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y chromosome evolution

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https://www.readbyqxmd.com/read/29783761/the-guppy-sex-chromosome-system-and-the-sexually-antagonistic-polymorphism-hypothesis-for-y-chromosome-recombination-suppression
#1
REVIEW
Deborah Charlesworth
Sex chromosomes regularly evolve suppressed recombination, distinguishing them from other chromosomes, and the reason for this has been debated for many years. It is now clear that non-recombining sex-linked regions have arisen in different ways in different organisms. A major hypothesis is that a sex-determining gene arises on a chromosome and that sexually antagonistic (SA) selection (sometimes called intra-locus sexual conflict) acting at a linked gene has led to the evolution of recombination suppression in the region, to reduce the frequency of low fitness recombinant genotypes produced...
May 19, 2018: Genes
https://www.readbyqxmd.com/read/29781541/the-two-rules-of-speciation-in-species-with-young-sex-chromosomes
#2
Dmitry A Filatov
The two "rules of speciation", Haldane's rule (HR) and the large-X effect (LXE), are thought to be caused by recessive species incompatibilities exposed in the phenotype due to the hemizygosity of X-linked genes in the heterogametic sex. Thus, the reports of HR and the LXE in species with recently evolved non- or partially-degenerate Y-chromosomes, such as Silene latifolia and its relatives, were surprising. Here I argue that rapid species-specific degeneration of Y-linked genes and associated adjustment of expression of X-linked gametologs (dosage compensation) may lead to rapid evolution of sex-linked species incompatibilities...
May 21, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29769284/dynamic-copy-number-evolution-of-x-and-y-linked-ampliconic-genes-in-human-populations
#3
Elise A Lucotte, Laurits Skov, Jacob Malte Jensen, Moisès Coll Macià, Kasper Munch, Mikkel H Schierup
Ampliconic genes are multicopy, in majority found on sex-chromosomes and enriched for testis-expressed genes. While ampliconic genes have been associated with the emergence of hybrid incompatibilities, we know little about their copy number distribution and their turnover in human populations. Here we explore the evolution of human X- and Y-linked ampliconic genes by investigating copy number variation (CNV) and coding variation between populations using the Simons Genome Diversity Project. We develop a method to assess CNVs using the read-depth on modified X and Y chromosome targets containing only one repetition of each ampliconic gene...
May 16, 2018: Genetics
https://www.readbyqxmd.com/read/29751570/shared-and-species-specific-patterns-of-nascent-y-chromosome-evolution-in-two-guppy-species
#4
Jake Morris, Iulia Darolti, Natasha I Bloch, Alison E Wright, Judith E Mank
Sex chromosomes form once recombination is halted around the sex-determining locus between a homologous pair of chromosomes, resulting in a male-limited Y chromosome. We recently characterized the nascent sex chromosome system in the Trinidadian guppy ( Poecilia reticulata ). The guppy Y is one of the youngest animal sex chromosomes yet identified, and therefore offers a unique window into the early evolutionary forces shaping sex chromosome formation, particularly the rate of accumulation of repetitive elements and Y-specific sequence...
May 3, 2018: Genes
https://www.readbyqxmd.com/read/29751495/a-comparison-of-selective-pressures-in-plant-x-linked-and-autosomal-genes
#5
Marc Krasovec, Bruno Nevado, Dmitry A Filatov
Selection is expected to work differently in autosomal and X-linked genes because of their ploidy difference and the exposure of recessive X-linked mutations to haploid selection in males. However, it is not clear whether these expectations apply to recently evolved sex chromosomes, where many genes retain functional X- and Y-linked gametologs. We took advantage of the recently evolved sex chromosomes in the plant Silene latifolia and its closely related species to compare the selective pressures between hemizygous and non-hemizygous X-linked genes as well as between X-linked genes and autosomal genes...
May 3, 2018: Genes
https://www.readbyqxmd.com/read/29743013/genome-wide-analysis-of-gras-transcription-factor-gene-family-in-gossypium-hirsutum-l
#6
Bin Zhang, J Liu, Zhao E Yang, Er Y Chen, Chao J Zhang, Xue Y Zhang, Fu G Li
BACKGROUND: Cotton is a major fiber and oil crop worldwide. Cotton production, however, is often threatened by abiotic environmental stresses. GRAS family proteins are among the most abundant transcription factors in plants and play important roles in regulating root and shoot development, which can improve plant resistance to abiotic stresses. However, few studies on the GRAS family have been conducted in cotton. Recently, the G. hirsutum genome sequences have been released, which provide us an opportunity to analyze the GRAS family in G...
May 9, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29739989/haplotypic-polymorphisms-and-mutation-rate-estimates-of-22-y-chromosome-strs-in-the-northern-chinese-han-father-son-pairs
#7
Yaran Yang, Weini Wang, Feng Cheng, Man Chen, Tong Chen, Jing Zhao, Chong Chen, Yan Shi, Chen Li, Chuguang Chen, Yacheng Liu, Jiangwei Yan
Y chromosome Short tandem repeats (Y-STRs) analysis has been widely used in forensic identification, kinship testing, and population evolution. An accurate understanding of haplotype and mutation rate will benefit these applications. In this work, we analyzed 1123 male samples from Northern Chinese Han population which including 578 DNA-confirmed father-son pairs at 22 Y-STRs loci. A total of 537 haplotypes were observed and the overall haplotype diversity was calculated as 1.0000 ± 0.0001. Except that only two haplotypes were observed twice, all the rest of the 535 were unique...
May 8, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29736013/utx-mediated-enhancer-and-chromatin-remodeling-suppresses-myeloid-leukemogenesis-through-noncatalytic-inverse-regulation-of-ets-and-gata-programs
#8
Malgorzata Gozdecka, Eshwar Meduri, Milena Mazan, Konstantinos Tzelepis, Monika Dudek, Andrew J Knights, Mercedes Pardo, Lu Yu, Jyoti S Choudhary, Emmanouil Metzakopian, Vivek Iyer, Haiyang Yun, Naomi Park, Ignacio Varela, Ruben Bautista, Grace Collord, Oliver Dovey, Dimitrios A Garyfallos, Etienne De Braekeleer, Saki Kondo, Jonathan Cooper, Berthold Göttgens, Lars Bullinger, Paul A Northcott, David Adams, George S Vassiliou, Brian J P Huntly
The histone H3 Lys27-specific demethylase UTX (or KDM6A) is targeted by loss-of-function mutations in multiple cancers. Here, we demonstrate that UTX suppresses myeloid leukemogenesis through noncatalytic functions, a property shared with its catalytically inactive Y-chromosome paralog, UTY (or KDM6C). In keeping with this, we demonstrate concomitant loss/mutation of KDM6A (UTX) and UTY in multiple human cancers. Mechanistically, global genomic profiling showed only minor changes in H3K27me3 but significant and bidirectional alterations in H3K27ac and chromatin accessibility; a predominant loss of H3K4me1 modifications; alterations in ETS and GATA-factor binding; and altered gene expression after Utx loss...
May 7, 2018: Nature Genetics
https://www.readbyqxmd.com/read/29734690/regulation-of-the-x-chromosome-in-the-germline-and-soma-of-drosophila-melanogaster-males
#9
Eliza Argyridou, John Parsch
During the evolution of heteromorphic sex chromosomes, the sex-specific Y chromosome degenerates, while the X chromosome evolves new mechanisms of regulation. Using bioinformatic and experimental approaches, we investigate the expression of the X chromosome in Drosophila melanogaster . We observe nearly complete X chromosome dosage compensation in male somatic tissues, but not in testis. The X chromosome contains disproportionately fewer genes with high expression in testis than the autosomes, even after accounting for the lack of dosage compensation, which suggests that another mechanism suppresses their expression in the male germline...
May 4, 2018: Genes
https://www.readbyqxmd.com/read/29718380/high-levels-of-copy-number-variation-of-ampliconic-genes-across-major-human-y-haplogroups
#10
Danling Ye, Arslan Zaidi, Marta Tomaszkiewicz, Kate Anthony, Corey Liebowitz, Michael DeGiorgio, Mark D Shriver, Kateryna D Makova
Due to its highly repetitive nature, the human male-specific Y chromosome remains understudied. It is important to investigate variation on the Y chromosome to understand its evolution and contribution to phenotypic variation, including infertility. Approximately 20% of the human Y chromosome consists of ampliconic regions which include nine multi-copy gene families. These gene families are expressed exclusively in testes and usually implicated in spermatogenesis. Here, to gain a better understanding of the role of the Y chromosome in human evolution and in determining sexually dimorphic traits, we studied ampliconic gene copy number variation in 100 males representing ten major Y haplogroups world-wide...
April 28, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29695139/comparative-analysis-of-repetitive-dna-between-the-main-vectors-of-chagas-disease-triatoma-infestans-and-rhodnius-prolixus
#11
Sebastián Pita, Pablo Mora, Jesús Vela, Teresa Palomeque, Antonio Sánchez, Francisco Panzera, Pedro Lorite
Chagas disease or American trypanosomiasis affects six to seven million people worldwide, mostly in Latin America. This disease is transmitted by hematophagous insects known as "kissing bugs" (Hemiptera, Triatominae), with Triatoma infestans and Rhodnius prolixus being the two most important vector species. Despite the fact that both species present the same diploid chromosome number (2 n = 22), they have remarkable differences in their total DNA content, chromosome structure and genome organization...
April 24, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29669830/evolution-guided-structural-and-functional-analyses-of-the-herc-family-reveals-an-ancient-marine-origin-and-determinants-of-antiviral-activity
#12
Ermela Paparisto, Matthew W Woods, Macon D Coleman, Seyed A Moghadasi, Divjyot S Kochar, Sean K Tom, Hinissan P Kohio, Richard M Gibson, Taryn J Rohringer, Nina R Hunt, Eric J Di Gravio, Jonathan Y Zhang, Meijuan Tian, Yong Gao, Eric J Arts, Stephen D Barr
In humans, 'homologous to the E6-AP carboxyl terminus (HECT) and regulator of chromosome condensation 1 (RCC1)-like domain-containing protein 5' (HERC5) is an interferon-induced protein that inhibits replication of evolutionarily diverse viruses including human immunodeficiency virus type 1 (HIV-1). To better understand the origin, evolution and function of HERC5, we performed phylogenetic, structural and functional analyses of the entire human small HERC family, which includes HERC3, HERC4, HERC5 and HERC6...
April 18, 2018: Journal of Virology
https://www.readbyqxmd.com/read/29617732/a-new-approach-for-comprehensively-describing-heterogametic-sex-chromosomes
#13
Shenglong Li, Masahiro Ajimura, Zhiwei Chen, Jianqiu Liu, Enxiang Chen, Huizhen Guo, Vidya Tadapatri, Chilakala Gangi Reddy, Jiwei Zhang, Hirohisa Kishino, Hiroaki Abe, Qingyou Xia, Kallare P Arunkumar, Kazuei Mita
Notwithstanding the rapid developments in sequencing techniques, Y and W sex chromosomes have still been mostly excluded from whole genome sequencing projects due to their high repetitive DNA content. Therefore, Y and W chromosomes are poorly described in most species despite their biological importance. Several methods were developed for identifying Y or W-linked sequences among unmapped scaffolds. However, it is not enough to discover functional regions from short unmapped scaffolds. Here, we provide a new and simple strategy based on k-mer comparison for comprehensive analysis of the W chromosome in Bombyx mori...
April 2, 2018: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29616077/karyotypic-diversity-and-evolution-in-a-sympatric-assemblage-of-neotropical-electric-knifefish
#14
Adauto L Cardoso, Julio C Pieczarka, William G R Crampton, Jonathan S Ready, Wilsea M B de Figueiredo Ready, Joseph C Waddell, Jonas A de Oliveira, Cleusa Y Nagamachi
Chromosome changes can perform an important role in speciation by acting as post-zygotic reproductive barriers. The Neotropical electric fish genus Brachyhypopomus (Gymnotiformes, Hypopomidae) has 28 described species, but cytogenetic data are hitherto available only for four of them. To understand karyotype evolution and investigate the possible role of chromosome changes in the diversification of this genus, we describe here the karyotype of eight species of Brachyhypopomus from a sympatric assemblage in the central Amazon basin...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29606909/early-stages-of-xy-sex-chromosomes-differentiation-in-the-fish-hoplias-malabaricus-characiformes-erythrinidae-revealed-by-dna-repeats-accumulation
#15
Natália Lourenço de Freitas, Ahmed Basheer Hamid Al-Rikabi, Luiz Antonio Carlos Bertollo, Tariq Ezaz, Cassia Fernanda Yano, Ezequiel Aguiar de Oliveira, Terumi Hatanaka, Marcelo de Bello Cioffi
Background: Species with 'young' or nascent sex chromosomes provide unique opportunities to understand early evolutionary mechanisms (e.g. accumulation of repetitive sequences, cessation of recombination and gene loss) that drive the evolution of sex chromosomes. Among vertebrates, fishes exhibit highly diverse and a wide spectrum of sex-determining mechanisms and sex chromosomes, ranging from cryptic to highly differentiated ones, as well as, from simple to multiple sex chromosome systems...
April 2018: Current Genomics
https://www.readbyqxmd.com/read/29518227/yleaf-software-for-human-y-chromosomal-haplogroup-inference-from-next-generation-sequencing-data
#16
Arwin Ralf, Diego Montiel González, Kaiyin Zhong, Manfred Kayser
Next-generation sequencing (NGS) technologies offer immense possibilities given the large genomic data they simultaneously deliver. The human Y-chromosome serves as good example how NGS benefits various applications in evolution, anthropology, genealogy, and forensics. Prior to NGS, the Y-chromosome phylogenetic tree consisted of a few hundred branches, based on NGS data, it now contains many thousands. The complexity of both, Y tree and NGS data provide challenges for haplogroup assignment. For effective analysis and interpretation of Y-chromosome NGS data, we present Yleaf, a publically available, automated, user-friendly software for high-resolution Y-chromosome haplogroup inference independently of library and sequencing methods...
May 1, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29471785/phylogeny-with-introgression-in-habronattus-jumping-spiders-araneae-salticidae
#17
Geneviève Leduc-Robert, Wayne P Maddison
BACKGROUND: Habronattus is a diverse clade of jumping spiders with complex courtship displays and repeated evolution of Y chromosomes. A well-resolved species phylogeny would provide an important framework to study these traits, but has not yet been achieved, in part because the few genes available in past studies gave conflicting signals. Such discordant gene trees could be the result of incomplete lineage sorting (ILS) in recently diverged parts of the phylogeny, but there are indications that introgression could be a source of conflict...
February 22, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29459623/rapid-emergence-of-independent-chromosomal-lineages-in-silvered-leaf-monkey-triggered-by-y-autosome-translocation
#18
Oronzo Capozzi, Roscoe Stanyon, Nicoletta Archidiacono, Takafumi Ishida, Svetlana A Romanenko, Mariano Rocchi
Sex/autosome translocations are rare events. The only known example in catarrhines is in the silvered-leaf monkey. Here the Y chromosome was reciprocally translocated with chromosome 1. The rearrangement produced an X1 X2 Y1 Y2 sex chromosome system. At least three chromosomal variants of the intact chromosome 1 are known to exist. We characterized in high resolution the translocation products (Y1 and Y2 ) and the polymorphic forms of the intact chromosome 1 with a panel of more than 150 human BAC clones. We showed that the translocation products were extremely rearranged, in contrast to the high level of marker order conservation of the other silvered-leaf monkey chromosomes...
February 19, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29458354/the-slowdown-of-y-chromosome-expansion-in-dioecious-silene-latifolia-due-to-dna-loss-and-male-specific-silencing-of-retrotransposons
#19
Janka Puterova, Zdenek Kubat, Eduard Kejnovsky, Wojciech Jesionek, Jana Cizkova, Boris Vyskot, Roman Hobza
BACKGROUND: The rise and fall of the Y chromosome was demonstrated in animals but plants often possess the large evolutionarily young Y chromosome that is thought has expanded recently. Break-even points dividing expansion and shrinkage phase of plant Y chromosome evolution are still to be determined. To assess the size dynamics of the Y chromosome, we studied intraspecific genome size variation and genome composition of male and female individuals in a dioecious plant Silene latifolia, a well-established model for sex-chromosomes evolution...
February 20, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29449410/conserved-microrna-targeting-reveals-preexisting-gene-dosage-sensitivities-that-shaped-amniote-sex-chromosome-evolution
#20
Sahin Naqvi, Daniel W Bellott, Kathy S Lin, David C Page
Mammalian X and Y Chromosomes evolved from an ordinary autosomal pair. Genetic decay of the Y led to X Chromosome inactivation (XCI) in females, but some Y-linked genes were retained during the course of sex chromosome evolution, and many X-linked genes did not become subject to XCI. We reconstructed gene-by-gene dosage sensitivities on the ancestral autosomes through phylogenetic analysis of microRNA (miRNA) target sites and compared these preexisting characteristics to the current status of Y-linked and X-linked genes in mammals...
April 2018: Genome Research
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