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y chromosome evolution

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https://www.readbyqxmd.com/read/28892047/a-system-for-detecting-high-impact-low-frequency-mutations-in-primary-tumors-and-metastases
#1
M Anjanappa, Y Hao, E R Simpson, P Bhat-Nakshatri, J B Nelson, S A Tersey, R G Mirmira, A A Cohen-Gadol, M R Saadatzadeh, L Li, F Fang, K P Nephew, K D Miller, Y Liu, H Nakshatri
Tumor complexity and intratumor heterogeneity contribute to subclonal diversity. Despite advances in next-generation sequencing (NGS) and bioinformatics, detecting rare mutations in primary tumors and metastases contributing to subclonal diversity is a challenge for precision genomics. Here, in order to identify rare mutations, we adapted a recently described epithelial reprograming assay for short-term propagation of epithelial cells from primary and metastatic tumors. Using this approach, we expanded minor clones and obtained epithelial cell-specific DNA/RNA for quantitative NGS analysis...
September 11, 2017: Oncogene
https://www.readbyqxmd.com/read/28874168/holocentric-chromosome-evolution-in-kissing-bugs-hemiptera-reduviidae-triatominae-diversification-of-repeated-sequences
#2
Sebastián Pita, Pedro Lorite, Jesús Vela, Pablo Mora, Teresa Palomeque, Khoa Pham Thi, Francisco Panzera
BACKGROUND: The analysis of the chromosomal and genome evolution in organisms with holocentric chromosomes is restricted by the lack of primary constriction or centromere. An interesting group is the hemipteran subfamily Triatominae, vectors of Chagas disease, which affects around 6 to 7 million people worldwide. This group exhibits extensive variability in the number and chromosomal location of repeated sequences such as heterochromatin and ribosomal genes. This paper tries to reveal the significant differences of the repeated sequences among Triatoma species through the use of genomic DNA probes...
September 6, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/28860320/cross-species-y-chromosome-function-between-malaria-vectors-of-the-anopheles-gambiae%C3%A2-species-complex
#3
Federica Bernardini, Roberto Galizi, Mariana Wunderlich, Chrysanthi Taxiarchi, Nace Kranjc, Kyros Kyrou, Andrew Hammond, Tony Nolan, Mara N K Lawniczak, Philippos Aris Papathanos, Andrea Crisanti, Nikolai Windbichler
Y chromosome function, structure and evolution is poorly understood in many species including the Anopheles genus of mosquitoes, an emerging model system for studying speciation that also represents the major vectors of malaria. While the Anopheline Y had previously been implicated in male mating behavior, recent data from the Anopheles gambiae complex suggests that, apart from the putative primary sex-determiner, no other genes are conserved on the Y. Studying the functional basis of the evolutionary divergence of the Y chromosome in the gambiae complex is complicated by complete F1 male hybrid sterility...
August 31, 2017: Genetics
https://www.readbyqxmd.com/read/28846694/analysis-of-62-hybrid-assembled-human-y-chromosomes-exposes-rapid-structural-changes-and-high-rates-of-gene-conversion
#4
Laurits Skov, Mikkel Heide Schierup
The human Y-chromosome does not recombine across its male-specific part and is therefore an excellent marker of human migrations. It also plays an important role in male fertility. However, its evolution is difficult to fully understand because of repetitive sequences, inverted repeats and the potentially large role of gene conversion. Here we perform an evolutionary analysis of 62 Y-chromosomes of Danish descent sequenced using a wide range of library insert sizes and high coverage, thus allowing large regions of these chromosomes to be well assembled...
August 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28811564/computational-identification-of-y-linked-markers-and-genes-in-the-grass-carp-genome-by-using-a-pool-and-sequence-method
#5
Aidi Zhang, Rong Huang, Liangming Chen, Lv Xiong, Libo He, Yongming Li, Lanjie Liao, Zuoyan Zhu, Yaping Wang
The molecular analysis of sex in vertebrates is important, as it has the potential to provide vital information for theoretical and applied research alike. Teleost fish are the ancient vertebrates that present a broad sex chromosome system but lack differentiated sex chromosomes in most species. Hence understanding the sex in fish would not only illuminate the sex determination evolution in vertebrates but also shed light on fish farming. In the present study, we used grass carp as a teleost fish model, studied the Y chromosome by using a pool-and-sequence strategy in combination with fragment-ratio method...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28811388/hill-robertson-interference-reduces-genetic-diversity-on-a-young-plant-y-chromosome
#6
Josh Hough, Wei Wang, Spencer C H Barrett, Stephen I Wright
X and Y chromosomes differ in effective population size (Ne ), rates of recombination, and exposure to natural selection, all of which can affect patterns of genetic diversity. On Y chromosomes with suppressed recombination, natural selection is expected to eliminate linked neutral variation and lower the Ne of Y compared to X chromosomes or autosomes. However, female-biased sex ratios and high variance in male reproductive success can also reduce Y-linked Ne , making it difficult to infer the causes of low Y-diversity...
August 15, 2017: Genetics
https://www.readbyqxmd.com/read/28782550/contribution-of-gene-flow-to-the-evolution-of-recombination-suppression-in-sex-chromosomes
#7
Tomotaka Matsumoto, Kohta Yoshida, Jun Kitano
Polymorphism of alleles that benefit one sex but harm the other (sexually antagonistic alleles) generates selective pressures for reduced recombination between themselves and sex-determination loci. Such polymorphism can be maintained within a population when selection coefficients are sufficiently balanced between males and females. However, if regulatory mutations restrict gene expression only to one sex, these alleles become neutral in the other sex and easily fixed within a population, removing the selective pressures for recombination suppression in sex chromosomes...
August 3, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28772266/evolution-of-the-sex-chromosomes-in-beetles-i-the-loss-of-the-y-chromosome
#8
Anne-Marie Dutrillaux, Bernard Dutrillaux
In the males of Coleoptera, the most frequent sex chromosome constitution is XY. At metaphase I of meiosis, the X and Y are linked by nucleolar proteins, forming the so-called parachute bivalent (Xyp), which is assumed to allow the non-synapsed X and Y to segregate correctly at anaphase I. However, X0 males are not exceptional, and we explored the relationships between the X and nucleolar proteins in the absence of the Y chromosome in 6 species belonging to different families/subfamilies. Using C-banding and silver staining, we show that nucleolar proteins always remain in contact with the X until anaphase I...
August 4, 2017: Cytogenetic and Genome Research
https://www.readbyqxmd.com/read/28743997/high-throughput-analysis-of-the-satellitome-revealed-enormous-diversity-of-satellite-dnas-in-the-neo-y-chromosome-of-the-cricket-eneoptera-surinamensis
#9
Octavio Manuel Palacios-Gimenez, Guilherme Borges Dias, Leonardo Gomes de Lima, Gustavo Campos E Silva Kuhn, Érica Ramos, Cesar Martins, Diogo Cavalcanti Cabral-de-Mello
Satellite DNAs (satDNAs) constitute large portion of eukaryote genomes, comprising non-protein-coding sequences tandemly repeated. They are mostly found in heterochromatic regions of chromosomes such as around centromere or near telomeres, in intercalary heterochromatin, and often in non-recombining segments of sex chromosomes. We examined the satellitome in the cricket Eneoptera surinamensis (2n = 9, neo-X1X2Y, males) to characterize the molecular evolution of its neo-sex chromosomes. To achieve this, we analyzed illumina reads using graph-based clustering and complementary analyses...
July 25, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28705249/vector-control-with-driving-y-chromosomes-modelling-the-evolution-of-resistance
#10
Andrea Beaghton, Pantelis John Beaghton, Austin Burt
BACKGROUND: The introduction of new malaria control interventions has often led to the evolution of resistance, both of the parasite to new drugs and of the mosquito vector to new insecticides, compromising the efficacy of the interventions. Recent progress in molecular and population biology raises the possibility of new genetic-based interventions, and the potential for resistance to evolve against these should be considered. Here, population modelling is used to determine the main factors affecting the likelihood that resistance will evolve against a synthetic, nuclease-based driving Y chromosome that produces a male-biased sex ratio...
July 14, 2017: Malaria Journal
https://www.readbyqxmd.com/read/28704543/the-transcriptional-regulator-ssrb-is-involved-in-a-molecular-switch-controlling-virulence-lifestyles-of-salmonella
#11
Deyanira Pérez-Morales, María M Banda, N Y Elizabeth Chau, Heladia Salgado, Irma Martínez-Flores, J Antonio Ibarra, Bushra Ilyas, Brian K Coombes, Víctor H Bustamante
The evolution of bacterial pathogenicity, heavily influenced by horizontal gene transfer, provides new virulence factors and regulatory connections that alter bacterial phenotypes. Salmonella pathogenicity islands 1 and 2 (SPI-1 and SPI-2) are chromosomal regions that were acquired at different evolutionary times and are essential for Salmonella virulence. In the intestine of mammalian hosts, Salmonella expresses the SPI-1 genes that mediate its invasion to the gut epithelium. Once inside the cells, Salmonella down-regulates the SPI-1 genes and induces the expression of the SPI-2 genes, which favor its intracellular replication...
July 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28675502/dmrt1-polymorphism-and-sex-chromosome-differentiation-in-rana-temporaria
#12
Nicolas Rodrigues, Tania Studer, Christophe Dufresnes, Wen-Juan Ma, Paris Veltsos, Nicolas Perrin
Sex-determination mechanisms vary both within and among populations of common frogs, opening opportunities to investigate the molecular pathways and ultimate causes shaping their evolution. We investigated the association between sex-chromosome differentiation (as assayed from microsatellites) and polymorphism at the candidate sex-determining gene Dmrt1 in two Alpine populations. Both populations harbored a diversity of X-linked and Y-linked Dmrt1 haplotypes. Some males had fixed male-specific alleles at all markers ('differentiated' Y chromosomes), others only at Dmrt1 ('proto-' Y chromosomes), while still others were genetically indistinguishable from females (undifferentiated X chromosomes)...
July 4, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28626004/sex-chromosome-evolution-heterochiasmy-and-physiological-qtl-in-the-salmonid-brook-charr-salvelinus-fontinalis
#13
Ben J G Sutherland, Ciro Rico, Céline Audet, Louis Bernatchez
Whole-genome duplication (WGD) can have large impacts on genome evolution, and much remains unknown about these impacts. This includes the mechanisms of coping with a duplicated sex determination system and whether this has an impact on increasing the diversity of sex determination mechanisms. Other impacts include sexual conflict, where alleles having different optimums in each sex can result in sequestration of genes into nonrecombining sex chromosomes. Sex chromosome development itself may involve sex-specific recombination rate (i...
August 7, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28619849/the-house-fly-y-chromosome-is-young-and-minimally-differentiated-from-its-ancient-x-chromosome-partner
#14
Richard P Meisel, Christopher A Gonzales, Hoang Luu
Canonical ancient sex chromosome pairs consist of a gene rich X (or Z) Chromosome and a male-limited (or female-limited) Y (or W) Chromosome that is gene poor. In contrast to highly differentiated sex chromosomes, nascent sex chromosome pairs are homomorphic or very similar in sequence content. Nascent sex chromosomes can arise if an existing sex chromosome fuses to an autosome or an autosome acquires a new sex-determining locus/allele. Sex chromosomes often differ between closely related species and can even be polymorphic within species, suggesting that nascent sex chromosomes arise frequently over the course of evolution...
August 2017: Genome Research
https://www.readbyqxmd.com/read/28611256/a-duplicated-truncated-amh-gene-is-involved-in-male-sex-determination-in-an-old-world-silverside
#15
Dilip Kumar Bej, Kaho Miyoshi, Ricardo S Hattori, Carlos A Strüssmann, Yoji Yamamoto
A master sex-determining gene, the Y chromosome-linked anti-Müllerian hormone (amhy) gene, has been described in two New World atheriniform species but little is known on the distribution, evolution, and function(s) of this gene in other Atheriniformes. Interestingly, amhy has been found to coexist with temperature-dependent sex determination (TSD), providing a unique opportunity to explore the interplay between genotypic and environmental sex determination. In this study, the search for an amhy homolog was extended to an Old World atheriniform, the cobaltcap silverside Hypoatherina tsurugae (Atherinidae)...
August 7, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28595587/multiple-gene-movements-into-and-out-of-haploid-sex-chromosomes
#16
Agnieszka P Lipinska, Nicholas R T Toda, Svenja Heesch, Akira F Peters, J Mark Cock, Susana M Coelho
BACKGROUND: Long-term evolution of sex chromosomes is a dynamic process shaped by gene gain and gene loss. Sex chromosome gene traffic has been studied in XY and ZW systems but no detailed analyses have been carried out for haploid phase UV sex chromosomes. Here, we explore sex-specific sequences of seven brown algal species to understand the dynamics of the sex-determining region (SDR) gene content across 100 million years of evolution. RESULTS: A core set of sex-linked genes is conserved across all the species investigated, but we also identify modifications of both the U and the V SDRs that occurred in a lineage-specific fashion...
June 8, 2017: Genome Biology
https://www.readbyqxmd.com/read/28571006/extensive-sex-chromosome-polymorphism-of-microtus-thomasi-microtus-atticus-species-complex-associated-with-cryptic-chromosomal-rearrangements-and-independent-accumulation-of-heterochromatin
#17
Michail T Rovatsos, Juan A Marchal, Ismael Romero-Fernández, Maria Arroyo, Eva B Athanasopoulou, Antonio Sánchez
The sibling species Microtus thomasi and M. atticus represent probably the highest karyotypic diversity within the genus Microtus and are an interesting model for chromosomal evolution studies. In addition to variation in autosomes, they show a high intraspecific variation in the size and morphology of both sex chromosomes. We analyzed individuals with different sex chromosome constitutions using 3 painting probes, 2 from Y chromosome variants and 1 from the small arm of the submetacentric X chromosome. Our comparative painting approach uncovered 12 variants of Y and 14 variants of X chromosomes, which demonstrates that the polymorphism of sex chromosomes is substantially larger than previously reported...
2017: Cytogenetic and Genome Research
https://www.readbyqxmd.com/read/28555659/human-y-chromosome-variation-in-the-genome-sequencing-era
#18
REVIEW
Mark A Jobling, Chris Tyler-Smith
The properties of the human Y chromosome - namely, male specificity, haploidy and escape from crossing over - make it an unusual component of the genome, and have led to its genetic variation becoming a key part of studies of human evolution, population history, genealogy, forensics and male medical genetics. Next-generation sequencing (NGS) technologies have driven recent progress in these areas. In particular, NGS has yielded direct estimates of mutation rates, and an unbiased and calibrated molecular phylogeny that has unprecedented detail...
August 2017: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/28536279/the-damaging-effect-of-passenger-mutations-on-cancer-progression
#19
Christopher D McFarland, Julia A Yaglom, Jonathan W Wojtkowiak, Jacob G Scott, David L Morse, Michael Y Sherman, Leonid A Mirny
Genomic instability and high mutation rates cause cancer to acquire numerous mutations and chromosomal alterations during its somatic evolution; most are termed passengers because they do not confer cancer phenotypes. Evolutionary simulations and cancer genomic studies suggest that mildly deleterious passengers accumulate and can collectively slow cancer progression. Clinical data also suggest an association between passenger load and response to therapeutics, yet no causal link between the effects of passengers and cancer progression has been established...
May 23, 2017: Cancer Research
https://www.readbyqxmd.com/read/28515739/patterns-of-inter-chromosomal-gene-conversion-on-the-male-specific-region-of-the-human-y-chromosome
#20
REVIEW
Beniamino Trombetta, Eugenia D'Atanasio, Fulvio Cruciani
The male-specific region of the human Y chromosome (MSY) is characterized by the lack of meiotic recombination and it has long been considered an evolutionary independent region of the human genome. In recent years, however, the idea that human MSY did not have an independent evolutionary history begun to emerge with the discovery that inter-chromosomal gene conversion (ICGC) can modulate the genetic diversity of some portions of this genomic region. Despite the study of the dynamics of this molecular mechanism in humans is still in its infancy, some peculiar features and consequences of it can be summarized...
2017: Frontiers in Genetics
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