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y chromosome evolution

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...
March 6, 2018: Molecular Biology and Evolution
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
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
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
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...
February 15, 2018: Genome Research
Felipe Cava
In this monographic issue, we have the pleasure to present contributions from six of the leading laboratories at the forefront of Vibrio cholerae genetics, ecology and evolution, together with a brief tribute by Diego Romero to Doctor Jaime Ferrán y Clua, a pioneering Spanish bacteriologist who developed the first vaccine against this pathogen. V. cholerae is a free-living aquatic bacterium that interacts with and infects a variety of organisms. In humans it causes cholera, the deadly diarrhoea that was responsible for millions of deaths during seven pandemics since 1817, and still thousands every year...
September 2017: International Microbiology: the Official Journal of the Spanish Society for Microbiology
Juan M Ferro, Dario E Cardozo, Pablo Suárez, Juan M Boeris, Ailin Blasco-Zúñiga, Gastón Barbero, Anderson Gomes, Thiago Gazoni, William Costa, Cleusa Y Nagamachi, Miryan Rivera, Patricia P Parise-Maltempi, John E Wiley, Julio C Pieczarka, Celio F B Haddad, Julián Faivovich, Diego Baldo
The hylid tribe Cophomantini is a diverse clade of Neotropical treefrogs composed of the genera Aplastodiscus, Boana, Bokermannohyla, Hyloscirtus, and Myersiohyla. The phylogenetic relationships of Cophomantini have been comprehensively reviewed in the literature, providing a suitable framework for the study of chromosome evolution. Employing different banding techniques, we studied the chromosomes of 25 species of Boana and 3 of Hyloscirtus; thus providing, for the first time, data for Hyloscirtus and for 15 species of Boana...
2018: PloS One
Milla de Andrade Machado, Julio C Pieczarka, Fernando H R Silva, Patricia C M O'Brien, Malcolm A Ferguson-Smith, Cleusa Y Nagamachi
The genus Gymnotus (Gymnotiformes) contains over 40 species of freshwater electric fishes exhibiting a wide distribution throughout Central and South America, and being particularly prevalent in the Amazon basin. Cytogenetics has been an important tool in the cytotaxonomy and elucidation of evolutionary processes in this genus, including the unraveling the variety of diploid chromosome number (2n = from 34 to 54), the high karyotype diversity among species with a shared diploid number, different sex chromosome systems, and variation in the distribution of several Repetitive DNAs and colocation and association between those sequences...
2018: Frontiers in Genetics
Nicolas Rodrigues, Tania Studer, Christophe Dufresnes, Nicolas Perrin
According to the canonical model of sex-chromosome evolution, the degeneration of Y or W chromosomes (as observed in mammals and birds respectively) results from an arrest of recombination in the heterogametic sex, driven by the fixation of sexually antagonistic mutations. However, sex chromosomes have remained homomorphic in many lineages of fishes, amphibians, and non-avian reptiles. According to the 'fountain-of-youth' model, this homomorphy results from occasional events of sex reversal. If recombination arrest in males is controlled by maleness per se (and not by genotype), then Y chromosomes are expected to recombine in XY females, preventing their long-term degeneration...
January 30, 2018: Molecular Biology and Evolution
Georgi Hudjashov, Phillip Endicott, Helen Post, Nano Nagle, Simon Y W Ho, Daniel J Lawson, Maere Reidla, Monika Karmin, Siiri Rootsi, Ene Metspalu, Lauri Saag, Richard Villems, Murray P Cox, R John Mitchell, Ralph L Garcia-Bertrand, Mait Metspalu, Rene J Herrera
The debate concerning the origin of the Polynesian speaking peoples has been recently reinvigorated by genetic evidence for secondary migrations to western Polynesia from the New Guinea region during the 2nd millennium BP. Using genome-wide autosomal data from the Leeward Society Islands, the ancient cultural hub of eastern Polynesia, we find that the inhabitants' genomes also demonstrate evidence of this episode of admixture, dating to 1,700-1,200 BP. This supports a late settlement chronology for eastern Polynesia, commencing ~1,000 BP, after the internal differentiation of Polynesian society...
January 29, 2018: Scientific Reports
Lei He, Hong-Xiang Zheng, Yanan Wang, Katherine Y Le, Qian Liu, Jun Shang, Yingxin Dai, Hongwei Meng, Xing Wang, Tianming Li, Qianqian Gao, Juanxiu Qin, Huiying Lu, Michael Otto, Min Li
BACKGROUND: Severe infections with highly virulent community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) are a global problem. However, the molecular events defining the evolution of CA-MRSA are still poorly understood. MRSA of sequence type (ST) 398 is known to frequently infect livestock, while ST398 isolates infecting humans are commonly methicillin-susceptible or represent MRSA originating from livestock-associated (LA)-MRSA. METHODS: We used whole genome sequencing of newly detected CA-MRSA ST398 isolates, in comparison to geographically matched LA-MRSA and methicillin-sensitive ST398, to determine their evolutionary history...
January 29, 2018: Genome Medicine
T Gazoni, C F B Haddad, H Narimatsu, D C Cabral-de-Mello, M L Lyra, P P Parise-Maltempi
Heteromorphic sex chromosomes are common in eukaryotes and largely ubiquitous in birds and mammals. The largest number of multiple sex chromosomes in vertebrates known today is found in the monotreme platypus (Ornithorhynchus anatinus, 2n = 52) which exhibits precisely 10 sex chromosomes. Interestingly, fish, amphibians, and reptiles have sex determination mechanisms that do or do not involve morphologically differentiated sex chromosomes. Relatively few amphibian species carry heteromorphic sex chromosomes, and when present, they are frequently represented by only one pair, either XX:XY or ZZ:ZW types...
January 26, 2018: Chromosoma
Kevin H-C Wei, Sarah E Lower, Ian V Caldas, Trevor J Sless, Daniel A Barbash, Andrew G Clark
Simple satellites are tandemly repeating short DNA motifs that can span megabases in eukaryotic genomes. Because they can cause genomic instability through non-allelic homologous exchange, they are primarily found in the repressive heterochromatin near centromeres and telomeres where recombination is minimal, and on the Y chromosome, where they accumulate as the chromosome degenerates. Interestingly, the types and abundances of simple satellites often vary dramatically between closely related species, suggesting that they turn over rapidly...
January 19, 2018: Molecular Biology and Evolution
Samuel F Bakhoum, Bryan Ngo, Ashley M Laughney, Julie-Ann Cavallo, Charles J Murphy, Peter Ly, Pragya Shah, Roshan K Sriram, Thomas B K Watkins, Neil K Taunk, Mercedes Duran, Chantal Pauli, Christine Shaw, Kalyani Chadalavada, Vinagolu K Rajasekhar, Giulio Genovese, Subramanian Venkatesan, Nicolai J Birkbak, Nicholas McGranahan, Mark Lundquist, Quincey LaPlant, John H Healey, Olivier Elemento, Christine H Chung, Nancy Y Lee, Marcin Imielenski, Gouri Nanjangud, Dana Pe'er, Don W Cleveland, Simon N Powell, Jan Lammerding, Charles Swanton, Lewis C Cantley
Chromosomal instability is a hallmark of cancer that results from ongoing errors in chromosome segregation during mitosis. Although chromosomal instability is a major driver of tumour evolution, its role in metastasis has not been established. Here we show that chromosomal instability promotes metastasis by sustaining a tumour cell-autonomous response to cytosolic DNA. Errors in chromosome segregation create a preponderance of micronuclei whose rupture spills genomic DNA into the cytosol. This leads to the activation of the cGAS-STING (cyclic GMP-AMP synthase-stimulator of interferon genes) cytosolic DNA-sensing pathway and downstream noncanonical NF-κB signalling...
January 17, 2018: Nature
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
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
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
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
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
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
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