Genetics and Genomics Commons^™

Cryptic Diversity And Discordance In Single‐Locus Species Delimitation Methods Within Horned Lizards (Phrynosomatidae: Phrynosoma), Christopher Blair, Robert W. Bryson Jr.

Publications and Research

Biodiversity reduction and loss continues to progress at an alarming rate, and thus there is widespread interest in utilizing rapid and efficient methods for quantifying and delimiting taxonomic diversity. Single-locus species-delimitation methods have become popular, in part due to the adoption of the DNA barcoding paradigm. These techniques can be broadly classified into tree-based and distance-based methods depending on whether species are delimited based on a constructed genealogy. Although the relative performance of these methods has been tested repeatedly with simulations, additional studies are needed to assess congruence with empirical data. We compiled a large data set of mitochondrial ND4 …

Draft Nuclear Genome Sequence Of The Halophilic And Beta-Carotene- Accumulating Green Alga Dunaliella Salina Strain Ccap19/18, Juergen Polle, Kerrie Barry, John Cushman, Jeremy Schmutz, Duc Tran, Leyla T. Hathwaik, Won C. Yin, Jerry Jenkins, Zaid Mckie-Krisberg, Simon Prochnik, Erika Lindquist, Rhyan B. Dockter, Catherine Adam, Henrik Molina, Jakob Bunkenborg, Eonseon Jin, Mark Buchheim, Jon Magnuson

Publications and Research

The halotolerant alga Dunaliella salina is a model for stress tolerance and is used commercially for production of beta-carotene (pro-vitamin A). The presented draft genome of the genuine strain CCAP19/18 will allow investigations into metabolic processes involved in regulation of stress responses, including carotenogenesis and adaptations to life in high-salinity environments.

A First Linkage Map And Downy Mildew Resistance Qtl Discovery For Sweet Basil (Ocimum Basilicum) Facilitated By Double Digestion Restriction Site Associated Dna Sequencing (Ddradseq), Robert M. Pyne, Josh Honig, Jennifer Vaiciunas, Adolfina R. Koroch, Christian Wyenandt, Stacy Bonos, James Simon

Publications and Research

Limited understanding of sweet basil (Ocimum basilicum L.) genetics and genome structure has reduced efficiency of breeding strategies. This is evidenced by the rapid, worldwide dissemination of basil downy mildew (Peronospora belbahrii) in the absence of resistant cultivars. In an effort to improve available genetic resources, expressed sequence tag simple sequence repeat (EST-SSR) and single nucleotide polymorphism (SNP) markers were developed and used to genotype the MRI x SB22 F2 mapping population, which segregates for response to downy mildew. SNP markers were generated from genomic sequences derived from double digestion restriction site associated DNA sequencing (ddRADseq). Disomic segregation was observed …

Strategies For Improving Approximate Bayesian Computation Tests For Synchronous Diversification, Isaac Overcast, Justin C. Bagley, Michael J. Hickerson

Publications and Research

Background: Estimating the variability in isolation times across co-distributed taxon pairs that may have experienced the same allopatric isolating mechanism is a core goal of comparative phylogeography. The use of hierarchical Approximate Bayesian Computation (ABC) and coalescent models to infer temporal dynamics of lineage co-diversification has been a contentious topic in recent years. Key issues that remain unresolved include the choice of an appropriate prior on the number of co-divergence events (Ψ), as well as the optimal strategies for data summarization.

Methods: Through simulation-based cross validation we explore the impact of the strategy for sorting summary statistics and the choice …

Draft Nuclear Genome, Complete Chloroplast Genome, And Complete Mitochondrial Genome For The Biofuel/ Bioproduct Feedstock Species Scenedesmus Obliquus Strain Doe0152z, S. R. Starkenburg, Juergen Polle, B. Hovde, H. E. Daligault, K. W. Davenport, A. Huang, P. Neofotis, Zaid Mckie-Krisberg

Publications and Research

The green alga Scenedesmus obliquus is an emerging platform species for the industrial production of biofuels. Here, we report the draft assembly and annotation for the nuclear, plastid, and mitochondrial genomes of S. obliquus strain DOE0152z.

Retrotransposons Are The Major Contributors To The Expansion Of The Drosophila Ananassae Muller F Element, Wilson Leung, Gerard Mcneil

Publications and Research

The discordance between genome size and the complexity of eukaryotes can partly be attributed to differences in repeat density. The Muller F element (5.2 Mb) is the smallest chromosome in Drosophila melanogaster, but it is substantially larger (.18.7 Mb) in D. ananassae. To identify the major contributors to the expansion of the F element and to assess their impact, we improved the genome sequence and annotated the genes in a 1.4-Mb region of the D. ananassae F element, and a 1.7-Mb region from the D element for comparison. We find that transposons (particularly LTR and LINE retrotransposons) are major contributors …

Large-Scale Differences In Microbial Biodiversity Discovery Between 16s Amplicon And Shotgun Sequencing, Michael Tessler, Johannes S. Neumann, Ebrahim Afshinnekoo, Michael Pineda, Rebecca Hersch, Luiz Felipe M. Velgo, Bianca T. Segovia, Fabio A. Lansac-Toha, Michael Lemke, Rob Desalle, Christopher E. Mason, Mercer R. Brugler

Publications and Research

Modern metagenomic environmental DNA studies are almost completely reliant on next-generation sequencing, making evaluations of these methods critical. We compare two next-generation sequencing techniques – amplicon and shotgun – on water samples across four of Brazil’s major river floodplain systems (Amazon, Araguaia, Paraná, and Pantanal). Less than 50% of phyla identified via amplicon sequencing were recovered from shotgun sequencing, clearly challenging the dogma that mid-depth shotgun recovers more diversity than amplicon-based approaches. Amplicon sequencing also revealed ~27% more families. Overall the amplicon data were more robust across both biodiversity and community ecology analyses at different taxonomic scales. Our work doubles …

T-Dna-Genome Junctions Form Early After Infection And Are Influenced By The Chromatin State Of The Host Genome, Shay Shilo, Pooja Tripathi, Cathy Melamed Bessudo, Oren Tzfadia, Theodore R. Muth, Avraham A. Levy

Publications and Research

Agrobacterium tumefaciens mediated T-DNA integration is a common tool for plant genome manipulation. However, there is controversy regarding whether T-DNA integration is biased towards genes or randomly distributed throughout the genome. In order to address this question, we performed high-throughput mapping of T-DNA-genome junctions obtained in the absence of selection at several time points after infection. T-DNA-genome junctions were detected as early as 6 hours post-infection. T-DNA distribution was apparently uniform throughout the chromosomes, yet local biases toward AT-rich motifs and T-DNA border sequence micro-homology were detected. Analysis of the epigenetic landscape of previously isolated sites of T-DNA integration in …

Tumor Necrosis Factor Dynamically Regulates The Mrna Stabilome In Rheumatoid Arthritis Fibroblast-Like Synoviocytes, Konstantinos Loupasakis, David Kuo, Upneet K. Sokhi, Christopher Sohn, Bethany Syracuse, Eugenia G. Giannopoulou, Sung Ho Park, Hyelim Kang, Gunnar Rätsch, Lionel B. Ivashkiv, George D. Kalliolias

Publications and Research

During rheumatoid arthritis (RA), Tumor Necrosis Factor (TNF) activates fibroblast-like synoviocytes (FLS) inducing in a temporal order a constellation of genes, which perpetuate synovial inflammation. Although the molecular mechanisms regulating TNF-induced transcription are well characterized, little is known about the impact of mRNA stability on gene expression and the impact of TNF on decay rates of mRNA transcripts in FLS. To address these issues we performed RNA sequencing and genome-wide analysis of the mRNA stabilome in RA FLS. We found that TNF induces a biphasic gene expression program: initially, the inducible transcriptome consists primarily of unstable transcripts but progressively switches …

Mutant Tdp-43 Does Not Impair Mitochondrial Bioenergetics In Vitro And In Viv, Hibiki Kawamata, Pablo Peixoto, Csaba Konrad, Gloria Palomo, Kirsten Bredvik, Meri Gerges, Federica Valsecchi, Leonard Petrucelli, John M. Ravits, Anatoly Starkov, Giovanni Manfredi

Publications and Research

Background: Mitochondrial dysfunction has been linked to the pathogenesis of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). Functional studies of mitochondrial bioenergetics have focused mostly on superoxide dismutase 1 (SOD1) mutants, and showed that mutant human SOD1 impairs mitochondrial oxidative phosphorylation, calcium homeostasis, and dynamics. However, recent reports have indicated that alterations in transactivation response element DNA-binding protein 43 (TDP-43) can also lead to defects of mitochondrial morphology and dynamics. Furthermore, it was proposed that TDP-43 mutations cause oxidative phosphorylation impairment associated with respiratory chain defects and that these effects were caused by mitochondrial localization of the mutant …

From Sexless To Sexy: Why It Is Time For Human Genetics To Consider And Report Analyses Of Sex, Matthew S. Powers, Phillip H. Smith, Sherry A. Mckee, Marissa A. Ehringer

Publications and Research

Science has come a long way with regard to the consideration of sex differences in clinical and preclinical research, but one field remains behind the curve: human statistical genetics. The goal of this commentary is to raise awareness and discussion about how to best consider and evaluate possible sex effects in the context of large-scale human genetic studies. Over the course of this commentary, we reinforce the importance of interpreting genetic results in the context of biological sex, establish evidence that sex differences are not being considered in human statistical genetics, and discuss how best to conduct and report such …

Rseqrep: Rna-Seq Reports, An Open-Source Cloud-Enabled Framework For Reproducible Rna-Seq Data Processing, Analysis, And Result Reporting, Travis L. Jensen, Michael Frasketi, Kevin Conway, Leigh Villarroel, Heather Hill, Konstantinos Krampis, Johannes B. Goll

Publications and Research

RNA-Seq is increasingly being used to measure human RNA expression on a genome-wide scale. Expression profiles can be interrogated to identify and functionally characterize treatment-responsive genes. Ultimately, such controlled studies promise to reveal insights into molecular mechanisms of treatment effects, identify biomarkers, and realize personalized medicine. RNA-Seq Reports (RSEQREP) is a new open-source cloud-enabled framework that allows users to execute start-to-end gene-level RNA-Seq analysis on a preconfigured RSEQREP Amazon Virtual Machine Image (AMI) hosted by AWS or on their own Ubuntu Linux machine. The framework works with unstranded, stranded, and paired-end sequence FASTQ files stored locally, on Amazon Simple Storage …

Mirnas Associated With Prostate Cancer Risk And Progression, Hung N. Luu, Hui-Yi Lin, Karina Dalsgaard Sorensen, Olorunseun O. Ogunwobi, Nagi Kumar, Ganna Chornokur, Catherine Phelan, Dominique Jones, Lacreis Kidd, Jyotsna Batra, Kosj Yamoah, Anders Berglund, Robert J. Rounbehler, Mihi Yang, Sang Haak Lee, Nahyeon Kang, Seung Joon Kim, Jong Y. Park, Giuliano Di Pietro

Publications and Research

Prostate cancer is the most common malignancy among men in the US. Though considerable improvement in the diagnosis of prostate cancer has been achieved in the past decade, predicting disease outcome remains a major clinical challenge. Recent expression profiling studies in prostate cancer suggest microRNAs (miRNAs) may serve as potential biomarkers for prostate cancer risk and disease progression. miRNAs comprise a large family of about 22-nucleotide-long non-protein coding RNAs, regulate gene expression post-transcriptionally and participate in the regulation of numerous cellular processes. In this review, we discuss the current status of miRNA in studies evaluating the disease progression of prostate …

Differential Methylation Between Ethnic Sub-Groups Reflects The Effect Of Genetic Ancestry And Environmental Exposures, Joshua M. Galanter, Christopher R. Gignoux, Sam S. Oh, Dara Torgerson, Maria Pino-Yanes, Neeta Thakur, Celeste Eng, Donglei Hu, Scott Huntsman, Harold J. Farber, Pedro C. Avila, Emerita Brigino-Buenaventura, Michael A. Lenoir, Kelly Meade, Denise Serebrisky, William Rodriguez-Cintron, Rajesh Kumar, Jose R. Rodrıguez-Cintron, Max A. Seibold, Luisa N. Borrell, Esteban G. Burchard, Noah Zaitlen

Publications and Research

Populations are often divided categorically into distinct racial/ethnic groups based on social rather than biological constructs. Genetic ancestry has been suggested as an alternative to this categorization. Herein, we typed over 450,000 CpG sites in whole blood of 573 individuals of diverse Hispanic origin who also had high-density genotype data. We found that both self- identified ethnicity and genetically determined ancestry were each significantly associated with methylation levels at 916 and 194 CpGs, respectively, and that shared genomic ancestry accounted for a median of 75.7% (IQR 45.8% to 92%) of the variance in methylation associated with ethnicity. There was a …

Review Of The Algal Biology Program Within The National Alliance For Advanced Biofuels And Bioproducts, Clifford J. Unkefer, Richard T. Sayre, Jon K. Magnuson, Daniel B. Anderson, Ivan Baxter, Ian K. Balby, Judith K. Brown, Michael Carleton, Rose Ann Cattolico, Taraka Dale, Timothy P. Devarenne, C. Meghan Downes, Susan K. Dutcher, David T. Fox, Ursula Goodenough, Jan Jaworski, Jonathan E. Holladay, David M. Kramer, Andrew T. Koppisch, Mary S. Lipton, Babetta L. Marrone, Margaret Mccormick, István Molnár, John B. Mott, Kimberly L. Ogden, Ellen A. Panisko, Matteo Pellegrini, Juergen Polle, James W. Richardson, Martin Sabarsky, Shawn R. Starkenburg, Gary D. Stormo, Munehiro Teshima, Scott N. Twary, Pat J. Unkefer, Joshua S. Yuan, José A. Olivares

Publications and Research

In 2010,when the National Alliance for Advanced Biofuels and Bioproducts (NAABB) consortiumbegan, littlewas known about themolecular basis of algal biomass or oil production. Very fewalgal genome sequenceswere available and efforts to identify the best-producing wild species through bioprospecting approaches had largely stalled after the U.S. Department of Energy's Aquatic Species Program. This lack of knowledge included how reduced carbon was partitioned into storage products like triglycerides or starch and the role played bymetabolite remodeling in the accumulation of energy-dense storage products. Furthermore, genetic transformation and metabolic engineering approaches to improve algal biomass and oil yields were in their infancy. Genome …

A Machine Learning Approach For Using The Postmortem Skin Microbiome To Estimate The Postmortem Interval, Hunter R. Johnson, Donovan D. Trinidad, Stephania Guzman, Zenab Khan, James V. Parziale, Jennifer M. Debruyn, Nathan H. Lents

Publications and Research

Research on the human microbiome, the microbiota that live in, on, and around the human person, has revolutionized our understanding of the complex interactions between microbial life and human health and disease. The microbiome may also provide a valuable tool in forensic death investigations by helping to reveal the postmortem interval (PMI) of a decedent that is discovered after an unknown amount of time since death. Current methods of estimating PMI for cadavers discovered in uncontrolled, unstudied environments have substantial limitations, some of which may be overcome through the use of microbial indicators. In this project, we sampled the microbiomes …

Improved Genome-Scale Multitarget Virtual Screening Via A Novel Collaborative Filtering Approach To Cold-Start Problem, Hansaim Lim, Paul Gray, Lei Xie, Aleksandar Poleksic

Publications and Research

Conventional one-drug-one-gene approach has been of limited success in modern drug discovery. Polypharmacology, which focuses on searching for multi-targeted drugs to perturb disease-causing networks instead of designing selective ligands to target individual proteins, has emerged as a new drug discovery paradigm. Although many methods for single-target virtual screening have been developed to improve the efficiency of drug discovery, few of these algorithms are designed for polypharmacology. Here, we present a novel theoretical framework and a corresponding algorithm for genome-scale multitarget virtual screening based on the one-class collaborative filtering technique. Our method overcomes the sparseness of the protein-chemical interaction data by …

Control Of Gene Expression By Rna Binding Protein Action On Alternative Translation Initiation Sites, Angela Re, Levi Waldron, Alessandro Quattrone

Publications and Research

Transcript levels do not faithfully predict protein levels, due to post-transcriptional regulation of gene expression mediated by RNA binding proteins (RBPs) and non-coding RNAs. We developed a multivariate linear regression model integrating RBP levels and predicted RBP-mRNA regulatory interactions from matched transcript and protein datasets. RBPs significantly improved the accuracy in predicting protein abundance of a portion of the total modeled mRNAs in three panels of tissues and cells and for different methods employed in the detection of mRNA and protein. The presence of upstream translation initiation sites (uTISs) at the mRNA 5' untranslated regions was strongly associated with improvement …

Evolutionary Interpretations Of Mycobacteriophage Biodiversity And Host-Range Through The Analysis Of Codon Usage Bias, Laura A. Esposito, Swati Gupta, Fraida Streiter, Ashley Prasad, John J. Dennehy

Publications and Research

In an genomics course sponsored by the Howard Hughes Medical Institute (HHMI), undergraduate students have isolated and sequenced the genomes of more than 1,150 mycobacteriophages, creating the largest database of sequenced bacteriophages able to infect a single host, Mycobacterium smegmatis, a soil bacterium. Genomic analysis indicates that these mycobacteriophages can be grouped into 26 clusters based on genetic similarity. These clusters span a continuum of genetic diversity, with extensive genomic mosaicism among phages in different clusters. However, little is known regarding the primary hosts of these mycobacteriophages in their natural habitats, nor of their broader host ranges. As such, it …

Ben Domain Protein Elba2 Can Functionally Substitute For Linker Histone H1 In Drosophila In Vivo, Na Xu, Xingwu Lu, Harsh Kavi, Alexander V. Emelyanov, Travis J. Bernardo, Elena Vershilova, Arthur I. Skoultchi, Dmitry V. Fyodorov

Publications and Research

Metazoan linker histones are essential for development and play crucial roles in organization of chromatin, modification of epigenetic states and regulation of genetic activity. Vertebrates express multiple linker histone H1 isoforms, which may function redundantly. In contrast, H1 isoforms are not present in Dipterans, including D. melanogaster, except for an embryo-specific, distantly related dBigH1. Here we show that Drosophila BEN domain protein Elba2, which is expressed in early embryos and was hypothesized to have insulator-specific functions, can compensate for the loss of H1 in vivo. Although the Elba2 gene is not essential, its mutation causes a disruption of normal internucleosomal …

Machine Learning Meta-Analysis Of Large Metagenomic Datasets: Tools And Biological Insight, Edoardo Pasolli, Duy Tin Truong, Faizan Malik, Levi Waldron, Nicola Segata

Publications and Research

Shotgun metagenomic analysis of the human associated microbiome provides a rich set of microbial features for prediction and biomarker discovery in the context of human diseases and health conditions. However, the use of such high-resolution microbial features presents new challenges, and validated computational tools for learning tasks are lacking. Moreover, classification rules have scarcely been validated in independent studies, posing questions about the generality and generalization of disease-predictive models across cohorts. In this paper, we comprehensively assess approaches to metagenomics-based prediction tasks and for quantitative assessment of the strength of potential microbiome-phenotype associations. We develop a computational framework for prediction …

Comparative Genomics Explains The Evolutionary Success Of Reef-Forming Corals, Debashish Bhattacharya, Shobhit Agrawal, Manuel Aranda, Sebastian Baumgarten, Mahdi Belcaid, Jeana L. Drake, Douglas Erwin, Sylvian Foret, Ruth D. Gates, David F. Gruber, Bishoy Kamel, Michael P. Lesser, Oren Levy, Yi Jin Liew, Matthew Macmanes, Tali Mass, Monica Medina, Shaadi Mehr, Eli Meyer, Dana C. Price, Hollie M. Putnam, Huan Qiu, Chuya Shinzato, Eiichi Shoguchi, Alexander J. Stokes, Sylvie Tambutté, Dan Tchernov, Christian R. Voolstra, Nicole Wagner, Charles W. Walker, Andreas Pm Weber, Virginia Weis, Ehud Zelzion, Didier Zoccola, Paul G. Falkowski

Publications and Research

Transcriptome and genome data from twenty stony coral species and a selection of reference bilaterians were studied to elucidate coral evolutionary history. We identified genes that encode the proteins responsible for the precipitation and aggregation of the aragonite skeleton on which the organisms live, and revealed a network of environmental sensors that coordinate responses of the host animals to temperature, light, and pH. Furthermore, we describe a variety of stress-related pathways, including apoptotic pathways that allow the host animals to detoxify reactive oxygen and nitrogen species that are generated by their intracellular photosynthetic symbionts, and determine the fate of corals …

Epigenetic Profiles Signify Cell Fate Plasticity In Unipotent Spermatogonial Stem And Progenitor Cells, Ying Liu, Eugenia G. Giannopoulou, Duacheng Wen, Ilaria Falciatori, Oliver Elemento, C. David Allis, Shahin Rafii, Marco Seandel

Publications and Research

Spermatogonial stem and progenitor cells (SSCs) generate adult male gametes. During in vitro expansion, these unipotent murine cells spontaneously convert to multipotent adult spermatogonial-derived stem cells (MASCs). Here we investigate this conversion process through integrative transcriptomic and epigenomic analyses. We find in SSCs that promoters essential to maintenance and differentiation of embryonic stem cells (ESCs) are enriched with histone H3-lysine4 and -lysine 27 trimethylations. These bivalent modifications are maintained at most somatic promoters after conversion, bestowing MASCs an ESC-like promoter chromatin. At enhancers, the core pluripotency circuitry is activated partially in SSCs and completely in MASCs, concomitant with loss of …

Comparative Error-Free And Error-Prone Translesion Synthesis Of N2‑2′-Deoxyguanosine Adducts Formed By Mitomycin C And Its Metabolite, 2,7-Diaminomitosene, In Human Cells, Arindam Bose, Chaitra Surugihalli, Paritosh Pande, Elise Champeil, Ashis K. Basu

Publications and Research

Mitomycin C (MC) is a cytotoxic and mutagenic antitumor agent that alkylates DNA upon reductive activation. 2,7-Diaminomitosene (2,7-DAM) is a major metabolite of MC in tumor cells, which also alkylates DNA. MC forms seven DNA adducts, including monoadducts and inter- and intrastrand cross-links, whereas 2,7-DAM forms two monoadducts. Herein, the biological effects of the dG-N2 adducts formed by MC and 2,7-DAM have been compared by constructing single-stranded plasmids containing these adducts and replicating them in human embryonic kidney 293T cells. Translesion synthesis (TLS) efficiencies of dG-N2-MC and dG-N2-2,7-DAM were 38 ± 3 and 27 …

Effects Of Choline On Dna Methylation And Macronutrient Metabolic Gene Expression In In Vitro Models Of Hyperglycemia, Xinyin Jiang, Esther Greenwald, Chauntelle Jack-Roberts

Publications and Research

Choline is an essential nutrient that plays an important role in lipid metabolism and DNA methylation. Studies in rodents suggest that choline may adversely affect glycemic control, yet studies in humans are lacking. Using the human hepatic and placental cells, HepG2 and BeWo, respectively, we examined the interaction between choline and glucose treatments. In HepG2 cells, choline supplementation (1 mM) increased global DNA methylation and DNA methyltransferase expression in both low-glucose (5 mM) and high-glucose (35 mM) conditions. Choline supplementation increased the expression of peroxisomal acyl-coenzyme A oxidase 1 (ACOX1), which mediates fatty acid β-oxidation, especially in the high-glucose condition. …

Diversity-Dependent Cladogenesis Throughout Western Mexico: Evolutionary Biogeography Of Rattlesnakes (Viperidae: Crotalinae: Crotalus And Sistrurus), Christopher Blair, Santiago Sánchez-Ramírez

Publications and Research

Rattlesnakes (Crotalus and Sistrurus) represent a radiation of approximately 42 species distributed throughout the New World from southern Canada to Argentina. Interest in this enigmatic group of snakes continues to accrue due, in part, to their ecomorphological diversity, contributions to global envenomations, and potential medicinal importance. Although the group has garnered substantial attention from systematists and evolutionary biologists for decades, little is still known regarding patterns of lineage diversification. In addition, few studies have statistically quantified broad-scale biogeographic patterns in rattlesnakes to ascertain how dispersal occurred throughout the New World, particularly among the different major biomes of the …

Genome Assembly And Geospatial Phylogenomics Of The Bed Bug Cimex Lectularius, Jeffrey A. Rosenfeld, Darryl Reeves, Mercer R. Brugler, Apurva Narechania, Sabrina Simon, Russell Durrett, Jonathan Foox, Kevin Shianna, Michael C. Schatz, Jorge Gandara, Ebrahim Afshinnekoo, Ernest T. Lam, Alex R. Hastie, Saki Chan, Han Cao, Michael Saghbini, Alex Kentsis, Paul J. Planet, Vladyslav Kholodovych, Michael Tessler, Richard Baker, Rob Desalle, Louis N. Sorkin, Sergios-Orestis Kolokotronis, Mark E. Siddall, George Amato, Christopher E. Mason

Publications and Research

The common bed bug (Cimex lectularius) has been a persistent pest of humans for thousands of years, yet the genetic basis of the bed bug’s basic biology and adaptation to dense human environments is largely unknown. Here we report the assembly, annotation and phylogenetic mapping of the 697.9-Mb Cimex lectularius genome, with an N50 of 971 kb, using both long and short read technologies. A RNA-seq time course across all five developmental stages and male and female adults generated 36,985 coding and noncoding gene models. The most pronounced change in gene expression during the life cycle occurs after feeding on …

Cellmapper: Rapid And Accurate Inference Of Gene Expression In Difficult-To-Isolate Cell Types, Bradlee D. Nelms, Levi Waldron, Luis A. Barrera, Andrew W. Weflen, Jeremy A. Goettel, Guoji Guo, Robert K. Montgomery, Marian R. Neutra, David T. Breault, Scott B. Snapper, Stuart H. Orkin, Martha L. Bulyk, Curtis Huttenhower, Wayne I. Lencer

Publications and Research

We present a sensitive approach to predict genes expressed selectively in specific cell types, by searching publicly available expression data for genes with a similar expression profile to known cell-specific markers. Our method, CellMapper, strongly outperforms previous computational algorithms to predict cell type-specific expression, especially for rare and difficult-to-isolate cell types. Furthermore, CellMapper makes accurate predictions for human brain cell types that have never been isolated, and can be rapidly applied to diverse cell types from many tissues. We demonstrate a clinically relevant application to prioritize candidate genes in disease susceptibility loci identified by GWAS.

The Mitogenome Of The Bed Bug Cimex Lectularius (Hemiptera: Cimicidae), Sergios-Orestis Kolokotronis, Jonathan Foox, Jeffrey A. Rosenfeld, Mercer R. Brugler, Darryl Reeves, Joshua B. Benoit, Warren Booth, Grant Robison, Michael Steffen, Zoe Sakas, Subba R. Palli, Coby Schal, Stephen Richards, Apurva Narechania, Richard H. Baker, Louis N. Sorkin, George Amato, Christopher E. Mason, Mark E. Siddall, Rob Desalle

Publications and Research

We report the extraction of a bed bug mitogenome from high-throughput sequencing projects originally focused on the nuclear genome of Cimex lectularius. The assembled mitogenome has a similar AT nucleotide composition bias found in other insects. Phylogenetic analysis of all protein-coding genes indicates that C. lectularius is clearly a member of a paraphyletic Cimicomorpha clade within the Order Hemiptera.

Elimination Of Chromosomal Island Spycim1 From Streptococcus Pyogenes Strain Sf370 Reverses The Mutator Phenotype And Alters Global Transcription, Christina Hendrickson, Chad W. Euler, Scott V. Nguyen, Maliha Rahman, Kimberly A. Mccullor, Catherine J. King, Vincent A. Fischetti, W. Michael Mcshan

Publications and Research

Streptococcus pyogenes chromosomal island M1 (SpyCIM1) integrates by site-specific recombination into the 5’ end of DNA mismatch repair (MMR) gene mutL in strain SF370SmR, blocking transcription of it and the downstream operon genes. During exponential growth, SpyCIM1 excises from the chromosome and replicates as an episome, restoring mutL transcription. This process is reversed in stationary phase with SpyCIM1 re-integrating into mutL, returning the cells to a mutator phenotype. Here we show that elimination of SpyCIM1 relieves this mutator phenotype. The downstream MMR operon genes, multidrug efflux pump lmrP, Holliday junction resolution helicase ruvA, and DNA base excision …