1
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Smith CF, Modahl CM, Ceja-Galindo D, Larson KY, Maroney SP, Bahrabadi L, Brandehoff NP, Perry BW, McCabe MC, Petras D, Lomonte B, Calvete JJ, Castoe TA, Mackessy SP, Hansen KC, Saviola AJ. ASSESSING TARGET SPECIFICITY OF THE SMALL MOLECULE INHIBITOR MARIMASTAT TO SNAKE VENOM TOXINS: A NOVEL APPLICATION OF THERMAL PROTEOME PROFILING. Mol Cell Proteomics 2024:100779. [PMID: 38679388 DOI: 10.1016/j.mcpro.2024.100779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 04/09/2024] [Accepted: 04/25/2024] [Indexed: 05/01/2024] Open
Abstract
New treatments that circumvent the pitfalls of traditional antivenom therapies are critical to address the problem of snakebite globally. Numerous snake venom toxin inhibitors have shown promising cross-species neutralization of medically significant venom toxins in vivo and in vitro. The development of high-throughput approaches for the screening of such inhibitors could accelerate their identification, testing, and implementation, and thus holds exciting potential for improving the treatments and outcomes of snakebite envenomation worldwide. Energetics-based proteomic approaches, including Thermal Proteome Profiling (TPP) and Proteome Integral Solubility Alteration (PISA) assays, represent "deep proteomics" methods for high throughput, proteome-wide identification of drug targets and ligands. In the following study, we apply TPP and PISA methods to characterize the interactions between venom toxin proteoforms in Crotalus atrox (Western Diamondback Rattlesnake) and the snake venom metalloprotease (SVMP) inhibitor marimastat. We investigate its venom proteome-wide effects and characterize its interactions with specific SVMP proteoforms, as well as its potential targeting of non-SVMP venom toxin families. We also compare the performance of PISA thermal window and soluble supernatant with insoluble precipitate using two inhibitor concentrations, providing the first demonstration of the utility of a sensitive high-throughput PISA-based approach to assess the direct targets of small molecule inhibitors for snake venom.
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Affiliation(s)
- Cara F Smith
- Department of Biochemistry and Molecular Genetics, 12801 East 17(th) Avenue, University of Colorado Denver, Aurora, CO, USA
| | - Cassandra M Modahl
- Centre for Snakebite Research and Interventions, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, UK
| | - David Ceja-Galindo
- Department of Biochemistry and Molecular Genetics, 12801 East 17(th) Avenue, University of Colorado Denver, Aurora, CO, USA
| | - Keira Y Larson
- Department of Biochemistry and Molecular Genetics, 12801 East 17(th) Avenue, University of Colorado Denver, Aurora, CO, USA
| | - Sean P Maroney
- Department of Biochemistry and Molecular Genetics, 12801 East 17(th) Avenue, University of Colorado Denver, Aurora, CO, USA
| | - Lilyrose Bahrabadi
- Department of Biochemistry and Molecular Genetics, 12801 East 17(th) Avenue, University of Colorado Denver, Aurora, CO, USA
| | - Nicklaus P Brandehoff
- Rocky Mountain Poison and Drug Center, Denver Health and Hospital Authority, Denver, CO, USA
| | - Blair W Perry
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Maxwell C McCabe
- Department of Biochemistry and Molecular Genetics, 12801 East 17(th) Avenue, University of Colorado Denver, Aurora, CO, USA
| | - Daniel Petras
- CMFI Cluster of Excellence, University of Tuebingen, Tuebingen, Germany; Department of Biochemistry, University of California Riverside, Riverside, CA, USA
| | - Bruno Lomonte
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José, 11501-2060, Costa Rica
| | - Juan J Calvete
- Evolutionary and Translational Venomics Laboratory, Consejo Superior de Investigaciones Científicas (CSIC), 46010 Valencia, Spain
| | - Todd A Castoe
- Department of Biology, The University of Texas Arlington, Texas, USA
| | - Stephen P Mackessy
- Department of Biological Sciences, 501 20th Street, University of Northern Colorado, Greeley, CO 80639 USA
| | - Kirk C Hansen
- Department of Biochemistry and Molecular Genetics, 12801 East 17(th) Avenue, University of Colorado Denver, Aurora, CO, USA
| | - Anthony J Saviola
- Department of Biochemistry and Molecular Genetics, 12801 East 17(th) Avenue, University of Colorado Denver, Aurora, CO, USA.
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2
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Vincent EP, Perry BW, Kelley JL, Robbins CT, Jansen HT. Circadian gene transcription plays a role in cellular metabolism in hibernating brown bears, Ursus arctos. J Comp Physiol B 2023; 193:699-713. [PMID: 37819371 DOI: 10.1007/s00360-023-01513-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/28/2023] [Accepted: 09/05/2023] [Indexed: 10/13/2023]
Abstract
Hibernation is a highly seasonal physiological adaptation that allows brown bears (Ursus arctos) to survive extended periods of low food availability. Similarly, daily or circadian rhythms conserve energy by coordinating body processes to optimally match the environmental light/dark cycle. Brown bears express circadian rhythms in vivo and their cells do in vitro throughout the year, suggesting that these rhythms may play important roles during periods of negative energy balance. Here, we use time-series analysis of RNA sequencing data and timed measurements of ATP production in adipose-derived fibroblasts from active and hibernation seasons under two temperature conditions to confirm that rhythmicity was present. Culture temperature matching that of hibernation body temperature (34 °C) resulted in a delay of daily peak ATP production in comparison with active season body temperatures (37 °C). The timing of peaks of mitochondrial gene transcription was altered as were the amplitudes of transcripts coding for enzymes of the electron transport chain. Additionally, we observed changes in mean expression and timing of key metabolic genes such as SIRT1 and AMPK which are linked to the circadian system and energy balance. The amplitudes of several circadian gene transcripts were also reduced. These results reveal a link between energy conservation and a functioning circadian system in hibernation.
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Affiliation(s)
- Ellery P Vincent
- School of Biological Sciences, Washington State University, Pullman, WA, 99163, USA
| | - Blair W Perry
- School of Biological Sciences, Washington State University, Pullman, WA, 99163, USA
| | - Joanna L Kelley
- Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
| | - Charles T Robbins
- School of Biological Sciences, Washington State University, Pullman, WA, 99163, USA
- School of the Environment, Washington State University, Pullman, WA, 99163, USA
| | - Heiko T Jansen
- School of Biological Sciences, Washington State University, Pullman, WA, 99163, USA.
- Department of Integrative Physiology and Neuroscience, Washington State University, Pullman, WA, 99163, USA.
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3
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McCabe MC, Okamura DM, Erickson CB, Perry BW, Brewer CM, Nguyen ED, Saviola AJ, Majesky MW, Hansen KC. ECM-Focused Proteomic Analysis of Ear Punch Regeneration in Acomys Cahirinus. bioRxiv 2023:2023.10.11.561940. [PMID: 37873317 PMCID: PMC10592745 DOI: 10.1101/2023.10.11.561940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
In mammals, significant injury is generally followed by the formation of a fibrotic scar which provides structural integrity but fails to functionally restore damaged tissue. Spiny mice of the genus Acomys represent the first example of full skin autotomy in mammals. Acomys cahirinus has evolved extremely weak skin as a strategy to avoid predation and is able to repeatedly regenerate healthy tissue without scar after severe skin injury or full-thickness ear punches. Extracellular matrix (ECM) composition is a critical regulator of wound repair and scar formation and previous studies have suggested that alterations in its expression may be responsible for the differences in regenerative capacity observed between Mus musculus and A. cahirinus , yet analysis of this critical tissue component has been limited in previous studies by its insolubility and resistance to extraction. Here, we utilize a 2-step ECM-optimized extraction to perform proteomic analysis of tissue composition during wound repair after full-thickness ear punches in A. cahirinus and M. musculus from weeks 1 to 4 post-injury. We observe changes in a wide range of ECM proteins which have been previously implicated in wound regeneration and scar formation, including collagens, coagulation and provisional matrix proteins, and matricryptic signaling peptides. We additionally report differences in crosslinking enzyme activity and ECM protein solubility between Mus and Acomys. Furthermore, we observed rapid and sustained increases in CD206, a marker of pro-regenerative M2 macrophages, in Acomys, whereas little or no increase in CD206 was detected in Mus. Together, these findings contribute to a comprehensive understanding of tissue cues which drive the regenerative capacity of Acomys and identify a number of potential targets for future pro-regenerative therapies.
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Smith CF, Nikolakis ZL, Perry BW, Schield DR, Meik JM, Saviola AJ, Castoe TA, Parker J, Mackessy SP. The best of both worlds? Rattlesnake hybrid zones generate complex combinations of divergent venom phenotypes that retain high toxicity. Biochimie 2023; 213:176-189. [PMID: 37451532 DOI: 10.1016/j.biochi.2023.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 06/27/2023] [Accepted: 07/10/2023] [Indexed: 07/18/2023]
Abstract
Studying the consequences of hybridization between closely related species with divergent traits can reveal patterns of evolution that shape and maintain extreme trophic adaptations. Snake venoms are an excellent model system for examining the evolutionary and ecological patterns that underlie highly selected polymorphic traits. Here we investigate hybrid venom phenotypes that result from natural introgression between two rattlesnake species that express highly divergent venom phenotypes: Crotalus o. concolor and C. v. viridis. Though not yet documented, interbreeding between these species may lead to novel venom phenotypes with unique activities that break the typical trends of venom composition in rattlesnakes. The characteristics of these unusual phenotypes could unveil the roles of introgression in maintaining patterns of venom composition and variation, including the near ubiquitous dichotomy between neurotoxic or degradative venoms observed across rattlesnakes. We use RADseq data to infer patterns of gene flow and hybrid ancestry between these diverged lineages and link these genetic data with analyses of venom composition, biological activity, and whole animal model toxicity tests to understand the impacts of introgression on venom composition. We find that introgressed populations express admixed venom phenotypes that do not sacrifice biological activity (lethal toxicity) or overall abundance of dominant toxins compared to parental venoms. These hybridized venoms therefore do not represent a trade-off in functionality between the typical phenotypic extremes but instead represent a unique combination of characters whose expression appears limited to the hybrid zone.
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Affiliation(s)
- Cara F Smith
- School of Biological Sciences, 501 20th Street, University of Northern Colorado, Greeley, CO, 80639, USA
| | - Zachary L Nikolakis
- Department of Biology, 501 S. Nedderman Drive, University of Texas at Arlington, Arlington, TX, 76019, USA
| | - Blair W Perry
- Department of Biology, 501 S. Nedderman Drive, University of Texas at Arlington, Arlington, TX, 76019, USA
| | - Drew R Schield
- Department of Biology, 501 S. Nedderman Drive, University of Texas at Arlington, Arlington, TX, 76019, USA
| | - Jesse M Meik
- Department of Biological Sciences, Tarleton State University, 1333 W. Washington Street, Stephenville, TX, 76402, USA
| | - Anthony J Saviola
- Department of Biochemistry and Molecular Genetics, 12801 East 17th Avenue, University of Colorado Denver, Aurora, CO, 80045, USA
| | - Todd A Castoe
- Department of Biology, 501 S. Nedderman Drive, University of Texas at Arlington, Arlington, TX, 76019, USA
| | - Joshua Parker
- Fresno City College, 1101 E. University Avenue, Fresno, CA, 93741, USA
| | - Stephen P Mackessy
- School of Biological Sciences, 501 20th Street, University of Northern Colorado, Greeley, CO, 80639, USA.
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Perry BW, McDonald AL, Trojahn S, Saxton MW, Vincent EP, Lowry C, Evans Hutzenbiler BD, Cornejo OE, Robbins CT, Jansen HT, Kelley JL. Feeding during hibernation shifts gene expression toward active season levels in brown bears ( Ursus arctos). Physiol Genomics 2023; 55:368-380. [PMID: 37486084 PMCID: PMC10642923 DOI: 10.1152/physiolgenomics.00030.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 06/28/2023] [Accepted: 07/17/2023] [Indexed: 07/25/2023] Open
Abstract
Hibernation in bears involves a suite of metabolical and physiological changes, including the onset of insulin resistance, that are driven in part by sweeping changes in gene expression in multiple tissues. Feeding bears glucose during hibernation partially restores active season physiological phenotypes, including partial resensitization to insulin, but the molecular mechanisms underlying this transition remain poorly understood. Here, we analyze tissue-level gene expression in adipose, liver, and muscle to identify genes that respond to midhibernation glucose feeding and thus potentially drive postfeeding metabolical and physiological shifts. We show that midhibernation feeding stimulates differential expression in all analyzed tissues of hibernating bears and that a subset of these genes responds specifically by shifting expression toward levels typical of the active season. Inferences of upstream regulatory molecules potentially driving these postfeeding responses implicate peroxisome proliferator-activated receptor gamma (PPARG) and other known regulators of insulin sensitivity, providing new insight into high-level regulatory mechanisms involved in shifting metabolic phenotypes between hibernation and active states.
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Affiliation(s)
- Blair W Perry
- School of Biological Sciences, Washington State University, Pullman, Washington, United States
| | - Anna L McDonald
- School of Biological Sciences, Washington State University, Pullman, Washington, United States
| | - Shawn Trojahn
- School of Biological Sciences, Washington State University, Pullman, Washington, United States
| | - Michael W Saxton
- School of Biological Sciences, Washington State University, Pullman, Washington, United States
| | - Ellery P Vincent
- School of Biological Sciences, Washington State University, Pullman, Washington, United States
| | - Courtney Lowry
- School of Biological Sciences, Washington State University, Pullman, Washington, United States
| | | | - Omar E Cornejo
- Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, California, United States
| | - Charles T Robbins
- School of the Environment, Washington State University, Pullman, Washington, United States
| | - Heiko T Jansen
- Department of Integrative Physiology and Neuroscience, Washington State University, Pullman, Washington, United States
| | - Joanna L Kelley
- Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, California, United States
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6
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Westfall AK, Gopalan SS, Perry BW, Adams RH, Saviola AJ, Mackessy SP, Castoe TA. Single-cell heterogeneity in snake venom expression is hardwired by co-option of regulators from progressively activated pathways. Genome Biol Evol 2023:evad109. [PMID: 37311204 DOI: 10.1093/gbe/evad109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 05/31/2023] [Accepted: 06/07/2023] [Indexed: 06/15/2023] Open
Abstract
The ubiquitous cellular heterogeneity underlying many organism-level phenotypes raises questions about what factors drive this heterogeneity and how these complex heterogeneous systems evolve. Here, we use single-cell expression data from a Prairie rattlesnake (Crotalus viridis) venom gland to evaluate hypotheses for signaling networks underlying snake venom regulation and the degree to which different venom gene families have evolutionarily recruited distinct regulatory architectures. Our findings suggest that snake venom regulatory systems have evolutionarily co-opted trans-regulatory factors from ERK and UPR pathways that specifically coordinate expression of distinct venom toxins in a phased sequence across a single population of secretory cells. This pattern of co-option results in extensive cell-to-cell variation in venom gene expression, even between tandemly-duplicated paralogs, suggesting this regulatory architecture has evolved to circumvent cellular constraints. While the exact nature of such constraints remains an open question, we propose that such regulatory heterogeneity may circumvent steric constraints on chromatin, cellular physiological constraints (e.g., endoplasmic reticulum stress or negative protein-protein interactions), or a combination of these. Regardless of the precise nature of these constraints, this example suggests that, in some cases, dynamic cellular constraints may impose previously unappreciated secondary constraints on the evolution of gene regulatory networks that favors heterogeneous expression.
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Affiliation(s)
- Aundrea K Westfall
- Department of Biology, 501 S. Nedderman Dr., The University of Texas Arlington, Arlington, TX 76019USA
| | - Siddharth S Gopalan
- Department of Biology, 501 S. Nedderman Dr., The University of Texas Arlington, Arlington, TX 76019USA
| | - Blair W Perry
- Department of Biology, 501 S. Nedderman Dr., The University of Texas Arlington, Arlington, TX 76019USA
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - Richard H Adams
- Department of Entomology and Plant Pathology, University of Arkansas Agricultural Experimental Station, University of Arkansas, Fayetteville, AR 72701USA
| | - Anthony J Saviola
- Department of Biochemistry and Molecular Genetics, 12801 East 17th Avenue, University of Colorado Denver, Aurora, CO 80045USA
| | - Stephen P Mackessy
- School of Biological Sciences, University of Northern Colorado, Greeley, CO 80639, USA
| | - Todd A Castoe
- Department of Biology, 501 S. Nedderman Dr., The University of Texas Arlington, Arlington, TX 76019USA
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7
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Perry BW, Saxton MW, Jansen HT, Quackenbush CR, Evans Hutzenbiler BD, Robbins CT, Kelley JL, Cornejo OE. A multi-tissue gene expression dataset for hibernating brown bears. BMC Genom Data 2023; 24:33. [PMID: 37291509 PMCID: PMC10251632 DOI: 10.1186/s12863-023-01136-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 06/06/2023] [Indexed: 06/10/2023] Open
Abstract
OBJECTIVES Complex physiological adaptations often involve the coordination of molecular responses across multiple tissues. Establishing transcriptomic resources for non-traditional model organisms with phenotypes of interest can provide a foundation for understanding the genomic basis of these phenotypes, and the degree to which these resemble, or contrast, those of traditional model organisms. Here, we present a one-of-a-kind gene expression dataset generated from multiple tissues of two hibernating brown bears (Ursus arctos). DATA DESCRIPTION This dataset is comprised of 26 samples collected from 13 tissues of two hibernating brown bears. These samples were collected opportunistically and are typically not possible to attain, resulting in a highly unique and valuable gene expression dataset. In combination with previously published datasets, this new transcriptomic resource will facilitate detailed investigation of hibernation physiology in bears, and the potential to translate aspects of this biology to treat human disease.
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Affiliation(s)
- Blair W Perry
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Michael W Saxton
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Heiko T Jansen
- Department of Integrative Physiology and Neuroscience, Washington State University, Pullman, WA, 99164, USA
| | - Corey R Quackenbush
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
| | | | - Charles T Robbins
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
- School of the Environment, Washington State University, Pullman, WA, 99164, USA
| | - Joanna L Kelley
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, 95060, USA
| | - Omar E Cornejo
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, 95060, USA.
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Smith CF, Nikolakis ZL, Ivey K, Perry BW, Schield DR, Balchan NR, Parker J, Hansen KC, Saviola AJ, Castoe TA, Mackessy SP. Snakes on a plain: biotic and abiotic factors determine venom compositional variation in a wide-ranging generalist rattlesnake. BMC Biol 2023; 21:136. [PMID: 37280596 DOI: 10.1186/s12915-023-01626-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 05/12/2023] [Indexed: 06/08/2023] Open
Abstract
BACKGROUND Snake venoms are trophic adaptations that represent an ideal model to examine the evolutionary factors that shape polymorphic traits under strong natural selection. Venom compositional variation is substantial within and among venomous snake species. However, the forces shaping this phenotypic complexity, as well as the potential integrated roles of biotic and abiotic factors, have received little attention. Here, we investigate geographic variation in venom composition in a wide-ranging rattlesnake (Crotalus viridis viridis) and contextualize this variation by investigating dietary, phylogenetic, and environmental variables that covary with venom. RESULTS Using shotgun proteomics, venom biochemical profiling, and lethality assays, we identify 2 distinct divergent phenotypes that characterize major axes of venom variation in this species: a myotoxin-rich phenotype and a snake venom metalloprotease (SVMP)-rich phenotype. We find that dietary availability and temperature-related abiotic factors are correlated with geographic trends in venom composition. CONCLUSIONS Our findings highlight the potential for snake venoms to vary extensively within species, for this variation to be driven by biotic and abiotic factors, and for the importance of integrating biotic and abiotic variation for understanding complex trait evolution. Links between venom variation and variation in biotic and abiotic factors indicate that venom variation likely results from substantial geographic variation in selection regimes that determine the efficacy of venom phenotypes across populations and snake species. Our results highlight the cascading influence of abiotic factors on biotic factors that ultimately shape venom phenotype, providing evidence for a central role of local selection as a key driver of venom variation.
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Affiliation(s)
- Cara F Smith
- Department of Biological Sciences, University of Northern Colorado, 501 20th Street, Greeley, CO, 80639, USA
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, 12801 East 17th Avenue, Aurora, CO, 80045, USA
| | - Zachary L Nikolakis
- Department of Biology, University of Texas at Arlington, 501 S. Nedderman Drive, Arlington, TX, 76019, USA
| | - Kathleen Ivey
- Department of Biology, University of Texas at Arlington, 501 S. Nedderman Drive, Arlington, TX, 76019, USA
| | - Blair W Perry
- Department of Biology, University of Texas at Arlington, 501 S. Nedderman Drive, Arlington, TX, 76019, USA
| | - Drew R Schield
- Department of Biology, University of Texas at Arlington, 501 S. Nedderman Drive, Arlington, TX, 76019, USA
- Current address: Department of Ecology & Evolutionary Biology, University of Colorado, 1900 Pleasant Street, Boulder, CO, 80309, USA
| | - Neil R Balchan
- Department of Biological Sciences, University of Northern Colorado, 501 20th Street, Greeley, CO, 80639, USA
| | - Joshua Parker
- Fresno City College, 1101 E. University Avenue, Fresno, CA, 93741, USA
| | - Kirk C Hansen
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, 12801 East 17th Avenue, Aurora, CO, 80045, USA
| | - Anthony J Saviola
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, 12801 East 17th Avenue, Aurora, CO, 80045, USA
| | - Todd A Castoe
- Department of Biology, University of Texas at Arlington, 501 S. Nedderman Drive, Arlington, TX, 76019, USA
| | - Stephen P Mackessy
- Department of Biological Sciences, University of Northern Colorado, 501 20th Street, Greeley, CO, 80639, USA.
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9
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Perry BW, Armstrong EE, Robbins CT, Jansen HT, Kelley JL. Temporal Analysis of Gene Expression and Isoform Switching in Brown Bears (Ursus arctos). Integr Comp Biol 2022; 62:1802-1811. [PMID: 35709393 DOI: 10.1093/icb/icac093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 06/01/2022] [Accepted: 06/09/2022] [Indexed: 01/05/2023] Open
Abstract
Hibernation in brown bears is an annual process involving multiple physiologically distinct seasons-hibernation, active, and hyperphagia. While recent studies have characterized broad patterns of differential gene regulation and isoform usage between hibernation and active seasons, patterns of gene and isoform expression during hyperphagia remain relatively poorly understood. The hyperphagia stage occurs between active and hibernation seasons and involves the accumulation of large fat reserves in preparation for hibernation. Here, we use time-series analyses of gene expression and isoform usage to interrogate transcriptomic regulation associated with all three seasons. We identify a large number of genes with significant differential isoform usage (DIU) across seasons and show that these patterns of isoform usage are largely tissue-specific. We also show that DIU and differential gene-level expression responses are generally non-overlapping, with only a small subset of multi-isoform genes showing evidence of both gene-level expression changes and changes in isoform usage across seasons. Additionally, we investigate nuanced regulation of candidate genes involved in the insulin signaling pathway and find evidence of hyperphagia-specific gene expression and isoform regulation that may enhance fat accumulation during hyperphagia. Our findings highlight the value of using temporal analyses of both gene- and isoform-level gene expression when interrogating complex physiological phenotypes and provide new insight into the mechanisms underlying seasonal changes in bear physiology.
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Affiliation(s)
- Blair W Perry
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - Ellie E Armstrong
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - Charles T Robbins
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA.,School of the Environment, Washington State University, Pullman, WA 99164, USA
| | | | - Joanna L Kelley
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
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10
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Nikolakis ZL, Schield DR, Westfall AK, Perry BW, Ivey KN, Orton RW, Hales NR, Adams RH, Meik JM, Parker JM, Smith CF, Gompert Z, Mackessy SP, Castoe TA. Evidence that genomic incompatibilities and other multilocus processes impact hybrid fitness in a rattlesnake hybrid zone. Evolution 2022; 76:2513-2530. [PMID: 36111705 DOI: 10.1111/evo.14612] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 06/24/2022] [Accepted: 08/15/2022] [Indexed: 01/22/2023]
Abstract
Hybrid zones provide valuable opportunities to understand the genomic mechanisms that promote speciation by providing insight into factors involved in intermediate stages of speciation. Here, we investigate introgression in a hybrid zone between two rattlesnake species (Crotalus viridis and Crotalus oreganus concolor) that have undergone historical allopatric divergence and recent range expansion and secondary contact. We use Bayesian genomic cline models to characterize genomic patterns of introgression between these lineages and identify loci potentially subject to selection in hybrids. We find evidence for a large number of genomic regions with biased ancestry that deviate from the genomic background in hybrids (i.e., excess ancestry loci), which tend to be associated with genomic regions with higher recombination rates. We also identify suites of excess ancestry loci that show highly correlated allele frequencies (including conspecific and heterospecific combinations) across physically unlinked genomic regions in hybrids. Our findings provide evidence for multiple multilocus evolutionary processes impacting hybrid fitness in this system.
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Affiliation(s)
- Zachary L Nikolakis
- Department of Biology, University of Texas at Arlington, Arlington, Texas, 76019
| | - Drew R Schield
- Department of Biology, University of Texas at Arlington, Arlington, Texas, 76019.,Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, 80309
| | - Aundrea K Westfall
- Department of Biology, University of Texas at Arlington, Arlington, Texas, 76019
| | - Blair W Perry
- Department of Biology, University of Texas at Arlington, Arlington, Texas, 76019
| | - Kathleen N Ivey
- Department of Biology, University of Texas at Arlington, Arlington, Texas, 76019
| | - Richard W Orton
- Department of Biology, University of Texas at Arlington, Arlington, Texas, 76019
| | - Nicole R Hales
- Department of Biology, University of Texas at Arlington, Arlington, Texas, 76019
| | - Richard H Adams
- Department of Biological and Environmental Sciences, Georgia College and State University, Milledgeville, Georgia, 31061
| | - Jesse M Meik
- Department of Biological Sciences, Tarleton State University, Stephenville, Texas, 76402
| | - Joshua M Parker
- Department of Life Sciences, Fresno City College, Fresno, California, 93741
| | - Cara F Smith
- School of Biological Sciences, University of Northern Colorado, Greeley, Colorado, 80639
| | | | - Stephen P Mackessy
- School of Biological Sciences, University of Northern Colorado, Greeley, Colorado, 80639
| | - Todd A Castoe
- Department of Biology, University of Texas at Arlington, Arlington, Texas, 76019
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11
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Saxton MW, Perry BW, Evans Hutzenbiler BD, Trojahn S, Gee A, Brown AP, Merrihew GE, Park J, Cornejo OE, MacCoss MJ, Robbins CT, Jansen HT, Kelley JL. Serum plays an important role in reprogramming the seasonal transcriptional profile of brown bear adipocytes. iScience 2022; 25:105084. [PMID: 36317158 PMCID: PMC9617460 DOI: 10.1016/j.isci.2022.105084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 06/30/2022] [Accepted: 09/01/2022] [Indexed: 11/19/2022] Open
Abstract
Understanding how metabolic reprogramming happens in cells will aid the progress in the treatment of a variety of metabolic disorders. Brown bears undergo seasonal shifts in insulin sensitivity, including reversible insulin resistance in hibernation. We performed RNA-sequencing on brown bear adipocytes and proteomics on serum to identify changes possibly responsible for reversible insulin resistance. We observed dramatic transcriptional changes, which depended on both the cell and serum season of origin. Despite large changes in adipocyte gene expression, only changes in eight circulating proteins were identified as related to the seasonal shifts in insulin sensitivity, including some that have not previously been associated with glucose homeostasis. The identified serum proteins may be sufficient for shifting hibernation adipocytes to an active-like state. Hibernation in grizzly bears is marked by insulin resistance Bear adipocytes were stimulated with active and hibernating bear blood serum Serum elicited dramatic gene expression responses related to insulin signaling Eight serum proteins were implicated in driving this transcriptional response
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Affiliation(s)
- Michael W. Saxton
- School of Biological Sciences, Washington State University, Pullman, WA 99163, USA
| | - Blair W. Perry
- School of Biological Sciences, Washington State University, Pullman, WA 99163, USA
| | | | - Shawn Trojahn
- School of Biological Sciences, Washington State University, Pullman, WA 99163, USA
| | - Alexia Gee
- School of Biological Sciences, Washington State University, Pullman, WA 99163, USA
| | - Anthony P. Brown
- School of Biological Sciences, Washington State University, Pullman, WA 99163, USA
| | | | - Jea Park
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Omar E. Cornejo
- School of Biological Sciences, Washington State University, Pullman, WA 99163, USA
| | - Michael J. MacCoss
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Charles T. Robbins
- School of Biological Sciences, Washington State University, Pullman, WA 99163, USA
- School of the Environment, Washington State University, Pullman, WA 99163, USA
| | - Heiko T. Jansen
- Department of Integrative Physiology and Neuroscience, Washington State University, Pullman, WA 99163, USA
| | - Joanna L. Kelley
- School of Biological Sciences, Washington State University, Pullman, WA 99163, USA
- Corresponding author
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12
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Schield DR, Perry BW, Adams RH, Holding ML, Nikolakis ZL, Gopalan SS, Smith CF, Parker JM, Meik JM, DeGiorgio M, Mackessy SP, Castoe TA. The roles of balancing selection and recombination in the evolution of rattlesnake venom. Nat Ecol Evol 2022; 6:1367-1380. [PMID: 35851850 PMCID: PMC9888523 DOI: 10.1038/s41559-022-01829-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 06/15/2022] [Indexed: 02/02/2023]
Abstract
The origin of snake venom involved duplication and recruitment of non-venom genes into venom systems. Several studies have predicted that directional positive selection has governed this process. Venom composition varies substantially across snake species and venom phenotypes are locally adapted to prey, leading to coevolutionary interactions between predator and prey. Venom origins and contemporary snake venom evolution may therefore be driven by fundamentally different selection regimes, yet investigations of population-level patterns of selection have been limited. Here, we use whole-genome data from 68 rattlesnakes to test hypotheses about the factors that drive genomic diversity and differentiation in major venom gene regions. We show that selection has resulted in long-term maintenance of genetic diversity within and between species in multiple venom gene families. Our findings are inconsistent with a dominant role of directional positive selection and instead support a role of long-term balancing selection in shaping venom evolution. We also detect rapid decay of linkage disequilibrium due to high recombination rates in venom regions, suggesting that venom genes have reduced selective interference with nearby loci, including other venom paralogues. Our results provide an example of long-term balancing selection that drives trans-species polymorphism and help to explain how snake venom keeps pace with prey resistance.
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Affiliation(s)
- Drew R Schield
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA.
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA.
| | - Blair W Perry
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Richard H Adams
- Department of Biological and Environmental Sciences, Georgia College and State University, Milledgeville, GA, USA
| | | | | | | | - Cara F Smith
- School of Biological Sciences, University of Northern Colorado, Greeley, CO, USA
| | - Joshua M Parker
- Life Science Department, Fresno City College, Fresno, CA, USA
| | - Jesse M Meik
- Department of Biological Sciences, Tarleton State University, Stephenville, TX, USA
| | - Michael DeGiorgio
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL, USA
| | - Stephen P Mackessy
- School of Biological Sciences, University of Northern Colorado, Greeley, CO, USA
| | - Todd A Castoe
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA.
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13
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Armstrong EE, Perry BW, Huang Y, Garimella KV, Jansen HT, Robbins CT, Tucker NR, Kelley JL. A beary good genome: Haplotype-resolved, chromosome-level assembly of the brown bear (Ursus arctos). Genome Biol Evol 2022; 14:6656105. [PMID: 35929770 PMCID: PMC9447482 DOI: 10.1093/gbe/evac125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/20/2022] [Indexed: 11/30/2022] Open
Abstract
The brown bear (Ursus arctos) is the second largest and most widespread extant terrestrial carnivore on Earth and has recently emerged as a medical model for human metabolic diseases. Here, we report a fully phased chromosome-level assembly of a male North American brown bear built by combining Pacific Biosciences (PacBio) HiFi data and publicly available Hi-C data. The final genome size is 2.47 Gigabases (Gb) with a scaffold and contig N50 length of 70.08 and 43.94 Megabases (Mb), respectively. Benchmarking Universal Single-Copy Ortholog (BUSCO) analysis revealed that 94.5% of single copy orthologs from Mammalia were present in the genome (the highest of any ursid genome to date). Repetitive elements accounted for 44.48% of the genome and a total of 20,480 protein coding genes were identified. Based on whole genome alignment to the polar bear, the brown bear is highly syntenic with the polar bear, and our phylogenetic analysis of 7,246 single-copy orthologs supports the currently proposed species tree for Ursidae. This highly contiguous genome assembly will support future research on both the evolutionary history of the bear family and the physiological mechanisms behind hibernation, the latter of which has broad medical implications.
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Affiliation(s)
- Ellie E Armstrong
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Blair W Perry
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Yongqing Huang
- Data Sciences Platform, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kiran V Garimella
- Data Sciences Platform, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Heiko T Jansen
- Integrative Physiology and Neuroscience, Washington State University, Pullman, WA, 99164, USA
| | - Charles T Robbins
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA.,School of the Environment, Washington State University, Pullman, WA, 99164, USA
| | - Nathan R Tucker
- Masonic Medical Research Institute, 2150 Bleecker St, Utica, NY, 13501, USA.,Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Joanna L Kelley
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
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14
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Schield DR, Perry BW, Card DC, Pasquesi GIM, Westfall AK, Mackessy SP, Castoe TA. The rattlesnake W chromosome: A GC-rich retroelement refugium with retained gene function across ancient evolutionary strata. Genome Biol Evol 2022; 14:6648526. [PMID: 35867356 PMCID: PMC9447483 DOI: 10.1093/gbe/evac116] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2022] [Indexed: 11/18/2022] Open
Abstract
Sex chromosomes diverge after the establishment of recombination suppression, resulting in differential sex-linkage of genes involved in genetic sex determination and dimorphic traits. This process produces systems of male or female heterogamety wherein the Y and W chromosomes are only present in one sex and are often highly degenerated. Sex-limited Y and W chromosomes contain valuable information about the evolutionary transition from autosomes to sex chromosomes, yet detailed characterizations of the structure, composition, and gene content of sex-limited chromosomes are lacking for many species. In this study, we characterize the female-specific W chromosome of the prairie rattlesnake (Crotalus viridis) and evaluate how recombination suppression and other processes have shaped sex chromosome evolution in ZW snakes. Our analyses indicate that the rattlesnake W chromosome is over 80% repetitive and that an abundance of GC-rich mdg4 elements has driven an overall high degree of GC-richness despite a lack of recombination. The W chromosome is also highly enriched for repeat sequences derived from endogenous retroviruses and likely acts as a “refugium” for these and other retroelements. We annotated 219 putatively functional W-linked genes across at least two evolutionary strata identified based on estimates of sequence divergence between Z and W gametologs. The youngest of these strata is relatively gene-rich, however gene expression across strata suggests retained gene function amidst a greater degree of degeneration following ancient recombination suppression. Functional annotation of W-linked genes indicates a specialization of the W chromosome for reproductive and developmental function since recombination suppression from the Z chromosome.
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Affiliation(s)
- Drew R Schield
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Blair W Perry
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA.,School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Daren C Card
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.,Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Giulia I M Pasquesi
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Aundrea K Westfall
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - Stephen P Mackessy
- School of Biological Sciences, University of Northern Colorado, Greeley, CO, USA
| | - Todd A Castoe
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
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15
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Gopalan SS, Perry BW, Schield DR, Smith CF, Mackessy SP, Castoe TA. Origins, genomic structure and copy number variation of snake venom myotoxins. Toxicon 2022; 216:92-106. [PMID: 35820472 DOI: 10.1016/j.toxicon.2022.06.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 06/21/2022] [Accepted: 06/27/2022] [Indexed: 10/17/2022]
Abstract
Crotamine, myotoxin a and homologs are short peptides that often comprise major fractions of rattlesnake venoms and have been extensively studied for their bioactive properties. These toxins are thought to be important for rapidly immobilizing mammalian prey and are implicated in serious, and sometimes fatal, responses to envenomation in humans. While high quality reference genomes for multiple venomous snakes are available, the loci that encode myotoxins have not been successfully assembled in any existing genome assembly. Here, we integrate new and existing genomic and transcriptomic data from the Prairie Rattlesnake (Crotalus viridis viridis) to reconstruct, characterize, and infer the chromosomal locations of myotoxin-encoding loci. We integrate long-read transcriptomics (Pacific Bioscience's Iso-Seq) and short-read RNA-seq to infer gene sequence diversity and characterize patterns of myotoxin and paralogous β-defensin expression across multiple tissues. We also identify two long non-coding RNA sequences which both encode functional myotoxins, demonstrating a newly discovered source of venom coding sequence diversity. We also integrate long-range mate-pair chromatin contact data and linked-read sequencing to infer the structure and chromosomal locations of the three myotoxin-like loci. Further, we conclude that the venom-associated myotoxin is located on chromosome 1 and is adjacent to non-venom paralogs. Consistent with this locus contributing to venom composition, we find evidence that the promoter of this gene is selectively open in venom gland tissue and contains transcription factor binding sites implicated in broad trans-regulatory pathways that regulate snake venoms. This study provides the best genomic reconstruction of myotoxin loci to date and raises questions about the physiological roles and interplay between myotoxin and related genes, as well as the genomic origins of snake venom variation.
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Affiliation(s)
- Siddharth S Gopalan
- Department of Biology, 501 S. Nedderman Dr., The University of Texas Arlington, Arlington, TX, 76019, USA
| | - Blair W Perry
- Department of Biology, 501 S. Nedderman Dr., The University of Texas Arlington, Arlington, TX, 76019, USA; School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Drew R Schield
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309, USA
| | - Cara F Smith
- School of Biological Sciences, 501 20th Street, University of Northern Colorado, Greeley, CO, 80639, USA; Department of Biochemistry and Molecular Biology, 12801 East 17th Avenue, University of Colorado Denver, Aurora, CO, 80045, USA
| | - Stephen P Mackessy
- School of Biological Sciences, 501 20th Street, University of Northern Colorado, Greeley, CO, 80639, USA
| | - Todd A Castoe
- Department of Biology, 501 S. Nedderman Dr., The University of Texas Arlington, Arlington, TX, 76019, USA.
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16
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Perry BW, Gopalan SS, Pasquesi GIM, Schield DR, Westfall AK, Smith CF, Koludarov I, Chippindale PT, Pellegrino MW, Chuong EB, Mackessy SP, Castoe TA. Snake venom gene expression is coordinated by novel regulatory architecture and the integration of multiple co-opted vertebrate pathways. Genome Res 2022; 32:1058-1073. [PMID: 35649579 PMCID: PMC9248877 DOI: 10.1101/gr.276251.121] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 04/11/2022] [Indexed: 11/25/2022]
Abstract
Understanding how regulatory mechanisms evolve is critical for understanding the processes that give rise to novel phenotypes. Snake venom systems represent a valuable and tractable model for testing hypotheses related to the evolution of novel regulatory networks, yet the regulatory mechanisms underlying venom production remain poorly understood. Here, we use functional genomics approaches to investigate venom regulatory architecture in the prairie rattlesnake and identify cis-regulatory sequences (enhancers and promoters), trans-regulatory transcription factors, and integrated signaling cascades involved in the regulation of snake venom genes. We find evidence that two conserved vertebrate pathways, the extracellular signal-regulated kinase and unfolded protein response pathways, were co-opted to regulate snake venom. In one large venom gene family (snake venom serine proteases), this co-option was likely facilitated by the activity of transposable elements. Patterns of snake venom gene enhancer conservation, in some cases spanning 50 million yr of lineage divergence, highlight early origins and subsequent lineage-specific adaptations that have accompanied the evolution of venom regulatory architecture. We also identify features of chromatin structure involved in venom regulation, including topologically associated domains and CTCF loops that underscore the potential importance of novel chromatin structure to coevolve when duplicated genes evolve new regulatory control. Our findings provide a model for understanding how novel regulatory systems may evolve through a combination of genomic processes, including tandem duplication of genes and regulatory sequences, cis-regulatory sequence seeding by transposable elements, and diverse transcriptional regulatory proteins controlled by a co-opted regulatory cascade.
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Affiliation(s)
- Blair W Perry
- Department of Biology, University of Texas at Arlington, Arlington, Texas 76019, USA.,School of Biological Sciences, Washington State University, Pullman, Washington 99164, USA
| | - Siddharth S Gopalan
- Department of Biology, University of Texas at Arlington, Arlington, Texas 76019, USA
| | - Giulia I M Pasquesi
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309, USA
| | - Drew R Schield
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado 80309, USA
| | - Aundrea K Westfall
- Department of Biology, University of Texas at Arlington, Arlington, Texas 76019, USA
| | - Cara F Smith
- School of Biological Sciences, University of Northern Colorado, Greeley, Colorado 80639, USA
| | - Ivan Koludarov
- Animal Venomics Group, Justus Liebig University, Giessen, 35390, Germany
| | - Paul T Chippindale
- Department of Biology, University of Texas at Arlington, Arlington, Texas 76019, USA
| | - Mark W Pellegrino
- Department of Biology, University of Texas at Arlington, Arlington, Texas 76019, USA
| | - Edward B Chuong
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309, USA
| | - Stephen P Mackessy
- School of Biological Sciences, University of Northern Colorado, Greeley, Colorado 80639, USA
| | - Todd A Castoe
- Department of Biology, University of Texas at Arlington, Arlington, Texas 76019, USA
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17
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Westfall AK, Perry BW, Kamal AHM, Hales NR, Kay JC, Sapkota M, Schield DR, Pellegrino MW, Secor SM, Chowdhury SM, Castoe TA. Identification of an integrated stress and growth response signaling switch that directs vertebrate intestinal regeneration. BMC Genomics 2022; 23:6. [PMID: 34983392 PMCID: PMC8725436 DOI: 10.1186/s12864-021-08226-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 12/01/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Snakes exhibit extreme intestinal regeneration following months-long fasts that involves unparalleled increases in metabolism, function, and tissue growth, but the specific molecular control of this process is unknown. Understanding the mechanisms that coordinate these regenerative phenotypes provides valuable opportunities to understand critical pathways that may control vertebrate regeneration and novel perspectives on vertebrate regenerative capacities. RESULTS Here, we integrate a comprehensive set of phenotypic, transcriptomic, proteomic, and phosphoproteomic data from boa constrictors to identify the mechanisms that orchestrate shifts in metabolism, nutrient uptake, and cellular stress to direct phases of the regenerative response. We identify specific temporal patterns of metabolic, stress response, and growth pathway activation that direct regeneration and provide evidence for multiple key central regulatory molecules kinases that integrate these signals, including major conserved pathways like mTOR signaling and the unfolded protein response. CONCLUSION Collectively, our results identify a novel switch-like role of stress responses in intestinal regeneration that forms a primary regulatory hub facilitating organ regeneration and could point to potential pathways to understand regenerative capacity in vertebrates.
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Affiliation(s)
- Aundrea K Westfall
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - Blair W Perry
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - Abu H M Kamal
- Advanced Technology Cores, Baylor College of Medicine, Houston, TX, USA.,Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, TX, USA
| | - Nicole R Hales
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA.,Department of Research Development and Commercialization, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Jarren C Kay
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, USA
| | - Madhab Sapkota
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA.,Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Drew R Schield
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA.,Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, USA
| | - Mark W Pellegrino
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - Stephen M Secor
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, USA
| | - Saiful M Chowdhury
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, TX, USA
| | - Todd A Castoe
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA.
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18
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Lund AJ, Wade KJ, Nikolakis ZL, Ivey KN, Perry BW, Pike HNC, Paull SH, Liu Y, Castoe TA, Pollock DD, Carlton EJ. Integrating genomic and epidemiologic data to accelerate progress toward schistosomiasis elimination. eLife 2022; 11:79320. [PMID: 36040013 PMCID: PMC9427098 DOI: 10.7554/elife.79320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 08/11/2022] [Indexed: 11/13/2022] Open
Abstract
The global community has adopted ambitious goals to eliminate schistosomiasis as a public health problem, and new tools are needed to achieve them. Mass drug administration programs, for example, have reduced the burden of schistosomiasis, but the identification of hotspots of persistent and reemergent transmission threaten progress toward elimination and underscore the need to couple treatment with interventions that reduce transmission. Recent advances in DNA sequencing technologies make whole-genome sequencing a valuable and increasingly feasible option for population-based studies of complex parasites such as schistosomes. Here, we focus on leveraging genomic data to tailor interventions to distinct social and ecological circumstances. We consider two priority questions that can be addressed by integrating epidemiological, ecological, and genomic information: (1) how often do non-human host species contribute to human schistosome infection? and (2) what is the importance of locally acquired versus imported infections in driving transmission at different stages of elimination? These questions address processes that can undermine control programs, especially those that rely heavily on treatment with praziquantel. Until recently, these questions were difficult to answer with sufficient precision to inform public health decision-making. We review the literature related to these questions and discuss how whole-genome approaches can identify the geographic and taxonomic sources of infection, and how such information can inform context-specific efforts that advance schistosomiasis control efforts and minimize the risk of reemergence.
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Affiliation(s)
- Andrea J Lund
- Department of Environmental and Occupational Health, Colorado School of Public Health, University of Colorado AnschutzAuroraUnited States
| | - Kristen J Wade
- Department of Biochemistry & Molecular Genetics, University of Colorado School of MedicineAuroraUnited States
| | - Zachary L Nikolakis
- Department of Biology, University of Texas at ArlingtonArlingtonUnited States
| | - Kathleen N Ivey
- Department of Biology, University of Texas at ArlingtonArlingtonUnited States
| | - Blair W Perry
- Department of Biology, University of Texas at ArlingtonArlingtonUnited States
| | - Hamish NC Pike
- Department of Biochemistry & Molecular Genetics, University of Colorado School of MedicineAuroraUnited States
| | - Sara H Paull
- Department of Environmental and Occupational Health, Colorado School of Public Health, University of Colorado AnschutzAuroraUnited States
| | - Yang Liu
- Sichuan Centers for Disease Control and PreventionChengduChina
| | - Todd A Castoe
- Department of Biology, University of Texas at ArlingtonArlingtonUnited States
| | - David D Pollock
- Department of Biochemistry & Molecular Genetics, University of Colorado School of MedicineAuroraUnited States
| | - Elizabeth J Carlton
- Department of Environmental and Occupational Health, Colorado School of Public Health, University of Colorado AnschutzAuroraUnited States
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19
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Pasquesi GIM, Perry BW, Vandewege MW, Ruggiero RP, Schield DR, Castoe TA. Vertebrate Lineages Exhibit Diverse Patterns of Transposable Element Regulation and Expression across Tissues. Genome Biol Evol 2021; 12:506-521. [PMID: 32271917 PMCID: PMC7211425 DOI: 10.1093/gbe/evaa068] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/02/2020] [Indexed: 12/11/2022] Open
Abstract
Transposable elements (TEs) comprise a major fraction of vertebrate genomes, yet little is known about their expression and regulation across tissues, and how this varies across major vertebrate lineages. We present the first comparative analysis integrating TE expression and TE regulatory pathway activity in somatic and gametic tissues for a diverse set of 12 vertebrates. We conduct simultaneous gene and TE expression analyses to characterize patterns of TE expression and TE regulation across vertebrates and examine relationships between these features. We find remarkable variation in the expression of genes involved in TE negative regulation across tissues and species, yet consistently high expression in germline tissues, particularly in testes. Most vertebrates show comparably high levels of TE regulatory pathway activity across gonadal tissues except for mammals, where reduced activity of TE regulatory pathways in ovarian tissues may be the result of lower relative germ cell densities. We also find that all vertebrate lineages examined exhibit remarkably high levels of TE-derived transcripts in somatic and gametic tissues, with recently active TE families showing higher expression in gametic tissues. Although most TE-derived transcripts originate from inactive ancient TE families (and are likely incapable of transposition), such high levels of TE-derived RNA in the cytoplasm may have secondary, unappreciated biological relevance.
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Affiliation(s)
- Giulia I M Pasquesi
- Department of Biology, University of Texas at Arlington.,Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder
| | - Blair W Perry
- Department of Biology, University of Texas at Arlington
| | | | | | - Drew R Schield
- Department of Biology, University of Texas at Arlington.,Department of Ecology and Evolutionary Biology, University of Colorado, Boulder
| | - Todd A Castoe
- Department of Biology, University of Texas at Arlington
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20
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Perry BW, Schield DR, Adams RH, Castoe TA. Microchromosomes Exhibit Distinct Features of Vertebrate Chromosome Structure and Function with Underappreciated Ramifications for Genome Evolution. Mol Biol Evol 2021; 38:904-910. [PMID: 32986808 PMCID: PMC7947875 DOI: 10.1093/molbev/msaa253] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Microchromosomes are common yet poorly understood components of many vertebrate genomes. Recent studies have revealed that microchromosomes contain a high density of genes and possess other distinct characteristics compared with macrochromosomes. Whether distinctive characteristics of microchromosomes extend to features of genome structure and organization, however, remains an open question. Here, we analyze Hi-C sequencing data from multiple vertebrate lineages and show that microchromosomes exhibit consistently high degrees of interchromosomal interaction (particularly with other microchromosomes), appear to be colocalized to a common central nuclear territory, and are comprised of a higher proportion of open chromatin than macrochromosomes. These findings highlight an unappreciated level of diversity in vertebrate genome structure and function, and raise important questions regarding the evolutionary origins and ramifications of microchromosomes and the genes that they house.
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Affiliation(s)
- Blair W Perry
- Department of Biology, University of Texas at Arlington, Arlington, TX
| | - Drew R Schield
- Department of Biology, University of Texas at Arlington, Arlington, TX
| | - Richard H Adams
- Department of Biology, University of Texas at Arlington, Arlington, TX
| | - Todd A Castoe
- Department of Biology, University of Texas at Arlington, Arlington, TX
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21
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Kazi MI, Perry BW, Card DC, Schargel RD, Ali HB, Obuekwe VC, Sapkota M, Kang KN, Pellegrino MW, Greenberg DE, Castoe TA, Boll JM. Discovery and characterization of New Delhi metallo-β-lactamase-1 inhibitor peptides that potentiate meropenem-dependent killing of carbapenemase-producing Enterobacteriaceae. J Antimicrob Chemother 2021; 75:2843-2851. [PMID: 32591801 DOI: 10.1093/jac/dkaa242] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 04/20/2020] [Accepted: 05/06/2020] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVES Metallo-β-lactamases (MBLs) are an emerging class of antimicrobial resistance enzymes that degrade β-lactam antibiotics, including last-resort carbapenems. Infections caused by carbapenemase-producing Enterobacteriaceae (CPE) are increasingly prevalent, but treatment options are limited. While several serine-dependent β-lactamase inhibitors are formulated with commonly prescribed β-lactams, no MBL inhibitors are currently approved for combinatorial therapies. New compounds that target MBLs to restore carbapenem activity against CPE are therefore urgently needed. Herein we identified and characterized novel synthetic peptide inhibitors that bound to and inhibited NDM-1, which is an emerging β-lactam resistance mechanism in CPE. METHODS We leveraged Surface Localized Antimicrobial displaY (SLAY) to identify and characterize peptides that inhibit NDM-1, which is a primary carbapenem resistance mechanism in CPE. Lead inhibitor sequences were chemically synthesized and MBCs and MICs were calculated in the presence/absence of carbapenems. Kinetic analysis with recombinant NDM-1 and select peptides tested direct binding and supported NDM-1 inhibitor mechanisms of action. Inhibitors were also tested for cytotoxicity. RESULTS We identified approximately 1700 sequences that potentiated carbapenem-dependent killing against NDM-1 Escherichia coli. Several also enhanced meropenem-dependent killing of other CPE. Biochemical characterization of a subset indicated the peptides penetrated the bacterial periplasm and directly bound NDM-1 to inhibit enzymatic activity. Additionally, each demonstrated minimal haemolysis and cytotoxicity against mammalian cell lines. CONCLUSIONS Our approach advances a molecular platform for antimicrobial discovery, which complements the growing need for alternative antimicrobials. We also discovered lead NDM-1 inhibitors, which serve as a starting point for further chemical optimization.
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Affiliation(s)
- Misha I Kazi
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - Blair W Perry
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - Daren C Card
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - Richard D Schargel
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - Hana B Ali
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - Victor C Obuekwe
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA.,Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Madhab Sapkota
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - Katie N Kang
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - Mark W Pellegrino
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - David E Greenberg
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Todd A Castoe
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - Joseph M Boll
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
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22
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Schield DR, Perry BW, Nikolakis ZL, Mackessy SP, Castoe TA. Population Genomic Analyses Confirm Male-Biased Mutation Rates in Snakes. J Hered 2021; 112:221-227. [PMID: 33502475 DOI: 10.1093/jhered/esab005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 01/21/2021] [Indexed: 11/13/2022] Open
Abstract
Male-biased mutation rates occur in a diverse array of organisms. The ratio of male-to-female mutation rate may have major ramifications for evolution across the genome, and for sex-linked genes in particular. In ZW species, the Z chromosome is carried by males two-thirds of the time, leading to the prediction that male-biased mutation rates will have a disproportionate effect on the evolution of Z-linked genes relative to autosomes and the W chromosome. Colubroid snakes (including colubrids, elapids, and viperids) have ZW sex determination, yet male-biased mutation rates have not been well studied in this group. Here we analyze a population genomic dataset from rattlesnakes to quantify genetic variation within and genetic divergence between species. We use a new method for unbiased estimation of population genetic summary statistics to compare variation between the Z chromosome and autosomes and to calculate net nucleotide differentiation between species. We find evidence for a 2.03-fold greater mutation rate in male rattlesnakes relative to females, corresponding to an average μZ/μA ratio of 1.1. Our results from snakes are quantitatively similar to birds, suggesting that male-biased mutation rates may be a common feature across vertebrate lineages with ZW sex determination.
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Affiliation(s)
- Drew R Schield
- Department of Biology, University of Texas at Arlington, Arlington, TX.,Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO
| | - Blair W Perry
- Department of Biology, University of Texas at Arlington, Arlington, TX
| | | | - Stephen P Mackessy
- School of Biological Sciences, University of Northern Colorado, Greeley, CO
| | - Todd A Castoe
- Department of Biology, University of Texas at Arlington, Arlington, TX
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23
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Schield DR, Pasquesi GIM, Perry BW, Adams RH, Nikolakis ZL, Westfall AK, Orton RW, Meik JM, Mackessy SP, Castoe TA. Snake Recombination Landscapes Are Concentrated in Functional Regions despite PRDM9. Mol Biol Evol 2021; 37:1272-1294. [PMID: 31926008 DOI: 10.1093/molbev/msaa003] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Meiotic recombination in vertebrates is concentrated in hotspots throughout the genome. The location and stability of hotspots have been linked to the presence or absence of PRDM9, leading to two primary models for hotspot evolution derived from mammals and birds. Species with PRDM9-directed recombination have rapid turnover of hotspots concentrated in intergenic regions (i.e., mammals), whereas hotspots in species lacking PRDM9 are concentrated in functional regions and have greater stability over time (i.e., birds). Snakes possess PRDM9, yet virtually nothing is known about snake recombination. Here, we examine the recombination landscape and test hypotheses about the roles of PRDM9 in rattlesnakes. We find substantial variation in recombination rate within and among snake chromosomes, and positive correlations between recombination rate and gene density, GC content, and genetic diversity. Like mammals, snakes appear to have a functional and active PRDM9, but rather than being directed away from genes, snake hotspots are concentrated in promoters and functional regions-a pattern previously associated only with species that lack a functional PRDM9. Snakes therefore provide a unique example of recombination landscapes in which PRDM9 is functional, yet recombination hotspots are associated with functional genic regions-a combination of features that defy existing paradigms for recombination landscapes in vertebrates. Our findings also provide evidence that high recombination rates are a shared feature of vertebrate microchromosomes. Our results challenge previous assumptions about the adaptive role of PRDM9 and highlight the diversity of recombination landscape features among vertebrate lineages.
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Affiliation(s)
- Drew R Schield
- Department of Biology, University of Texas at Arlington, Arlington, TX
| | | | - Blair W Perry
- Department of Biology, University of Texas at Arlington, Arlington, TX
| | - Richard H Adams
- Department of Biology, University of Texas at Arlington, Arlington, TX.,Department of Computer & Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL
| | | | | | - Richard W Orton
- Department of Biology, University of Texas at Arlington, Arlington, TX
| | - Jesse M Meik
- Department of Biological Sciences, Tarleton State University, Stephenville, TX
| | - Stephen P Mackessy
- School of Biological Sciences, University of Northern Colorado, Greeley, CO
| | - Todd A Castoe
- Department of Biology, University of Texas at Arlington, Arlington, TX
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24
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Nikolakis ZL, Hales NR, Perry BW, Schield DR, Timm LE, Liu Y, Zhong B, Kechris KJ, Carlton EJ, Pollock DD, Castoe TA. Patterns of relatedness and genetic diversity inferred from whole genome sequencing of archival blood fluke miracidia (Schistosoma japonicum). PLoS Negl Trop Dis 2021; 15:e0009020. [PMID: 33406094 PMCID: PMC7815185 DOI: 10.1371/journal.pntd.0009020] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 01/19/2021] [Accepted: 11/30/2020] [Indexed: 02/05/2023] Open
Abstract
Genomic approaches hold great promise for resolving unanswered questions about transmission patterns and responses to control efforts for schistosomiasis and other neglected tropical diseases. However, the cost of generating genomic data and the challenges associated with obtaining sufficient DNA from individual schistosome larvae (miracidia) from mammalian hosts have limited the application of genomic data for studying schistosomes and other complex macroparasites. Here, we demonstrate the feasibility of utilizing whole genome amplification and sequencing (WGS) to analyze individual archival miracidia. As an example, we sequenced whole genomes of 22 miracidia from 11 human hosts representing two villages in rural Sichuan, China, and used these data to evaluate patterns of relatedness and genetic diversity. We also down-sampled our dataset to test how lower coverage sequencing could increase the cost effectiveness of WGS while maintaining power to accurately infer relatedness. Collectively, our results illustrate that population-level WGS datasets are attainable for individual miracidia and represent a powerful tool for ultimately providing insight into overall genetic diversity, parasite relatedness, and transmission patterns for better design and evaluation of disease control efforts.
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Affiliation(s)
- Zachary L. Nikolakis
- Department of Biology, University of Texas at Arlington, Arlington, Texas, United States of America
| | - Nicole R. Hales
- Department of Biology, University of Texas at Arlington, Arlington, Texas, United States of America
| | - Blair W. Perry
- Department of Biology, University of Texas at Arlington, Arlington, Texas, United States of America
| | - Drew R. Schield
- Department of Biology, University of Texas at Arlington, Arlington, Texas, United States of America
| | - Laura E. Timm
- Department of Biochemistry & Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Yang Liu
- Institute of Parasitic Disease, Sichuan Center for Disease Control and Prevention, Chengdu, The People’s Republic of China
| | - Bo Zhong
- Institute of Parasitic Disease, Sichuan Center for Disease Control and Prevention, Chengdu, The People’s Republic of China
| | - Katerina J. Kechris
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado, Anschutz, Aurora, Colorado, United States of America
| | - Elizabeth J. Carlton
- Department of Environmental and Occupational Health, Colorado School of Public Health, University of Colorado, Anschutz, Aurora, Colorado, United States of America
| | - David D. Pollock
- Department of Biochemistry & Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Todd A. Castoe
- Department of Biology, University of Texas at Arlington, Arlington, Texas, United States of America
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25
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Boni MF, Lemey P, Jiang X, Lam TTY, Perry BW, Castoe TA, Rambaut A, Robertson DL. Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic. Nat Microbiol 2020; 5:1408-1417. [PMID: 32724171 DOI: 10.1101/2020.03.30.015008] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 07/10/2020] [Indexed: 05/22/2023]
Abstract
There are outstanding evolutionary questions on the recent emergence of human coronavirus SARS-CoV-2 including the role of reservoir species, the role of recombination and its time of divergence from animal viruses. We find that the sarbecoviruses-the viral subgenus containing SARS-CoV and SARS-CoV-2-undergo frequent recombination and exhibit spatially structured genetic diversity on a regional scale in China. SARS-CoV-2 itself is not a recombinant of any sarbecoviruses detected to date, and its receptor-binding motif, important for specificity to human ACE2 receptors, appears to be an ancestral trait shared with bat viruses and not one acquired recently via recombination. To employ phylogenetic dating methods, recombinant regions of a 68-genome sarbecovirus alignment were removed with three independent methods. Bayesian evolutionary rate and divergence date estimates were shown to be consistent for these three approaches and for two different prior specifications of evolutionary rates based on HCoV-OC43 and MERS-CoV. Divergence dates between SARS-CoV-2 and the bat sarbecovirus reservoir were estimated as 1948 (95% highest posterior density (HPD): 1879-1999), 1969 (95% HPD: 1930-2000) and 1982 (95% HPD: 1948-2009), indicating that the lineage giving rise to SARS-CoV-2 has been circulating unnoticed in bats for decades.
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Affiliation(s)
- Maciej F Boni
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA, USA.
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, Leuven, Belgium.
| | - Xiaowei Jiang
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, China
| | - Tommy Tsan-Yuk Lam
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong SAR, China
| | - Blair W Perry
- Department of Biology, University of Texas Arlington, Arlington, TX, USA
| | - Todd A Castoe
- Department of Biology, University of Texas Arlington, Arlington, TX, USA
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.
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26
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Perry BW, Schield DR, Westfall AK, Mackessy SP, Castoe TA. Physiological demands and signaling associated with snake venom production and storage illustrated by transcriptional analyses of venom glands. Sci Rep 2020; 10:18083. [PMID: 33093509 PMCID: PMC7582160 DOI: 10.1038/s41598-020-75048-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 10/09/2020] [Indexed: 01/30/2023] Open
Abstract
Despite the extensive body of research on snake venom, many facets of snake venom systems, such as the physiology and regulation of the venom gland itself, remain virtually unstudied. Here, we use time series gene expression analyses of the rattlesnake venom gland in comparison with several non-venom tissues to characterize physiological and cellular processes associated with venom production and to highlight key distinctions of venom gland cellular and physiological function. We find consistent evidence for activation of stress response pathways in the venom gland, suggesting that mitigation of cellular stress is a crucial component of venom production. Additionally, we demonstrate evidence for an unappreciated degree of cellular and secretory activity in the steady state venom gland relative to other secretory tissues and identify vacuolar ATPases as the likely mechanisms driving acidification of the venom gland lumen during venom production and storage.
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Affiliation(s)
- Blair W Perry
- Department of Biology, The University of Texas Arlington, 501 S. Nedderman Dr., Arlington, TX, 76019, USA
| | - Drew R Schield
- Department of Biology, The University of Texas Arlington, 501 S. Nedderman Dr., Arlington, TX, 76019, USA.,Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309, USA
| | - Aundrea K Westfall
- Department of Biology, The University of Texas Arlington, 501 S. Nedderman Dr., Arlington, TX, 76019, USA
| | - Stephen P Mackessy
- School of Biological Sciences, University of Northern Colorado, 501 20th Street, Greeley, CO, 80639, USA
| | - Todd A Castoe
- Department of Biology, The University of Texas Arlington, 501 S. Nedderman Dr., Arlington, TX, 76019, USA.
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27
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Pollock DD, Castoe TA, Perry BW, Lytras S, Wade KJ, Robertson DL, Holmes EC, Boni MF, Kosakovsky Pond SL, Parry R, Carlton EJ, Wood JLN, Pennings PS, Goldstein RA. Viral CpG Deficiency Provides No Evidence That Dogs Were Intermediate Hosts for SARS-CoV-2. Mol Biol Evol 2020; 37:2706-2710. [PMID: 32658964 PMCID: PMC7454803 DOI: 10.1093/molbev/msaa178] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Due to the scope and impact of the COVID-19 pandemic there exists a strong desire to understand where the SARS-CoV-2 virus came from and how it jumped species boundaries to humans. Molecular evolutionary analyses can trace viral origins by establishing relatedness and divergence times of viruses and identifying past selective pressures. However, we must uphold rigorous standards of inference and interpretation on this topic because of the ramifications of being wrong. Here, we dispute the conclusions of Xia (2020. Extreme genomic CpG deficiency in SARS-CoV-2 and evasion of host antiviral defense. Mol Biol Evol. doi:10.1093/molbev/masa095) that dogs are a likely intermediate host of a SARS-CoV-2 ancestor. We highlight major flaws in Xia's inference process and his analysis of CpG deficiencies, and conclude that there is no direct evidence for the role of dogs as intermediate hosts. Bats and pangolins currently have the greatest support as ancestral hosts of SARS-CoV-2, with the strong caveat that sampling of wildlife species for coronaviruses has been limited.
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Affiliation(s)
- David D Pollock
- Department of Biochemistry & Molecular Genetics, University of Colorado School of Medicine, Aurora, CO
| | - Todd A Castoe
- Department of Biology, University of Texas Arlington, Arlington, TX
| | - Blair W Perry
- Department of Biology, University of Texas Arlington, Arlington, TX
| | - Spyros Lytras
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Kristen J Wade
- Department of Biochemistry & Molecular Genetics, University of Colorado School of Medicine, Aurora, CO
| | - David L Robertson
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases & Biosecurity, School of Life & Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Maciej F Boni
- 5Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA
| | | | - Rhys Parry
- Australian Infectious Disease Research Centre, School of Biological Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Elizabeth J Carlton
- Department of Environmental and Occupational Health, Colorado School of Public Health, University of Colorado, Anschutz, Aurora, CO
| | - James L N Wood
- Disease Dynamics Unit, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Pleuni S Pennings
- Department of Biology, San Francisco State University, San Francisco, CA
| | - Richard A Goldstein
- Division of Infection & Immunity, University College London, London, United Kingdom
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28
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Boni MF, Lemey P, Jiang X, Lam TTY, Perry BW, Castoe TA, Rambaut A, Robertson DL. Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic. Nat Microbiol 2020; 5:1408-1417. [DOI: 10.1038/s41564-020-0771-4] [Citation(s) in RCA: 568] [Impact Index Per Article: 142.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 07/10/2020] [Indexed: 02/07/2023]
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29
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Card DC, Adams RH, Schield DR, Perry BW, Corbin AB, Pasquesi GIM, Row K, Van Kleeck MJ, Daza JM, Booth W, Montgomery CE, Boback SM, Castoe TA. Genomic Basis of Convergent Island Phenotypes in Boa Constrictors. Genome Biol Evol 2020; 11:3123-3143. [PMID: 31642474 PMCID: PMC6836717 DOI: 10.1093/gbe/evz226] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/10/2019] [Indexed: 12/14/2022] Open
Abstract
Convergent evolution is often documented in organisms inhabiting isolated environments with distinct ecological conditions and similar selective regimes. Several Central America islands harbor dwarf Boa populations that are characterized by distinct differences in growth, mass, and craniofacial morphology, which are linked to the shared arboreal and feast-famine ecology of these island populations. Using high-density RADseq data, we inferred three dwarf island populations with independent origins and demonstrate that selection, along with genetic drift, has produced both divergent and convergent molecular evolution across island populations. Leveraging whole-genome resequencing data for 20 individuals and a newly annotated Boa genome, we identify four genes with evidence of phenotypically relevant protein-coding variation that differentiate island and mainland populations. The known roles of these genes involved in body growth (PTPRS, DMGDH, and ARSB), circulating fat and cholesterol levels (MYLIP), and craniofacial development (DMGDH and ARSB) in mammals link patterns of molecular evolution with the unique phenotypes of these island forms. Our results provide an important genome-wide example for quantifying expectations of selection and convergence in closely related populations. We also find evidence at several genomic loci that selection may be a prominent force of evolutionary change—even for small island populations for which drift is predicted to dominate. Overall, while phenotypically convergent island populations show relatively few loci under strong selection, infrequent patterns of molecular convergence are still apparent and implicate genes with strong connections to convergent phenotypes.
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Affiliation(s)
- Daren C Card
- Department of Biology, University of Texas Arlington.,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts.,Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts
| | | | | | - Blair W Perry
- Department of Biology, University of Texas Arlington
| | | | | | | | | | - Juan M Daza
- Grupo Herpetológico de Antioquia, Instituto de Biología, Universidad de Antioquia, Medellín, Colombia
| | - Warren Booth
- Department of Biological Science, University of Tulsa, Oklahoma
| | | | - Scott M Boback
- Department of Biology, Dickinson College, Carlisle, Pennsylvania
| | - Todd A Castoe
- Department of Biology, University of Texas Arlington
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30
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Perry BW, Andrew AL, Mostafa Kamal AH, Card DC, Schield DR, Pasquesi GIM, Pellegrino MW, Mackessy SP, Chowdhury SM, Secor SM, Castoe TA. Multi-species comparisons of snakes identify coordinated signalling networks underlying post-feeding intestinal regeneration. Proc Biol Sci 2019; 286:20190910. [PMID: 31288694 DOI: 10.1098/rspb.2019.0910] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Several snake species that feed infrequently in nature have evolved the ability to massively upregulate intestinal form and function with each meal. While fasting, these snakes downregulate intestinal form and function, and upon feeding restore intestinal structure and function through major increases in cell growth and proliferation, metabolism and upregulation of digestive function. Previous studies have identified changes in gene expression that underlie this regenerative growth of the python intestine, but the unique features that differentiate this extreme regenerative growth from non-regenerative post-feeding responses exhibited by snakes that feed more frequently remain unclear. Here, we leveraged variation in regenerative capacity across three snake species-two distantly related lineages ( Crotalus and Python) that experience regenerative growth, and one ( Nerodia) that does not-to infer molecular mechanisms underlying intestinal regeneration using transcriptomic and proteomic approaches. Using a comparative approach, we identify a suite of growth, stress response and DNA damage response signalling pathways with inferred activity specifically in regenerating species, and propose a hypothesis model of interactivity between these pathways that may drive regenerative intestinal growth in snakes.
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Affiliation(s)
- Blair W Perry
- 1 Department of Biology, The University of Texas Arlington , 501 South Nedderman Drive, Arlington, TX 76019 , USA
| | - Audra L Andrew
- 1 Department of Biology, The University of Texas Arlington , 501 South Nedderman Drive, Arlington, TX 76019 , USA
| | - Abu Hena Mostafa Kamal
- 2 Department of Chemistry and Biochemistry, The University of Texas Arlington , 501 South Nedderman Drive, Arlington, TX 76019 , USA
| | - Daren C Card
- 1 Department of Biology, The University of Texas Arlington , 501 South Nedderman Drive, Arlington, TX 76019 , USA
| | - Drew R Schield
- 1 Department of Biology, The University of Texas Arlington , 501 South Nedderman Drive, Arlington, TX 76019 , USA
| | - Giulia I M Pasquesi
- 1 Department of Biology, The University of Texas Arlington , 501 South Nedderman Drive, Arlington, TX 76019 , USA
| | - Mark W Pellegrino
- 1 Department of Biology, The University of Texas Arlington , 501 South Nedderman Drive, Arlington, TX 76019 , USA
| | - Stephen P Mackessy
- 3 School of Biological Sciences, University of Northern Colorado , 501 20th Street, Greeley, CO 80639 , USA
| | - Saiful M Chowdhury
- 2 Department of Chemistry and Biochemistry, The University of Texas Arlington , 501 South Nedderman Drive, Arlington, TX 76019 , USA
| | - Stephen M Secor
- 4 Department of Biological Sciences, University of Alabama , Box 870344, Tuscaloosa, AL 35487 , USA
| | - Todd A Castoe
- 1 Department of Biology, The University of Texas Arlington , 501 South Nedderman Drive, Arlington, TX 76019 , USA
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31
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Schield DR, Perry BW, Adams RH, Card DC, Jezkova T, Pasquesi GIM, Nikolakis ZL, Row K, Meik JM, Smith CF, Mackessy SP, Castoe TA. Allopatric divergence and secondary contact with gene flow: a recurring theme in rattlesnake speciation. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz077] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
The study of recently diverged lineages whose geographical ranges come into contact can provide insight into the early stages of speciation and the potential roles of reproductive isolation in generating and maintaining species. Such insight can also be important for understanding the strategies and challenges for delimiting species within recently diverged species complexes. Here, we use mitochondrial and nuclear genetic data to study population structure, gene flow and demographic history across a geographically widespread rattlesnake clade, the western rattlesnake species complex (Crotalus cerberus, Crotalus viridis, Crotalus oreganus and relatives), which contains multiple lineages with ranges that overlap geographically or contact one another. We find evidence that the evolutionary history of this group does not conform to a bifurcating tree model and that pervasive gene flow has broadly influenced patterns of present-day genetic diversity. Our results suggest that lineage diversity has been shaped largely by drift and divergent selection in isolation, followed by secondary contact, in which reproductive isolating mechanisms appear weak and insufficient to prevent introgression, even between anciently diverged lineages. The complexity of divergence and secondary contact with gene flow among lineages also provides new context for why delimiting species within this complex has been difficult and contentious historically.
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Affiliation(s)
- Drew R Schield
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - Blair W Perry
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - Richard H Adams
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - Daren C Card
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Tereza Jezkova
- Department of Biology, Miami University of Ohio, Oxford, OH, USA
| | | | | | - Kristopher Row
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - Jesse M Meik
- Department of Biological Sciences, Tarleton State University, Stephenville, TX, USA
| | - Cara F Smith
- School of Biological Sciences, University of Northern Colorado, Greeley, CO, USA
| | - Stephen P Mackessy
- School of Biological Sciences, University of Northern Colorado, Greeley, CO, USA
| | - Todd A Castoe
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
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Schield DR, Card DC, Hales NR, Perry BW, Pasquesi GM, Blackmon H, Adams RH, Corbin AB, Smith CF, Ramesh B, Demuth JP, Betrán E, Tollis M, Meik JM, Mackessy SP, Castoe TA. The origins and evolution of chromosomes, dosage compensation, and mechanisms underlying venom regulation in snakes. Genome Res 2019; 29:590-601. [PMID: 30898880 PMCID: PMC6442385 DOI: 10.1101/gr.240952.118] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 02/15/2019] [Indexed: 01/28/2023]
Abstract
Here we use a chromosome-level genome assembly of a prairie rattlesnake (Crotalus viridis), together with Hi-C, RNA-seq, and whole-genome resequencing data, to study key features of genome biology and evolution in reptiles. We identify the rattlesnake Z Chromosome, including the recombining pseudoautosomal region, and find evidence for partial dosage compensation driven by an evolutionary accumulation of a female-biased up-regulation mechanism. Comparative analyses with other amniotes provide new insight into the origins, structure, and function of reptile microchromosomes, which we demonstrate have markedly different structure and function compared to macrochromosomes. Snake microchromosomes are also enriched for venom genes, which we show have evolved through multiple tandem duplication events in multiple gene families. By overlaying chromatin structure information and gene expression data, we find evidence for venom gene-specific chromatin contact domains and identify how chromatin structure guides precise expression of multiple venom gene families. Further, we find evidence for venom gland-specific transcription factor activity and characterize a complement of mechanisms underlying venom production and regulation. Our findings reveal novel and fundamental features of reptile genome biology, provide insight into the regulation of snake venom, and broadly highlight the biological insight enabled by chromosome-level genome assemblies.
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Affiliation(s)
- Drew R Schield
- Department of Biology, University of Texas at Arlington, Arlington, Texas 76010, USA
| | - Daren C Card
- Department of Biology, University of Texas at Arlington, Arlington, Texas 76010, USA
| | - Nicole R Hales
- Department of Biology, University of Texas at Arlington, Arlington, Texas 76010, USA
| | - Blair W Perry
- Department of Biology, University of Texas at Arlington, Arlington, Texas 76010, USA
| | - Giulia M Pasquesi
- Department of Biology, University of Texas at Arlington, Arlington, Texas 76010, USA
| | - Heath Blackmon
- Department of Biology, Texas A&M University, College Station, Texas 77843, USA
| | - Richard H Adams
- Department of Biology, University of Texas at Arlington, Arlington, Texas 76010, USA
| | - Andrew B Corbin
- Department of Biology, University of Texas at Arlington, Arlington, Texas 76010, USA
| | - Cara F Smith
- School of Biological Sciences, University of Northern Colorado, Greeley, Colorado 80639, USA
| | - Balan Ramesh
- Department of Biology, University of Texas at Arlington, Arlington, Texas 76010, USA
| | - Jeffery P Demuth
- Department of Biology, University of Texas at Arlington, Arlington, Texas 76010, USA
| | - Esther Betrán
- Department of Biology, University of Texas at Arlington, Arlington, Texas 76010, USA
| | - Marc Tollis
- School of Life Sciences, Arizona State University, Tempe, Arizona 85287, USA
| | - Jesse M Meik
- Department of Biological Sciences, Tarleton State University, Stephenville, Texas 76402, USA
| | - Stephen P Mackessy
- School of Biological Sciences, University of Northern Colorado, Greeley, Colorado 80639, USA
| | - Todd A Castoe
- Department of Biology, University of Texas at Arlington, Arlington, Texas 76010, USA
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Card DC, Perry BW, Adams RH, Schield DR, Young AS, Andrew AL, Jezkova T, Pasquesi GI, Hales NR, Walsh MR, Rochford MR, Mazzotti FJ, Hart KM, Hunter ME, Castoe TA. Novel ecological and climatic conditions drive rapid adaptation in invasive Florida Burmese pythons. Mol Ecol 2018; 27:4744-4757. [DOI: 10.1111/mec.14885] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 08/24/2018] [Accepted: 09/14/2018] [Indexed: 12/30/2022]
Affiliation(s)
- Daren C. Card
- Department of Biology The University of Texas at Arlington Arlington Texas
| | - Blair W. Perry
- Department of Biology The University of Texas at Arlington Arlington Texas
| | - Richard H. Adams
- Department of Biology The University of Texas at Arlington Arlington Texas
| | - Drew R. Schield
- Department of Biology The University of Texas at Arlington Arlington Texas
| | - Acacia S. Young
- Department of Biology The University of Texas at Arlington Arlington Texas
| | - Audra L. Andrew
- Department of Biology The University of Texas at Arlington Arlington Texas
| | | | | | - Nicole R. Hales
- Department of Biology The University of Texas at Arlington Arlington Texas
| | - Matthew R. Walsh
- Department of Biology The University of Texas at Arlington Arlington Texas
| | - Michael R. Rochford
- Fort Lauderdale Research & Education Center University of Florida Fort Lauderdale Florida
| | - Frank J. Mazzotti
- Fort Lauderdale Research & Education Center University of Florida Fort Lauderdale Florida
| | - Kristen M. Hart
- U. S. Geological Survey Wetland and Aquatic Research Center Davie Florida
| | - Margaret E. Hunter
- U. S. Geological Survey Wetland and Aquatic Research Center Gainesville Florida
| | - Todd A. Castoe
- Department of Biology The University of Texas at Arlington Arlington Texas
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Schield DR, Adams RH, Card DC, Corbin AB, Jezkova T, Hales NR, Meik JM, Perry BW, Spencer CL, Smith LL, García GC, Bouzid NM, Strickland JL, Parkinson CL, Borja M, Castañeda-Gaytán G, Bryson RW, Flores-Villela OA, Mackessy SP, Castoe TA. Cryptic genetic diversity, population structure, and gene flow in the Mojave rattlesnake (Crotalus scutulatus). Mol Phylogenet Evol 2018; 127:669-681. [DOI: 10.1016/j.ympev.2018.06.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 05/30/2018] [Accepted: 06/06/2018] [Indexed: 10/28/2022]
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35
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Perry BW, Card DC, McGlothlin JW, Pasquesi GIM, Adams RH, Schield DR, Hales NR, Corbin AB, Demuth JP, Hoffmann FG, Vandewege MW, Schott RK, Bhattacharyya N, Chang BSW, Casewell NR, Whiteley G, Reyes-Velasco J, Mackessy SP, Gamble T, Storey KB, Biggar KK, Passow CN, Kuo CH, McGaugh SE, Bronikowski AM, de Koning APJ, Edwards SV, Pfrender ME, Minx P, Brodie ED, Brodie ED, Warren WC, Castoe TA. Molecular Adaptations for Sensing and Securing Prey and Insight into Amniote Genome Diversity from the Garter Snake Genome. Genome Biol Evol 2018; 10:2110-2129. [PMID: 30060036 PMCID: PMC6110522 DOI: 10.1093/gbe/evy157] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/26/2018] [Indexed: 12/26/2022] Open
Abstract
Colubridae represents the most phenotypically diverse and speciose family of snakes, yet no well-assembled and annotated genome exists for this lineage. Here, we report and analyze the genome of the garter snake, Thamnophis sirtalis, a colubrid snake that is an important model species for research in evolutionary biology, physiology, genomics, behavior, and the evolution of toxin resistance. Using the garter snake genome, we show how snakes have evolved numerous adaptations for sensing and securing prey, and identify features of snake genome structure that provide insight into the evolution of amniote genomes. Analyses of the garter snake and other squamate reptile genomes highlight shifts in repeat element abundance and expansion within snakes, uncover evidence of genes under positive selection, and provide revised neutral substitution rate estimates for squamates. Our identification of Z and W sex chromosome-specific scaffolds provides evidence for multiple origins of sex chromosome systems in snakes and demonstrates the value of this genome for studying sex chromosome evolution. Analysis of gene duplication and loss in visual and olfactory gene families supports a dim-light ancestral condition in snakes and indicates that olfactory receptor repertoires underwent an expansion early in snake evolution. Additionally, we provide some of the first links between secreted venom proteins, the genes that encode them, and their evolutionary origins in a rear-fanged colubrid snake, together with new genomic insight into the coevolutionary arms race between garter snakes and highly toxic newt prey that led to toxin resistance in garter snakes.
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Affiliation(s)
- Blair W Perry
- Department of Biology, University of Texas at Arlington, Arlington
| | - Daren C Card
- Department of Biology, University of Texas at Arlington, Arlington
| | - Joel W McGlothlin
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia
| | | | - Richard H Adams
- Department of Biology, University of Texas at Arlington, Arlington
| | - Drew R Schield
- Department of Biology, University of Texas at Arlington, Arlington
| | - Nicole R Hales
- Department of Biology, University of Texas at Arlington, Arlington
| | - Andrew B Corbin
- Department of Biology, University of Texas at Arlington, Arlington
| | - Jeffery P Demuth
- Department of Biology, University of Texas at Arlington, Arlington
| | - Federico G Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State.,Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Starkville
| | - Michael W Vandewege
- Department of Biology, Institute for Genomics and Evolutionary Medicine, Temple University
| | - Ryan K Schott
- Department of Ecology and Evolutionary Biology, Department of Cell and Systems Biology, Centre for the Analysis of Genome Evolution & Function, University of Toronto, Ontario, Canada.,Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia
| | - Nihar Bhattacharyya
- Department of Cell and Systems Biology, University of Toronto, Ontario, Canada
| | - Belinda S W Chang
- Department of Ecology and Evolutionary Biology, Department of Cell and Systems Biology, Centre for the Analysis of Genome Evolution & Function, University of Toronto, Ontario, Canada
| | - Nicholas R Casewell
- Alistair Reid Venom Research Unit, Parasitology Department, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, United Kingdom
| | - Gareth Whiteley
- Alistair Reid Venom Research Unit, Parasitology Department, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, United Kingdom
| | - Jacobo Reyes-Velasco
- Department of Biology, University of Texas at Arlington, Arlington.,Department of Biology, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates
| | | | - Tony Gamble
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53201, USA.,Bell Museum of Natural History, University of Minnesota, Saint Paul, MN, USA
| | - Kenneth B Storey
- Institute of Biochemistry, Carleton University, Ottawa, Ontario, Canada
| | - Kyle K Biggar
- Institute of Biochemistry, Carleton University, Ottawa, Ontario, Canada
| | | | - Chih-Horng Kuo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | | | - Anne M Bronikowski
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University
| | - A P Jason de Koning
- Department of Biochemistry and Molecular Biology, Department of Medical Genetics, Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Alberta, Canada
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University
| | - Michael E Pfrender
- Department of Biological Sciences and Environmental Change Initiative, University of Notre Dame
| | - Patrick Minx
- The McDonnell Genome Institute, Washington University School of Medicine, St. Louis
| | | | | | - Wesley C Warren
- The McDonnell Genome Institute, Washington University School of Medicine, St. Louis
| | - Todd A Castoe
- Department of Biology, University of Texas at Arlington, Arlington
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Pasquesi GIM, Adams RH, Card DC, Schield DR, Corbin AB, Perry BW, Reyes-Velasco J, Ruggiero RP, Vandewege MW, Shortt JA, Castoe TA. Squamate reptiles challenge paradigms of genomic repeat element evolution set by birds and mammals. Nat Commun 2018; 9:2774. [PMID: 30018307 PMCID: PMC6050309 DOI: 10.1038/s41467-018-05279-1] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 06/25/2018] [Indexed: 12/14/2022] Open
Abstract
Broad paradigms of vertebrate genomic repeat element evolution have been largely shaped by analyses of mammalian and avian genomes. Here, based on analyses of genomes sequenced from over 60 squamate reptiles (lizards and snakes), we show that patterns of genomic repeat landscape evolution in squamates challenge such paradigms. Despite low variance in genome size, squamate genomes exhibit surprisingly high variation among species in abundance (ca. 25–73% of the genome) and composition of identifiable repeat elements. We also demonstrate that snake genomes have experienced microsatellite seeding by transposable elements at a scale unparalleled among eukaryotes, leading to some snake genomes containing the highest microsatellite content of any known eukaryote. Our analyses of transposable element evolution across squamates also suggest that lineage-specific variation in mechanisms of transposable element activity and silencing, rather than variation in species-specific demography, may play a dominant role in driving variation in repeat element landscapes across squamate phylogeny. Large-scale patterns of genomic repeat element evolution have been studied mainly in birds and mammals. Here, the authors analyze the genomes of over 60 squamate reptiles and show high variation in repeat elements compared to mammals and birds, and particularly high microsatellite seeding in snakes.
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Affiliation(s)
- Giulia I M Pasquesi
- Department of Biology, University of Texas at Arlington, 501S. Nedderman Drive, Arlington, TX, 76019, USA
| | - Richard H Adams
- Department of Biology, University of Texas at Arlington, 501S. Nedderman Drive, Arlington, TX, 76019, USA
| | - Daren C Card
- Department of Biology, University of Texas at Arlington, 501S. Nedderman Drive, Arlington, TX, 76019, USA
| | - Drew R Schield
- Department of Biology, University of Texas at Arlington, 501S. Nedderman Drive, Arlington, TX, 76019, USA
| | - Andrew B Corbin
- Department of Biology, University of Texas at Arlington, 501S. Nedderman Drive, Arlington, TX, 76019, USA
| | - Blair W Perry
- Department of Biology, University of Texas at Arlington, 501S. Nedderman Drive, Arlington, TX, 76019, USA
| | - Jacobo Reyes-Velasco
- Department of Biology, University of Texas at Arlington, 501S. Nedderman Drive, Arlington, TX, 76019, USA.,Department of Biology, New York University Abu Dhabi, Saadiyat Island, United Arab Emirates
| | - Robert P Ruggiero
- Department of Biology, New York University Abu Dhabi, Saadiyat Island, United Arab Emirates
| | - Michael W Vandewege
- Department of Biology, Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, 19122, USA
| | - Jonathan A Shortt
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Todd A Castoe
- Department of Biology, University of Texas at Arlington, 501S. Nedderman Drive, Arlington, TX, 76019, USA.
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Andrew AL, Perry BW, Card DC, Schield DR, Ruggiero RP, McGaugh SE, Choudhary A, Secor SM, Castoe TA. Growth and stress response mechanisms underlying post-feeding regenerative organ growth in the Burmese python. BMC Genomics 2017; 18:338. [PMID: 28464824 PMCID: PMC5412052 DOI: 10.1186/s12864-017-3743-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 04/27/2017] [Indexed: 12/26/2022] Open
Abstract
Background Previous studies examining post-feeding organ regeneration in the Burmese python (Python molurus bivittatus) have identified thousands of genes that are significantly differentially regulated during this process. However, substantial gaps remain in our understanding of coherent mechanisms and specific growth pathways that underlie these rapid and extensive shifts in organ form and function. Here we addressed these gaps by comparing gene expression in the Burmese python heart, liver, kidney, and small intestine across pre- and post-feeding time points (fasted, one day post-feeding, and four days post-feeding), and by conducting detailed analyses of molecular pathways and predictions of upstream regulatory molecules across these organ systems. Results Identified enriched canonical pathways and upstream regulators indicate that while downstream transcriptional responses are fairly tissue specific, a suite of core pathways and upstream regulator molecules are shared among responsive tissues. Pathways such as mTOR signaling, PPAR/LXR/RXR signaling, and NRF2-mediated oxidative stress response are significantly differentially regulated in multiple tissues, indicative of cell growth and proliferation along with coordinated cell-protective stress responses. Upstream regulatory molecule analyses identify multiple growth factors, kinase receptors, and transmembrane receptors, both within individual organs and across separate tissues. Downstream transcription factors MYC and SREBF are induced in all tissues. Conclusions These results suggest that largely divergent patterns of post-feeding gene regulation across tissues are mediated by a core set of higher-level signaling molecules. Consistent enrichment of the NRF2-mediated oxidative stress response indicates this pathway may be particularly important in mediating cellular stress during such extreme regenerative growth. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3743-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Audra L Andrew
- Department of Biology, The University of Texas Arlington, 501 S. Nedderman Dr, Arlington, TX, 76019, USA
| | - Blair W Perry
- Department of Biology, The University of Texas Arlington, 501 S. Nedderman Dr, Arlington, TX, 76019, USA
| | - Daren C Card
- Department of Biology, The University of Texas Arlington, 501 S. Nedderman Dr, Arlington, TX, 76019, USA
| | - Drew R Schield
- Department of Biology, The University of Texas Arlington, 501 S. Nedderman Dr, Arlington, TX, 76019, USA
| | - Robert P Ruggiero
- Department of Biology, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates
| | - Suzanne E McGaugh
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN, 55108, USA
| | - Amit Choudhary
- Harvard Medical School, Renal Division, Brigham and Woman's Hospital, Cambridge, MA, 02142, USA.,Center for the Science of Therapeutics, Broad Institute, Cambridge, MA, 02142, USA
| | - Stephen M Secor
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, 35487, Box 870344, USA
| | - Todd A Castoe
- Department of Biology, The University of Texas Arlington, 501 S. Nedderman Dr, Arlington, TX, 76019, USA.
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Schield DR, Adams RH, Card DC, Perry BW, Pasquesi GM, Jezkova T, Portik DM, Andrew AL, Spencer CL, Sanchez EE, Fujita MK, Mackessy SP, Castoe TA. Insight into the roles of selection in speciation from genomic patterns of divergence and introgression in secondary contact in venomous rattlesnakes. Ecol Evol 2017; 7:3951-3966. [PMID: 28616190 PMCID: PMC5468163 DOI: 10.1002/ece3.2996] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 03/21/2017] [Indexed: 01/03/2023] Open
Abstract
Investigating secondary contact of historically isolated lineages can provide insight into how selection and drift influence genomic divergence and admixture. Here, we studied the genomic landscape of divergence and introgression following secondary contact between lineages of the Western Diamondback Rattlesnake (Crotalus atrox) to determine whether genomic regions under selection in allopatry also contribute to reproductive isolation during introgression. We used thousands of nuclear loci to study genomic differentiation between two lineages that have experienced recent secondary contact following isolation, and incorporated sampling from a zone of secondary contact to identify loci that are resistant to gene flow in hybrids. Comparisons of patterns of divergence and introgression revealed a positive relationship between allelic differentiation and resistance to introgression across the genome, and greater‐than‐expected overlap between genes linked to lineage‐specific divergence and loci that resist introgression. Genes linked to putatively selected markers were related to prominent aspects of rattlesnake biology that differ between populations of Western Diamondback rattlesnakes (i.e., venom and reproductive phenotypes). We also found evidence for selection against introgression of genes that may contribute to cytonuclear incompatibility, consistent with previously observed biased patterns of nuclear and mitochondrial alleles suggestive of partial reproductive isolation due to cytonuclear incompatibilities. Our results provide a genome‐scale perspective on the relationships between divergence and introgression in secondary contact that is relevant for understanding the roles of selection in maintaining partial isolation of lineages, causing admixing lineages to not completely homogenize.
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Affiliation(s)
- Drew R Schield
- Department of Biology The University of Texas at Arlington Arlington TX USA
| | - Richard H Adams
- Department of Biology The University of Texas at Arlington Arlington TX USA
| | - Daren C Card
- Department of Biology The University of Texas at Arlington Arlington TX USA
| | - Blair W Perry
- Department of Biology The University of Texas at Arlington Arlington TX USA
| | - Giulia M Pasquesi
- Department of Biology The University of Texas at Arlington Arlington TX USA
| | - Tereza Jezkova
- Department of Ecology and Evolutionary Biology University of Arizona Tucson AZ USA
| | - Daniel M Portik
- Department of Biology The University of Texas at Arlington Arlington TX USA
| | - Audra L Andrew
- Department of Biology The University of Texas at Arlington Arlington TX USA
| | - Carol L Spencer
- Museum of Vertebrate Zoology University of California Berkeley CA USA
| | - Elda E Sanchez
- National Natural Toxins Research Center and Department of Chemistry Texas A&M University Kingsville Kingsville TX USA
| | - Matthew K Fujita
- Department of Biology The University of Texas at Arlington Arlington TX USA
| | - Stephen P Mackessy
- School of Biological Sciences University of Northern Colorado Greeley CO USA
| | - Todd A Castoe
- Department of Biology The University of Texas at Arlington Arlington TX USA
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Card DC, Schield DR, Adams RH, Corbin AB, Perry BW, Andrew AL, Pasquesi GIM, Smith EN, Jezkova T, Boback SM, Booth W, Castoe TA. Phylogeographic and population genetic analyses reveal multiple species of Boa and independent origins of insular dwarfism. Mol Phylogenet Evol 2016; 102:104-16. [PMID: 27241629 DOI: 10.1016/j.ympev.2016.05.034] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Revised: 05/05/2016] [Accepted: 05/26/2016] [Indexed: 10/21/2022]
Abstract
Boa is a Neotropical genus of snakes historically recognized as monotypic despite its expansive distribution. The distinct morphological traits and color patterns exhibited by these snakes, together with the wide diversity of ecosystems they inhabit, collectively suggest that the genus may represent multiple species. Morphological variation within Boa also includes instances of dwarfism observed in multiple offshore island populations. Despite this substantial diversity, the systematics of the genus Boa has received little attention until very recently. In this study we examined the genetic structure and phylogenetic relationships of Boa populations using mitochondrial sequences and genome-wide SNP data obtained from RADseq. We analyzed these data at multiple geographic scales using a combination of phylogenetic inference (including coalescent-based species delimitation) and population genetic analyses. We identified extensive population structure across the range of the genus Boa and multiple lines of evidence for three widely-distributed clades roughly corresponding with the three primary land masses of the Western Hemisphere. We also find both mitochondrial and nuclear support for independent origins and parallel evolution of dwarfism on offshore island clusters in Belize and Cayos Cochinos Menor, Honduras.
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Affiliation(s)
- Daren C Card
- Department of Biology, 501 S. Nedderman Drive, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Drew R Schield
- Department of Biology, 501 S. Nedderman Drive, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Richard H Adams
- Department of Biology, 501 S. Nedderman Drive, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Andrew B Corbin
- Department of Biology, 501 S. Nedderman Drive, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Blair W Perry
- Department of Biology, 501 S. Nedderman Drive, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Audra L Andrew
- Department of Biology, 501 S. Nedderman Drive, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Giulia I M Pasquesi
- Department of Biology, 501 S. Nedderman Drive, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Eric N Smith
- Department of Biology, 501 S. Nedderman Drive, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Tereza Jezkova
- Department of Ecology & Evolutionary Biology, University of Arizona, P.O. Box 210088, Tucson, AZ 85721, USA
| | - Scott M Boback
- Department of Biology, P.O. Box 1773, Dickinson College, Carlisle, PA 17013, USA
| | - Warren Booth
- Department of Biological Science, 800 South Tucker Drive, University of Tulsa, Tulsa, OK 74104, USA
| | - Todd A Castoe
- Department of Biology, 501 S. Nedderman Drive, University of Texas at Arlington, Arlington, TX 76019, USA.
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40
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Koethe SM, Zielinski J, Perry BW. Glycohemoglobin results in samples with C or S trait measured on the Bio-Rad Diamat and Variant Express. Clin Chem 1999; 45:2041. [PMID: 10545088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
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Abstract
Transient co-transfection of receptor cDNA and suitable reporter genes was used to study human glucocorticoid receptor (hGR) function in a neutral mammalian cell background. A variety of natural and synthetic steroids were analyzed for their ability to activate gene expression through the hGR and to bind to extracts of cells expressing the hGR cDNA. There was very good correlation between these two in vitro parameters for these compounds. Furthermore, correlation of these data with reported in vivo anti-inflammatory potencies was surprisingly close, with two exceptions. The in vitro data suggest an explanation for the discrepant compounds, consistent with published data on their metabolic fate in vivo. The co-transfection assay has utility as a quantitative predictor of in vivo glucocorticoid pharmacology.
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Affiliation(s)
- T S Berger
- Ligand Pharmaceuticals Inc., San Diego, CA 92121
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42
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Doumas BT, Perry BW, McComb RB, Kessner A, Vader HL, Vink KL, Koedam JC, Paule RC. Molar absorptivities of bilirubin (NIST SRM 916a) and its neutral and alkaline azopigments. Clin Chem 1990. [DOI: 10.1093/clinchem/36.9.1698] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Three laboratories in the U.S. and two in the Netherlands determined molar absorptivities (epsilon) of Standard Reference Material (SRM) 916a Bilirubin from the National Institute of Standards and Technology. In caffeine reagent the average epsilon values were 50,060 and 48, 980 L.mol-1.cm-1 at 432 and 457 nm, respectively. The epsilon value of the blue azopigment, obtained with the Reference Method for total serum bilirubin, was 76,490 L.mol-1.cm-1 at 598 nm. When the addition of alkaline tartrate was omitted, the molar absorptivity of the red azopigment was 56,600 L.mol-1.cm-1 at 530 nm.
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Affiliation(s)
- B T Doumas
- Department of Pathology, Medical College of Wisconsin, Milwaukee 53226
| | - B W Perry
- Department of Pathology, Medical College of Wisconsin, Milwaukee 53226
| | - R B McComb
- Department of Pathology, Medical College of Wisconsin, Milwaukee 53226
| | - A Kessner
- Department of Pathology, Medical College of Wisconsin, Milwaukee 53226
| | - H L Vader
- Department of Pathology, Medical College of Wisconsin, Milwaukee 53226
| | - K L Vink
- Department of Pathology, Medical College of Wisconsin, Milwaukee 53226
| | - J C Koedam
- Department of Pathology, Medical College of Wisconsin, Milwaukee 53226
| | - R C Paule
- Department of Pathology, Medical College of Wisconsin, Milwaukee 53226
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43
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Doumas BT, Perry BW, McComb RB, Kessner A, Vader HL, Vink KL, Koedam JC, Paule RC. Molar absorptivities of bilirubin (NIST SRM 916a) and its neutral and alkaline azopigments. Clin Chem 1990; 36:1698-701. [PMID: 2208723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Three laboratories in the U.S. and two in the Netherlands determined molar absorptivities (epsilon) of Standard Reference Material (SRM) 916a Bilirubin from the National Institute of Standards and Technology. In caffeine reagent the average epsilon values were 50,060 and 48, 980 L.mol-1.cm-1 at 432 and 457 nm, respectively. The epsilon value of the blue azopigment, obtained with the Reference Method for total serum bilirubin, was 76,490 L.mol-1.cm-1 at 598 nm. When the addition of alkaline tartrate was omitted, the molar absorptivity of the red azopigment was 56,600 L.mol-1.cm-1 at 530 nm.
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Affiliation(s)
- B T Doumas
- Department of Pathology, Medical College of Wisconsin, Milwaukee 53226
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Doumas BT, Kwok-Cheung PP, Perry BW, Jendrzejczak B, McComb RB, Schaffer R, Hause LL. Candidate reference method for determination of total bilirubin in serum: development and validation. Clin Chem 1985; 31:1779-89. [PMID: 4053346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
This candidate Reference Method for measuring total bilirubin in serum is based on the Jendrassik-Gróf principle (Clin Chem 29: 297-301, 1983). Standard Reference Material no. 916 bilirubin (National Bureau of Standards) is used as the standard. Bilirubin standard solutions may be prepared either in human serum or in 40 g/L albumin solution (human or bovine), because we found the molar absorptivity of the azopigment at 598 nm to be identical in these media. The absorptivities of the unconjugated and conjugated azopigments appear to be identical, but the conjugated azopigment is completely hydrolyzed in the final reaction mixture. Bilirubin added to serum from adults or neonates was quantitatively accounted for. Interference by hemoglobin (up to 2 g/L), ascorbic acid (up to 20 mg/L), or zinc (at physiological concentrations) is negligible. Of the therapeutic drugs we tested, only L-dopa and alpha-methyldopa interfere. We established normal adult reference values for total bilirubin and examined the intraindividual variation in 19 subjects.
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Doumas BT, Kwok-Cheung PP, Perry BW, Jendrzejczak B, McComb RB, Schaffer R, Hause LL. Candidate reference method for determination of total bilirubin in serum: development and validation. Clin Chem 1985. [DOI: 10.1093/clinchem/31.11.1779] [Citation(s) in RCA: 118] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
This candidate Reference Method for measuring total bilirubin in serum is based on the Jendrassik-Gróf principle (Clin Chem 29: 297-301, 1983). Standard Reference Material no. 916 bilirubin (National Bureau of Standards) is used as the standard. Bilirubin standard solutions may be prepared either in human serum or in 40 g/L albumin solution (human or bovine), because we found the molar absorptivity of the azopigment at 598 nm to be identical in these media. The absorptivities of the unconjugated and conjugated azopigments appear to be identical, but the conjugated azopigment is completely hydrolyzed in the final reaction mixture. Bilirubin added to serum from adults or neonates was quantitatively accounted for. Interference by hemoglobin (up to 2 g/L), ascorbic acid (up to 20 mg/L), or zinc (at physiological concentrations) is negligible. Of the therapeutic drugs we tested, only L-dopa and alpha-methyldopa interfere. We established normal adult reference values for total bilirubin and examined the intraindividual variation in 19 subjects.
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Mateer JR, Perry BW, Thompson BM, Tucker JF, Aprahamian C. Effects of rapid infusion with high pressure and large-bore i.v. tubing on red blood cell lysis and warming. Ann Emerg Med 1985; 14:966-9. [PMID: 4037476 DOI: 10.1016/s0196-0644(85)80238-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A prototype large-bore intravenous tubing was developed and tested. Mean flow rates for blood (Hct 45%) and tap water were determined for several catheters at 600 mm Hg, 300 mm Hg, and gravity flow and were statistically analyzed by calculating the 95% confidence intervals. The degree of hemolysis during high pressure and flow was determined by measuring the plasma free hemoglobin using the spectrophotometric method. To determine if cold banked blood can be adequately warmed at high flow rates, thermocouples were used to measure the blood temperature before and after rapid infusion through a blood warmer. Results included maximum flow rates of 1,764 mL/min for tap water, and 1,714 mL/min for blood (Hct 45%) at 600 mm Hg through the large-bore tubing and an 8.5-F catheter. Flow rates for other pressure and catheter combinations were tabulated. The plasma-free hemoglobin increased slightly compared to controls with high pressure (less than or equal to 600 mm Hg) and flow rates. The increase correlated with less than 1% red blood cell lysis in all trials. When 13 C blood was infused through a warmer, blood temperature increased to 25.3 C at the maximum flow rate of 732 mL/min. Slightly higher heat gain resulted with slower infusion rates. We conclude that the prototype large-bore tubing and up to 600 mm Hg pressure provide rapid flow rates without significant hemolysis. Blood warming may be inadequate at higher flow rates.
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Abstract
A microcomputer-based information system that integrates the concepts of text processing, data base processing, and data base analysis has been designed for cost evaluation in our laboratories. This forms a flexible package that is directed by the needs of the user. The package, which has been used to calculate various cost parameters and productivity on the basis of comprehensive data and user-defined rules, serves as a tool for good financial management at various organizational levels in the clinical laboratory.
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Perry BW, Doumas BT, Bayse DD, Butler T, Cohen A, Fellows W, Garber CC, Howell B, Koch T, Krishnamurthy S, Louderback A, McComb RB, Miller D, Miller RR, Rand RN, Schaffer R. A candidate reference method for determination of bilirubin in serum. Test for transferability. Clin Chem 1983. [DOI: 10.1093/clinchem/29.2.297] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Perry BW, Doumas BT, Bayse DD, Butler T, Cohen A, Fellows W, Garber CC, Howell B, Koch T, Krishnamurthy S, Louderback A, McComb RB, Miller D, Miller RR, Rand RN, Schaffer R. A candidate reference method for determination of bilirubin in serum. Test for transferability. Clin Chem 1983; 29:297-301. [PMID: 6821933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Doumas BT, Perry BW, Jendrzejczak B, Katona V. Pitfalls in the American Monitor kit methods for determination of total and "direct" bilirubin. Clin Chem 1982. [DOI: 10.1093/clinchem/28.11.2305] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
We evaluated the American Monitor Corporation kit for total and direct-reacting bilirubin and found that it suffers serious deficiencies, which lead to inaccurate and imprecise results. The main problem with the total-bilirubin procedure is that the short reaction time (2 min) is inadequate for completion of the reaction. The poor precision of the direct-bilirubin method is due to the short reaction time and the inability of the "stabilizer" (hydroxylamine sulfate) to completely destroy the diazo reagent. Depending on when Fehling's reagent is added, the reaction time may vary from 2 min to 7 min. Values for direct bilirubin at 7 min exceed those obtained at 2 min by 17 to 29%. The short reaction time makes color development temperature dependent, an additional source of imprecision. The suboptimal concentration of the diazo reagent results in underestimation of direct-reacting bilirubin. We recommend changes that improve both precision and accuracy of the kit procedures.
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