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y chromosome evolution

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https://www.readbyqxmd.com/read/28220980/the-fire-ant-social-chromosome-supergene-variant-sb-shows-low-diversity-but-high-divergence-from-sb
#1
Rodrigo Pracana, Anurag Priyam, Ilya Levantis, Richard A Nichols, Yannick Wurm
Variation in social behavior is common yet little is known about the genetic architectures underpinning its evolution. A rare exception is in the fire ant Solenopsis invicta: Alternative variants of a supergene region determine whether a colony will have exactly one or up to dozens of queens. The two variants of this region are carried by a pair of "social chromosomes", SB and Sb, which resemble a pair of sex chromosomes. Recombination is suppressed between the two chromosomes in the supergene region. While the X-like SB can recombine with itself in SB/SB queens, recombination is effectively absent in the Y-like Sb because Sb/Sb queens die before reproducing...
February 21, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28193284/selective-intra-dinucleotide-interactions-and-periodicities-of-bases-separated-by-k-sites-a-new-vision-and-tool-for-phylogeny-analyses
#2
REVIEW
Carlos Y Valenzuela
Direct tests of the random or non-random distribution of nucleotides on genomes have been devised to test the hypothesis of neutral, nearly-neutral or selective evolution. These tests are based on the direct base distribution and are independent of the functional (coding or non-coding) or structural (repeated or unique sequences) properties of the DNA. The first approach described the longitudinal distribution of bases in tandem repeats under the Bose-Einstein statistics. A huge deviation from randomness was found...
February 13, 2017: Biological Research
https://www.readbyqxmd.com/read/28179393/triploid-production-from-interspecific-crosses-of-two-diploid-perennial-helianthus-with-diploid-cultivated-sunflower-helianthus-annuus-l
#3
Zhao Liu, Gerald J Seiler, Thomas J Gulya, Jiuhuan Feng, Khalid Y Rashid, Xiwen Cai, Chao-Chien Jan
Wild Helianthus species are a valuable genetic resource for the improvement of cultivated sunflower. We report the discovery and characterization of a unique high frequency production of triploids when cultivated sunflower was pollinated by specific accessions of diploid Helianthus nuttallii T. &. G. and H. maximiliani Schr. Genomic in situ hybridization (GISH) analyses indicated that the triploid F1s had two genomes from the wild pollen sources and one from the cultivated line. Mitotic chromosome analyses indicated that the frequency of triploid progenies from the crosses of cultivated lines × H...
February 7, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28177827/genomic-constitution-and-intergenomic-translocations-in-elymus-dahuricus-complex-revealed-by-multicolor-gish
#4
Cairong Yang, Zhang Haiqin, Weihuan Chen, Houyang Kang, Yi Wang, Sha Lina, Xing Fan, Jian Zeng, Yong-Hong Zhou
Multicolor genomic in situ hybridization was used to investigate genomic constitution and intergenomic translocations in Elymus dahuricus complex. The genomic constitution of species in E. dahuricus complex was confirmed as StYH. H/Y and H/St intergenomic translocations were identified in the present study with 7H and 1Y chromosomes involved in reciprocal translocations for all the accessions investigated in the complex. We propose that the translocations are species-specific in the E. dahuricus complex, are associated with allopolyploidy and may serve as important structural alterations for allopolyploid stability...
January 11, 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28139647/convergent-recombination-suppression-suggests-role-of-sexual-selection-in-guppy-sex-chromosome-formation
#5
Alison E Wright, Iulia Darolti, Natasha I Bloch, Vicencio Oostra, Ben Sandkam, Severine D Buechel, Niclas Kolm, Felix Breden, Beatriz Vicoso, Judith E Mank
Sex chromosomes evolve once recombination is halted between a homologous pair of chromosomes. The dominant model of sex chromosome evolution posits that recombination is suppressed between emerging X and Y chromosomes in order to resolve sexual conflict. Here we test this model using whole genome and transcriptome resequencing data in the guppy, a model for sexual selection with many Y-linked colour traits. We show that although the nascent Y chromosome encompasses nearly half of the linkage group, there has been no perceptible degradation of Y chromosome gene content or activity...
January 31, 2017: Nature Communications
https://www.readbyqxmd.com/read/28128398/mitochondrial-dna-insertions-in-the-nuclear-capra-hircus-genome
#6
F Y Ning, J Fu, Z H Du
Nuclear mitochondrial pseudogenes (numts), originating from mtDNA insertions into the nuclear genome, have been detected in many species. However, the distribution of numts in the newly published nuclear genome of domestic goat (Capra hircus) has not yet been explored. We used the entire goat mtDNA sequence and nuclear genome, to identify 118 numts using BLAST. Of these, 79 were able to map sequences to the genome. Further analysis showed that the size of the numts ranged from 318 to 9608 bp, and the homologous identity between numts and their respective corresponding mtDNA fragments varied between 65 and 99%...
January 23, 2017: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28115992/sex-specific-chromatin-landscapes-in-an-ultra-compact-chordate-genome
#7
Pavla Navratilova, Gemma Barbara Danks, Abby Long, Stephen Butcher, John Robert Manak, Eric M Thompson
BACKGROUND: In multicellular organisms, epigenome dynamics are associated with transitions in the cell cycle, development, germline specification, gametogenesis and inheritance. Evolutionarily, regulatory space has increased in complex metazoans to accommodate these functions. In tunicates, the sister lineage to vertebrates, we examine epigenome adaptations to strong secondary genome compaction, sex chromosome evolution and cell cycle modes. RESULTS: Across the 70 MB Oikopleura dioica genome, we profiled 19 histone modifications, and RNA polymerase II, CTCF and p300 occupancies, to define chromatin states within two homogeneous tissues with distinct cell cycle modes: ovarian endocycling nurse nuclei and mitotically proliferating germ nuclei in testes...
2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28100589/meiotic-consequences-of-genetic-divergence-across-the-murine-pseudoautosomal-region
#8
Beth L Dumont
The production of haploid gametes during meiosis is dependent on the homology-driven processes of pairing, synapsis, and recombination. On the mammalian heterogametic sex chromosomes, these key meiotic activities are confined to the pseudoautosomal region (PAR), a short region of near-perfect sequence homology between the X and Y chromosomes. Despite its established importance for meiosis, the PAR is rapidly evolving, raising the question of how proper X/Y segregation is buffered against the accumulation of homology-disrupting mutations...
January 18, 2017: Genetics
https://www.readbyqxmd.com/read/28081279/karyotype-analysis-and-ribosomal-gene-localization-of-spotted-knifejaw-oplegnathus-punctatus
#9
P Z Li, D D Cao, X B Liu, Y J Wang, H Y Yu, X J Li, Q Q Zhang, X B Wang
The spotted knifejaw, Oplegnathus punctatus, is an important aquaculture fish species in China. To better understand the chromosomal microstructure and the karyotypic origin of this species, cytogenetic analysis was performed using Giemsa staining to identify metaphase chromosomes, C-banding to detect C-positive heterochromatin, silver staining to identify the nucleolus organizer regions (Ag-NORs), and fluorescence in situ hybridization (FISH) for physical mapping of the major (18S rDNA) and minor (5S rDNA) ribosomal genes...
December 23, 2016: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28057732/satellite-dna-and-transposable-elements-in-seabuckthorn-hippophae-rhamnoides-a-dioecious-plant-with-small-y-and-large-x-chromosomes
#10
Janka Puterova, Olga Razumova, Tomas Martinek, Oleg Alexandrov, Mikhail Divashuk, Zdenek Kubat, Roman Hobza, Gennady Karlov, Eduard Kejnovsky
Seabuckthorn (Hippophae rhamnoides) is a dioecious shrub commonly used in the pharmaceutical, cosmetic and environmental industry as a source of oil, minerals and vitamins. In this study, we analyzed the transposable elements and satellites in its genome. We carried out Illumina DNA sequencing and reconstructed the main repetitive DNA sequences. For data analysis, we developed a new bioinformatics approach for advanced satellite DNA analysis and showed that about 25% of the genome consists of satellite DNA and about 24% is formed of transposable elements, dominated by Ty3/Gypsy and Ty1/Copia LTR retrotransposons...
January 4, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/27999113/the-composite-regulatory-basis-of-the-large-x-effect-in-mouse-speciation
#11
Erica L Larson, Sara Keeble, Dan Vanderpool, Matthew D Dean, Jeffrey M Good
The disruption of meiotic sex chromosome inactivation (MSCI) has been proposed to be a major developmental mechanism underlying the rapid evolution of hybrid male sterility. We tested this idea by analyzing cell-specific gene expression across spermatogenesis in two lineages of house mice and their sterile and fertile reciprocal hybrids. We found pervasive disruption of sex chromosome gene expression in sterile hybrids at every stage of spermatogenesis. Failure of MSCI was developmentally preceded by increased silencing of autosomal genes, supporting the hypothesis that divergence at the hybrid incompatibility gene, Prdm9, results in increased rates of autosomal asynapsis which in turn triggers widespread silencing of unsynapsed chromatin...
December 20, 2016: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/27923910/a-new-approach-to-chromosomal-evolution-in-the-giant-water-bug-heteroptera-belostomatidae
#12
Raquel Bozini Gallo, Rachel Colauto Milanezi Aguiar, Ana Paula Scaramal Ricietto, Laurival Vilas-Boas, Carlos Roberto Maximiano da Silva, José Ricardo Inacio Ribeiro, Renata Da Rosa
The genus Belostoma, known colloquially as 'giant water bugs', presents striking cytogenetic diversity and extensive chromosome variability. Notwithstanding, its karyotype evolution is not well understood. We analyzed eight species of Belostoma (77 samples). The meiotic analysis revealed 2n=14+XY for B. horvathi and B. candidulum; 2n=22+XY for B. cummings; 2n=26+X1X2Y for B. dentatum, B. elongatum, and B. discretum; and 2n=26+X1X2X3Y for B. testacopallidum and B. dilatatum. All species showed holokinetic chromosomes...
December 6, 2016: Journal of Heredity
https://www.readbyqxmd.com/read/27889059/chad-genetic-diversity-reveals-an-african-history-marked-by-multiple-holocene-eurasian-migrations
#13
Marc Haber, Massimo Mezzavilla, Anders Bergström, Javier Prado-Martinez, Pille Hallast, Riyadh Saif-Ali, Molham Al-Habori, George Dedoussis, Eleftheria Zeggini, Jason Blue-Smith, R Spencer Wells, Yali Xue, Pierre A Zalloua, Chris Tyler-Smith
Understanding human genetic diversity in Africa is important for interpreting the evolution of all humans, yet vast regions in Africa, such as Chad, remain genetically poorly investigated. Here, we use genotype data from 480 samples from Chad, the Near East, and southern Europe, as well as whole-genome sequencing from 19 of them, to show that many populations today derive their genomes from ancient African-Eurasian admixtures. We found evidence of early Eurasian backflow to Africa in people speaking the unclassified isolate Laal language in southern Chad and estimate from linkage-disequilibrium decay that this occurred 4,750-7,200 years ago...
December 1, 2016: American Journal of Human Genetics
https://www.readbyqxmd.com/read/27879256/determination-and-regulation-of-body-composition-in-elite-athletes
#14
Peter Sonksen
In 2011, the International Association of Athletics Federations (IAAF) and IOC introduced a 'hyperandrogenism' rule that excluded women with a serum testosterone >10 nmol/L from participating in elite sport. This rule was based on the false premise that the greater lean body mass in men was a consequence of their higher serum testosterone. This rule did not have scientific backing and the Court of Arbitration for Sport subsequently rescinded the rule following an appeal from an Indian athlete barred from the Commonwealth Games...
November 22, 2016: British Journal of Sports Medicine
https://www.readbyqxmd.com/read/27827389/recombination-changes-at-the-boundaries-of-fully-and-partially-sex-linked-regions-between-closely-related-silene-species-pairs
#15
J L Campos, S Qiu, S Guirao-Rico, R Bergero, D Charlesworth
The establishment of a region of suppressed recombination is a critical change during sex chromosome evolution, leading to such properties as Y (and W) chromosome genetic degeneration, accumulation of repetitive sequences and heteromorphism. Although chromosome inversions can cause large regions to have suppressed recombination, and inversions are sometimes involved in sex chromosome evolution, gradual expansion of the non-recombining region could potentially sometimes occur. We here test whether closer linkage has recently evolved between the sex-determining region and several genes that are partially sex-linked in Silene latifolia, using Silene dioica, a closely related dioecious plants whose XY sex chromosome system is inherited from a common ancestor...
November 9, 2016: Heredity
https://www.readbyqxmd.com/read/27817057/the-y-chromosome-as-the-most-popular-marker-in-genetic-genealogy-benefits-interdisciplinary-research
#16
REVIEW
Francesc Calafell, Maarten H D Larmuseau
The Y chromosome is currently by far the most popular marker in genetic genealogy that combines genetic data and family history. This popularity is based on its haploid character and its close association with the patrilineage and paternal inherited surname. Other markers have not been found (yet) to overrule this status due to the low sensitivity and precision of autosomal DNA for genetic genealogical applications, given the vagaries of recombination, and the lower capacities of mitochondrial DNA combined with an in general much lower interest in maternal lineages...
November 5, 2016: Human Genetics
https://www.readbyqxmd.com/read/27808231/evolution-of-sex-biased-gene-expression-in-a-dioecious-plant
#17
Niklaus Zemp, Raquel Tavares, Aline Muyle, Deborah Charlesworth, Gabriel A B Marais, Alex Widmer
Separate sexes and sex-biased gene expression have repeatedly evolved in animals and plants, but the underlying changes in gene expression remain unknown. Here, we studied a pair of plant species, one in which separate sexes and sex chromosomes evolved recently and one which maintained hermaphrodite flowers resembling the ancestral state, to reconstruct expression changes associated with the evolution of dioecy. We found that sex-biased gene expression has evolved in autosomal and sex-linked genes in the dioecious species...
November 3, 2016: Nature Plants
https://www.readbyqxmd.com/read/27796355/evolutionary-study-of-yersinia-genomes-deciphers-emergence-of-human-pathogenic-species
#18
Shi Yang Tan, Irene Kit Ping Tan, Mui Fern Tan, Avirup Dutta, Siew Woh Choo
On record, there are 17 species in the Yersinia genus, of which three are known to be pathogenic to human. While the chromosomal and pYV (or pCD1) plasmid-borne virulence genes as well as pathogenesis of these three species are well studied, their genomic evolution is poorly understood. Our study aims to predict the key evolutionary events that led to the emergence of pathogenic Yersinia species by analyzing gene gain-and-loss, virulence genes, and "Clustered regularly-interspaced short palindromic repeats"...
October 31, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27793085/genome-sequence-of-phormia-regina-meigen-diptera-calliphoridae-implications-for-medical-veterinary-and-forensic-research
#19
Anne A Andere, Roy N Platt, David A Ray, Christine J Picard
BACKGROUND: Blow flies (Diptera: Calliphoridae) are important medical, veterinary and forensic insects encompassing 8 % of the species diversity observed in the calyptrate insects. Few genomic resources exist to understand the diversity and evolution of this group. RESULTS: We present the hybrid (short and long reads) draft assemblies of the male and female genomes of the common North American blow fly, Phormia regina (Diptera: Calliphoridae). The 550 and 534 Mb draft assemblies contained 8312 and 9490 predicted genes in the female and male genomes, respectively; including > 93 % conserved eukaryotic genes...
October 28, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27756226/comparative-analysis-of-a-sex-chromosome-from-the-blackchin-tilapia-sarotherodon-melanotheron
#20
William J Gammerdinger, Matthew A Conte, Jean-François Baroiller, Helena D'Cotta, Thomas D Kocher
BACKGROUND: Inversions and other structural polymorphisms often reduce the rate of recombination between sex chromosomes, making it impossible to fine map sex-determination loci using traditional genetic mapping techniques. Here we compare distantly related species of tilapia that each segregate an XY system of sex-determination on linkage group 1. We use whole genome sequencing to identify shared sex-patterned polymorphisms, which are candidates for the ancestral sex-determination mutation...
October 18, 2016: BMC Genomics
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