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https://www.readbyqxmd.com/read/28226421/opening-plenary-speaker-human-genomics-precision-medicine-and-advancing-human-health
#1
Eric D Green
Starting with the launch of the Human Genome Project in 1990, the past quarter-century has brought spectacular achievements in genomics that dramatically empower the study of human biology and disease. The human genomics enterprise is now in the midst of an important transition, as the growing foundation of genomic knowledge is being used by researchers and clinicians to tackle increasingly complex problems in biomedicine. Of particular prominence is the use of revolutionary new DNA sequencing technologies for generating prodigious amounts of DNA sequence data to elucidate the complexities of genome structure, function, and evolution, as well as to unravel the genomic bases of rare and common diseases...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28226237/novel-insights-into-tree-biology-and-genome-evolution-as-revealed-through-genomics
#2
David B Neale, Pedro J Martínez-García, Amanda R De La Torre, Sara Montanari, Xiao-Xin Wei
Reference genome sequences are the key to the discovery of genes and gene families that determine traits of interest. Recent progress in sequencing technologies has enabled a rapid increase in genome sequencing of tree species, allowing the dissection of complex characters of economic importance, such as fruit and wood quality and resistance to biotic and abiotic stresses. Although the number of reference genome sequences for trees lags behind those for other plant species, it is not too early to gain insight into the unique features that distinguish trees from nontree plants...
February 6, 2017: Annual Review of Plant Biology
https://www.readbyqxmd.com/read/28226236/new-strategies-and-tools-in-quantitative-genetics-how-to-go-from-the-phenotype-to-the-genotype
#3
C Bazakos, M Hanemian, C Trontin, J M Jiménez-Gómez, O Loudet
Quantitative genetics has a long history in plants: It has been used to study specific biological processes, identify the factors important for trait evolution, and breed new crop varieties. These classical approaches to quantitative trait locus mapping have naturally improved with technology. In this review, we show how quantitative genetics has evolved recently in plants and how new developments in phenotyping, population generation, sequencing, gene manipulation, and statistics are rejuvenating both the classical linkage mapping approaches (for example, through nested association mapping) as well as the more recently developed genome-wide association studies...
February 6, 2017: Annual Review of Plant Biology
https://www.readbyqxmd.com/read/28226235/plant-mitochondrial-genomes-dynamics-and-mechanisms-of-mutation
#4
José M Gualberto, Kathleen J Newton
The large mitochondrial genomes of angiosperms are unusually dynamic because of recombination activities involving repeated sequences. These activities generate subgenomic forms and extensive genomic variation even within the same species. Such changes in genome structure are responsible for the rapid evolution of plant mitochondrial DNA and for the variants associated with cytoplasmic male sterility and abnormal growth phenotypes. Nuclear genes modulate these processes, and over the past decade, several of these genes have been identified...
February 9, 2017: Annual Review of Plant Biology
https://www.readbyqxmd.com/read/28225773/whole-genome-duplication-and-molecular-evolution-in-cornus-l-cornaceae-insights-from-transcriptome-sequences
#5
Yan Yu, Qiuyun Xiang, Paul S Manos, Douglas E Soltis, Pamela S Soltis, Bao-Hua Song, Shifeng Cheng, Xin Liu, Gane Wong
The pattern and rate of genome evolution have profound consequences in organismal evolution. Whole-genome duplication (WGD), or polyploidy, has been recognized as an important evolutionary mechanism of plant diversification. However, in non-model plants the molecular signals of genome duplications have remained largely unexplored. High-throughput transcriptome data from next-generation sequencing have set the stage for novel investigations of genome evolution using new bioinformatic and methodological tools in a phylogenetic framework...
2017: PloS One
https://www.readbyqxmd.com/read/28224497/hidden-markov-models-in-population-genomics
#6
Julien Y Dutheil
With the advent of sequencing techniques population genomics took a major shift. The structure of data sets has evolved from a sample of a few loci in the genome, sequenced in dozens of individuals, to collections of complete genomes, virtually comprising all available loci. Initially sequenced in a few individuals, such genomic data sets are now reaching and even exceeding the size of traditional data sets in the number of haplotypes sequenced. Because all loci in a genome are not independent, this evolution of data sets is mirrored by a methodological change...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28224054/variant-profiling-of-evolving-prokaryotic-populations
#7
Markus Zojer, Lisa N Schuster, Frederik Schulz, Alexander Pfundner, Matthias Horn, Thomas Rattei
Genomic heterogeneity of bacterial species is observed and studied in experimental evolution experiments and clinical diagnostics, and occurs as micro-diversity of natural habitats. The challenge for genome research is to accurately capture this heterogeneity with the currently used short sequencing reads. Recent advances in NGS technologies improved the speed and coverage and thus allowed for deep sequencing of bacterial populations. This facilitates the quantitative assessment of genomic heterogeneity, including low frequency alleles or haplotypes...
2017: PeerJ
https://www.readbyqxmd.com/read/28224003/darwinism-for-the-genomic-age-connecting-mutation-to-diversification
#8
Xia Hua, Lindell Bromham
A growing body of evidence suggests that rates of diversification of biological lineages are correlated with differences in genome-wide mutation rate. Given that most research into differential patterns of diversification rate have focused on species traits or ecological parameters, a connection to the biochemical processes of genome change is an unexpected observation. While the empirical evidence for a significant association between mutation rate and diversification rate is mounting, there has been less effort in explaining the factors that mediate this connection between genetic change and species richness...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28223993/diacylglycerol-kinases-are-widespread-in-higher-plants-and-display-inducible-gene-expression-in-response-to-beneficial-elements-metal-and-metalloid-ions
#9
Hugo F Escobar-Sepúlveda, Libia I Trejo-Téllez, Paulino Pérez-Rodríguez, Juan V Hidalgo-Contreras, Fernando C Gómez-Merino
Diacylglycerol kinases (DGKs) are pivotal signaling enzymes that phosphorylate diacylglycerol (DAG) to yield phosphatidic acid (PA). The biosynthesis of PA from phospholipase D (PLD) and the coupled phospholipase C (PLC)/DGK route is a crucial signaling process in eukaryotic cells. Next to PLD, the PLC/DGK pathway is the second most important generator of PA in response to biotic and abiotic stresses. In eukaryotic cells, DGK, DAG, and PA are implicated in vital processes such as growth, development, and responses to environmental cues...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28223462/fallacy-of-the-unique-genome-sequence-diversity-within-single-helicobacter-pylori-strains
#10
Jenny L Draper, Lori M Hansen, David L Bernick, Samar Abedrabbo, Jason G Underwood, Nguyet Kong, Bihua C Huang, Allison M Weis, Bart C Weimer, Arnoud H M van Vliet, Nader Pourmand, Jay V Solnick, Kevin Karplus, Karen M Ottemann
Many bacterial genomes are highly variable but nonetheless are typically published as a single assembled genome. Experiments tracking bacterial genome evolution have not looked at the variation present at a given point in time. Here, we analyzed the mouse-passaged Helicobacter pylori strain SS1 and its parent PMSS1 to assess intra- and intergenomic variability. Using high sequence coverage depth and experimental validation, we detected extensive genome plasticity within these H. pylori isolates, including movement of the transposable element IS607, large and small inversions, multiple single nucleotide polymorphisms, and variation in cagA copy number...
February 21, 2017: MBio
https://www.readbyqxmd.com/read/28223459/evolution-and-epidemiology-of-multidrug-resistant-klebsiella-pneumoniae-in-the-united-kingdom-and-ireland
#11
Danesh Moradigaravand, Veronique Martin, Sharon J Peacock, Julian Parkhill
Klebsiella pneumoniae is a human commensal and opportunistic pathogen that has become a leading causative agent of hospital-based infections over the past few decades. The emergence and global expansion of hypervirulent and multidrug-resistant (MDR) clones of K. pneumoniae have been increasingly reported in community-acquired and nosocomial infections. Despite this, the population genomics and epidemiology of MDR K. pneumoniae at the national level are still poorly understood. To obtain insights into these, we analyzed a systematic large-scale collection of invasive MDR K...
February 21, 2017: MBio
https://www.readbyqxmd.com/read/28223401/transcriptome-analyses-of-rhesus-monkey-pre-implantation-embryos-reveal-a-reduced-capacity-for-dna-double-strand-break-repair-in-primate-oocytes-and-early-embryos
#12
Xinyi Wang, Denghui Liu, Dajian He, Shengbo Suo, Xian Xia, Xiechao He, Jing-Dong Han, Ping Zheng
Pre-implantation embryogenesis encompasses several critical events including genome reprogramming, zygotic genome activation (ZGA), and cell fate commitment, most of which remain mechanistically unclear in primates. In addition, primates display a high rate of embryo wastage without any clear molecular basis. Understanding the factors involved in genome reprogramming and ZGA will help the generation of induced pluripotent stem cells with high efficiency. Moreover, explaining the molecular basis responsible for embryo wastage in primates will greatly expand our knowledge of species evolution...
February 21, 2017: Genome Research
https://www.readbyqxmd.com/read/28223399/centromere-location-in-arabidopsis-is-unaltered-by-extreme-divergence-in-cenh3-protein-sequence
#13
Shamoni Maheshwari, Takayoshi Ishii, C Titus Brown, Andreas Houben, Luca Comai
During cell division, spindle fibers attach to chromosomes at centromeres. The DNA sequence at regional centromeres is fast evolving with no conserved genetic signature for centromere identity. Instead CENH3, a centromere-specific histone H3 variant, is the epigenetic signature that specifies centromere location across both plant and animal kingdoms. Paradoxically, CENH3 is also adaptively evolving. An ongoing question is whether CENH3 evolution is driven by a functional relationship with the underlying DNA sequence...
February 21, 2017: Genome Research
https://www.readbyqxmd.com/read/28223252/the-origin-and-evolution-of-basigin-bsg-gene-a-comparative-genomic-and-phylogenetic-analysis
#14
Xinyan Zhu, Shenglan Wang, Mingjie Shao, Jie Yan, Fei Liu
Basigin (BSG), also known as extracellular matrix metalloproteinase inducer (EMMPRIN) or cluster of differentiation 147 (CD147), plays various fundamental roles in the intercellular recognition involved in immunologic phenomena, differentiation, and development. In this study, we aimed to compare the similarities and differences of BSG among organisms and explore possible evolutionary relationships based on the comparison result. We used the extensive BLAST tool to search the metazoan genomes, N-glycosylation sites, the transmembrane region and other functional sites...
February 18, 2017: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/28222808/detection-and-genome-characterization-of-four-novel-bat-hepadnaviruses-and-a-hepevirus-in-china
#15
Bo Wang, Xing-Lou Yang, Wen Li, Yan Zhu, Xing-Yi Ge, Li-Biao Zhang, Yun-Zhi Zhang, Claus-Thomas Bock, Zheng-Li Shi
BACKGROUND: In recent years, novel hepadnaviruses, hepeviruses, hepatoviruses, and hepaciviruses have been discovered in various species of bat around the world, indicating that bats may act as natural reservoirs for these hepatitis viruses. In order to further assess the distribution of hepatitis viruses in bat populations in China, we tested the presence of these hepatitis viruses in our archived bat liver samples that originated from several bat species and various geographical regions in China...
February 22, 2017: Virology Journal
https://www.readbyqxmd.com/read/28222791/epig-statistical-inference-and-profiling-of-dna-methylation-from-whole-genome-bisulfite-sequencing-data
#16
Martin Vincent, Kamilla Mundbjerg, Jakob Skou Pedersen, Gangning Liang, Peter A Jones, Torben Falck Ørntoft, Karina Dalsgaard Sørensen, Carsten Wiuf
The study of epigenetic heterogeneity at the level of individual cells and in whole populations is the key to understanding cellular differentiation, organismal development, and the evolution of cancer. We develop a statistical method, epiG, to infer and differentiate between different epi-allelic haplotypes, annotated with CpG methylation status and DNA polymorphisms, from whole-genome bisulfite sequencing data, and nucleosome occupancy from NOMe-seq data. We demonstrate the capabilities of the method by inferring allele-specific methylation and nucleosome occupancy in cell lines, and colon and tumor samples, and by benchmarking the method against independent experimental data...
February 21, 2017: Genome Biology
https://www.readbyqxmd.com/read/28222765/new-h6-influenza-virus-reassortment-strains-isolated-from-anser-fabalis-in-anhui-province-china
#17
Ye Ge, Hongliang Chai, Zhiqiang Fan, Xianfu Wang, Qiucheng Yao, Jian Ma, Si Chen, Yuping Hua, Guohua Deng, Hualan Chen
BACKGROUND: H6 subtype avian influenza viruses are globally distributed and, in recent years, have been isolated with increasing frequency from both domestic and wild bird species as well as infected humans. Many reports have examined the viruses in the context of poultry or several wild bird species, but there is less information regarding their presence in migratory birds. METHODS: Hemagglutination and hemagglutination inhibition tests were used to measure HA activity for different HA subtypes...
February 21, 2017: Virology Journal
https://www.readbyqxmd.com/read/28222695/evolution-and-expression-of-the-fructokinase-gene-family-in-saccharum
#18
Yihong Chen, Qing Zhang, Weichang Hu, Xingtan Zhang, Liming Wang, Xiuting Hua, Qingyi Yu, Ray Ming, Jisen Zhang
BACKGROUND: Sugarcane is an important sugar crop contributing up to about 80% of the world sugar production. Efforts to characterize the genes involved in sugar metabolism at the molecular level are growing since increasing sugar content is a major goal in the breeding of new sugarcane varieties. Fructokinases (FRK) are the main fructose phosphorylating enzymes with high substrate specificity and affinity. RESULTS: In this study, by combining comparative genomics approaches with BAC resources, seven fructokinase genes were identified in S...
February 21, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28222679/comparative-mitogenomics-indicates-respiratory-competence-in%C3%A2-parasitic-viscum-despite%C3%A2-loss-of-complex-i%C3%A2-and-extreme-sequence%C3%A2-divergence-and-reveals-horizontal-gene-transfer-and-remarkable%C3%A2-variation-in-genome-size
#19
Elizabeth Skippington, Todd J Barkman, Danny W Rice, Jeffrey D Palmer
BACKGROUND: Aerobically respiring eukaryotes usually contain four respiratory-chain complexes (complexes I-IV) and an ATP synthase (complex V). In several lineages of aerobic microbial eukaryotes, complex I has been lost, with an alternative, nuclear-encoded NADH dehydrogenase shown in certain cases to bypass complex I and oxidize NADH without proton translocation. The first loss of complex I in any multicellular eukaryote was recently reported in two studies; one sequenced the complete mitogenome of the hemiparasitic aerial mistletoe, Viscum scurruloideum, and the other sequenced the V...
February 21, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28220980/the-fire-ant-social-chromosome-supergene-variant-sb-shows-low-diversity-but-high-divergence-from-sb
#20
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
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