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https://www.readbyqxmd.com/read/28098486/identification-and-characterization-of-genes-on-a-single-subgenome-in-the-hexaploid-wheat-triticum-aestivum-l-genotype-chinese-spring
#1
Jian Ma, Zhi Zheng, Jiri Stiller, Xiu-Jin Lan, Yaxi Liu, Mei Deng, Penghao Wang, Zhien Pu, Guangdeng Chen, Qian-Tao Jiang, Yuming Wei, You-Liang Zheng
Gene loss during the formation of hexaploid bread wheat has been repeatedly reported. However, our knowledge on genome-wide analysis of the genes present on a single subgenome (SSG) in bread wheat is still limited. In this study, by analysing the 'Chinese Spring' chromosome arm shotgun sequences together with high-confidence gene models, we detected 433 genes on a SSG. Greater gene loss was observed in A and D subgenomes compared with B subgenome. More than 79% of the orthologs for these SSG genes were detected in diploid and tetraploid relatives of hexaploid wheat...
November 1, 2016: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28096526/telomeres-in-cancer-tumour-suppression-and-genome-instability
#2
John Maciejowski, Titia de Lange
The shortening of human telomeres has two opposing effects during cancer development. On the one hand, telomere shortening can exert a tumour-suppressive effect through the proliferation arrest induced by activating the kinases ATM and ATR at unprotected chromosome ends. On the other hand, loss of telomere protection can lead to telomere crisis, which is a state of extensive genome instability that can promote cancer progression. Recent data, reviewed here, provide new evidence for the telomere tumour suppressor pathway and has revealed that telomere crisis can induce numerous cancer-relevant changes, including chromothripsis, kataegis and tetraploidization...
January 18, 2017: Nature Reviews. Molecular Cell Biology
https://www.readbyqxmd.com/read/28096351/uncovering-hidden-variation-in-polyploid-wheat
#3
Ksenia V Krasileva, Hans A Vasquez-Gross, Tyson Howell, Paul Bailey, Francine Paraiso, Leah Clissold, James Simmonds, Ricardo H Ramirez-Gonzalez, Xiaodong Wang, Philippa Borrill, Christine Fosker, Sarah Ayling, Andrew L Phillips, Cristobal Uauy, Jorge Dubcovsky
Comprehensive reverse genetic resources, which have been key to understanding gene function in diploid model organisms, are missing in many polyploid crops. Young polyploid species such as wheat, which was domesticated less than 10,000 y ago, have high levels of sequence identity among subgenomes that mask the effects of recessive alleles. Such redundancy reduces the probability of selection of favorable mutations during natural or human selection, but also allows wheat to tolerate high densities of induced mutations...
January 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28090264/drought-stress-induced-changes-of-micrornas-in-diploid-and-autotetraploid-paulownia-tomentosa
#4
Xibing Cao, Guoqiang Fan, Lin Cao, Minjie Deng, Zhenli Zhao, Suyan Niu, Zhe Wang, Yuanlong Wang
Drought stress adversely affects plant productivity. Growth and timber production of Paulownia trees are limited under drought stress. Changes in gene expression patterns and miRNA in different ploidy of Paulownia tomentosa have been investigated. However, the responses of P. tomentosa to drought stress at the microRNA (miRNA) level have not been reported so far. To identify miRNA candidates and their target genes involved in the drought stress response in diploid and tetraploid P. tomentosa, four small RNA and four degradome libraries from diploid and autotetraploid P...
2017: Genes & Genomics
https://www.readbyqxmd.com/read/28080987/ploidy-dynamics-and-evolvability-in-fungi
#5
REVIEW
Noa Blutraich Wertheimer, Neil Stone, Judith Berman
Rapid responses to acute stresses are essential for stress survival and are critical to the ability of fungal pathogens to adapt to new environments or hosts. The rapid emergence of drug resistance is used as a model for how fungi adapt and survive stress conditions that inhibit the growth of progenitor cells. Aneuploidy and loss of heterozygosity (LOH), which are large-scale genome shifts involving whole chromosomes or chromosome arms, occur at higher frequency than point mutations and have the potential to mediate stress survival...
December 5, 2016: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/28071676/transcriptome-analysis-of-neo-tetraploid-rice-reveals-specific-differential-gene-expressions-associated-with-fertility-and-heterosis
#6
Haibin Guo, Jean Nestor Mendrikahy, Lei Xie, Junfeng Deng, Zijun Lu, Jinwen Wu, Xiang Li, Muhammad Qasim Shahid, Xiangdong Liu
Polyploid rice hybrids have a powerful biological and yield potential that may become a new way for rice breeding; however, low fertility is major hindrance in commercial utilization. Here, we developed a neo-tetraploid rice that could overcome the sterility of autotetraploid rice and produce high heterosis. Transcriptome analysis of F1 hybrid developed by crossing neo-tetraploid with autotetraploid rice displayed 807, 663 and 866 differentially expressed genes that uniquely associated with F1 and specific to (DEGFu-sp) anther, ovary and leaf, respectively...
January 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28070610/automated-tetraploid-genotype-calling-by-hierarchical-clustering
#7
Cari A Schmitz Carley, Joseph J Coombs, David S Douches, Paul C Bethke, Jiwan P Palta, Richard G Novy, Jeffrey B Endelman
New software to make tetraploid genotype calls from SNP array data was developed, which uses hierarchical clustering and multiple F1 populations to calibrate the relationship between signal intensity and allele dosage. SNP arrays are transforming breeding and genetics research for autotetraploids. To fully utilize these arrays, the relationship between signal intensity and allele dosage must be calibrated for each marker. We developed an improved computational method to automate this process, which is provided as the R package ClusterCall...
January 9, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28069571/apc-c-dysfunction-limits-excessive-cancer-chromosomal-instability
#8
Laurent Sansregret, James O Patterson, Sally Dewhurst, Carlos López-García, André Koch, Nicholas McGranahan, William Chong Hang Chao, David J Barry, Andrew Rowan, Rachael Instrell, Stuart Horswell, Michael Way, Michael Howell, Martin R Singleton, René H Medema, Paul Nurse, Mark Petronczki, Charles Swanton
: Intercellular heterogeneity, exacerbated by chromosomal instability (CIN), fosters tumor heterogeneity and drug resistance. However, extreme CIN correlates with improved cancer outcome, suggesting that karyotypic diversity required to adapt to selection pressures might be balanced in tumors against the risk of excessive instability. Here, we used a functional genomics screen, genome editing, and pharmacologic approaches to identify CIN-survival factors in diploid cells. We find partial anaphase-promoting complex/cyclosome (APC/C) dysfunction lengthens mitosis, suppresses pharmacologically induced chromosome segregation errors, and reduces naturally occurring lagging chromosomes in cancer cell lines or following tetraploidization...
January 9, 2017: Cancer Discovery
https://www.readbyqxmd.com/read/28065918/exploiting-next-generation-sequencing-to-solve-the-haplotyping-puzzle-in-polyploids-a-simulation-study
#9
Ehsan Motazedi, Richard Finkers, Chris Maliepaard, Dick de Ridder
Haplotypes are the units of inheritance in an organism, and many genetic analyses depend on their precise determination. Methods for haplotyping single individuals use the phasing information available in next-generation sequencing reads, by matching overlapping single-nucleotide polymorphisms while penalizing post hoc nucleotide corrections made. Haplotyping diploids is relatively easy, but the complexity of the problem increases drastically for polyploid genomes, which are found in both model organisms and in economically relevant plant and animal species...
January 8, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28065301/incomplete-cytokinesis-binucleation-in-mammals-the-powerful-system-of-hepatocytes
#10
M Fortier, S Celton-Morizur, C Desdouets
Polyploidy, the state of having greater than a diploid DNA content (tetraploid, octoploid, etc.) is a characteristic feature of mammalian hepatocytes and accompanies late fetal development and postnatal maturation of the liver. During the weaning period, diploid hepatocytes can engage either into normal cell division cycle giving rise to two diploid hepatocytes or follow a scheduled division program characterized by incomplete cytokinesis. In that case, diploid hepatocytes undergo mitosis, but do not form a contractile ring...
2017: Methods in Cell Biology
https://www.readbyqxmd.com/read/28060351/ploidy-manipulation-of-zebrafish-embryos-with-heat-shock-2-treatment
#11
Destiny L Baars, Kendra A Takle, Jonathon Heier, Francisco Pelegri
Manipulation of ploidy allows for useful transformations, such as diploids to tetraploids, or haploids to diploids. In the zebrafish Danio rerio, specifically the generation of homozygous gynogenetic diploids is useful in genetic analysis because it allows the direct production of homozygotes from a single heterozygous mother. This article describes a modified protocol for ploidy duplication based on a heat pulse during the first cell cycle, Heat Shock 2 (HS2). Through inhibition of centriole duplication, this method results in a precise cell division stall during the second cell cycle...
December 16, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28059097/fibrous-hamartoma-of-infancy-a-clinicopathologic-study-of-145-cases-including-2-with-sarcomatous-features
#12
Alyaa Al-Ibraheemi, Anthony Martinez, Sharon W Weiss, Harry P Kozakewich, Antonio R Perez-Atayde, Henry Tran, David M Parham, William R Sukov, Karen J Fritchie, Andrew L Folpe
Fibrous hamartoma of infancy is a rare soft tissue lesion of infants and young children with characteristic triphasic morphology, which typically occurs in the axilla and less commonly in other locations. We reviewed 145 cases of fibrous hamartoma of infancy from our consultation archives. Cases occurred in 106 males and 39 females (mean age-15 months; range-birth to 14 years), and involved both typical sites (eg, axilla/back/upper arm) (n=69) and unusual locations (n=76). Six were congenital. The tumors presented as subcutaneous masses and ranged from 0...
January 6, 2017: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/28049060/a-comparative-study-of-the-dynamic-accumulation-of-polyphenol-components-and-the-changes-in-their-antioxidant-activities-in-diploid-and-tetraploid-lonicera-japonica
#13
Dexin Kong, Yanqun Li, Mei Bai, Yali Deng, Guangxin Liang, Hong Wu
Polyploidization is an effective method to achieve a higher yield of secondary metabolism active ingredients in medicinal plants. Polyphenols are the main active substances that contribute to the antioxidant activity of Lonicera japonica. For studying on the effect of chromosome doubling and harvest time on the dynamic accumulation of the main active substances and antioxidant capabilities of L. japonica, the polyphenol composition contents (7 phenolic acids and 3 flavonoids) and the antioxidant capacity in buds and flowers of diploid and tetraploid L...
December 28, 2016: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/28039515/genome-wide-association-mapping-for-seedling-and-field-resistance-to-puccinia-striiformis-f-sp-tritici-in-elite-durum-wheat
#14
Weizhen Liu, Marco Maccaferri, Peter Bulli, Sheri Rynearson, Roberto Tuberosa, Xianming Chen, Michael Pumphrey
Genome-wide association analysis in tetraploid wheat revealed novel and diverse loci for seedling and field resistance to stripe rust in elite spring durum wheat accessions from worldwide. Improving resistance to stripe rust, caused by Puccinia striiformis f. sp. tritici, is a major objective for wheat breeding. To identify effective stripe rust resistance loci, a genome-wide association study (GWAS) was conducted using 232 elite durum wheat (Triticum turgidum ssp. durum) lines from worldwide breeding programs...
December 30, 2016: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28038458/chromosome-nondisjunction-during-bipolar-mitoses-of-binucleated-intermediates-promote-aneuploidy-formation-along-with-multipolar-mitoses-rather-than-chromosome-loss-in-micronuclei-induced-by-asbestos
#15
Tianwei Zhang, Lei Lv, Yun Huang, Xiaohui Ren, Qinghua Shi
Asbestos is a well-known occupational carcinogen that can cause aneuploidy during the early stages of neoplastic development. To explore the origins of asbestos-induced aneuploidy, we performed long-term live-cell imaging followed by fluorescence in situ hybridization of chromosomes 8 and 12 in human bronchial epithelial (HBEC) and mesothelial (MeT5A) cells. We demonstrate that asbestos induces aneuploidy via binucleated intermediates resulting from cytokinesis failure. On the one hand, asbestos increases chromosome nondisjunction during bipolar divisions of binucleated intermediates and produces near-tetraploidy...
December 26, 2016: Oncotarget
https://www.readbyqxmd.com/read/28035071/heterogeneity-in-sarcoma-cell-lines-reveals-enhanced-motility-of-tetraploid-versus-diploid-cells
#16
Mohamed Jemaà, Samer Abdallah, Gwendaline Lledo, Gaelle Perot, Tom Lesluyes, Catherine Teyssier, Pierre Roux, Juliette van Dijk, Frederic Chibon, Ariane Abrieu, Nathalie Morin
Soft tissue sarcomas with complex genomics are very heterogeneous tumors lacking simple prognosis markers or targeted therapies. Overexpression of a subset of mitotic genes from a signature called CINSARC is of bad prognosis, but the significance of this signature remains elusive. Here we precisely measure the cell cycle and mitosis duration of sarcoma cell lines and we found that the mitotic gene products overexpression does not reflect variation in the time spent during mitosis or G2/M. We also found that the CINSARC cell lines, we studied, are composed of a mixture of aneuploid, diploid, and tetraploid cells that are highly motile in vitro...
December 27, 2016: Oncotarget
https://www.readbyqxmd.com/read/28034842/effects-of-genome-doubling-on-expression-of-genes-regulating-grain-size-in-rice
#17
Zhang Hongyu, Cui Xiaoyun, Hou Feixue, Wang Yiyi, Wu Tingkai, Liu Yutong, Yang Dingqian, Zhang Hongkai, Fu Yao, Zhang Xiangyang, Li Wenli, Wu Xianjun
Rice is one of the most important staple crops. It has been the major focus in breeding program to improve grain yield. A unique feature of tetraploid rice is the increased grain size and weight compared to diploid. Therefore, investigating the effects of genome doubling on expression of genes regulating grain size is important for yield improvement in rice breeding program. In this study, we analyzed differential expression of six genes regulating grain size in young panicles of various developmental stages between diploid and tetraploid rice...
December 20, 2016: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/28032246/identification-and-characterization-of-diploid-and-tetraploid-in-platycodon-grandiflorum
#18
Jeoung-Hwa Shin, Yun Gyong Ahn, Ju-Hee Jung, Sun-Hee Woo, Hag-Hyun Kim, Shela Gorinstein, Hee-Ock Boo
Platycodon grandiflorum (PG), a species of herbaceous flowering perennial plant of the family Campanulaceae, has been used as a traditional oriental medicine for bronchitis, asthma, pulmonary tuberculosis, diabetes, hepatic fibrosis, bone disorders and many others similar diseases and as a food supplement. For the primary profiling of PG gas chromatography coupled with high resolution - time of flight mass spectrometry (GC/HR-TOF MS) was used as an analytical tool. A comparison of optimal extraction of metabolites was carried out with a number of solvents [hexane, methylene chloride, methanol, ethanol, methanol: ethanol (70:30, v:v)]...
December 28, 2016: Plant Foods for Human Nutrition
https://www.readbyqxmd.com/read/28013251/contrasting-effects-of-ploidy-level-on-seed-production-in-a-diploid-tetraploid-system
#19
Zuzana MÜnzbergová, Jiří Skuhrovec
Previous studies demonstrated the effects of polyploidy on various aspects of plant life. It is, however, difficult to determine which plant characteristics are responsible for fitness differences between cytotypes. We assessed the relationship between polyploidy and seed production. To separate the effects of flowering phenology, flower head size and herbivores from other possible causes, we collected data on these characteristics in single flower heads of diploid and tetraploid Centaurea phrygia in an experimental garden...
December 23, 2016: AoB Plants
https://www.readbyqxmd.com/read/28008701/entire-nucleotide-sequences-of-gossypium-raimondii-and-g-arboreum-mitochondrial-genomes-revealed-a-genome-species-as-cytoplasmic-donor-of-the-allotetraploid-species
#20
Zhiwen Chen, Hushuai Nie, Corrinne E Grover, Yumei Wang, Pengbo Li, Meiyan Wang, Haili Pei, Yanpeng Zhao, Shuangshuang Li, Jonathan F Wendel, Jinping Hua
Cotton (Gossypium spp.) is commonly grouped into eight diploid genomic groups, designated A-G and K, and an allotetraploid genomic group, AD. Gossypium raimondii (D5 ) and Gossypium arboreum (A2 ) are the putative contributors to the progenitor of G. hirsutum (AD1 ), the economically important fiber-producing cotton species. Mitochondrial DNA from week-old etiolated seedlings was extracted from isolated organelles using discontinuous sucrose density gradient method. Mitochondrial genomes were sequenced, assembled, annotated and analyzed orderly...
December 23, 2016: Plant Biology
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