A multiple genome alignment workflow shows the impact of repeat masking and parameter tuning on alignment of functional regions in plants

Alignments of multiple genomes are a cornerstone of comparative genomics, but generating these alignments remains technically challenging and often impractical. We developed the msa_pipeline workflow (https://bitbucket.org/bucklerlab/msa_pipeline) based on the LAST aligner to allow practical and sensitive multiple alignment of diverged plant genomes with minimal user inputs. Our workflow only requires a set of genomes in FASTA format as input. The workflow outputs multiple alignments in MAF format, and includes utilities to help calculate genome-wide conservation scores. As high repeat content and genomic divergence are substantial challenges in plant genome alignment, we also explored the impact of different masking approaches and alignment parameters using genome assemblies of 33 grass species. Compared to conventional masking with RepeatMasker, a k-mer masking approach increased the alignment rate of CDS and non-coding functional regions by 25% and 14% respectively. We further found that default alignment parameters generally perform well, but parameter tuning can increase the alignment rate for non-coding functional regions by over 52% compared to default LAST settings. Finally, by increasing alignment sensitivity from the default baseline, parameter tuning can increase the number of non-coding sites that can be scored for conservation by over 76%.

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Effect of fire regime on the grass community of the humid savanna of Lamto, Ivory Coast

Journal of Tropical Ecology ◽

10.1017/s0266467418000391 ◽

2018 ◽

Vol 35 (1) ◽

pp. 1-7 ◽

Cited By ~ 2

Author(s):

Kouamé Fulgence Koffi ◽

Aya Brigitte N’Dri ◽

Jean-Christophe Lata ◽

Souleymane Konaté ◽

Tharaniya Srikanthasamy ◽

...

Keyword(s):

Relative Abundance ◽

Ivory Coast ◽

Fire Regime ◽

Fire Regimes ◽

Abundant Species ◽

Grass Species ◽

The Third ◽

Humid Savanna ◽

The Impact ◽

Tussock Grasses

AbstractThis study assesses the impact of four fire treatments applied yearly over 3 y, i.e. early fire, mid-season fire, late fire and no fire treatments, on the grass communities of Lamto savanna, Ivory Coast. We describe communities of perennial tussock grasses on three replicated 5 × 5-m or 10 × 5-m plots of each fire treatment. Tussock density did not vary with fire treatment. The relative abundance of grass species, the circumference of grass tussocks and the probability of having a tussock with a central die-back, varied with fire treatment. Mid-season fire had the highest proportion of tussocks with a central die-back while the late fire had the smallest tussocks. Tussock density, circumference, relative abundance and probability of having a central die-back varied with species. Andropogon canaliculatus and Hyparrhenia diplandra were the most abundant of the nine grass species. They had the largest tussocks and the highest proportion of tussock with a central die-back. Loudetia simplex was the third most abundant species but was very rare in no fire plots. The distribution of tussock circumferences was right skewed and dominated by small tussocks. The proportion of the tussocks with a central die-back strongly increased with circumference, which could lead to tussock fragmentation. Taken together, this study suggests that fire regimes impact grass demography and that this impact depends on grass species and tussock size.

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Response of dry grassland vegetation to fluctuations in weather conditions: a 9-year case study in Prague (Czech Republic)

Biologia ◽

10.2478/s11756-011-0079-1 ◽

2011 ◽

Vol 66 (5) ◽

Cited By ~ 6

Author(s):

Jiří Dostálek ◽

Tomáš Frantík

Keyword(s):

Species Richness ◽

Czech Republic ◽

Weather Conditions ◽

Grass Species ◽

Individual Species ◽

Weather Variability ◽

Grassland Vegetation ◽

Dry Grassland ◽

Local Climate ◽

The Impact

AbstractThe extreme habitats of dry grasslands are suitable for investigations of the response of vegetation to local climate changes. The impact of weather variability on the dynamics of a plant community in a dry grassland was studied. Correlations were found between different functional groups of species and individual species and weather variability. During a 9-year study in five nature reserves in Prague (Czech Republic), the following responses of dry grassland vegetation to weather conditions were observed: (i) wetter conditions, especially in the winter, affected the dominance and species richness of perennial grass species and the decline of rosette plants; (ii) the year-to-year higher temperatures in the winter produced a decline in the dominance of short graminoids and creeping forbs; (iii) spring drought adversely impacted the overall abundance, especially the abundance of dicotyledonous species, and the species richness. However, these relationships may be manifested in different ways in different locations, and in some cases the vegetation of different locations may respond to weather conditions in opposite manners.

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Facial Expression Recognition of Instructor Using Deep Features and Extreme Learning Machine

Computational Intelligence and Neuroscience ◽

10.1155/2021/5570870 ◽

2021 ◽

Vol 2021 ◽

pp. 1-17

Author(s):

Yusra Khalid Bhatti ◽

Afshan Jamil ◽

Nudrat Nida ◽

Muhammad Haroon Yousaf ◽

Serestina Viriri ◽

...

Keyword(s):

Facial Expression ◽

Extreme Learning Machine ◽

Facial Expressions ◽

Classroom Environment ◽

Facial Expression Recognition ◽

Parameter Tuning ◽

Expression Recognition ◽

Fast Learning ◽

Learning Machine ◽

The Impact

Classroom communication involves teacher’s behavior and student’s responses. Extensive research has been done on the analysis of student’s facial expressions, but the impact of instructor’s facial expressions is yet an unexplored area of research. Facial expression recognition has the potential to predict the impact of teacher’s emotions in a classroom environment. Intelligent assessment of instructor behavior during lecture delivery not only might improve the learning environment but also could save time and resources utilized in manual assessment strategies. To address the issue of manual assessment, we propose an instructor’s facial expression recognition approach within a classroom using a feedforward learning model. First, the face is detected from the acquired lecture videos and key frames are selected, discarding all the redundant frames for effective high-level feature extraction. Then, deep features are extracted using multiple convolution neural networks along with parameter tuning which are then fed to a classifier. For fast learning and good generalization of the algorithm, a regularized extreme learning machine (RELM) classifier is employed which classifies five different expressions of the instructor within the classroom. Experiments are conducted on a newly created instructor’s facial expression dataset in classroom environments plus three benchmark facial datasets, i.e., Cohn–Kanade, the Japanese Female Facial Expression (JAFFE) dataset, and the Facial Expression Recognition 2013 (FER2013) dataset. Furthermore, the proposed method is compared with state-of-the-art techniques, traditional classifiers, and convolutional neural models. Experimentation results indicate significant performance gain on parameters such as accuracy, F1-score, and recall.

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The challenge of abandonment for the sustainable management of Palaearctic natural and semi-natural grasslands

Hacquetia ◽

10.1515/hacq-2017-0018 ◽

2018 ◽

Vol 17 (1) ◽

pp. 5-16 ◽

Cited By ~ 30

Author(s):

Orsolya Valkó ◽

Stephen Venn ◽

Michał Żmihorski ◽

Idoia Biurrun ◽

Rocco Labadessa ◽

...

Keyword(s):

Sustainable Management ◽

Grassland Management ◽

Grass Species ◽

Economic Changes ◽

The Core ◽

Natural Grasslands ◽

Biomass Removal ◽

Management Regimes ◽

The Impact ◽

Grassland Biodiversity

Abstract Disturbance by biomass removal is a crucial mechanism maintaining the diversity of Palaearctic grasslands, which are unique biodiversity hotspots. The century-long traditional land use of mowing, grazing and burning, has been fundamentally changed in many parts of the Palaearctic. Due to socio-economic changes, large areas of former pastures and meadows have been abandoned, leading to a succession towards secondary scrublands or forest and the encroachment of competitor grass species, all leading to a decrease in biodiversity. Here we report the causes and consequences of the cessation of traditional grassland management regimes, provide strategies for reducing the impact of abandonment and consider these from the perspective of sustainability. We consider the possibilities for initiating sustainable management regimes in the contemporary socio-economic environment, and discuss the prospects and limitation of alternative management regimes in the conservation of grassland biodiversity. These themes are also the core topics of this Special Feature, edited by the EDGG. We hope that this Special Feature will encourage steps towards more sustainable strategies for the conservation of Palaearctic grasslands and the integration of the sustainability perspective into their conservation.

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A phased, diploid assembly of the Cascade hop (Humulus lupulus) genome reveals patterns of selection and haplotype variation

10.1101/786145 ◽

2019 ◽

Cited By ~ 4

Author(s):

Lillian K. Padgitt-Cobb ◽

Sarah B. Kingan ◽

Jackson Wells ◽

Justin Elser ◽

Brent Kronmiller ◽

...

Keyword(s):

Large Scale ◽

Humulus Lupulus ◽

Plant Genome ◽

Repeat Content ◽

Haplotype Variation ◽

Genomic Landscape ◽

Cannabidiolic Acid ◽

Long Read ◽

History Of ◽

Insight Into

AbstractHop (Humulus lupulus L. var Lupulus) is a diploid, dioecious plant with a history of cultivation spanning more than one thousand years. Hop cones are valued for their use in brewing, and around the world, hop has been used in traditional medicine to treat a variety of ailments. Efforts to determine how biochemical pathways responsible for desirable traits are regulated have been challenged by the large, repetitive, and heterozygous genome of hop. We present the first report of a haplotype-phased assembly of a large plant genome. Our assembly and annotation of the Cascade cultivar genome is the most extensive to date. PacBio long-read sequences from hop were assembled with FALCON and phased with FALCON-Unzip. Using the diploid assembly to assess haplotype variation, we discovered genes under positive selection enriched for stress-response, growth, and flowering functions. Comparative analysis of haplotypes provides insight into large-scale structural variation and the selective pressures that have driven hop evolution. Previous studies estimated repeat content at around 60%. With improved resolution of long terminal retrotransposons (LTRs) due to long-read sequencing, we found that hop is nearly 78% repetitive. Our quantification of repeat content provides context for the size of the hop genome, and supports the hypothesis of whole genome duplication (WGD), rather than expansion due to LTRs. With our more complete assembly, we have identified a homolog of cannabidiolic acid synthase (CBDAS) that is expressed in multiple tissues. The approaches we developed to analyze a phased, diploid assembly serve to deepen our understanding of the genomic landscape of hop and may have broader applicability to the study of other large, complex genomes.

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Improved Understanding of the Role of Gene and Genome Duplications in Chordate Evolution With New Genome and Transcriptome Sequences

Frontiers in Ecology and Evolution ◽

10.3389/fevo.2021.703163 ◽

2021 ◽

Vol 9 ◽

Author(s):

Madeleine E. Aase-Remedios ◽

David E. K. Ferrier

Keyword(s):

Chromosomal Rearrangements ◽

Expression Patterns ◽

Gene Families ◽

Evolutionary Transitions ◽

Whole Genome Duplications ◽

Chordate Evolution ◽

Genome Duplications ◽

The Many ◽

Genome Assemblies ◽

The Impact

Comparative approaches to understanding chordate genomes have uncovered a significant role for gene duplications, including whole genome duplications (WGDs), giving rise to and expanding gene families. In developmental biology, gene families created and expanded by both tandem and WGDs are paramount. These genes, often involved in transcription and signalling, are candidates for underpinning major evolutionary transitions because they are particularly prone to retention and subfunctionalisation, neofunctionalisation, or specialisation following duplication. Under the subfunctionalisation model, duplication lays the foundation for the diversification of paralogues, especially in the context of gene regulation. Tandemly duplicated paralogues reside in the same regulatory environment, which may constrain them and result in a gene cluster with closely linked but subtly different expression patterns and functions. Ohnologues (WGD paralogues) often diversify by partitioning their expression domains between retained paralogues, amidst the many changes in the genome during rediploidisation, including chromosomal rearrangements and extensive gene losses. The patterns of these retentions and losses are still not fully understood, nor is the full extent of the impact of gene duplication on chordate evolution. The growing number of sequencing projects, genomic resources, transcriptomics, and improvements to genome assemblies for diverse chordates from non-model and under-sampled lineages like the coelacanth, as well as key lineages, such as amphioxus and lamprey, has allowed more informative comparisons within developmental gene families as well as revealing the extent of conserved synteny across whole genomes. This influx of data provides the tools necessary for phylogenetically informed comparative genomics, which will bring us closer to understanding the evolution of chordate body plan diversity and the changes underpinning the origin and diversification of vertebrates.

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PaaS Optimization of Apache Applications Using System Parameter Tuning of Big Data Platforms in Distributed Computing

International Journal of Distributed Systems and Technologies ◽

10.4018/ijdst.2020100102 ◽

2020 ◽

Vol 11 (4) ◽

pp. 23-38

Author(s):

Tanuja Pattanshetti ◽

Vahida Attar

Keyword(s):

Parameter Tuning ◽

Service Level ◽

System Parameters ◽

Second Stage ◽

Huge Data ◽

Optimal Value ◽

System Output ◽

Software Quality Metrics ◽

The Impact ◽

Individual Input

Widely used data processing platforms use distributed systems to process huge data efficiently. The aim of this article is to optimize the platform services by tuning only the relevant, tunable, system parameters and to identify the relation between the software quality metrics. The system parameters of data platforms based on the service level agreements can be defined and customized. In the first stage, the most significant parameters are identified and shortlisted using various feature selection approaches. In the second stage, the iterative runs of applications are executed for tuning these shortlisted parameters to identify the optimal value and to understand the impact of individual input parameters on the system output parameter. The empirical results imply significant improvement in performance and with which it is possible to render the proposed work optimizing the services offered by these data platforms.

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Evolutionary Dynamics of Transposable Elements Following a Shared Polyploidization Event in the Tribe Andropogoneae

G3 Genes|Genome|Genetics ◽

10.1534/g3.120.401596 ◽

2020 ◽

Vol 10 (12) ◽

pp. 4387-4398

Author(s):

Dhanushya Ramachandran ◽

Michael R. McKain ◽

Elizabeth A. Kellogg ◽

Jennifer S. Hawkins

Keyword(s):

Insertional Mutagenesis ◽

Evolutionary Dynamics ◽

Diploid Species ◽

Duplicate Gene ◽

Plant Genome ◽

Abiotic Stress Response ◽

Repeat Content ◽

Gene Copies ◽

Polyploidization Event ◽

Plant Genome Evolution

Both polyploidization and transposable element (TE) activity are known to be major drivers of plant genome evolution. Here, we utilize the Zea-Tripsacum clade to investigate TE activity and accumulation after a shared polyploidization event. Comparisons of TE evolutionary dynamics in various Zea and Tripsacum species, in addition to two closely related diploid species, Urelytrum digitatum and Sorghum bicolor, revealed variation in repeat content among all taxa included in the study. The repeat composition of Urelytrum is more similar to that of Zea and Tripsacum compared to Sorghum, despite the similarity in genome size with the latter. Although LTR-retrotransposons were abundant in all species, we observed an expansion of the copia superfamily, specifically in Z. mays and T. dactyloides, species that have adapted to more temperate environments. Additional analyses of the genomic distribution of these retroelements provided evidence of biased insertions near genes involved in various biological processes including plant development, defense, and macromolecule biosynthesis. Specifically, copia insertions in Zea and T. dactyloides were significantly enriched near genes involved in abiotic stress response, suggesting independent evolution post Zea-Tripsacum divergence. The lack of copia insertions near the orthologous genes in S. bicolor suggests that duplicate gene copies generated during polyploidization may offer novel neutral sites for TEs to insert, thereby providing an avenue for subfunctionalization via TE insertional mutagenesis.

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Vegetation and Fluvial Geomorphology Dynamics after an Urban Fire

Geosciences ◽

10.3390/geosciences10080317 ◽

2020 ◽

Vol 10 (8) ◽

pp. 317

Author(s):

Lauren E. H. Mathews ◽

Alicia M. Kinoshita

Keyword(s):

Laser Scanning ◽

Small Sample Size ◽

Arundo Donax ◽

Small Sample ◽

Giant Reed ◽

Grass Species ◽

Native Vegetation ◽

Absolute Maximum ◽

Field Observations ◽

The Impact

The goal of this research was to characterize the impact of invasive riparian vegetation on burn severity patterns and fluvial topographic change in an urban Mediterranean riverine system (Med-sys) after fire in San Diego, California. We assessed standard post-fire metrics under urban conditions with non-native vegetation and utilized field observations to quantify vegetation and fluvial geomorphic processes. Field observations noted both high vegetation loss in the riparian area and rapidly resprouting invasive grass species such as Arundo donax (Giant Reed) after fire. Satellite-based metrics that represent vegetation biomass underestimated the initial green canopy loss, as did volumetric data derived from three-dimensional terrestrial laser scanning data. Field measurements were limited to a small sample size but demonstrated that the absolute maximum topographic changes were highest in stands of Arundo donax (0.18 to 0.67 m). This work is the first quantification of geomorphic alterations promoted by non-native vegetation after fire and highlights potential grass–fire feedbacks that can contribute to geomorphic disruption. Our results support the need for ground-truthing or higher resolution when using standard satellite-based indices to assess post-fire conditions in urban open spaces, especially when productive invasive vegetation are present, and they also emphasize restoring urban waterways to native vegetation conditions.

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The impact of drought stress on the yields and food value of selected forage grasses

Acta Agrobotanica ◽

10.5586/aa.1663 ◽

2016 ◽

Vol 69 (2) ◽

Cited By ~ 4

Author(s):

Mariola Staniak

Keyword(s):

Soil Moisture ◽

Water Stress ◽

Drought Stress ◽

Dry Matter ◽

Nutritional Value ◽

Lolium Multiflorum ◽

Grass Species ◽

Forage Grasses ◽

The Impact

The aim of the study was to compare yields and nutritional value of selected species and cultivars of forage grasses under the optimal moisture conditions and long-term drought stress. The regenerative capacity of plants after dehydration was also assessed. The pot experiment was conducted in years 2009–2010 in IUNG-PIB’s greenhouse in Puławy, Poland. Nine cultivars of four species: Dactylis glomerata (‘Amera’, ‘Minora’), Festuca pratensis (‘Skra’, ‘Fantazja’), Festulolium braunii (‘Felopa’, ‘Agula’, ‘Sulino’), and Lolium multiflorum (‘Gisel’, ‘Lotos’) were investigated in well-watered conditions (70% field water capacity – FWC) and under a long-term drought stress (40% FWC).The study showed that stress caused by soil moisture deficiency significantly reduced yields of D. glomerata, F. pratensis, F. braunii, and L. multiflorum. The total yield of dry matter under stress conditions was about 31% lower, compared to the performance achieved on the optimally moisturized treatment. The smallest reduction in dry matter yield under the conditions of water deficit was recorded for D. glomerata, which makes it the most resistant to stress, followed by F. pratensis. The resistance of F. braunii and L. multiflorum to stress was similar and significantly lower. There was a various response of different grasses to the water stress. On the basis of the value of the DSI (drought susceptibility index), the tested cultivars were ranked depending on the sensitivity to drought, starting with the most resistant cultivar: ‘Minora’, ‘Skra’, ‘Fantazja’, ‘Amera’, ‘Sulino’, ‘Agula’, ‘Gisel’, ‘Lotos’, and ‘Felopa’. The digestibility of dry matter and nutrient value of the grasses depended on both the level of soil moisture and grass species. Under the water stress, the digestibility and protein value increased compared to the control objects. Lolium multiflorum and F. braunii had the best nutritional value, while D. glomerata – the weakest.

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