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Extension of Lander-Waterman theory for sequencing filtered DNA libraries
Michael C Wendl, W Brad Barbazuk
BMC Bioinformatics , 2005, DOI: 10.1186/1471-2105-6-245
Abstract: The edge effect cannot be neglected in most cases. Specifically, rates of coverage and gap reduction are appreciably lower than those for conventional libraries, as predicted by standard theory. Performance decreases as read length increases relative to island size. Although opposite of what happens in a conventional library, this apparent paradox is readily explained in terms of the edge effect. The model agrees well with prototype gene-tagging experiments for Zea mays and Sorghum bicolor. Moreover, the associated density function suggests well-defined probabilistic milestones for the number of reads necessary to capture a given fraction of the gene space. An exception for applying standard theory arises if sequence redundancy is less than about 1-fold. Here, evolution of the random quantities is independent of library gaps and edge effects. This observation effectively validates the practice of using standard theory to estimate the genic enrichment of a library based on light shotgun sequencing.Coverage performance using a filtered library is significantly lower than that for an equivalent-sized conventional library, suggesting that directed methods may be more critical for the former. The proposed model should be useful for analyzing future projects.Over the last few decades, DNA sequencing has firmly established its role in the broader enterprises of scientific and medical research. Enabled by ongoing development and refinement of laboratory techniques, instruments, and software, investigators are now studying a wide array of genomes at a level of sophistication not before possible. While a number of sequencing approaches have been devised, experience indicates that the efficacy of any particular one depends strongly upon the context of the target sequence. For instance, the whole genome shotgun (WGS) procedure has proved especially suited to microbes [1]. Conversely, mammalian projects are being completed using large-insert mapped clones, which are better able
Exploring Diversification and Genome Size Evolution in Extant Gymnosperms through Phylogenetic Synthesis
J. Gordon Burleigh,W. Brad Barbazuk,John M. Davis,Alison M. Morse,Pamela S. Soltis
Journal of Botany , 2012, DOI: 10.1155/2012/292857
Abstract: Gymnosperms, comprising cycads, Ginkgo, Gnetales, and conifers, represent one of the major groups of extant seed plants. Yet compared to angiosperms, little is known about the patterns of diversification and genome evolution in gymnosperms. We assembled a phylogenetic supermatrix containing over 4.5 million nucleotides from 739 gymnosperm taxa. Although 93.6% of the cells in the supermatrix are empty, the data reveal many strongly supported nodes that are generally consistent with previous phylogenetic analyses, including weak support for Gnetales sister to Pinaceae. A lineage through time plot suggests elevated rates of diversification within the last 100 million years, and there is evidence of shifts in diversification rates in several clades within cycads and conifers. A likelihood-based analysis of the evolution of genome size in 165 gymnosperms finds evidence for heterogeneous rates of genome size evolution due to an elevated rate in Pinus. 1. Introduction Recent advances in sequencing technology offer the possibility of identifying the genetic mechanisms that influence evolutionarily important characters and ultimately drive diversification. Within angiosperms, large-scale phylogenetic analyses have identified complex patterns of diversification (e.g., [1–3]), and numerous genomes are at least partially sequenced. Yet the other major clade of seed plants, the gymnosperms, have received far less attention, with few comprehensive studies of diversification and no sequenced genomes. Note that throughout this paper “gymnosperms” specifies only the approximately 1000 extant species within cycads, Ginkgo, Gnetales, and conifers. These comprise the Acrogymnospermae clade described by Cantino et al. [4]. Many gymnosperms have exceptionally large genomes (e.g., [5–7]), and this has hindered whole-genome sequencing projects, especially among economically important Pinus species. This large genome size is interesting because one suggested mechanism for rapid increases in genome size, polyploidy, is rare among gymnosperms [8]. Recent sequencing efforts have elucidated some of genomic characteristics associated with the large genome size in Pinus. Morse et al. [9] identified a large retrotransposon family in Pinus, that, with other retrotransposon families, accounts for much of the genomic complexity. Similarly, recent sequencing of 10 BAC (bacterial artificial chromosome) clones from Pinus taeda identified many conifer-specific LTR (long terminal repeat) retroelements [10]. These studies suggest that the large genome size may be caused by rapid expansion of
Novel and nodulation-regulated microRNAs in soybean roots
Senthil Subramanian, Yan Fu, Ramanjulu Sunkar, W Brad Barbazuk, Jian-Kang Zhu, Oliver Yu
BMC Genomics , 2008, DOI: 10.1186/1471-2164-9-160
Abstract: We sequenced ~350000 small RNAs from soybean roots inoculated with B. japonicum and identified conserved miRNAs based on similarity to miRNAs known in other plant species and new miRNAs based on potential hairpin-forming precursors within soybean EST and shotgun genomic sequences. These bioinformatics analyses identified 55 families of miRNAs of which 35 were novel. A subset of these miRNAs were validated by Northern analysis and miRNAs differentially responding to B. japonicum inoculation were identified. We also identified putative target genes of the identified miRNAs and verified in vivo cleavage of a subset of these targets by 5'-RACE analysis. Using conserved miRNAs as internal control, we estimated that our analysis identified ~50% of miRNAs in soybean roots.Construction and analysis of a small RNA library led to the identification of 20 conserved and 35 novel miRNA families in soybean. The availability of complete and assembled genome sequence information will enable identification of many other miRNAs. The conserved miRNA loci and novel miRNAs identified in this study enable investigation of the role of miRNAs in rhizobial symbiosis.Symbiotic association between leguminous plants and rhizobia bacteria results in specialized nitrogen-fixing structures called root nodules. The interaction between the symbiotic partners starts with the exchange of chemical signals. Legumes release specific flavonoids (a group of small phenolic compounds) as signal molecules into the soil through root exudates. Compatible rhizobia bacteria (Bradyrhizobium japonicum in case of soybean) respond by producing specific lipochitooligosaccharide (LCO) bacterial signals which are in turn recognized by plants [1-3] resulting in the attachment of bacterial cells to plant root hairs. Signal transduction leading to the process of nodule development commences upon recognition of compatible bacterial LCOs on the root surface by the plants. The immediate responses are ion fluxes (Ca2+ influx
High-Resolution Genotyping via Whole Genome Hybridizations to Microarrays Containing Long Oligonucleotide Probes
Yan Fu,Nathan M. Springer,Kai Ying,Cheng-Ting Yeh,A. Leonardo Iniguez,Todd Richmond,Wei Wu,Brad Barbazuk,Dan Nettleton,Jeff Jeddeloh,Patrick S. Schnable
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0014178
Abstract: To date, microarray-based genotyping of large, complex plant genomes has been complicated by the need to perform genome complexity reduction to obtain sufficiently strong hybridization signals. Genome complexity reduction techniques are, however, tedious and can introduce unwanted variables into genotyping assays. Here, we report a microarray-based genotyping technology for complex genomes (such as the 2.3 GB maize genome) that does not require genome complexity reduction prior to hybridization. Approximately 200,000 long oligonucleotide probes were identified as being polymorphic between the inbred parents of a mapping population and used to genotype two recombinant inbred lines. While multiple hybridization replicates provided ~97% accuracy, even a single replicate provided ~95% accuracy. Genotyping accuracy was further increased to >99% by utilizing information from adjacent probes. This microarray-based method provides a simple, high-density genotyping approach for large, complex genomes.
Optical mapping as a routine tool for bacterial genome sequence finishing
Phil Latreille, Stacie Norton, Barry S Goldman, John Henkhaus, Nancy Miller, Brad Barbazuk, Helge B Bode, Creg Darby, Zijin Du, Steve Forst, Sophie Gaudriault, Brad Goodner, Heidi Goodrich-Blair, Steven Slater
BMC Genomics , 2007, DOI: 10.1186/1471-2164-8-321
Abstract: Whole genome restriction maps of the sequenced strains were produced through optical mapping technology. These maps allowed rapid resolution of sequence assembly problems, permitted closing of the genome, and allowed correction of a large inversion in a genome assembly that we had considered finished.Our experience suggests that routine use of optical mapping in bacterial genome sequence finishing is warranted. When combined with data produced through 454 sequencing, an optical map can rapidly and inexpensively generate an ordered and oriented set of contigs to produce a nearly complete genome sequence assembly.Xenorhabdus species are symbiotic bacteria associated with insectivorous nematodes of the genus Steinernema (for review see [1]) They reside in a specialized segment of the nematode gut [2,3], and provide insecticidal proteins [4,5] and small molecules [6-10] that help to kill the insect larvae that are the prey of the nematode. Both organisms reproduce in the dead larvae, the Xenorhabdus colonize the young nematodes, and the cycle repeats [11]. Xenorhabdus are closely related to the enteric gamma proteobacteria such as Escherichia coli [12], and are an emerging model for both mutualism and pathogenicity in invertebrate hosts. To better understand the genetic basis of these relationships, we are sequencing the genomes of two Xenorhabdus species: X. nematophila ATCC 19061 and an X. bovienii strain from Monsanto's collection.In the course of this work, we found that the X. nematophila genome contained large numbers of highly repetitive DNA regions, and efforts to finish the genome stalled. We sought a means to produce whole-genome maps for comparison with the genomic DNA sequence, and identified optical mapping as a useful means to align and orient the genome sections in silico. In addition, we produced an optical map of a second genome that we had considered finished, and identified a large sequence inversion that would have otherwise been unnoticed.Eight-fold
Consciousness & Time: A Time-Based Model of the Evolution of Consciousness  [PDF]
Brad Bowins
Journal of Behavioral and Brain Science (JBBS) , 2017, DOI: 10.4236/jbbs.2017.71002
Abstract: A novel theoretical model is presented maintaining that consciousness evolved on the basis of time distinctions. Various models of time pertain to the existence of future, present and past. It is proposed that the future represents potentialities, the present the actualization of certain potentialities, and the past a record of actualized potentialities. Actualization of potentialities derives from micro quantum wave function collapses with specific constellations corresponding to macro level form. Consciousness provides for an awareness of potentialities being actualized in the present, the time frame of consciousness closely aligning with the time frame of potentialities being actualized in the moment. Evolution of such awareness is highly probable, given the ensuing motivation enabling behavior to be altered in the moment to minimize the actualization of maladaptive potentialities, and maximize the actualization of adaptive potentialities. The model also provides a logical proof for the occurrence of time distinctions.
Maize Inbreds Exhibit High Levels of Copy Number Variation (CNV) and Presence/Absence Variation (PAV) in Genome Content
Nathan M. Springer equal contributor,Kai Ying equal contributor,Yan Fu,Tieming Ji,Cheng-Ting Yeh,Yi Jia,Wei Wu,Todd Richmond,Jacob Kitzman,Heidi Rosenbaum,A. Leonardo Iniguez,W. Brad Barbazuk,Jeffrey A. Jeddeloh,Dan Nettleton,Patrick S. Schnable
PLOS Genetics , 2009, DOI: 10.1371/journal.pgen.1000734
Abstract: Following the domestication of maize over the past ~10,000 years, breeders have exploited the extensive genetic diversity of this species to mold its phenotype to meet human needs. The extent of structural variation, including copy number variation (CNV) and presence/absence variation (PAV), which are thought to contribute to the extraordinary phenotypic diversity and plasticity of this important crop, have not been elucidated. Whole-genome, array-based, comparative genomic hybridization (CGH) revealed a level of structural diversity between the inbred lines B73 and Mo17 that is unprecedented among higher eukaryotes. A detailed analysis of altered segments of DNA conservatively estimates that there are several hundred CNV sequences among the two genotypes, as well as several thousand PAV sequences that are present in B73 but not Mo17. Haplotype-specific PAVs contain hundreds of single-copy, expressed genes that may contribute to heterosis and to the extraordinary phenotypic diversity of this important crop.
Influence of deficit irrigation on nutrient indices in wine grape (Vitis vinifera L.)  [PDF]
Krista Shellie, Brad Brown
Agricultural Sciences (AS) , 2012, DOI: 10.4236/as.2012.32031
Abstract: Deficit irrigation is widely used in wine grape production (Vitis vinifera L.) to meet wine quality goals yet its influence on tissue nutrient indices has not been well studied. The objective of this research was to determine whether response to water deficit compromised the prescriptive usefulness of tissue nutrient analyses. Tissue macro and micronutrient composition at bloom and veraison were evaluated over multiple seasons in nine wine grape cultivars grown under well-watered or deficit-irrigated conditions. Deficit-irrigated vines sampled at veraison had 2 to 12-fold higher petiole nitrate-nitrogen concentration, 6% lower blade nitrogen concentration and 13% lower blade copper concentration compared to well-watered vines. Water deficit influenced blade potassium concentration at veraison differently according to cultivar and was lower (cv. Malbec, Petite syrah, Viognier, Lemberger and Sangiovese), higher (cv. Merlot, Cabernet franc and Cabernet Sauvignon) or similar (cv. Grenache) to well-watered vines. Results from this study indicate that nutrient analysis of petiole or blade tissue sampled at veraison has limited diagnostic and prescriptive usefulness when vines are grown under a water deficit.
A physical map for the Amborella trichopoda genome sheds light on the evolution of angiosperm genome structure
Andrea Zuccolo, John E Bowers, James C Estill, Zhiyong Xiong, Meizhong Luo, Aswathy Sebastian, José Goicoechea, Kristi Collura, Yeisoo Yu, Yuannian Jiao, Jill Duarte, Haibao Tang, Saravanaraj Ayyampalayam, Steve Rounsley, Dave Kudrna, Andrew H Paterson, J Pires, Andre Chanderbali, Douglas E Soltis, Srikar Chamala, Brad Barbazuk, Pamela S Soltis, Victor A Albert, Hong Ma, Dina Mandoli, Jody Banks, John E Carlson, Jeffrey Tomkins, Claude W dePamphilis, Rod A Wing, Jim Leebens-Mack
Genome Biology , 2011, DOI: 10.1186/gb-2011-12-5-r48
Abstract: Analysis of Amborella BAC ends sequenced from each contig suggests that the density of long terminal repeat retrotransposons is negatively correlated with that of protein coding genes. Syntenic, presumably ancestral, gene blocks were identified in comparisons of the Amborella BAC contigs and the sequenced Arabidopsis thaliana, Populus trichocarpa, Vitis vinifera and Oryza sativa genomes. Parsimony mapping of the loss of synteny corroborates previous analyses suggesting that the rate of structural change has been more rapid on lineages leading to Arabidopsis and Oryza compared with lineages leading to Populus and Vitis. The gamma paleohexiploidy event identified in the Arabidopsis, Populus and Vitis genomes is shown to have occurred after the divergence of all other known angiosperms from the lineage leading to Amborella.When placed in the context of a physical map, BAC end sequences representing just 5.4% of the Amborella genome have facilitated reconstruction of gene blocks that existed in the last common ancestor of all flowering plants. The Amborella genome is an invaluable reference for inferences concerning the ancestral angiosperm and subsequent genome evolution.The origin and rapid diversification of the angiosperms (flowering plants) were pivotal events in the evolutionary history of Earth's biota. Over the past 130 to 150 million years angiosperms have diversified to include approximately 350,000 species occupying nearly all habitable terrestrial and many aquatic environments. Angiosperms generate the vast majority of human food either directly or indirectly as animal feed, and they account for a huge proportion of land-based photosynthesis and carbon sequestration. Comparative analyses of genome sequences and gene function for a growing number of species are shedding light on how gene and genome duplications have contributed to the diversification within major flowering plant lineages (for example, Rosidae, Asteridae, Monocotyledoneae [1]), but elucidation
Novel Insights into Disseminated Candidiasis: Pathogenesis Research and Clinical Experience Converge
Brad Spellberg
PLOS Pathogens , 2008, DOI: 10.1371/journal.ppat.0040038
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