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https://www.readbyqxmd.com/read/29150717/genetic-diversity-and-phylogenetic-study-of-the-chinese-gelao-ethnic-minority-via-23-y-str-loci
#1
Pengyu Chen, Yanyan Han, Guanglin He, Haibo Luo, Tianzhen Gao, Feng Song, Dengfu Wan, Jian Yu, Yiping Hou
Haplotype diversity for 23 Y chromosomal short tandem repeat (Y-STR) loci included in the PowerPlex(®) Y23 System was analyzed in the Chinese Gelao minority group of 234 unrelated males living in Daozhen Gelao-Miao Autonomous County in Guizhou Province, southwest China. A total of 216 different haplotypes were detected, of which 199 haplotypes were unique. The overall haplotype diversity (HD) and discrimination capacity (DC) were 0.9996 and 0.9231, respectively. The gene diversity (GD) ranged from 0.4159 (DYS438) to 0...
November 17, 2017: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/29150183/genetic-analysis-of-29-y-str-loci-in-the-chinese-han-population-from-shanghai
#2
Yuxiang Zhou, Chengchen Shao, Liming Li, Yaqi Zhang, Baonian Liu, Qinrui Yang, Qiqun Tang, Shilin Li, Jianhui Xie
The analysis of Y chromosomal short tandem repeats (Y-STRs) provides important information that can be used to forensic investigation and population studies. In this study, typing of 29 Y-STRs included in the PowerPlex(®) Y23 system (PPY23) and Yfiler™ Plus system (Yfiler plus) was performed on 843 unrelated male samples from Han population in Shanghai. Besides null, duplicate, and intermediate alleles reported in previous studies, an allele of 10 at DYS643 with a 2-base deletion in the flanking region was initially observed...
November 11, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/29137168/origin-and-evolution-of-the-neo-sex-chromosomes-in-pamphagidae-grasshoppers-through-chromosome-fusion-and-following-heteromorphization
#3
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
#4
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
#5
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/29128546/a-1204-single-nucleotide-polymorphism-and-insertion-deletion-polymorphism-panel-for-massively-parallel-sequencing-analysis-of-dna-mixtures
#6
Hsiao-Lin Hwa, Wan-Chia Chung, Pei-Lung Chen, Chih-Peng Lin, Huei-Ying Li, Hsiang-I Yin, James Chun-I Lee
Massively parallel sequencing (MPS) technology enables the simultaneous analysis of a huge number of single nucleotide polymorphisms (SNPs) and insertion-deletion polymorphisms (indels). MPS also enables the detection of the alleles of minor contributors in a highly unbalanced DNA mixture. In this study, we established a 1204-marker panel optimized for MPS consisting of 987 autosomal markers (964 SNPs and 23 indels), 27 X-chromosome SNPs, 61 Y-chromosome markers (56 SNPs and 5 indels), and 129 mitochondrial SNPs...
November 6, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/29125104/polymorphisms-of-23-y-chromosome-str-loci-in-a-han-population-in-jiangsu-province
#7
Jun Ma, Ai-Hua Zhu, Jin-Wei Shi, Ming Jin, Hua-Jie Ba, Zhi-Guang Ping
Objective To investigate the polymorphisms of 23 Y-STR loci in a Han population in Jiangsu province. Methods Blood samples were collected from 4821 unrelated healthy Han males in Jiangsu province. DNA templates were amplified by PowerPlex Y23 kit,and the amplification products were detected by 3500xL genetic analyzer. Then,we calculated the allele frequencies and gene diversities respectively,as well as the haplotype frequencies and haplotype diversities. Results The gene diversity of these 23 Y-STR loci ranged 0...
October 30, 2017: Zhongguo Yi Xue Ke Xue Yuan Xue Bao. Acta Academiae Medicinae Sinicae
https://www.readbyqxmd.com/read/29121539/clinical-and-biological-significance-of-isolated-y-chromosome-loss-in-myelodysplastic-syndromes-and-chronic-myelomonocytic-leukemia-a-report-from-the-spanish-mds-group
#8
Meritxell Nomdedeu, Arturo Pereira, Xavier Calvo, Joan Colomer, Francesc Sole, Amparo Arias, Candida Gomez, Elisa Luño, Jose Cervera, Montserrat Arnan, Helena Pomares, Fernando Ramos, Itziar Oiartzabal, Blanca Espinet, Carme Pedro, Beatriz Arrizabalaga, María Laura Blanco, Mar Tormo, Jesus Maria Hernandez-Rivas, María Díez-Campelo, Margarita Ortega, David Valcárcel, Maria-Teresa Cedena, Rosa Collado, Javier Grau, Isabel Granada, Guillermo Sanz, Elias Campo, Jordi Esteve, Dolors Costa
Isolate loss of chromosome Y (-Y) in myelodysplastic syndromes (MDS) is associated to a better outcome but it is also well described as an age-related phenomenon. In this study we aimed to analyze the prognostic impact of -Y in the context of the IPSS-R cytogenetic classification, evaluate the clinical significance of the percentage of metaphases with isolated -Y, and test whether finding -Y may predispose to over-diagnose MDS in patients with borderline morphological features. We evaluated 3581 male patients from the Spanish MDS Registry with a diagnosis of MDS or chronic myelomonocytic leukemia (CMML)...
October 28, 2017: Leukemia Research
https://www.readbyqxmd.com/read/29116665/reproductive-isolation-and-environmental-adaptation-shape-the-phylogeography-of-mountain-pine-beetle-dendroctonus-ponderosae
#9
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/29114362/comparative-cytogenetics-of-some-marsupial-species-didelphimorphia-didelphidae-from-the-amazon-basin
#10
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/29107554/genomic-analyses-of-pre-european-conquest-human-remains-from-the-canary-islands-reveal-close-affinity-to-modern-north-africans
#11
Ricardo Rodríguez-Varela, Torsten Günther, Maja Krzewińska, Jan Storå, Thomas H Gillingwater, Malcolm MacCallum, Juan Luis Arsuaga, Keith Dobney, Cristina Valdiosera, Mattias Jakobsson, Anders Götherström, Linus Girdland-Flink
The origins and genetic affinity of the aboriginal inhabitants of the Canary Islands, commonly known as Guanches, are poorly understood. Though radiocarbon dates on archaeological remains such as charcoal, seeds, and domestic animal bones suggest that people have inhabited the islands since the 5(th) century BCE [1-3], it remains unclear how many times, and by whom, the islands were first settled [4, 5]. Previously published ancient DNA analyses of uniparental genetic markers have shown that the Guanches carried common North African Y chromosome markers (E-M81, E-M78, and J-M267) and mitochondrial lineages such as U6b, in addition to common Eurasian haplogroups [6-8]...
November 6, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/29104214/impact-of-repetitive-elements-on-the-y-chromosome-formation-in-plants
#12
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/29099847/a-glimpse-at-the-intricate-mosaic-of-ethnicities-from-mesopotamia-paternal-lineages-of-the-northern-iraqi-arabs-kurds-syriacs-turkmens-and-yazidis
#13
Serkan Dogan, Cemal Gurkan, Mustafa Dogan, Hasan Emin Balkaya, Ramazan Tunc, Damla Kanliada Demirdov, Nihad Ahmed Ameen, Damir Marjanovic
Widely considered as one of the cradles of human civilization, Mesopotamia is largely situated in the Republic of Iraq, which is also the birthplace of the Sumerian, Akkadian, Assyrian and Babylonian civilizations. These lands were subsequently ruled by the Persians, Greeks, Romans, Arabs, Mongolians, Ottomans and finally British prior to the independence. As a direct consequence of this rich history, the contemporary Iraqi population comprises a true mosaic of different ethnicities, which includes Arabs, Kurds, Turkmens, Assyrians, and Yazidis among others...
2017: PloS One
https://www.readbyqxmd.com/read/29099833/how-convincing-is-a-matching-y-chromosome-profile
#14
Mikkel M Andersen, David J Balding
The introduction of forensic autosomal DNA profiles was controversial, but the problems were successfully addressed, and DNA profiling has gone on to revolutionise forensic science. Y-chromosome profiles are valuable when there is a mixture of male-source and female-source DNA, and interest centres on the identity of the male source(s) of the DNA. The problem of evaluating evidential weight is even more challenging for Y profiles than for autosomal profiles. Numerous approaches have been proposed, but they fail to deal adequately with the fact that men with matching Y-profiles are related in extended patrilineal clans, many of which may not be represented in available databases...
November 2017: PLoS Genetics
https://www.readbyqxmd.com/read/29099806/chromosomal-evolution-in-mole-voles-ellobius-cricetidae-rodentia-bizarre-sex-chromosomes-variable-autosomes-and-meiosis
#15
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/29099633/aging-deteriorates-quality-of-sperm-produced-by-male-mice-with-partial-yq-deletion
#16
Katarzyna Kotarska, Andrzej Doniec, Magdalena Bednarska, Zbigniew Polański, Józefa Styrna
The aim of the study was to assess the cumulative effects of aging and Y-chromosome long arm deletion on sperm quality parameters. Motility, mitochondrial activity, and head morphology were evaluated for sperm of 3- and 12-month-old males from B10.BR-Y(del) and B10.BR congenic mouse strains. The study revealed that quality and fertilizing potential of sperm produced by younger and older B10.BR males persist on similar levels, but worsen significantly with age of B10.BR-Y(del) males. The findings imply that partial Yq deletions might be more harmful for spermiogenesis in advancing age and may be applicable to other species including humans...
November 3, 2017: Systems Biology in Reproductive Medicine
https://www.readbyqxmd.com/read/29098495/persistent-one-way-walking-in-a-circular-arena-in-drosophila-melanogaster-canton-s-strain
#17
Chengfeng Xiao, Shuang Qiu, R Meldrum Robertson
We describe persistent one-way walking of Drosophila melanogaster in a circular arena. Wild-type Canton-S adult flies walked in one direction, counter-clockwise or clockwise, for minutes, whereas white-eyed mutant [Formula: see text] changed directions frequently. Locomotion in the circular arena could be classified into four components: counter-clockwise walking, clockwise walking, nondirectional walking and pausing. Genetic analysis revealed that while wild-type genetic background was associated with reduced directional change and reduced numbers of one-way (including counter-clockwise and clockwise) and nondirectional walks, the white ([Formula: see text]) locus promoted persistent one-way walking by increasing the maximal duration of one-way episodes...
November 2, 2017: Behavior Genetics
https://www.readbyqxmd.com/read/29097670/the-genetic-variation-in-the-r1a-clade-among-the-ashkenazi-levites-y-chromosome
#18
Doron M Behar, Lauri Saag, Monika Karmin, Meir G Gover, Jeffrey D Wexler, Luisa Fernanda Sanchez, Elliott Greenspan, Alena Kushniarevich, Oleg Davydenko, Hovhannes Sahakyan, Levon Yepiskoposyan, Alessio Boattini, Stefania Sarno, Luca Pagani, Shai Carmi, Shay Tzur, Ene Metspalu, Concetta Bormans, Karl Skorecki, Mait Metspalu, Siiri Rootsi, Richard Villems
Approximately 300,000 men around the globe self-identify as Ashkenazi Levites, of whom two thirds were previously shown to descend from a single male. The paucity of whole Y-chromosome sequences precluded conclusive identification of this ancestor's age, geographic origin and migration patterns. Here, we report the variation of 486 Y-chromosomes within the Ashkenazi and non-Ashkenazi Levite R1a clade, other Ashkenazi Jewish paternal lineages, as well as non-Levite Jewish and non-Jewish R1a samples. Cumulatively, the emerging profile is of a Middle Eastern ancestor, self-affiliating as Levite, and carrying the highly resolved R1a-Y2619 lineage, which was likely a minor haplogroup among the Hebrews...
November 2, 2017: Scientific Reports
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/29090985/an-unusual-accumulation-of-ribosomal-multigene-families-and-microsatellite-dnas-in-the-xx-xy-sex-chromosome-system-in-the-trans-andean-catfish-pimelodella-cf-chagresi-siluriformes-heptapteridae
#20
Cristhian Camilo Conde-Saldaña, Cynthia Aparecida Valiati Barreto, Francisco Antonio Villa-Navarro, Jorge Abdala Dergam
This work constitutes the first cytogenetic characterization of a trans-Andean species of Heptapteridae. The catfish Pimelodella cf. chagresi from the Upper Rio Magdalena was studied, applying standard cytogenetic techniques (Giemsa, C-banding, and argyrophilic nucleolar organizer region [Ag-NOR]) and fluorescence in situ hybridization techniques using repetitive DNA probes: microsatellites (CA15 and GA15) and ribosomal RNA (rRNA) multigene families (18S and 5S recombinant DNA [rDNA] probes). The species showed a unique diploid chromosome number 2n = 50 (32m [metacentrics] +14sm [submetacentrics] +4st [subtelocentrics]) and a XX/XY sex chromosomal system, where the heteromorphic Y-chromosome revealed a conspicuous accumulation of all the assayed domains of repetitive DNA...
November 1, 2017: Zebrafish
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