A Maize Practical Haplotype Graph Leverages Diverse NAM Assemblies

AbstractAs a result of millions of years of transposon activity, multiple rounds of ancient polyploidization, and large populations that preserve diversity, maize has an extremely structurally diverse genome, evidenced by high-quality genome assemblies that capture substantial levels of both tropical and temperate diversity. We generated a pangenome representation (the Practical Haplotype Graph, PHG) of these assemblies in a database, representing the pangenome haplotype diversity and providing an initial estimate of structural diversity. We leveraged the pangenome to accurately impute haplotypes and genotypes of taxa using various kinds of sequence data, ranging from WGS to extremely-low coverage GBS. We imputed the genotypes of the recombinant inbred lines of the NAM population with over 99% mean accuracy, while unrelated germplasm attained a mean imputation accuracy of 92 or 95% when using GBS or WGS data, respectively. Most of the imputation errors occur in haplotypes within European or tropical germplasm, which have yet to be represented in the maize PHG database. Also, the PHG stores the imputation data in a 30,000-fold more space-efficient manner than a standard genotype file, which is a key improvement when dealing with large scale data.

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A Phylogenomic Supertree of Birds

Diversity ◽

10.3390/d11070109 ◽

2019 ◽

Vol 11 (7) ◽

pp. 109 ◽

Cited By ~ 17

Author(s):

Rebecca T. Kimball ◽

Carl H. Oliveros ◽

Ning Wang ◽

Noor D. White ◽

F. Keith Barker ◽

...

Keyword(s):

Large Scale ◽

Sequence Data ◽

Bird Species ◽

Divide And Conquer ◽

Clear Understanding ◽

Whole Genome ◽

Efficient Manner ◽

Sequence Capture ◽

Branch Lengths ◽

Supertree Methods

It has long been appreciated that analyses of genomic data (e.g., whole genome sequencing or sequence capture) have the potential to reveal the tree of life, but it remains challenging to move from sequence data to a clear understanding of evolutionary history, in part due to the computational challenges of phylogenetic estimation using genome-scale data. Supertree methods solve that challenge because they facilitate a divide-and-conquer approach for large-scale phylogeny inference by integrating smaller subtrees in a computationally efficient manner. Here, we combined information from sequence capture and whole-genome phylogenies using supertree methods. However, the available phylogenomic trees had limited overlap so we used taxon-rich (but not phylogenomic) megaphylogenies to weave them together. This allowed us to construct a phylogenomic supertree, with support values, that included 707 bird species (~7% of avian species diversity). We estimated branch lengths using mitochondrial sequence data and we used these branch lengths to estimate divergence times. Our time-calibrated supertree supports radiation of all three major avian clades (Palaeognathae, Galloanseres, and Neoaves) near the Cretaceous-Paleogene (K-Pg) boundary. The approach we used will permit the continued addition of taxa to this supertree as new phylogenomic data are published, and it could be applied to other taxa as well.

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Limited haplotype diversity underlies polygenic trait architecture across 70 years of wheat breeding

10.1101/2020.09.15.296533 ◽

2020 ◽

Cited By ~ 1

Author(s):

Michael F. Scott ◽

Nick Fradgley ◽

Alison R. Bentley ◽

Thomas Brabbs ◽

Fiona Corke ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Bread Wheat ◽

Genome Sequencing ◽

Recombinant Inbred Lines ◽

Crop Improvement ◽

Imputation Accuracy ◽

Wheat Yield ◽

Haplotype Diversity ◽

Wheat Breeding ◽

Whole Genome

AbstractBackgroundBreeding has helped improve bread wheat yield significantly over the last century. Understanding the potential for future crop improvement depends on relating segregating genetic variation to agronomic traits.ResultsWe bred NIAB Diverse MAGIC population, comprising over 500 recombinant inbred lines, descended from sixteen bread wheat varieties released between 1935-2004. We sequenced the founders’ exomes and promotors by capture. Despite being highly representative of North-West European wheat and capturing 73% of global polymorphism, we found 89% of genes contained no more than three haplotypes. We sequenced each line with 0.3x coverage whole-genome sequencing, and imputed 1.1M high-quality SNPs that were over 99% concordant with array genotypes. Imputation accuracy remained high at coverage as low as 0.076x, with or without the use of founder genomes as reference panels. We created a genotype-phenotype map for 47 traits over two years. We found 136 genome-wide significant associations, concentrated at 42 genetic loci with large and often pleiotropic effects. Outside of these loci most traits are polygenic, as revealed by multi-locus shrinkage modelling.ConclusionsHistorically, wheat breeding has reshuffled a limited palette of haplotypes; continued improvement will require selection at dozens of loci of diminishing effect, as most of the major loci we mapped are known. Breeding to optimise one trait generates correlated trait changes, exemplified by the negative trade-off between yield and protein content, unless selection and recombination can break critical unfavourable trait-trait associations. Finally, low coverage whole genome sequencing of bread wheat populations is an economical and accurate genotyping strategy.

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The Use of Medical Record Linkage for Population and Genetic Studies

Methods of Information in Medicine ◽

10.1055/s-0038-1635962 ◽

1969 ◽

Vol 08 (01) ◽

pp. 07-11 ◽

Cited By ~ 9

Author(s):

H. B. Newcombe

Keyword(s):

Record Linkage ◽

Large Scale ◽

Medical Record Linkage ◽

Canadian Province ◽

Genetic Studies ◽

Parental Characteristics ◽

Family Histories ◽

The Family ◽

Large Populations ◽

Machine Readable

Methods are described for deriving personal and family histories of birth, marriage, procreation, ill health and death, for large populations, from existing civil registrations of vital events and the routine records of ill health. Computers have been used to group together and »link« the separately derived records pertaining to successive events in the lives of the same individuals and families, rapidly and on a large scale. Most of the records employed are already available as machine readable punchcards and magnetic tapes, for statistical and administrative purposes, and only minor modifications have been made to the manner in which these are produced.As applied to the population of the Canadian province of British Columbia (currently about 2 million people) these methods have already yielded substantial information on the risks of disease: a) in the population, b) in relation to various parental characteristics, and c) as correlated with previous occurrences in the family histories.

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Dynamic Planning of Bicycle Stations in Dockless Public Bicycle-sharing System Using Gated Graph Neural Network

ACM Transactions on Intelligent Systems and Technology ◽

10.1145/3446342 ◽

2021 ◽

Vol 12 (2) ◽

pp. 1-22

Author(s):

Jianguo Chen ◽

Kenli Li ◽

Keqin Li ◽

Philip S. Yu ◽

Zeng Zeng

Keyword(s):

Large Scale ◽

Sequence Data ◽

Location Prediction ◽

City Management ◽

Dynamic Planning ◽

Graph Sequence ◽

Graph Modeling ◽

The Government ◽

Location Clustering ◽

Station Location

Benefiting from convenient cycling and flexible parking locations, the Dockless Public Bicycle-sharing (DL-PBS) network becomes increasingly popular in many countries. However, redundant and low-utility stations waste public urban space and maintenance costs of DL-PBS vendors. In this article, we propose a Bicycle Station Dynamic Planning (BSDP) system to dynamically provide the optimal bicycle station layout for the DL-PBS network. The BSDP system contains four modules: bicycle drop-off location clustering, bicycle-station graph modeling, bicycle-station location prediction, and bicycle-station layout recommendation. In the bicycle drop-off location clustering module, candidate bicycle stations are clustered from each spatio-temporal subset of the large-scale cycling trajectory records. In the bicycle-station graph modeling module, a weighted digraph model is built based on the clustering results and inferior stations with low station revenue and utility are filtered. Then, graph models across time periods are combined to create a graph sequence model. In the bicycle-station location prediction module, the GGNN model is used to train the graph sequence data and dynamically predict bicycle stations in the next period. In the bicycle-station layout recommendation module, the predicted bicycle stations are fine-tuned according to the government urban management plan, which ensures that the recommended station layout is conducive to city management, vendor revenue, and user convenience. Experiments on actual DL-PBS networks verify the effectiveness, accuracy, and feasibility of the proposed BSDP system.

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The Evolution of Life Modes in Stictidaceae, with Three Novel Taxa

Journal of Fungi ◽

10.3390/jof7020105 ◽

2021 ◽

Vol 7 (2) ◽

pp. 105

Author(s):

Vinodhini Thiyagaraja ◽

Robert Lücking ◽

Damien Ertz ◽

Samantha C. Karunarathna ◽

Dhanushka N. Wanasinghe ◽

...

Keyword(s):

New Species ◽

Large Scale ◽

Sequence Data ◽

Large Subunit ◽

Monte Carlo Sampling ◽

Small Subunit ◽

Sensu Stricto ◽

Internal Transcribed Spacers ◽

Character State ◽

Phenotypic Data

Ostropales sensu lato is a large group comprising both lichenized and non-lichenized fungi, with several lineages expressing optional lichenization where individuals of the same fungal species exhibit either saprotrophic or lichenized lifestyles depending on the substrate (bark or wood). Greatly variable phenotypic characteristics and large-scale phylogenies have led to frequent changes in the taxonomic circumscription of this order. Ostropales sensu lato is currently split into Graphidales, Gyalectales, Odontotrematales, Ostropales sensu stricto, and Thelenellales. Ostropales sensu stricto is now confined to the family Stictidaceae, which includes a large number of species that are poorly known, since they usually have small fruiting bodies that are rarely collected, and thus, their taxonomy remains partly unresolved. Here, we introduce a new genus Ostropomyces to accommodate a novel lineage related to Ostropa, which is composed of two new species, as well as a new species of Sphaeropezia, S. shangrilaensis. Maximum likelihood and Bayesian inference analyses of mitochondrial small subunit spacers (mtSSU), large subunit nuclear rDNA (LSU), and internal transcribed spacers (ITS) sequence data, together with phenotypic data documented by detailed morphological and anatomical analyses, support the taxonomic affinity of the new taxa in Stictidaceae. Ancestral character state analysis did not resolve the ancestral nutritional status of Stictidaceae with confidence using Bayes traits, but a saprotrophic ancestor was indicated as most likely in a Bayesian binary Markov Chain Monte Carlo sampling (MCMC) approach. Frequent switching in nutritional modes between lineages suggests that lifestyle transition played an important role in the evolution of this family.

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Whole-genome sequence data suggests environmental adaptation of Ethiopian sheep populations

Genome Biology and Evolution ◽

10.1093/gbe/evab014 ◽

2021 ◽

Author(s):

Pamela Wiener ◽

Christelle Robert ◽

Abulgasim Ahbara ◽

Mazdak Salavati ◽

Ayele Abebe ◽

...

Keyword(s):

High Altitude ◽

Environmental Variables ◽

Large Scale ◽

Sequence Data ◽

Strong Association ◽

Environmental Adaptation ◽

Whole Genome Sequence ◽

Single Nucleotide Variants ◽

High Altitude Adaptation ◽

Altitude Adaptation

Abstract Great progress has been made over recent years in the identification of selection signatures in the genomes of livestock species. This work has primarily been carried out in commercial breeds for which the dominant selection pressures, are associated with artificial selection. As agriculture and food security are likely to be strongly affected by climate change, a better understanding of environment-imposed selection on agricultural species is warranted. Ethiopia is an ideal setting to investigate environmental adaptation in livestock due to its wide variation in geo-climatic characteristics and the extensive genetic and phenotypic variation of its livestock. Here, we identified over three million single nucleotide variants across 12 Ethiopian sheep populations and applied landscape genomics approaches to investigate the association between these variants and environmental variables. Our results suggest that environmental adaptation for precipitation-related variables is stronger than that related to altitude or temperature, consistent with large-scale meta-analyses of selection pressure across species. The set of genes showing association with environmental variables was enriched for genes highly expressed in human blood and nerve tissues. There was also evidence of enrichment for genes associated with high-altitude adaptation although no strong association was identified with hypoxia-inducible-factor (HIF) genes. One of the strongest altitude-related signals was for a collagen gene, consistent with previous studies of high-altitude adaptation. Several altitude-associated genes also showed evidence of adaptation with temperature, suggesting a relationship between responses to these environmental factors. These results provide a foundation to investigate further the effects of climatic variables on small ruminant populations.

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Cytochrome P450 mono-oxygenases in conifer genomes: discovery of members of the terpenoid oxygenase superfamily in spruce and pine

Biochemical Society Transactions ◽

10.1042/bst0341209 ◽

2006 ◽

Vol 34 (6) ◽

pp. 1209-1214 ◽

Cited By ~ 32

Author(s):

B. Hamberger ◽

J. Bohlmann

Keyword(s):

Cytochrome P450 ◽

Loblolly Pine ◽

Large Scale ◽

Expressed Sequence Tag ◽

Resin Acid ◽

Functional Characterization ◽

Structural Diversity ◽

Resin Acids ◽

Full Length Sequence ◽

Diterpene Resin Acids

Diterpene resin acids, together with monoterpenes and sesquiterpenes, are the most prominent defence chemicals in conifers. These compounds belong to the large group of structurally diverse terpenoids formed by enzymes known as terpenoid synthases. CYPs (cytochrome P450-dependent mono-oxygenases) can further increase the structural diversity of these terpenoids. While most terpenoids are characterized as specialized or secondary metabolites, some terpenoids, such as the phytohormones GA (gibberellic acid), BRs (brassinosteroids) and ABA (abscisic acid), have essential functions in plant growth and development. To date, very few CYP genes involved in conifer terpenoid metabolism have been functionally characterized and were limited to two systems, yew (Taxus) and loblolly pine (Pinus taeda). The characterized yew CYP genes are involved in taxol diterpene biosynthesis, while the only characterized pine terpenoid CYP gene is part of DRA (diterpene resin acid) biosynthesis. These CYPs from yew and pine are members of two apparently conifer-specific CYP families within the larger CYP85 clan, one of four plant CYP multifamily clans. Other CYP families within the CYP85 clan were characterized from a variety of angiosperms with functions in terpenoid phytohormone metabolism of GA, BR, and ABA. The recent development of EST (expressed sequence tag) and FLcDNA (where FL is full-length) sequence databases and cDNA collections for species of two conifers, spruce (Picea) and pine, allows for the discovery of new terpenoid CYPs in gymnosperms by means of large-scale sequence mining, phylogenetic analysis and functional characterization. Here, we present a snapshot of conifer CYP data mining, discovery of new conifer CYPs in all but one family within the CYP85 clan, and suggestions for their functional characterization. This paper will focus on the discovery of conifer CYPs associated with diterpene metabolism and CYP with possible functions in the formation of GA, BR, and ABA in conifers.

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Self-organizing Clustering: Non-hierarchical Clustering for Large Scale DNA Sequence Data

IPSJ Digital Courier ◽

10.2197/ipsjdc.3.193 ◽

2007 ◽

Vol 3 ◽

pp. 193-197 ◽

Cited By ~ 1

Author(s):

Kou Amano ◽

Hiroaki Ichikawa ◽

Hidemitsu Nakamura ◽

Hisataka Numa ◽

Kaoru Fukami-Kobayashi ◽

...

Keyword(s):

Dna Sequence ◽

Hierarchical Clustering ◽

Large Scale ◽

Sequence Data ◽

Dna Sequence Data ◽

Self Organizing

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Fast two-stage phasing of large-scale sequence data

The American Journal of Human Genetics ◽

10.1016/j.ajhg.2021.08.005 ◽

2021 ◽

Author(s):

Brian L. Browning ◽

Xiaowen Tian ◽

Ying Zhou ◽

Sharon R. Browning

Keyword(s):

Large Scale ◽

Sequence Data ◽

Two Stage ◽

Scale Sequence

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A High-Speed, Light-Weight Scalar Magnetometer Bird for km Scale UAV Magnetic Surveying: On Sensor Choice, Bird Design, and Quality of Output Data

Remote Sensing ◽

10.3390/rs13040649 ◽

2021 ◽

Vol 13 (4) ◽

pp. 649

Author(s):

Arne Døssing ◽

Eduardo Lima Simoes da Silva ◽

Guillaume Martelet ◽

Thorkild Maack Rasmussen ◽

Eric Gloaguen ◽

...

Keyword(s):

High Speed ◽

Large Scale ◽

Signal To Noise Ratio ◽

Regional Scale ◽

Weather Conditions ◽

Light Weight ◽

Output Data ◽

Efficient Manner ◽

Flexible System ◽

Scalar Data

Magnetic surveying is a widely used and cost-efficient remote sensing method for the detection of subsurface structures at all scales. Traditionally, magnetic surveying has been conducted as ground or airborne surveys, which are cheap and provide large-scale consistent data coverage, respectively. However, ground surveys are often incomplete and slow, whereas airborne surveys suffer from being inflexible, expensive and characterized by a reduced signal-to-noise ratio, due to increased sensor-to-source distance. With the rise of reliable and affordable survey-grade Unmanned Aerial Vehicles (UAVs), and the developments of light-weight magnetometers, the shortcomings of traditional magnetic surveying systems may be bypassed by a carefully designed UAV-borne magnetometer system. Here, we present a study on the development and testing of a light-weight scalar field UAV-integrated magnetometer bird system (the CMAGTRES-S100). The idea behind the CMAGTRES-S100 is the need for a high-speed and flexible system that is easily transported in the field without a car, deployable in most terrain and weather conditions, and provides high-quality scalar data in an operationally efficient manner and at ranges comparable to sub-regional scale helicopter-borne magnetic surveys. We discuss various steps in the development, including (i) choice of sensor based on sensor specifications and sensor stability tests, (ii) design considerations of the bird, (iii) operational efficiency and flexibility and (iv) output data quality. The current CMAGTRES-S100 system weighs ∼5.9 kg (including the UAV) and has an optimal surveying speed of 50 km/h. The system was tested along a complex coastal setting in Brittany, France, targeting mafic dykes and fault contacts with magnetite infill and magnetite nuggets (skarns). A 2.0 × 0.3 km area was mapped with a 10 m line-spacing by four sub-surveys (due to regulatory restrictions). The sub-surveys were completed in 3.5 h, including >2 h for remobilisation and the safety clearance of the area. A noise-level of ±0.02 nT was obtained and several of the key geological structures were mapped by the system.

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