Abstract:
:Detecting and quantifying the differences in individual genomes (i.e., genotyping), plays a fundamental role in most modern bioinformatics pipelines. Many scientists now use reduced representation next-generation sequencing (NGS) approaches for genotyping. Genotyping diploid individuals using NGS is a well-studied field, and similar methods for polyploid individuals are just emerging. However, there are many aspects of NGS data, particularly in polyploids, that remain unexplored by most methods. Our contributions in this paper are fourfold: (i) We draw attention to, and then model, common aspects of NGS data: sequencing error, allelic bias, overdispersion, and outlying observations. (ii) Many datasets feature related individuals, and so we use the structure of Mendelian segregation to build an empirical Bayes approach for genotyping polyploid individuals. (iii) We develop novel models to account for preferential pairing of chromosomes, and harness these for genotyping. (iv) We derive oracle genotyping error rates that may be used for read depth suggestions. We assess the accuracy of our method in simulations, and apply it to a dataset of hexaploid sweet potato (Ipomoea batatas). An R package implementing our method is available at https://cran.r-project.org/package=updog.
journal_name
Geneticsjournal_title
Geneticsauthors
Gerard D,Ferrão LFV,Garcia AAF,Stephens Mdoi
10.1534/genetics.118.301468subject
Has Abstractpub_date
2018-11-01 00:00:00pages
789-807issue
3eissn
0016-6731issn
1943-2631pii
genetics.118.301468journal_volume
210pub_type
杂志文章相关文献
GENETICS文献大全abstract::Drosophila melanogaster males dosage compensate by twofold upregulation of the expression of genes on their single X chromosome. This process requires at least five proteins and two noncoding RNAs, roX1 and roX2, which paint the male X chromosome. We used a deletion analysis to search for functional RNA domains within...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:2003-07-01 00:00:00
abstract::To investigate the regulation of Drosophila melanogaster behavior by biogenic amines, we have exploited the broad requirement of the vesicular monoamine transporter (VMAT) for the vesicular storage and exocytotic release of all monoamine neurotransmitters. We used the Drosophila VMAT (dVMAT) null mutant to globally ab...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.112.142042
更新日期:2013-01-01 00:00:00
abstract::F1 hybrids between mouse inbred strains PWD and C57BL/6 represent the most thoroughly genetically defined model of hybrid sterility in vertebrates. Hybrid male sterility can be fully reconstituted from three components of this model, the Prdm9 gene, intersubspecific homeology of Mus musculus musculus and Mus musculus ...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.119.302554
更新日期:2019-11-01 00:00:00
abstract::Aimed at investigating the recovery of a specific mutant allele of the mating type locus (MAT) by switching a defective MAT allele, these experiments provide information bearing on several models proposed for MAT interconversion in bakers yeast, Saccharomyces cerevisiae. Hybrids between heterothallic (ho) cells carryi...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1979-07-01 00:00:00
abstract::About 450 black rats (Rattus rattus) were collected from 25 localities in Asia and Oceania. Their serum transferrins were analyzed by a newly developed thin layer acrylamide gel electrophoresis accompanied with acrinol pretreatment, exhibiting 12 transferrin bands. Generally, Asian type rats (2N=42) had fast-moving tr...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1975-02-01 00:00:00
abstract::A radiation-induced translocation, T(IIR----IIIL), has been shown to be nonreciprocal and to have most of IIR, including its terminus, attached uninverted to the terminus of IIIL.--Progeny with the IIR segment in duplicate, obtained from crosses of T(IIR----IIIL) to strains with a standard genome, were unstable at mit...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1985-06-01 00:00:00
abstract::The pathogenic life cycle of the rice blast fungus Magnaporthe oryzae involves a series of morphogenetic changes, essential for its ability to cause disease. The smo mutation was identified > 25 years ago, and affects the shape and development of diverse cell types in M. oryzae, including conidia, appressoria, and asc...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.118.301490
更新日期:2019-01-01 00:00:00
abstract::This paper studies the properties of a new class of demographic parameters for age-structured populations and analyzes the effect of natural selection on these parameters. Two new demographic variables are introduced: the entropy of a population and the reproductive potential. The entropy of a population measures the ...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1975-03-01 00:00:00
abstract::Mutants of Salmonella typhimurium lacking DNA adenine methylase were isolated; they include insertion and deletion alleles. The dam locus maps at 75 min between cysG and aroB, similar to the Escherichia coli dam gene. Dam- mutants of S. typhimurium resemble those of E coli in the following phenotypes: (1) increased sp...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1996-09-01 00:00:00
abstract::The genomes of all organisms are subject to continuous bombardment of deleterious genomic mutations (DGM). Our ability to accurately estimate various parameters of DGM has profound significance in population and evolutionary genetics. The Deng-Lynch method can estimate the parameters of DGM in natural selfing and outc...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:2002-11-01 00:00:00
abstract::fl(2)d, the Drosophila homolog of Wilms'-tumor-1-associated protein (WTAP), regulates the alternative splicing of Sex-lethal (Sxl), transformer (tra), and Ultrabithorax (Ubx). Although WTAP has been found in functional human spliceosomes, exactly how it contributes to the splicing process remains unknown. Here we atte...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.107.081679
更新日期:2008-02-01 00:00:00
abstract::The protein phosphatase calcineurin is central to Ca2+ signaling pathways from yeast to humans. Full activation of calcineurin requires Ca2+ binding to the regulatory subunit CNB, comprised of four Ca2+-binding EF hand domains, and recruitment of Ca2+-calmodulin. Here we report the consequences of disrupting Ca2+ bind...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.118.300911
更新日期:2018-07-01 00:00:00
abstract::Studies of transcriptional gene silencing in Drosophila melanogaster suggest that most of chromosome 4 resembles pericentric heterochromatin. However, some modifiers of position-effect variegation, including chromosome 4 dosage and loss of SU(VAR)3-9, have different effects on silencing in pericentric vs. distal arm c...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.106.066407
更新日期:2007-03-01 00:00:00
abstract::Two-dimensional paper chromatography was performed on methanol extracts of leaves of hexaploid bread wheat, Triticum aestivum L. em. Thell. cultivar Chinese Spring, and of the available nullisomic-tetrasomic compensating lines, the tetrasomic lines and the ditelocentric lines. The chromatograms had 27 spots identified...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1983-02-01 00:00:00
abstract::Hybrid matings between the sexual species Poeciliopsis monacha and Poeciliopsis lucida produced a series of diploid all-female lineages of P. monacha-lucida that inhabit the Río Fuerte of northwestern Mexico. Restriction site analyses of mitochondrial DNA (mtDNA) clearly revealed that P. monacha was the maternal ances...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1991-02-01 00:00:00
abstract::Lethal and sterility mutations were accumulated in a cage population which was initiated with lethal- and sterility-free second chromosomes of D. melanogaster. It took about 2,000 days for the frequencies of these genes to reach equilibrium levels, i.e., 18% lethal and 9% male-sterile chromosomes. Two other cage popul...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1977-07-01 00:00:00
abstract::Sexual isolating mechanisms that act before fertilization are often considered the most important genetic barriers leading to speciation in animals. While recent progress has been made toward understanding the genetic basis of the postzygotic isolating mechanisms of hybrid sterility and inviability, little is known ab...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.103.024364
更新日期:2004-07-01 00:00:00
abstract::DnaB is the helicase associated with the DNA polymerase III replication fork in Escherichia coli. Previously we observed that the dnaB107(ts) mutation, at its permissive temperature, greatly stimulated deletion events at chromosomal tandem repeats. This stimulation required recA, which suggests a recombinational mecha...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1999-05-01 00:00:00
abstract::This report examines five different naturally occurring alcohol dehydrogenase-1 alleles via the recombinational behavior of Adh1(-) mutants induced within them. Twenty-two biochemically characterized Adh1(-) mutants have been assessed for ability to recombine intragenically, using data generated by specifically staini...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1978-05-01 00:00:00
abstract::We formalize the use of allele frequency and geographic information for the construction of gene trees at the intraspecific level and extend the concept of evolutionary parsimony to molecular variance parsimony. The central principle is to consider a particular gene tree as a variable to be optimized in the estimation...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1994-01-01 00:00:00
abstract::To test genetic recombination in the vicinity of insertions of the transposon Tn5, crosses were performed by transduction between M. xanthus strains carrying different insertions of Tn5. One member of each pair carried resistance to kanamycin (Tn5-Km); the other carried resistance to tetracycline (Tn5-Tc). The distanc...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1983-10-01 00:00:00
abstract::Chromosomal double-strand breaks (DSBs) that have only one end with homology to a donor duplex undergo repair by strand invasion followed by replication to the chromosome terminus (break-induced replication, BIR). Using a transformation-based assay system, it was previously shown that BIR could occur by several rounds...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.114.162297
更新日期:2014-04-01 00:00:00
abstract::A natural population of Culex tritaeniorhynchus was sampled to test the efficacy of a proposed method to detect and measure concealed variability. Thirty-nine lethals and ten recessive visible mutations were uncovered out of a total of 125 chromosomes tested. ...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1972-06-01 00:00:00
abstract::The occurrence and patterns of linkage disequilibrium between an inversion and allozymic loci within it or nearby have been used in attempts to discriminate among different hypotheses for the maintenance of variability. The interpretation of the data on the best-documented case, that of the nonrandom association betwe...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1987-01-01 00:00:00
abstract::The multigene family of rDNA in Drosophila reveals high levels of within-species homogeneity and between-species diversity. This pattern of mutation distribution is known as concerted evolution and is considered to be due to a variety of genomic mechanisms of turnover (e.g., unequal crossing over and gene conversion) ...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1998-05-01 00:00:00
abstract::The Mus101 family of chromosomal proteins, identified initially in Drosophila, is widely conserved and has been shown to function in a variety of DNA metabolic processes. Such functions include DNA replication, DNA damage repair, postreplication repair, damage checkpoint activation, chromosome stability, and chromosom...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.104.036137
更新日期:2005-03-01 00:00:00
abstract::The maize ligule is an adaxial membranous structure on the leaf that develops at the boundary of the sheath and blade. The ligule and the associated auricle are dispensable structures, amenable to genetic manipulation. We present here a genetic analysis of liguleless1 (lg1) and liguleless2 (lg2), the two genes known t...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1996-12-01 00:00:00
abstract::The K1 killer plasmid, [KIL-k1], of Saccharomyces cerevisiae is a 1.25 x 10(6) dalton linear double-stranded RNA plasmid coding for a protein toxin and immunity to that toxin. The [KIL-sd1] plasmid is a replication-defective mutant of [KIL-k1] that depends on one of the recessive chromosomal superkiller (ski-) mutatio...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1982-02-01 00:00:00
abstract::Many insects feed on only one or a few types of host. These host specialists often evolve a preference for chemical cues emanating from their host and develop mechanisms for circumventing their host's defenses. Adaptations like these are central to evolutionary biology, yet our understanding of their genetics remains ...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.113.154773
更新日期:2013-11-01 00:00:00
abstract::While mitochondria are renowned for their role in energy production, they also perform several other integral functions within the cell. Thus, it is not surprising that mitochondrial dysfunction can negatively impact cell viability. Although mitochondria have received an increasing amount of attention in recent years,...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.110.117200
更新日期:2010-08-01 00:00:00