nobuko Ohmido, Yasuyuki Onodera
Spinach (Spinacia oleracea L.) is a dioecious plant with male heterogametic sex determination and homomorphic sex chromosomes (XY). The dioecism is utilized for producing commercial hybrid seeds, and hence understanding the molecular-genetic basis of the species' sex determining locus is an important issue for spinach breeding. In this study, seven dominant DNA markers were shown to completely co-segregate with the male-determining gene in segregating spinach populations comprising > 1500 plants. In addition, these seven dominant DNA markers were completely associated with the male-determining gene in over 100 spinach germplasm accessions and cultivars...
December 8, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/29202694/alternative-patterns-of-sex-chromosome-differentiation-in-aedes-aegypti-l
#5
Corey L Campbell, Laura B Dickson, Saul Lozano-Fuentes, Punita Juneja, Francis M Jiggins, William C Black
BACKGROUND: Some populations of West African Aedes aegypti, the dengue and zika vector, are reproductively incompatible; our earlier study showed that divergence and rearrangements of genes on chromosome 1, which bears the sex locus (M), may be involved. We also previously described a proposed cryptic subspecies SenAae (PK10, Senegal) that had many more high inter-sex FST genes on chromosome 1 than did Ae.aegypti aegypti (Aaa, Pai Lom, Thailand). The current work more thoroughly explores the significance of those findings...
December 4, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29186474/whole-mitochondrial-genomic-and-y-chromosomal-phylogenies-of-burmese-long-tailed-macaque-macaca-fascicularis-aurea-suggest-ancient-hybridization-between-fascicularis-and-sinica-species-groups
#6
Kazunari Matsudaira, Yuzuru Hamada, Srichan Bunlungsup, Takafumi Ishida, Aye Mi San, Suchinda Malaivijitnond
Macaca fascicularis aurea (Burmese long-tailed macaque) is 1 of the 10 subspecies of M. fascicularis. Despite having few morphological differences from other subspecies, a recent phylogeographic study showed that M. f. aurea is clearly distinct genetically from M. f. fascicularis (common long-tailed macaque) and suggests that M. f. aurea experienced a disparate evolutionary pathway versus other subspecies. To construct a detailed evolutionary history of M. f. aurea and its relationships with other macaque species, we performed phylogenetic analyses and divergence time estimation of whole mitochondrial genomes (2 M...
November 23, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/29150608/rapid-neo-sex-chromosome-evolution-and-incipient-speciation-in-a-major-forest-pest
#7
Ryan R Bracewell, Barbara J Bentz, Brian T Sullivan, Jeffrey M Good
Genome evolution is predicted to be rapid following the establishment of new (neo) sex chromosomes, but it is not known if neo-sex chromosome evolution plays an important role in speciation. Here we combine extensive crossing experiments with population and functional genomic data to examine neo-XY chromosome evolution and incipient speciation in the mountain pine beetle. We find a broad continuum of intrinsic incompatibilities in hybrid males that increase in strength with geographic distance between reproductively isolated populations...
November 17, 2017: Nature Communications
https://www.readbyqxmd.com/read/29144072/relapse-and-cytogenetic-evolution-in-myeloid-neoplasms
#8
Natalie Ertz-Archambault, Katalin Kelemen
Based on the current WHO Classification of Myeloid Neoplasms, cytogenetic findings play a central role in the diagnostic classification of the myeloid malignancies. Cytogenetic abnormalities detected at primary diagnosis may change over time. Karyotype changes can be characterized as cytogenetic evolution, cytogenetic regression or a combination of both. While the exact mechanism of cytogenetic evolution is not completely understood, the process of cytogenetic evolution is not random, but follows different, and often disease-specific patterns during progression and relapse of myeloid neoplasms...
December 2017: Panminerva Medica
https://www.readbyqxmd.com/read/29137168/origin-and-evolution-of-the-neo-sex-chromosomes-in-pamphagidae-grasshoppers-through-chromosome-fusion-and-following-heteromorphization
#9
Ilyas Yerkinovich Jetybayev, Alexander Gennadievich Bugrov, Olesya Georgievna Buleu, Anton Gennadievich Bogomolov, Nikolay Borisovich Rubtsov
In most phylogenetic lineages, the evolution of sex chromosomes is accompanied by their heteromorphization and degradation of one of them. The neo-sex chromosomes are useful model for studying early stages of these processes. Recently two lineages of the neo-sex chromosomes on different stages of heteromorphization was discovered in Pamphagidae family. The neo-sex chromosome heteromorphization was analyzed by generation of DNA probes derived from the neo-Xs and neo-Ys followed with chromosome painting in nineteen species of Pamphagidae family...
November 13, 2017: Genes
https://www.readbyqxmd.com/read/29134711/x-exceptionalism-in-caenorhabditis-speciation
#10
Asher D Cutter
Speciation genetics research in diverse organisms shows the X-chromosome to be exceptional in how it contributes to 'rules' of speciation. Until recently, however, the nematode phylum has been nearly silent on this issue, despite the model organism Caenorhabditis elegans having touched most other topics in biology. Studies of speciation with Caenorhabditis accelerated with the recent discovery of species pairs showing partial inter-fertility. The resulting genetic analyses of reproductive isolation in nematodes demonstrate key roles for the X-chromosome in hybrid male sterility and inviability, opening up new understanding of the genetic causes of Haldane's rule, Darwin's corollary to Haldane's rule, and enabling tests of the large-X effect hypothesis...
November 13, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29133310/convergent-origination-of-a-drosophila-like-dosage-compensation-mechanism-in-a-reptile-lineage
#11
Ray Marin, Diego Cortez, Francesco Lamanna, Madapura M Pradeepa, Evgeny Leushkin, Philippe Julien, Angélica Liechti, Jean Halbert, Thoomke Brüning, Katharina Mössinger, Timo Trefzer, Christian Conrad, Halie N Kerver, Juli Wade, Patrick Tschopp, Henrik Kaessmann
Sex chromosomes differentiated from different ancestral autosomes in various vertebrate lineages. Here, we trace the functional evolution of the XY Chromosomes of the green anole lizard (Anolis carolinensis), on the basis of extensive high-throughput genome, transcriptome and histone modification sequencing data and revisit dosage compensation evolution in representative mammals and birds with substantial new expression data. Our analyses show that Anolis sex chromosomes represent an ancient XY system that originated at least ≈160 million years ago in the ancestor of Iguania lizards, shortly after the separation from the snake lineage...
November 13, 2017: Genome Research
https://www.readbyqxmd.com/read/29121353/secondary-structure-forming-sequences-drive-sd-mmej-repair-of-dna-double-strand-breaks
#12
Varandt Y Khodaverdian, Terrence Hanscom, Amy Marie Yu, Taylor L Yu, Victoria Mak, Alexander J Brown, Steven A Roberts, Mitch McVey
Alternative end-joining (alt-EJ) repair of DNA double-strand breaks is associated with deletions, chromosome translocations, and genome instability. Alt-EJ frequently uses annealing of microhomologous sequences to tether broken ends. When accessible pre-existing microhomologies do not exist, we have postulated that new microhomologies can be created via limited DNA synthesis at secondary-structure forming sequences. This model, called synthesis-dependent microhomology-mediated end joining (SD-MMEJ), predicts that differences between DNA sequences near double-strand breaks should alter repair outcomes in predictable ways...
November 7, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29116665/reproductive-isolation-and-environmental-adaptation-shape-the-phylogeography-of-mountain-pine-beetle-dendroctonus-ponderosae
#13
Eddy J Dowle, Ryan R Bracewell, Michael E Pfrender, Karen E Mock, Barbara J Bentz, Gregory J Ragland
Chromosomal rearrangement can be an important mechanism driving population differentiation and incipient speciation. In the mountain pine beetle (MPB, Dendroctonus ponderosae), deletions on the Y chromosome that are polymorphic among populations are associated with reproductive incompatibility. Here, we used RAD sequencing across the entire MPB range in western North America to reveal the extent of the phylogeographic differences between Y haplotypes compared to autosomal and X-linked loci. Clustering and geneflow analyses revealed three distinct Y haplogroups geographically positioned within and on either side of the Great Basin Desert...
November 8, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29114402/comparative-scaffolding-and-gap-filling-of-ancient-bacterial-genomes-applied-to-two-ancient-yersinia-pestis-genomes
#14
Nina Luhmann, Daniel Doerr, Cedric Chauve
Yersinia pestis is the causative agent of the bubonic plague, a disease responsible for several dramatic historical pandemics. Progress in ancient DNA (aDNA) sequencing rendered possible the sequencing of whole genomes of important human pathogens, including the ancient Y. pestis strains responsible for outbreaks of the bubonic plague in London in the 14th century and in Marseille in the 18th century, among others. However, aDNA sequencing data are still characterized by short reads and non-uniform coverage, so assembling ancient pathogen genomes remains challenging and often prevents a detailed study of genome rearrangements...
September 2017: Microbial Genomics
https://www.readbyqxmd.com/read/29114362/comparative-cytogenetics-of-some-marsupial-species-didelphimorphia-didelphidae-from-the-amazon-basin
#15
Carlos Eduardo Faresin E Silva, Rodrigo Amaral de Andrade, Érica Martinha Silva de Souza, Eduardo Schmidt Eler, Maria Nazareth Ferreira da Silva, Eliana Feldberg
We investigated the karyotype of 18 didelphid species captured at 13 localities in the Brazilian Amazon, after conventional staining, C-banding, Ag-NOR and fluorescent in situ hybridization (FISH) using the 18S rDNA probe. Variations were found in the X chromosome, heterochromatin distribution and the 18S rDNA sequence. The main variation observed was in the position of the centromere in the X chromosome of Caluromys philander Linnaeus, 1758 and Marmosa murina Linnaeus, 1758. For both species, the X chromosome showed a geographical segregation in the pattern of variation between eastern and western Brazil, with a possible contact area in the central Amazon...
2017: Comparative Cytogenetics
https://www.readbyqxmd.com/read/29114356/comparative-analysis-of-chromosomal-localization-of-ribosomal-and-telomeric-dna-markers-in-three-species-of-pyrgomorphidae-grasshoppers
#16
REVIEW
Olesya G Buleu, Ilyas Y Jetybayev, Alexander G Bugrov
The karyotypes of three species of Pyrgomorphidae grasshoppers were studied: Zonocerus elegans (Thunberg, 1815), Pyrgomorpha guentheri (Burr, 1899) and Atractomorpha lata (Mochulsky, 1866). Data on karyotypes of P. guentheri and Z. elegans are reported here for the first time. All species have karyotypes consisting of 19 acrocentric chromosomes in males and 20 acrocentric chromosomes in females (2n♂=19, NF=19; 2n♀=20, NF=20) and X0/XX sex determination system. A comparative analysis of the localization of C-heterochromatin, clusters of ribosomal DNA, and telomere repeats revealed inter-species diversity in these cytogenetic markers...
2017: Comparative Cytogenetics
https://www.readbyqxmd.com/read/29104214/impact-of-repetitive-elements-on-the-y-chromosome-formation-in-plants
#17
REVIEW
Roman Hobza, Radim Cegan, Wojciech Jesionek, Eduard Kejnovsky, Boris Vyskot, Zdenek Kubat
In contrast to animals, separate sexes and sex chromosomes in plants are very rare. Although the evolution of sex chromosomes has been the subject of numerous studies, the impact of repetitive sequences on sex chromosome architecture is not fully understood. New genomic approaches shed light on the role of satellites and transposable elements in the process of Y chromosome evolution. We discuss the impact of repetitive sequences on the structure and dynamics of sex chromosomes with specific focus on Rumex acetosa and Silene latifolia...
November 1, 2017: Genes
https://www.readbyqxmd.com/read/29099806/chromosomal-evolution-in-mole-voles-ellobius-cricetidae-rodentia-bizarre-sex-chromosomes-variable-autosomes-and-meiosis
#18
Sergey Matveevsky, Oxana Kolomiets, Alexey Bogdanov, Mikhayil Hakhverdyan, Irina Bakloushinskaya
This study reports on extensive experimental material covering more than 30 years of studying the genetics of mole voles. Sex chromosomes of Ellobius demonstrate an extraordinary case of mammalian sex chromosomes evolution. Five species of mole voles own three types of sex chromosomes; typical for placentals: XY♂/XX♀; and atypical X0♂/X0♀; or XX♂/XX♀. Mechanisms of sex determination in all Ellobius species remain enigmatic. It was supposed that the Y chromosome was lost twice and independently in subgenera Bramus and Ellobius...
November 3, 2017: Genes
https://www.readbyqxmd.com/read/29093472/the-asparagus-genome-sheds-light-on-the-origin-and-evolution-of-a-young-y-chromosome
#19
Alex Harkess, Jinsong Zhou, Chunyan Xu, John E Bowers, Ron Van der Hulst, Saravanaraj Ayyampalayam, Francesco Mercati, Paolo Riccardi, Michael R McKain, Atul Kakrana, Haibao Tang, Jeremy Ray, John Groenendijk, Siwaret Arikit, Sandra M Mathioni, Mayumi Nakano, Hongyan Shan, Alexa Telgmann-Rauber, Akira Kanno, Zhen Yue, Haixin Chen, Wenqi Li, Yanling Chen, Xiangyang Xu, Yueping Zhang, Shaochun Luo, Helong Chen, Jianming Gao, Zichao Mao, J Chris Pires, Meizhong Luo, Dave Kudrna, Rod A Wing, Blake C Meyers, Kexian Yi, Hongzhi Kong, Pierre Lavrijsen, Francesco Sunseri, Agostino Falavigna, Yin Ye, James H Leebens-Mack, Guangyu Chen
Sex chromosomes evolved from autosomes many times across the eukaryote phylogeny. Several models have been proposed to explain this transition, some involving male and female sterility mutations linked in a region of suppressed recombination between X and Y (or Z/W, U/V) chromosomes. Comparative and experimental analysis of a reference genome assembly for a double haploid YY male garden asparagus (Asparagus officinalis L.) individual implicates separate but linked genes as responsible for sex determination...
November 2, 2017: Nature Communications
https://www.readbyqxmd.com/read/29079134/impact-of-chromosome-alterations-genetic-mutations-and-clonal-hematopoiesis-of-indeterminate-potential-chip-on-the-classification-and-risk-stratification-of-mds
#20
REVIEW
Bani Bandana Ganguly, Debasis Banerjee, Mohan B Agarwal
The advent of technological development has undoubtedly advanced biological and molecular inputs for better understanding the heterogeneous hematopoietic pre-malignant disorder of the stem cells known as myelodysplastic syndromes (MDS). Chromosomal rearrangements, including del(3q/5q/7q/11q/12p/20q), loss of 5/7/Y, trisomy 8/19, i(17q), etc. frequently detected in MDS with variable frequencies and combinations, are the integral components of the 5-tier risk-stratification and WHO-2016 classification. Observations on mutations in genes involved in RNA-splicing, DNA methylation, chromatin modification, transcription factor, signal transduction/kinases, RAS pathway, cohesin complex, DNA repair and other pathways have given insights in independent effects and biological interaction of co-occurrence on disease-phenotype and treatment outcome...
October 16, 2017: Blood Cells, Molecules & Diseases
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