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- Phylogeny (2)
- Activational plasticity (1)
- Alarm cues (1)
- Behavioral plasticity (1)
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- Bisulfite sequencing (1)
- Boldness (1)
- Brown-rot fungi (1)
- C-start (1)
- Cell lines (1)
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- Cyanobacteria (1)
- DNA binding (1)
- DNA methylation (1)
- Development; embryo; fossil; metazoa; morphology; organ system; phylogeny; ScRNA-seq (1)
- Dictyostelium (1)
- Dictyostelium discoideum (1)
- Disease transmission (1)
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- Embryo (1)
- Fibroporia radiculosa (1)
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- Horizontal gene transfer (1)
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Articles 1 - 12 of 12
Full-Text Articles in Entire DC Network
Phylogenomics Reveals The History Of Host Use In Mosquitoes, John Soghigan, Charles Sither, Silvia Andrade Justi, Gen Morinaga, Brian K. Cassel, Christopher J. Vitek, Todd P. Livdahl, Siyang Xia, Andrea Gloria-Soria, Jeffrey R. Powell, Thomas Zavortink, Christopher M. Hardy, Nathan D. Burkett-Cadena, Lawrence E. Reeves, Richard C. Wilkerson, Robert R. Dunn, David K. Yeates, Maria Anice Sallum, Brian D. Byrd, Michelle D. Trautwein, Yvonne-Marie Linton, Michael H. Reiskind, Brian M. Wiegmann
Phylogenomics Reveals The History Of Host Use In Mosquitoes, John Soghigan, Charles Sither, Silvia Andrade Justi, Gen Morinaga, Brian K. Cassel, Christopher J. Vitek, Todd P. Livdahl, Siyang Xia, Andrea Gloria-Soria, Jeffrey R. Powell, Thomas Zavortink, Christopher M. Hardy, Nathan D. Burkett-Cadena, Lawrence E. Reeves, Richard C. Wilkerson, Robert R. Dunn, David K. Yeates, Maria Anice Sallum, Brian D. Byrd, Michelle D. Trautwein, Yvonne-Marie Linton, Michael H. Reiskind, Brian M. Wiegmann
Biology
Mosquitoes have profoundly affected human history and continue to threaten human health through the transmission of a diverse array of pathogens. The phylogeny of mosquitoes has remained poorly characterized due to difficulty in taxonomic sampling and limited availability of genomic data beyond the most important vector species. Here, we used phylogenomic analysis of 709 single copy ortholog groups from 256 mosquito species to produce a strongly supported phylogeny that resolves the position of the major disease vector species and the major mosquito lineages. Our analyses support an origin of mosquitoes in the early Triassic (217 MYA [highest posterior density region: …
Unraveling The Functional Dark Matter Through Global Metagenomics, Georgios A. Pavlopoulos, Fotis A. Baltoumas, Sirui Liu, Oguz Selvitopi, Antonio Pedro Camargo, Stephen Nayfach, Ariful Azad, Simon Roux, Lee Call, Natalia N. Ivanova, Min I. Chen, David Paez-Espino, Evangelos Karatzas, Nathan Ahlgren
Unraveling The Functional Dark Matter Through Global Metagenomics, Georgios A. Pavlopoulos, Fotis A. Baltoumas, Sirui Liu, Oguz Selvitopi, Antonio Pedro Camargo, Stephen Nayfach, Ariful Azad, Simon Roux, Lee Call, Natalia N. Ivanova, Min I. Chen, David Paez-Espino, Evangelos Karatzas, Nathan Ahlgren
Biology
Metagenomes encode an enormous diversity of proteins, reflecting a multiplicity of functions and activities1,2. Exploration of this vast sequence space has been limited to a comparative analysis against reference microbial genomes and protein families derived from those genomes. Here, to examine the scale of yet untapped functional diversity beyond what is currently possible through the lens of reference genomes, we develop a computational approach to generate reference-free protein families from the sequence space in metagenomes. We analyse 26,931 metagenomes and identify 1.17 billion protein sequences longer than 35 amino acids with no similarity to any sequences from 102,491 …
Transcriptomics Of Temporal- Versus Substrate-Specific Wood Decay In The Brown-Rot Fungus Fibroporia Radiculosa, Byoungnam Min, Steven Ahrendt, Anna Lipzen, Cristina E. Toapanta, Robert A. Blanchette, Dan Cullen, David Hibbett
Transcriptomics Of Temporal- Versus Substrate-Specific Wood Decay In The Brown-Rot Fungus Fibroporia Radiculosa, Byoungnam Min, Steven Ahrendt, Anna Lipzen, Cristina E. Toapanta, Robert A. Blanchette, Dan Cullen, David Hibbett
Biology
Brown-rot fungi lack many enzymes associated with complete wood degradation, such as lignin-attacking peroxidases, and have developed alternative mechanisms for rapid wood breakdown. To identify the effects of culture conditions and wood substrates on gene expression, we grew Fibroporia radiculosa in submerged cultures containing Wiley milled wood (5 days) and solid wood wafers (30 days), using aspen, pine, and spruce as a substrate.
Loggerhead Shrike Occurrence Along Urban Gradients In South Carolina’S Coastal Plain, Michelle A. Krauser, Christopher E. Hill
Loggerhead Shrike Occurrence Along Urban Gradients In South Carolina’S Coastal Plain, Michelle A. Krauser, Christopher E. Hill
Biology
The urban landscape is understudied compared to less developed ecosystems, despite providing suitable habitat for wildlife, including some species of grassland birds. Loggerhead Shrikes (Lanius ludovicianus) are predatory songbirds that frequent grasslands and have been observed using grassy areas in developed and more natural landscapes, yet remain largely unstudied in developed landscapes. We investigated the effects of development, measured as impervious surface percentage, on Loggerhead Shrike occurrence in urban areas in South Carolina, U.S.A, and also tracked canopy cover (%), highway density (m/ha), non-highway road density (m/ha), total road density (m/ha), and powerline density (m/ha). The first author searched 300 …
Investigating The Sequence Landscape In The Drosophila Initiator Core Promoter Element Using An Enhanced Marz Algorithm, Jacqueline Dresch, Regan D. Conrad, Daniel Klonaros, Robert Drewell
Investigating The Sequence Landscape In The Drosophila Initiator Core Promoter Element Using An Enhanced Marz Algorithm, Jacqueline Dresch, Regan D. Conrad, Daniel Klonaros, Robert Drewell
Biology
The core promoter elements are important DNA sequences for the regulation of RNA polymerase II transcription in eukaryotic cells. Despite the broad evolutionary conservation of these elements, there is extensive variation in the nucleotide composition of the actual sequences. In this study, we aim to improve our understanding of the complexity of this sequence variation in the TATA box and initiator core promoter elements in Drosophila melanogaster. Using computational approaches, including an enhanced version of our previously developed MARZ algorithm that utilizes gapped nucleotide matrices, several sequence landscape features are uncovered, including an interdependency between the nucleotides in position 2 …
The Dictyostelium Discoideum Genome Lacks Significant Dna Methylation And Uncovers Palindromic Sequences As A Source Of False Positives In Bisulfite Sequencing, Robert Drewell, Tayla C. Cormier, Jacob L. Steenwyk, James St Denis, Javier F. Tabima, Jacqueline Dresch, Denis A. Larochelle
The Dictyostelium Discoideum Genome Lacks Significant Dna Methylation And Uncovers Palindromic Sequences As A Source Of False Positives In Bisulfite Sequencing, Robert Drewell, Tayla C. Cormier, Jacob L. Steenwyk, James St Denis, Javier F. Tabima, Jacqueline Dresch, Denis A. Larochelle
Biology
DNA methylation, the addition of a methyl (CH3) group to a cytosine residue, is an evolutionarily conserved epigenetic mark involved in a number of different biological functions in eukaryotes, including transcriptional regulation, chromatin structural organization, cellular differentiation and development. In the social amoeba Dictyostelium, previous studies have shown the existence of a DNA methyltransferase (DNMA) belonging to the DNMT2 family, but the extent and function of 5-methylcytosine in the genome are unclear. Here, we present the whole genome DNA methylation profile of Dictyostelium discoideum using deep coverage replicate sequencing of bisulfite-converted gDNA extracted from post-starvation cells. We find an overall …
Transcriptome Profile In Drosophila Kc And S2 Embryonic Cell Lines, Daniel Klonaros, Jacqueline M. Dresch, Robert A. Drewell
Transcriptome Profile In Drosophila Kc And S2 Embryonic Cell Lines, Daniel Klonaros, Jacqueline M. Dresch, Robert A. Drewell
Biology
Drosophila melanogaster cell lines are an important resource for a range of studies spanning genomics, molecular genetics, and cell biology. Amongst these valuable lines are Kc167 (Kc) and Schneider 2 (S2) cells, which were originally isolated in the late 1960s from embryonic sources and have been used extensively to investigate a broad spectrum of biological activities including cell-cell signaling and immune system function. Whole-genome tiling microarray analysis of total RNA from these two cell types was performed as part of the modENCODE project over a decade ago and revealed that they share a number of gene expression features. Here, we …
Diverse Marine T4-Like Cyanophage Communities Are Primarily Comprised Of Low-Abundance Species Including Species With Distinct Seasonal, Persistent, Occasional, Or Sporadic Dynamics, Emily Dart, Jed A. Fuhrman, Nathan A. Ahlgren
Diverse Marine T4-Like Cyanophage Communities Are Primarily Comprised Of Low-Abundance Species Including Species With Distinct Seasonal, Persistent, Occasional, Or Sporadic Dynamics, Emily Dart, Jed A. Fuhrman, Nathan A. Ahlgren
Biology
Cyanophages exert important top-down controls on their cyanobacteria hosts; however, concurrent analysis of both phage and host populations is needed to better assess phage-host interaction models. We analyzed picocyanobacteria Prochlorococcus and Synechococcus and T4-like cyanophage communities in Pacific Ocean surface waters using five years of monthly viral and cellular fraction metagenomes. Cyanophage communities contained thousands of mostly low-abundance (<2% relative abundance) species with varying temporal dynamics, categorized as seasonally recurring or non-seasonal and occurring persistently, occasionally, or sporadically (detected in ≥85%, 15-85%, or <15% of samples, respectively). Viromes contained mostly seasonal and persistent phages (~40% each), while cellular fraction metagenomes had mostly sporadic species (~50%), reflecting that these sample sets capture different steps of the infection cycle-virions from prior infections or within currently infected cells, respectively. Two groups of seasonal phages correlated to Synechococcus or Prochlorococcus were abundant in spring/summer or fall/winter, respectively. Cyanophages likely have a strong influence on the host community structure, as their communities explained up to 32% of host community variation. These results support how both seasonally recurrent and apparent stochastic processes, likely determined by host availability and different host-range strategies among phages, are critical to phage-host interactions and dynamics, consistent with both the Kill-the-Winner and the Bank models.
Evolution Of Chemical-Cue-Mediated Antipredator Behavior In Threespine Stickleback Populations Experiencing Northern Pike Predation, Dale R. Stevens, Melissa A. Graham, Christina I. Bardjis, Susan A. Foster, John A. Baker, Kaitlyn A. Mathis
Evolution Of Chemical-Cue-Mediated Antipredator Behavior In Threespine Stickleback Populations Experiencing Northern Pike Predation, Dale R. Stevens, Melissa A. Graham, Christina I. Bardjis, Susan A. Foster, John A. Baker, Kaitlyn A. Mathis
Biology
Human-mediated environmental challenges are severely impacting local and global levels of biodiversity. Phenotypic plasticity can play a major role in aiding population persistence because plasticity can buffer populations from novel challenges. Given this role, it is possible for the degree of plasticity to evolve rapidly as it may place phenotypes near, but not exactly on, an adaptive peak for the new environment. Here, we asked if behavioral plasticity evolves following the introduction of a novel predator. We measured behavioral responses of threespine stickleback (Gasterosteus aculeatus) populations, with and without the introduced apex predator northern pike (Esox lucius), to three different …
Comparative Genomic Analysis Of 31 Phytophthora Genomes Reveals Genome Plasticity And Horizontal Gene Transfer, Brent A. Kronmiller, Nicolas Feau, Danyu Shen, Javier F. Tabima, Shahin S. Ali, Andrew D. Armitage, Felipe Arredondo, Bryan A. Bailey, Stephanie R. Bollmann, Angela Dale, Richard J. Harrison, Kelly Hrywkiw, Takao Kasuga, Rebecca Mcdougal, Charlotte F. Nellist, Preeti Panda, Sucheta Tripathy, Nari M. Williams, Wenwu Ye, Yuanchao Wang, Richard C. Hamelin, Niklaus Grünwald
Comparative Genomic Analysis Of 31 Phytophthora Genomes Reveals Genome Plasticity And Horizontal Gene Transfer, Brent A. Kronmiller, Nicolas Feau, Danyu Shen, Javier F. Tabima, Shahin S. Ali, Andrew D. Armitage, Felipe Arredondo, Bryan A. Bailey, Stephanie R. Bollmann, Angela Dale, Richard J. Harrison, Kelly Hrywkiw, Takao Kasuga, Rebecca Mcdougal, Charlotte F. Nellist, Preeti Panda, Sucheta Tripathy, Nari M. Williams, Wenwu Ye, Yuanchao Wang, Richard C. Hamelin, Niklaus Grünwald
Biology
Phytophthora species are oomycete plant pathogens that cause great economic and ecological impacts. The Phytophthora genus includes over 180 known species, infecting a wide range of plant hosts, including crops, trees, and ornamentals. We sequenced the genomes of 31 individual Phytophthora species and 24 individual transcriptomes to study genetic relationships across the genus. De novo genome assemblies revealed variation in genome sizes, numbers of predicted genes, and in repetitive element content across the Phytophthora genus. A genus-wide comparison evaluated orthologous groups of genes. Predicted effector gene counts varied across Phytophthora species by effector family, genome size, and plant host range. …
Editorial: Morphoevodevo: A Multilevel Approach To Elucidate The Evolution Of Metazoan Organ Systems, Andreas Wanninger, Pedro Martinez, Néva P. Meyer
Editorial: Morphoevodevo: A Multilevel Approach To Elucidate The Evolution Of Metazoan Organ Systems, Andreas Wanninger, Pedro Martinez, Néva P. Meyer
Biology
Editorial on the Research Topic MorphoEvoDevo: a multilevel approach to elucidate the evolution of metazoan organ systems.
Behavioral Diversity And Biomechanical Determinants Of The Outcome Of A Fish Predator–Prey Interaction, Milton Q.G.A., Iii, Philip Bergmann
Behavioral Diversity And Biomechanical Determinants Of The Outcome Of A Fish Predator–Prey Interaction, Milton Q.G.A., Iii, Philip Bergmann
Biology
Predator–prey interactions are ubiquitous and under strong selection because of the consequences experienced by both predator and prey if they lose the interaction. Biomechanics and behavior play important roles in the outcome of these interactions, but many studies focus on the prey, restrict the range of behaviors considered, and the role of prey boldness in the outcome is not understood. We used high-speed video to test for effects of multiple measures of performance and kinematics of both the predator and prey, and boldness of prey on the outcome of interactions between Pike Cichlids (Crenicichla sp.) and Guppies (Poecilia reticulata). We …