1
|
Ellsworth SA, Rautsaw RM, Ward MJ, Holding ML, Rokyta DR. Selection Across the Three-Dimensional Structure of Venom Proteins from North American Scolopendromorph Centipedes. J Mol Evol 2024:10.1007/s00239-024-10191-y. [PMID: 39026042 DOI: 10.1007/s00239-024-10191-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Accepted: 07/09/2024] [Indexed: 07/20/2024]
Abstract
Gene duplication followed by nucleotide differentiation is one of the simplest mechanisms to develop new functions for genes. However, the evolutionary processes underlying the divergence of multigene families remain controversial. We used multigene families found within the diversity of toxic proteins in centipede venom to test two hypotheses related to venom evolution: the two-speed mode of venom evolution and the rapid accumulation of variation in exposed residues (RAVER) model. The two-speed mode of venom evolution proposes that different types of selection impact ancient and younger venomous lineages with negative selection being the predominant form in ancient lineages and positive selection being the dominant form in younger lineages. The RAVER hypothesis proposes that, instead of different types of selection acting on different ages of venomous lineages, the different types of selection will selectively contribute to amino acid variation based on whether the residue is exposed to the solvent where it can potentially interact directly with toxin targets. This hypothesis parallels the longstanding understanding of protein evolution that suggests that residues found within the structural or active regions of the protein will be under negative or purifying selection, and residues that do not form part of these areas will be more prone to positive selection. To test these two hypotheses, we compared the venom of 26 centipedes from the order Scolopendromorpha from six currently recognized species from across North America using both transcriptomics and proteomics. We first estimated their phylogenetic relationships and uncovered paraphyly among the genus Scolopendra and evidence for cryptic diversity among currently recognized species. Using our phylogeny, we then characterized the diverse venom components from across the identified clades using a combination of transcriptomics and proteomics. We conducted selection-based analyses in the context of predicted three-dimensional properties of the venom proteins and found support for both hypotheses. Consistent with the two-speed hypothesis, we found a prevalence of negative selection across all proteins. Consistent with the RAVER hypothesis, we found evidence of positive selection on solvent-exposed residues, with structural and less-exposed residues showing stronger signal for negative selection. Through the use of phylogenetics, transcriptomics, proteomics, and selection-based analyses, we were able to describe the evolution of venom from an ancient venomous lineage and support principles of protein evolution that directly relate to multigene family evolution.
Collapse
Affiliation(s)
- Schyler A Ellsworth
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA
| | - Rhett M Rautsaw
- Department of Integrative Biology, University of South Florida, Tampa, FL, 33620, USA
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Micaiah J Ward
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA
| | - Matthew L Holding
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Darin R Rokyta
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA.
| |
Collapse
|
2
|
Frandsen PB, Holzenthal RW, Espeland M, Breinholt J, Thomas Thorpe JA, Simon S, Kawahara AY, Plotkin D, Hotaling S, Li Y, Nelson CR, Niehuis O, Mayer C, Podsiadlowski L, Donath A, Misof B, Moriarty Lemmon E, Lemmon A, Morse JC, Liu S, Pauls SU, Zhou X. Phylogenomics recovers multiple origins of portable case making in caddisflies (Insecta: Trichoptera), nature's underwater architects. Proc Biol Sci 2024; 291:20240514. [PMID: 38955232 DOI: 10.1098/rspb.2024.0514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 06/10/2024] [Indexed: 07/04/2024] Open
Abstract
Caddisflies (Trichoptera) are among the most diverse groups of freshwater animals with more than 16 000 described species. They play a fundamental role in freshwater ecology and environmental engineering in streams, rivers and lakes. Because of this, they are frequently used as indicator organisms in biomonitoring programmes. Despite their importance, key questions concerning the evolutionary history of caddisflies, such as the timing and origin of larval case making, remain unanswered owing to the lack of a well-resolved phylogeny. Here, we estimated a phylogenetic tree using a combination of transcriptomes and targeted enrichment data for 207 species, representing 48 of 52 extant families and 174 genera. We calibrated and dated the tree with 33 carefully selected fossils. The first caddisflies originated approximately 295 million years ago in the Permian, and major suborders began to diversify in the Triassic. Furthermore, we show that portable case making evolved in three separate lineages, and shifts in diversification occurred in concert with key evolutionary innovations beyond case making.
Collapse
Affiliation(s)
- Paul B Frandsen
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, USA
| | | | - Marianne Espeland
- Museum Koenig Bonn, Leibniz Institute for the Analysis of Biodiversity Change (LIB), Bonn, Germany
| | | | | | - Sabrina Simon
- Rosenheim University of Applied Sciences, Rosenheim, Germany
| | - Akito Y Kawahara
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
- Entomology and Nematology Department, University of Florida, Gainesville, FL, USA
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - David Plotkin
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - Scott Hotaling
- Department of Watershed Sciences, Utah State University, Logan, UT, USA
| | - Yiyuan Li
- Institute of Plant Virology, Ningbo University, Ningbo, Zhejiang Province, People's Republic of China
| | - C Riley Nelson
- Department of Biology, Brigham Young University, Provo, UT, USA
| | - Oliver Niehuis
- Department of Evolutionary Biology and Ecology, Institute of Biology I (Zoology), University of Freiburg, Freiburg, Germany
| | - Christoph Mayer
- Museum Koenig Bonn, Leibniz Institute for the Analysis of Biodiversity Change (LIB), Bonn, Germany
| | - Lars Podsiadlowski
- Museum Koenig Bonn, Leibniz Institute for the Analysis of Biodiversity Change (LIB), Bonn, Germany
| | - Alexander Donath
- Museum Koenig Bonn, Leibniz Institute for the Analysis of Biodiversity Change (LIB), Bonn, Germany
| | - Bernhard Misof
- Museum Koenig Bonn, Leibniz Institute for the Analysis of Biodiversity Change (LIB), Bonn, Germany
- Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | | | - Alan Lemmon
- Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, FL, USA
| | - John C Morse
- Department of Plant & Environmental Sciences, Clemson University, Clemson, SC, USA
| | - Shanlin Liu
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, People's Republic of China
| | - Steffen U Pauls
- LOEWE Center for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt, Germany
- Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt, Germany
- Department of Insect Biotechnology, Justus-Liebig-University Gießen, Gießen, Germany
| | - Xin Zhou
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, People's Republic of China
| |
Collapse
|
3
|
Entiauspe-Neto OM, Nachtigall PG, Borges-Martins M, Junqueira-de-Azevedo ILM, Grazziotin FG. Highly conserved and extremely variable: The paradoxical pattern of toxin expression revealed by comparative venom-gland transcriptomics of Phalotris (Serpentes: Dipsadidae). Toxicon 2024; 244:107740. [PMID: 38705487 DOI: 10.1016/j.toxicon.2024.107740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 04/11/2024] [Accepted: 04/27/2024] [Indexed: 05/07/2024]
Abstract
Although non-front fanged snakes account for almost two-thirds of snake diversity, most studies on venom composition and evolution focus exclusively on front-fanged species, which comprise most of the clinically relevant accidents. Comprehensive reports on venom composition of non-front fanged snakes are still scarce for several groups. In this study, we address such shortage of knowledge by providing new insights about the venom composition among species of Phalotris, a poorly studied Neotropical dipsadid genus. Phalotris are known for their specialized venom delivery system and toxic venoms, which can cause life-threatening accidents in humans. We evaluate the venom-gland transcriptome of Phalotris, comparing the following three South American species: P. reticulatus for the Araucaria Pine forests, P. lemniscatus for the Pampa grasslands, and P. mertensi for the Brazilian Cerrado. Our results indicate similar venom profiles, in which they share a high expression level of Kunitz-type inhibitors (KUNZ). On the other hand, comparative analyses revealed substantial differences in the expression levels of C-type lectins (CTL) and snake venom metalloproteinases (SVMP). The diverse set of SVMP and CTL isoforms shows signals of positive selection, and we also identified truncated forms of type III SVMPs, which resemble type II and type I SVMPs of viperids. Additionally, we identified a CNP precursor hosting a proline-rich region containing a BPP motif resembling those commonly detected in viperid venoms with hypotensive activity. Altogether, our results suggest an evolutionary history favoring high expression levels of few KUNZ isoforms in Phalotris venoms, contrasting with a highly diverse set of SVMP and CTL isoforms. Such diversity can be comparable with the venom variability observed in some viperids. Our findings highlight the extreme phenotypic diversity of non-front fanged snakes and the importance to allocate greater effort to study neglected groups of Colubroidea.
Collapse
Affiliation(s)
- Omar M Entiauspe-Neto
- Laboratório de Coleções Zoológicas, Instituto Butantan, 05503-900, Av. Vital Brazil, 1500, Butantã, São Paulo, SP, Brazil; Programa de Pós-graduação em Biologia Animal, Departamento de Zoologia, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves, CEP 91501-970, Porto Alegre, RS, Brazil.
| | - Pedro G Nachtigall
- Laboratório de Toxinologia Aplicada, Instituto Butantan, 05503-900, Av. Vital Brazil, 1500, Butantã, São Paulo, SP, Brazil
| | - Márcio Borges-Martins
- Programa de Pós-graduação em Biologia Animal, Departamento de Zoologia, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves, CEP 91501-970, Porto Alegre, RS, Brazil
| | | | - Felipe G Grazziotin
- Laboratório de Coleções Zoológicas, Instituto Butantan, 05503-900, Av. Vital Brazil, 1500, Butantã, São Paulo, SP, Brazil
| |
Collapse
|
4
|
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; 23:100779. [PMID: 38679388 PMCID: PMC11154231 DOI: 10.1016/j.mcpro.2024.100779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [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 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 thermal proteome profiling 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.
Collapse
Affiliation(s)
- Cara F Smith
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado, USA
| | - Cassandra M Modahl
- Centre for Snakebite Research and Interventions, Liverpool School of Tropical Medicine, Liverpool, UK
| | - David Ceja Galindo
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado, USA
| | - Keira Y Larson
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado, USA
| | - Sean P Maroney
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado, USA
| | - Lilyrose Bahrabadi
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado, USA
| | - Nicklaus P Brandehoff
- Rocky Mountain Poison and Drug Center, Denver Health and Hospital Authority, Denver, Colorado, USA
| | - Blair W Perry
- School of Biological Sciences, Washington State University, Pullman, Washington, USA
| | - Maxwell C McCabe
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado, USA
| | - Daniel Petras
- CMFI Cluster of Excellence, University of Tuebingen, Tuebingen, Germany; Department of Biochemistry, University of California Riverside, Riverside, California, USA
| | - Bruno Lomonte
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Juan J Calvete
- Evolutionary and Translational Venomics Laboratory, Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
| | - Todd A Castoe
- Department of Biology, The University of Texas Arlington, Texas, USA
| | - Stephen P Mackessy
- Department of Biological Sciences, University of Northern Colorado, Greeley, Colorado, USA
| | - Kirk C Hansen
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado, USA
| | - Anthony J Saviola
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado, USA.
| |
Collapse
|
5
|
Saldarriaga-Córdoba M, Clavero-León C, Rey-Suarez P, Nuñez-Rangel V, Avendaño-Herrera R, Solano-González S, Alzate JF. Unveiling Novel Kunitz- and Waprin-Type Toxins in the Micrurus mipartitus Coral Snake Venom Gland: An In Silico Transcriptome Analysis. Toxins (Basel) 2024; 16:224. [PMID: 38787076 PMCID: PMC11126030 DOI: 10.3390/toxins16050224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 04/23/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024] Open
Abstract
Kunitz-type peptide expression has been described in the venom of snakes of the Viperidae, Elapidae and Colubridae families. This work aimed to identify these peptides in the venom gland transcriptome of the coral snake Micrurus mipartitus. Transcriptomic analysis revealed a high diversity of venom-associated Kunitz serine protease inhibitor proteins (KSPIs). A total of eight copies of KSPIs were predicted and grouped into four distinctive types, including short KSPI, long KSPI, Kunitz-Waprin (Ku-WAP) proteins, and a multi-domain Kunitz-type protein. From these, one short KSPI showed high identity with Micrurus tener and Austrelaps superbus. The long KSPI group exhibited similarity within the Micrurus genus and showed homology with various elapid snakes and even with the colubrid Pantherophis guttatus. A third group suggested the presence of Kunitz domains in addition to a whey-acidic-protein-type four-disulfide core domain. Finally, the fourth group corresponded to a transcript copy with a putative 511 amino acid protein, formerly annotated as KSPI, which UniProt classified as SPINT1. In conclusion, this study showed the diversity of Kunitz-type proteins expressed in the venom gland transcriptome of M. mipartitus.
Collapse
Affiliation(s)
| | - Claudia Clavero-León
- Centro de Investigación en Recursos Naturales y Sustentabilidad (CIRENYS), Universidad Bernardo O’Higgins, Santiago 8320000, Chile
| | - Paola Rey-Suarez
- Grupo de Investigación en Toxinología, Alternativas Terapéuticas y Alimentarias, Facultad de Ciencias Farmacéuticas y Alimentarias, Universidad de Antioquia, Medellín 50010, Colombia; (P.R.-S.); (V.N.-R.)
| | - Vitelbina Nuñez-Rangel
- Grupo de Investigación en Toxinología, Alternativas Terapéuticas y Alimentarias, Facultad de Ciencias Farmacéuticas y Alimentarias, Universidad de Antioquia, Medellín 50010, Colombia; (P.R.-S.); (V.N.-R.)
- Escuela de Microbiología, Universidad de Antioquia, Medellín 50010, Colombia
| | - Ruben Avendaño-Herrera
- Facultad de Ciencias de la Vida & Centro de Investigación Marina Quintay (CIMARQ), Universidad Andrés Bello, Viña del Mar 2531015, Chile;
| | - Stefany Solano-González
- Laboratorio de Bioinformática Aplicada, Escuela de Ciencias Biológicas, Universidad Nacional, Heredia 86-3000, Costa Rica
| | - Juan F. Alzate
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia, Medellín 50010, Colombia;
| |
Collapse
|
6
|
Myers EA, Rautsaw RM, Borja M, Jones J, Grünwald CI, Holding ML, Grazziotin F, Parkinson CL. Phylogenomic discordance is driven by wide-spread introgression and incomplete lineage sorting during rapid species diversification within rattlesnakes (Viperidae: Crotalus and Sistrurus). Syst Biol 2024:syae018. [PMID: 38695290 DOI: 10.1093/sysbio/syae018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Indexed: 08/11/2024] Open
Abstract
Phylogenomics allows us to uncover the historical signal of evolutionary processes through time and estimate phylogenetic networks accounting for these signals. Insight from genome-wide data further allows us to pinpoint the contributions to phylogenetic signal from hybridization, introgression, and ancestral polymorphism across the genome. Here we focus on how these processes have contributed to phylogenetic discordance among rattlesnakes (genera Crotalus and Sistrurus), a group for which there are numerous conflicting phylogenetic hypotheses based on a diverse array of molecular datasets and analytical methods. We address the instability of the rattlesnake phylogeny using genomic data generated from transcriptomes sampled from nearly all known species. These genomic data, analyzed with coalescent and network-based approaches, reveal numerous instances of rapid speciation where individual gene trees conflict with the species tree. Moreover, the evolutionary history of rattlesnakes is dominated by incomplete speciation and frequent hybridization, both of which have likely influenced past interpretations of phylogeny. We present a new framework in which the evolutionary relationships of this group can only be understood in light of genome-wide data and network-based analytical methods. Our data suggest that network radiations, like seen within the rattlesnakes, can only be understood in a phylogenomic context, necessitating similar approaches in our attempts to understand evolutionary history in other rapidly radiating species.
Collapse
Affiliation(s)
- Edward A Myers
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
- Department of Herpetology, California Academy of Sciences, San Francisco, CA 94118, USA
| | - Rhett M Rautsaw
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
| | - Miguel Borja
- Facultad de Ciencias Biológicas, Universdad Juárez del Estado de Durango, Av. Universidad s/n. Fracc. Filadelfia, Gómez Palacio, Durango., Mex
| | - Jason Jones
- Herp.mx A.C. C.P. 28989, Villa de Álvarez, Colima, Mexico
| | - Christoph I Grünwald
- Herp.mx A.C. C.P. 28989, Villa de Álvarez, Colima, Mexico
- Biodiversa A.C., Avenida de la Ribera #203, C.P. 45900, Chapala, Jalisco, Mexico
| | - Matthew L Holding
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Felipe Grazziotin
- Laboratório Especial de Coleções Zoológicas, Instituto Butantan, Avenida Vital Brasil, São Paulo, 05503-900, Brazil
| | | |
Collapse
|
7
|
Gvoždík V, Dolinay M, Zassi-Boulou AG, Lemmon AR, Lemmon EM, Procházka M. Central African dwarf crocodiles found in syntopy are comparably divergent to South American dwarf caimans. Biol Lett 2024; 20:20230448. [PMID: 38716586 PMCID: PMC11135362 DOI: 10.1098/rsbl.2023.0448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 12/18/2023] [Accepted: 03/04/2024] [Indexed: 05/31/2024] Open
Abstract
Recent molecular taxonomic advancements have expanded our understanding of crocodylian diversity, revealing the existence of previously overlooked species, including the Congo dwarf crocodile (Osteolaemus osborni) in the central Congo Basin rainforests. This study explores the genomic divergence between O. osborni and its better-known relative, the true dwarf crocodile (Osteolaemus tetraspis), shedding light on their evolutionary history. Field research conducted in the northwestern Republic of the Congo uncovered a locality where both species coexist in sympatry/syntopy. Genomic analysis of sympatric individuals reveals a level of divergence comparable to that between ecologically similar South American dwarf caimans (Paleosuchus palpebrosus and Paleosuchus trigonatus), suggesting parallel speciation in the Afrotropics and Neotropics during the Middle to Late Miocene, 10-12 Ma. Comparison of the sympatric and allopatric dwarf crocodiles indicates no gene flow between the analysed sympatric individuals of O. osborni and O. tetraspis. However, a larger sample will be required to answer the question of whether or to what extent these species hybridize. This study emphasizes the need for further research on the biology and conservation status of the Congo dwarf crocodile, highlighting its significance in the unique biodiversity of the Congolian rainforests and thus its potential as a flagship species.
Collapse
Affiliation(s)
- Václav Gvoždík
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic
- Department of Zoology, National Museum of the Czech Republic, Prague, Czech Republic
| | - Matej Dolinay
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic
| | - Ange-Ghislain Zassi-Boulou
- Department of Biology, National Institute for Research in Exact and Natural Sciences (IRSEN), Brazzaville, Republic of the Congo
| | - Alan R. Lemmon
- Department of Scientific Computing, Dirac Science Library, Florida State University, Tallahassee, FL, USA
| | - Emily M. Lemmon
- Department of Biological Sciences, Florida State University, Tallahassee, FL, USA
| | | |
Collapse
|
8
|
Karimi N, Krieg CP, Spalink D, Lemmon AR, Lemmon EM, Eifler E, Hernández AI, Chan PW, Rodríguez A, Landis JB, Strickler SR, Specht CD, Givnish TJ. Chromosomal evolution, environmental heterogeneity, and migration drive spatial patterns of species richness in Calochortus (Liliaceae). Proc Natl Acad Sci U S A 2024; 121:e2305228121. [PMID: 38394215 DOI: 10.1073/pnas.2305228121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 12/20/2023] [Indexed: 02/25/2024] Open
Abstract
We used nuclear genomic data and statistical models to evaluate the ecological and evolutionary processes shaping spatial variation in species richness in Calochortus (Liliaceae, 74 spp.). Calochortus occupies diverse habitats in the western United States and Mexico and has a center of diversity in the California Floristic Province, marked by multiple orogenies, winter rainfall, and highly divergent climates and substrates (including serpentine). We used sequences of 294 low-copy nuclear loci to produce a time-calibrated phylogeny, estimate historical biogeography, and test hypotheses regarding drivers of present-day spatial patterns in species number. Speciation and species coexistence require reproductive isolation and ecological divergence, so we examined the roles of chromosome number, environmental heterogeneity, and migration in shaping local species richness. Six major clades-inhabiting different geographic/climatic areas, and often marked by different base chromosome numbers (n = 6 to 10)-began diverging from each other ~10.3 Mya. As predicted, local species number increased significantly with local heterogeneity in chromosome number, elevation, soil characteristics, and serpentine presence. Species richness is greatest in the Transverse/Peninsular Ranges where clades with different chromosome numbers overlap, topographic complexity provides diverse conditions over short distances, and several physiographic provinces meet allowing immigration by several clades. Recently diverged sister-species pairs generally have peri-patric distributions, and maximum geographic overlap between species increases over the first million years since divergence, suggesting that chromosomal evolution, genetic divergence leading to gametic isolation or hybrid inviability/sterility, and/or ecological divergence over small spatial scales may permit species co-occurrence.
Collapse
Affiliation(s)
- Nisa Karimi
- Science and Conservation Division, Missouri Botanical Garden, St. Louis, MO 63110
- Department of Botany, University of Wisconsin-Madison, Madison, WI 53706
| | | | - Daniel Spalink
- Department of Ecology and Conservation Biology, Texas A&M University, College Station, TX 77845
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL 32306
| | | | - Evan Eifler
- Department of Botany, University of Wisconsin-Madison, Madison, WI 53706
| | - Adriana I Hernández
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
- L. H. Bailey Hortorium, Cornell University, Ithaca, NY 14853
| | - Patricia W Chan
- Department of Botany, University of Wisconsin-Madison, Madison, WI 53706
| | - Aarón Rodríguez
- Departamento de Botánica y Zoología, Universidad de la Guadalajara, Zapopan, Jalisco 45200, Mexico
| | - Jacob B Landis
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
- Departamento de Botánica y Zoología, Universidad de la Guadalajara, Zapopan, Jalisco 45200, Mexico
- Boyce Thompson Institute for Plant Research, Ithaca, NY 14853
| | | | - Chelsea D Specht
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
- L. H. Bailey Hortorium, Cornell University, Ithaca, NY 14853
| | - Thomas J Givnish
- Department of Botany, University of Wisconsin-Madison, Madison, WI 53706
| |
Collapse
|
9
|
Modahl CM, Han SX, van Thiel J, Vaz C, Dunstan NL, Frietze S, Jackson TNW, Mackessy SP, Kini RM. Distinct regulatory networks control toxin gene expression in elapid and viperid snakes. BMC Genomics 2024; 25:186. [PMID: 38365592 PMCID: PMC10874052 DOI: 10.1186/s12864-024-10090-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 02/05/2024] [Indexed: 02/18/2024] Open
Abstract
BACKGROUND Venom systems are ideal models to study genetic regulatory mechanisms that underpin evolutionary novelty. Snake venom glands are thought to share a common origin, but there are major distinctions between venom toxins from the medically significant snake families Elapidae and Viperidae, and toxin gene regulatory investigations in elapid snakes have been limited. Here, we used high-throughput RNA-sequencing to profile gene expression and microRNAs between active (milked) and resting (unmilked) venom glands in an elapid (Eastern Brown Snake, Pseudonaja textilis), in addition to comparative genomics, to identify cis- and trans-acting regulation of venom production in an elapid in comparison to viperids (Crotalus viridis and C. tigris). RESULTS Although there is conservation in high-level mechanistic pathways regulating venom production (unfolded protein response, Notch signaling and cholesterol homeostasis), there are differences in the regulation of histone methylation enzymes, transcription factors, and microRNAs in venom glands from these two snake families. Histone methyltransferases and transcription factor (TF) specificity protein 1 (Sp1) were highly upregulated in the milked elapid venom gland in comparison to the viperids, whereas nuclear factor I (NFI) TFs were upregulated after viperid venom milking. Sp1 and NFI cis-regulatory elements were common to toxin gene promoter regions, but many unique elements were also present between elapid and viperid toxins. The presence of Sp1 binding sites across multiple elapid toxin gene promoter regions that have been experimentally determined to regulate expression, in addition to upregulation of Sp1 after venom milking, suggests this transcription factor is involved in elapid toxin expression. microRNA profiles were distinctive between milked and unmilked venom glands for both snake families, and microRNAs were predicted to target a diversity of toxin transcripts in the elapid P. textilis venom gland, but only snake venom metalloproteinase transcripts in the viperid C. viridis venom gland. These results suggest differences in toxin gene posttranscriptional regulation between the elapid P. textilis and viperid C. viridis. CONCLUSIONS Our comparative transcriptomic and genomic analyses between toxin genes and isoforms in elapid and viperid snakes suggests independent toxin regulation between these two snake families, demonstrating multiple different regulatory mechanisms underpin a venomous phenotype.
Collapse
Affiliation(s)
- Cassandra M Modahl
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore.
- Centre for Snakebite Research and Interventions, Liverpool School of Tropical Medicine, Liverpool, U.K..
| | - Summer Xia Han
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
- Fulcrum Therapeutics, Cambridge, MA, U.S.A
| | - Jory van Thiel
- Centre for Snakebite Research and Interventions, Liverpool School of Tropical Medicine, Liverpool, U.K
- Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
| | - Candida Vaz
- Human Development, Institute for Clinical Sciences (SICS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | | | - Seth Frietze
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT, U.S.A
| | - Timothy N W Jackson
- Australian Venom Research Unit, Department of Biochemistry and Pharmacology, University of Melbourne, Melbourne, Australia
| | - Stephen P Mackessy
- Department of Biological Sciences, University of Northern Colorado, Greeley, CO, U.S.A
| | - R Manjunatha Kini
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore.
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Singapore Eye Research Institute, Singapore, Singapore.
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, VA, U.S.A..
| |
Collapse
|
10
|
Freitas-de-Sousa LA, Colombini M, Souza VC, Silva JPC, Mota-da-Silva A, Almeida MRN, Machado RA, Fonseca WL, Sartim MA, Sachett J, Serrano SMT, Junqueira-de-Azevedo ILM, Grazziotin FG, Monteiro WM, Bernarde PS, Moura-da-Silva AM. Venom Composition of Neglected Bothropoid Snakes from the Amazon Rainforest: Ecological and Toxinological Implications. Toxins (Basel) 2024; 16:83. [PMID: 38393161 PMCID: PMC10891915 DOI: 10.3390/toxins16020083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/18/2024] [Accepted: 01/30/2024] [Indexed: 02/25/2024] Open
Abstract
Snake venoms have evolved in several families of Caenophidae, and their toxins have been assumed to be biochemical weapons with a role as a trophic adaptation. However, it remains unclear how venom contributes to the success of venomous species for adaptation to different environments. Here we compared the venoms from Bothrocophias hyoprora, Bothrops taeniatus, Bothrops bilineatus smaragdinus, Bothrops brazili, and Bothrops atrox collected in the Amazon Rainforest, aiming to understand the ecological and toxinological consequences of venom composition. Transcriptomic and proteomic analyses indicated that the venoms presented the same toxin groups characteristic from bothropoids, but with distinct isoforms with variable qualitative and quantitative abundances, contributing to distinct enzymatic and toxic effects. Despite the particularities of each venom, commercial Bothrops antivenom recognized the venom components and neutralized the lethality of all species. No clear features could be observed between venoms from arboreal and terrestrial habitats, nor in the dispersion of the species throughout the Amazon habitats, supporting the notion that venom composition may not shape the ecological or toxinological characteristics of these snake species and that other factors influence their foraging or dispersal in different ecological niches.
Collapse
Affiliation(s)
| | - Mônica Colombini
- Laboratório de Imunopatologia, Instituto Butantan, São Paulo 05503-900, SP, Brazil; (L.A.F.-d.-S.); (M.C.)
| | - Vinicius C. Souza
- Laboratório de Toxinologia Aplicada, Instituto Butantan, São Paulo 05503-900, SP, Brazil; (V.C.S.); (J.P.C.S.); (S.M.T.S.); (I.L.M.J.-d.-A.)
| | - Joanderson P. C. Silva
- Laboratório de Toxinologia Aplicada, Instituto Butantan, São Paulo 05503-900, SP, Brazil; (V.C.S.); (J.P.C.S.); (S.M.T.S.); (I.L.M.J.-d.-A.)
| | - Ageane Mota-da-Silva
- Instituto Federal do Acre, Campus de Cruzeiro do Sul, Cruzeiro do Sul 69980-000, AC, Brazil;
| | - Marllus R. N. Almeida
- Laboratório de Herpetologia, Universidade Federal do Acre, Campus Floresta, Cruzeiro do Sul 69895-000, AC, Brazil; (M.R.N.A.); (R.A.M.); (W.L.F.); (P.S.B.)
| | - Reginaldo A. Machado
- Laboratório de Herpetologia, Universidade Federal do Acre, Campus Floresta, Cruzeiro do Sul 69895-000, AC, Brazil; (M.R.N.A.); (R.A.M.); (W.L.F.); (P.S.B.)
| | - Wirven L. Fonseca
- Laboratório de Herpetologia, Universidade Federal do Acre, Campus Floresta, Cruzeiro do Sul 69895-000, AC, Brazil; (M.R.N.A.); (R.A.M.); (W.L.F.); (P.S.B.)
| | - Marco A. Sartim
- Instituto de Pesquisa Clínica Carlos Borborema, Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus 69040-000, AM, Brazil; (M.A.S.); (J.S.); (W.M.M.)
| | - Jacqueline Sachett
- Instituto de Pesquisa Clínica Carlos Borborema, Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus 69040-000, AM, Brazil; (M.A.S.); (J.S.); (W.M.M.)
| | - Solange M. T. Serrano
- Laboratório de Toxinologia Aplicada, Instituto Butantan, São Paulo 05503-900, SP, Brazil; (V.C.S.); (J.P.C.S.); (S.M.T.S.); (I.L.M.J.-d.-A.)
| | - Inácio L. M. Junqueira-de-Azevedo
- Laboratório de Toxinologia Aplicada, Instituto Butantan, São Paulo 05503-900, SP, Brazil; (V.C.S.); (J.P.C.S.); (S.M.T.S.); (I.L.M.J.-d.-A.)
| | - Felipe G. Grazziotin
- Laboratório de Coleções Zoológicas, Instituto Butantan, São Paulo 05503-900, SP, Brazil;
| | - Wuelton M. Monteiro
- Instituto de Pesquisa Clínica Carlos Borborema, Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus 69040-000, AM, Brazil; (M.A.S.); (J.S.); (W.M.M.)
| | - Paulo S. Bernarde
- Laboratório de Herpetologia, Universidade Federal do Acre, Campus Floresta, Cruzeiro do Sul 69895-000, AC, Brazil; (M.R.N.A.); (R.A.M.); (W.L.F.); (P.S.B.)
| | - Ana M. Moura-da-Silva
- Laboratório de Imunopatologia, Instituto Butantan, São Paulo 05503-900, SP, Brazil; (L.A.F.-d.-S.); (M.C.)
| |
Collapse
|
11
|
Phan P, Deshwal A, McMahon TA, Slikas M, Andrews E, Becker B, Kumar TKS. A Review of Rattlesnake Venoms. Toxins (Basel) 2023; 16:2. [PMID: 38276526 PMCID: PMC10818703 DOI: 10.3390/toxins16010002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/08/2023] [Accepted: 12/12/2023] [Indexed: 01/27/2024] Open
Abstract
Venom components are invaluable in biomedical research owing to their specificity and potency. Many of these components exist in two genera of rattlesnakes, Crotalus and Sistrurus, with high toxicity and proteolytic activity variation. This review focuses on venom components within rattlesnakes, and offers a comparison and itemized list of factors dictating venom composition, as well as presenting their known characteristics, activities, and significant applications in biosciences. There are 64 families and subfamilies of proteins present in Crotalus and Sistrurus venom. Snake venom serine proteases (SVSP), snake venom metalloproteases (SVMP), and phospholipases A2 (PLA2) are the standard components in Crotalus and Sistrurus venom. Through this review, we highlight gaps in the knowledge of rattlesnake venom; there needs to be more information on the venom composition of three Crotalus species and one Sistrurus subspecies. We discuss the activity and importance of both major and minor components in biomedical research and drug development.
Collapse
Affiliation(s)
- Phuc Phan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA;
| | - Anant Deshwal
- Department of Biology, Bradley University, Peoria, IL 61625, USA; (T.A.M.); (M.S.); (E.A.)
| | - Tyler Anthony McMahon
- Department of Biology, Bradley University, Peoria, IL 61625, USA; (T.A.M.); (M.S.); (E.A.)
| | - Matthew Slikas
- Department of Biology, Bradley University, Peoria, IL 61625, USA; (T.A.M.); (M.S.); (E.A.)
| | - Elodie Andrews
- Department of Biology, Bradley University, Peoria, IL 61625, USA; (T.A.M.); (M.S.); (E.A.)
| | - Brian Becker
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA;
| | | |
Collapse
|
12
|
Nystrom GS, Ellsworth SA, Ward MJ, Rokyta DR. Varying Modes of Selection Among Toxin Families in the Venoms of the Giant Desert Hairy Scorpions (Hadrurus). J Mol Evol 2023; 91:935-962. [PMID: 38091038 DOI: 10.1007/s00239-023-10148-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 11/12/2023] [Indexed: 12/21/2023]
Abstract
Venoms are primarily believed to evolve under strong diversifying selection resulting from persistent coevolution between predator and prey. Recent research has challenged this hypothesis, proposing that venoms from younger venomous lineages (e.g., snakes and cone snails) are governed predominantly by diversifying selection, while venoms from older venomous lineages (e.g., centipedes, scorpions, and spiders) are under stronger purifying selection. However, most research in older lineages has tested selection at more diverse phylogenetic scales. Although these tests are important for evaluating broad macroevolutionary trends underlying venom evolution, they are less equipped to detect species-level evolutionary trends, which likely have large impacts on venom variation seen at more diverse phylogenetic scales. To test for selection among closely related species from an older venomous lineage, we generated high-throughput venom-gland transcriptomes and venom proteomes for four populations of Giant Desert Hairy Scorpions (Hadrurus), including three Hadrurus arizonensis populations and one Hadrurus spadix population. We detected significant episodic and pervasive diversifying selection across a highly abundant toxin family that likely has a major role in venom function ([Formula: see text]KTxs), providing a contrast to the stronger purifying selection identified from other studies on scorpion venoms. Conversely, we detected weak episodic diversifying and/or stronger purifying selection in four toxin families (non-disulfide bridged peptides, phospholipase A2s, scorpine-like antimicrobial peptides, and serine proteases), most of which were less abundant and likely have ancillary functional roles. Finally, although we detected several major toxin families at disproportionate transcriptomic and/or proteomic abundances, we did not identify significant sex-based variation in Hadrurus venoms.
Collapse
Affiliation(s)
- Gunnar S Nystrom
- Department of Biological Science, Florida State University, 319 Stadium Dr., Tallahassee, FL, 32306-4295, USA
| | - Schyler A Ellsworth
- Department of Biological Science, Florida State University, 319 Stadium Dr., Tallahassee, FL, 32306-4295, USA
| | - Micaiah J Ward
- Department of Biological Science, Florida State University, 319 Stadium Dr., Tallahassee, FL, 32306-4295, USA
| | - Darin R Rokyta
- Department of Biological Science, Florida State University, 319 Stadium Dr., Tallahassee, FL, 32306-4295, USA.
| |
Collapse
|
13
|
Oliveira LD, Nachtigall PG, Vialla VL, Campos PF, Costa-Neves AD, Zaher H, Silva NJD, Grazziotin FG, Wilkinson M, Junqueira-de-Azevedo ILM. Comparing morphological and secretory aspects of cephalic glands among the New World coral snakes brings novel insights on their biological roles. Toxicon 2023; 234:107285. [PMID: 37683698 DOI: 10.1016/j.toxicon.2023.107285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 09/05/2023] [Accepted: 09/06/2023] [Indexed: 09/10/2023]
Abstract
Oral and other cephalic glands have been surveyed by several studies with distinct purposes. Despite the wide diversity and medical relevance of the New World coral snakes, studies focusing on understanding the biological roles of the glands within this group are still scarce. Specifically, the venom glands of some coral snakes were previously investigated but all other cephalic glands remain uncharacterized. In this sense, performing morphological and molecular analysis of these glands may help better understand their biological role. Here, we studied the morphology of the venom, infralabial, rictal, and harderian glands of thirteen species of Micrurus and Micruroides euryxanthus. We also performed a molecular characterization of these glands from selected species of Micrurus using transcriptomic and proteomic approaches. We described substantial morphological variation in the cephalic glands of New World coral snakes and structural evidence for protein-secreting cells in the inferior rictal glands. Our molecular analysis revealed that the venom glands, as expected, are majorly devoted to toxin production, however, the infralabial and inferior rictal glands also expressed some toxin genes at low to medium levels, despite the marked morphological differences. On the other hand, the harderian glands were dominated by the expression of lipocalins, but do not produce toxins. Our integrative analysis, including the prediction of biological processes and pathways, helped decipher some important traits of cephalic glands and better understand their biology.
Collapse
Affiliation(s)
- Leonardo de Oliveira
- Laboratório de Toxinologia Aplicada, Centre of Toxins, Immune-Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, 05503-900, Brazil; Herpetology, The Natural History Museum, London, SW7 5BD, United Kingdom.
| | - Pedro Gabriel Nachtigall
- Laboratório de Toxinologia Aplicada, Centre of Toxins, Immune-Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, 05503-900, Brazil
| | - Vincent Louis Vialla
- Laboratório de Toxinologia Aplicada, Centre of Toxins, Immune-Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, 05503-900, Brazil
| | - Pollyanna F Campos
- Laboratório de Toxinologia Aplicada, Centre of Toxins, Immune-Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, 05503-900, Brazil
| | | | - Hussam Zaher
- Museu de Zoologia da Universidade de São Paulo, Avenida Nazaré 481, Ipiranga, 04263-000, São Paulo, Brazil
| | - Nelson Jorge da Silva
- Programa de Pós-Graduação em Ciências Ambientais e Saúde, Pontifícia Universidade Católica de Goiás, Goiânia, Goiás, 74605-140, Brazil
| | - Felipe G Grazziotin
- Laboratório de Coleções Zoológicas, Instituto Butantan, São Paulo, 05503-900, Brazil
| | - Mark Wilkinson
- Herpetology, The Natural History Museum, London, SW7 5BD, United Kingdom
| | - Inácio L M Junqueira-de-Azevedo
- Laboratório de Toxinologia Aplicada, Centre of Toxins, Immune-Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, 05503-900, Brazil
| |
Collapse
|
14
|
Liao X, Guo S, Liao B, Shen X, He W, Meng Y, Liang C, Pei J, Liu J, Zhang Y, Xu J, Chen S. Chromatin architecture of two different strains of Artemisia annua reveals the alterations in interaction and gene expression. PLANTA 2023; 258:74. [PMID: 37668722 DOI: 10.1007/s00425-023-04223-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 08/02/2023] [Indexed: 09/06/2023]
Abstract
MAIN CONCLUSION The hierarchical architecture of chromatins affects the gene expression level of glandular secreting trichomes and the artemisinin biosynthetic pathway-related genes, consequently bringing on huge differences in the content of artemisinin and its derivatives of A. annua. The plant of traditional Chinese medicine "Qinghao" is called Artemisia annua L. in Chinese Pharmacopoeia. High content and the total amount of artemisinin is the main goal of A. annua breeding, nevertheless, the change of chromatin organization during the artemisinin synthesis process has not been discovered yet. This study intended to find the roles of chromatin structure in the production of artemisinin through bioinformatics and experimental validation. Chromosome conformation capture analysis was used to scrutinize the interactions among chromosomes and categorize various scales of chromatin during artemisinin synthesis in A. annua. To confirm the effect of the changes in chromatin structure, Hi-C and RNA-sequencing were performed on two different strains to find the correlation between chromatin structure and gene expression levels on artemisinin synthesis progress and regulation. Our results revealed that the frequency of intra-chromosomal interactions was higher in the inter-chromosomal interactions between the root and leaves on a high artemisinin production strain (HAP) compared to a low artemisinin production strain (LAP). We found that compartmental transition was connected with interactions among different chromatins. Interestingly, glandular secreting trichomes (GSTs) and the artemisinin biosynthetic pathway (ABP) related genes were enriched in the areas which have the compartmental transition, reflecting the regulation of artemisinin synthesis. Topologically associated domain boundaries were associated with various distributions of genes and expression levels. Genes associated with ABP and GST in the adjacent loop were highly expressed, suggesting that epigenetic regulation plays an important role during artemisinin synthesis and glandular secreting trichomes production process. Chromatin structure could show an important status in the mechanisms of artemisinin synthesis process in A. annua.
Collapse
Affiliation(s)
- Xuejiao Liao
- Pharmacy College, Shandong University of Traditional Chinese Medicine, Jinan, 250355, China
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Shuai Guo
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Baosheng Liao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Xiaofeng Shen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Wenrui He
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Ying Meng
- Pharmacy College, Shandong University of Traditional Chinese Medicine, Jinan, 250355, China
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Conglian Liang
- Pharmacy College, Shandong University of Traditional Chinese Medicine, Jinan, 250355, China
| | - Jin Pei
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Jiushi Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing, 100193, China
| | - Yongqing Zhang
- Pharmacy College, Shandong University of Traditional Chinese Medicine, Jinan, 250355, China.
| | - Jiang Xu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Shilin Chen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
| |
Collapse
|
15
|
Lane AN, Nash PD, Ellsworth SA, Nystrom GS, Rokyta DR. The arylsulfatase- and phospholipase-rich venom of the plutoniumid centipede Theatops posticus. Toxicon 2023; 233:107231. [PMID: 37517595 DOI: 10.1016/j.toxicon.2023.107231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 08/01/2023]
Abstract
Research on centipede venoms has led to the discovery of a diverse array of novel proteins and peptides, including those with homology to previously discovered toxin families (e.g., phospholipase A2s and pM12a metalloproteases) and novel toxin families not previously detected in venoms (e.g., β-pore forming toxins and scoloptoxins). Most of this research has focused on centipedes in the order Scolopendromorpha, particularly those in the families Scolopendridae, Cryptopidae, and Scolopocryptopidae. To generate the first high-throughput venom characterization for a centipede in the scolopendromorph family Plutoniumidae, we performed venom-gland transcriptomics and venom proteomics on two Theatops posticus. We identified a total of 64 venom toxins, 60 of which were detected in both the venom-gland transcriptome and venom proteome and four of which were only detected transcriptomically. We detected a single highly abundant arylsulfatase B (ARSB) toxin, the first ARSB toxin identified from centipede venoms. As ARSBs have been detected in other venomous species (e.g., scorpions), ARSBs in T. posticus highlights a new case of convergent evolution across venoms. Theatops posticus venom also contained a much higher abundance and diversity of phospholipase A2 toxins compared to other characterized centipede venoms. Conversely, we detected other common centipedes toxins, such as CAPs and scoloptoxins, at relatively low abundances and diversities. Our observation of a diverse set of toxins from T. posticus venom, including those from novel toxin families, emphasizes the importance of studying unexplored centipede taxonomic groups and the continued potential of centipede venoms for novel toxin discovery and unraveling the molecular mechanisms underlying trait evolution.
Collapse
Affiliation(s)
- Aaliyah N Lane
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA
| | - Pauline D Nash
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA
| | - Schyler A Ellsworth
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA
| | - Gunnar S Nystrom
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA
| | - Darin R Rokyta
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA.
| |
Collapse
|
16
|
Srodawa K, Cerda PA, Davis Rabosky AR, Crowe-Riddell JM. Evolution of Three-Finger Toxin Genes in Neotropical Colubrine Snakes (Colubridae). Toxins (Basel) 2023; 15:523. [PMID: 37755949 PMCID: PMC10534312 DOI: 10.3390/toxins15090523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 08/16/2023] [Accepted: 08/23/2023] [Indexed: 09/28/2023] Open
Abstract
Snake venom research has historically focused on front-fanged species (Viperidae and Elapidae), limiting our knowledge of venom evolution in rear-fanged snakes across their ecologically diverse phylogeny. Three-finger toxins (3FTxs) are a known neurotoxic component in the venoms of some rear-fanged snakes (Colubridae: Colubrinae), but it is unclear how prevalent 3FTxs are both in expression within venom glands and more broadly among colubrine species. Here, we used a transcriptomic approach to characterize the venom expression profiles of four species of colubrine snakes from the Neotropics that were dominated by 3FTx expression (in the genera Chironius, Oxybelis, Rhinobothryum, and Spilotes). By reconstructing the gene trees of 3FTxs, we found evidence of putative novel heterodimers in the sequences of Chironius multiventris and Oxybelis aeneus, revealing an instance of parallel evolution of this structural change in 3FTxs among rear-fanged colubrine snakes. We also found positive selection at sites within structural loops or "fingers" of 3FTxs, indicating these areas may be key binding sites that interact with prey target molecules. Overall, our results highlight the importance of exploring the venoms of understudied species in reconstructing the full evolutionary history of toxins across the tree of life.
Collapse
Affiliation(s)
- Kristy Srodawa
- Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA; (K.S.); (A.R.D.R.); (J.M.C.-R.)
- Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Peter A. Cerda
- Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA; (K.S.); (A.R.D.R.); (J.M.C.-R.)
- Museum of Zoology, University of Michigan, Ann Arbor, MI 48108, USA
| | - Alison R. Davis Rabosky
- Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA; (K.S.); (A.R.D.R.); (J.M.C.-R.)
- Museum of Zoology, University of Michigan, Ann Arbor, MI 48108, USA
| | - Jenna M. Crowe-Riddell
- Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA; (K.S.); (A.R.D.R.); (J.M.C.-R.)
- Museum of Zoology, University of Michigan, Ann Arbor, MI 48108, USA
- School of Agriculture, Biomedicine and Environment, La Trobe University, Melbourne, VIC 3086, Australia
| |
Collapse
|
17
|
Rosales-García RA, Rautsaw RM, Hofmann EP, Grünwald CI, Franz-Chavez H, Ahumada-Carrillo IT, Ramirez-Chaparro R, de la Torre-Loranca MA, Strickland JL, Mason AJ, Holding ML, Borja M, Castañeda-Gaytan G, Myers EA, Sasa M, Rokyta DR, Parkinson CL. Sequence Divergence in Venom Genes Within and Between Montane Pitviper (Viperidae: Crotalinae: Cerrophidion) Species is Driven by Mutation-Drift Equilibrium. J Mol Evol 2023; 91:514-535. [PMID: 37269364 PMCID: PMC10995822 DOI: 10.1007/s00239-023-10115-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 05/03/2023] [Indexed: 06/05/2023]
Abstract
Snake venom can vary both among and within species. While some groups of New World pitvipers-such as rattlesnakes-have been well studied, very little is known about the venom of montane pitvipers (Cerrophidion) found across the Mesoamerican highlands. Compared to most well-studied rattlesnakes, which are widely distributed, the isolated montane populations of Cerrophidion may facilitate unique evolutionary trajectories and venom differentiation. Here, we describe the venom gland transcriptomes for populations of C. petlalcalensis, C. tzotzilorum, and C. godmani from Mexico, and a single individual of C. sasai from Costa Rica. We explore gene expression variation in Cerrophidion and sequence evolution of toxins within C. godmani specifically. Cerrophidion venom gland transcriptomes are composed primarily of snake venom metalloproteinases, phospholipase A[Formula: see text]s (PLA[Formula: see text]s), and snake venom serine proteases. Cerrophidion petlalcalensis shows little intraspecific variation; however, C. godmani and C. tzotzilorum differ significantly between geographically isolated populations. Interestingly, intraspecific variation was mostly attributed to expression variation as we did not detect signals of selection within C. godmani toxins. Additionally, we found PLA[Formula: see text]-like myotoxins in all species except C. petlalcalensis, and crotoxin-like PLA[Formula: see text]s in the southern population of C. godmani. Our results demonstrate significant intraspecific venom variation within C. godmani and C. tzotzilorum. The toxins of C. godmani show little evidence of directional selection where variation in toxin sequence is consistent with evolution under a model of mutation-drift equilibrium. Cerrophidion godmani individuals from the southern population may exhibit neurotoxic venom activity given the presence of crotoxin-like PLA[Formula: see text]s; however, further research is required to confirm this hypothesis.
Collapse
Affiliation(s)
| | - Rhett M Rautsaw
- Department of Biological Sciences, Clemson University, 190 Collings St., Clemson, SC, 29634, USA
| | - Erich P Hofmann
- Department of Biological Sciences, Clemson University, 190 Collings St., Clemson, SC, 29634, USA
- Science Department, Cape Fear Community College, Wilmington, NC, 28401, USA
| | | | - Hector Franz-Chavez
- Herp.mx A.C., Colima, Mexico
- Biodiversa A. C., Chapala, Jalisco, 45900, Mexico
| | | | | | | | - Jason L Strickland
- Department of Biological Sciences, Clemson University, 190 Collings St., Clemson, SC, 29634, USA
- Department of Biology, University of South Alabama, Mobile, AL, 36688, USA
| | - Andrew J Mason
- Department of Biological Sciences, Clemson University, 190 Collings St., Clemson, SC, 29634, USA
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH, 43210, USA
| | - Matthew L Holding
- Department of Biological Sciences, Clemson University, 190 Collings St., Clemson, SC, 29634, USA
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Miguel Borja
- Facultad de Ciencias Biológicas, Universdad Juárez del Estado de Durango, Gómez Palacio, Durango, 35010, Mexico
| | - Gamaliel Castañeda-Gaytan
- Facultad de Ciencias Biológicas, Universdad Juárez del Estado de Durango, Gómez Palacio, Durango, 35010, Mexico
| | - Edward A Myers
- Department of Biological Sciences, Clemson University, 190 Collings St., Clemson, SC, 29634, USA
| | - Mahmood Sasa
- Centro Investigaciones en Biodiversidad y Ecología Tropical and Instituto Clodomiro Picado, Universidad de Costa Rica, San José, Costa Rica
| | - Darin R Rokyta
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA
| | - Christopher L Parkinson
- Department of Biological Sciences, Clemson University, 190 Collings St., Clemson, SC, 29634, USA.
| |
Collapse
|
18
|
Tioyama EC, Bayona-Serrano JD, Portes-Junior JA, Nachtigall PG, de Souza VC, Beraldo-Neto E, Grazziotin FG, Junqueira-de-Azevedo ILM, Moura-da-Silva AM, Freitas-de-Sousa LA. The Venom Composition of the Snake Tribe Philodryadini: 'Omic' Techniques Reveal Intergeneric Variability among South American Racers. Toxins (Basel) 2023; 15:415. [PMID: 37505684 PMCID: PMC10467154 DOI: 10.3390/toxins15070415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 05/31/2023] [Accepted: 06/03/2023] [Indexed: 07/29/2023] Open
Abstract
Snakes of the Philodryadini tribe are included in the Dipsadidae family, which is a diverse group of rear-fanged snakes widespread in different ecological conditions, including habitats and diet. However, little is known about the composition and effects of their venoms despite their relevance for understanding the evolution of these snakes or even their impact on the occasional cases of human envenoming. In this study, we integrated venom gland transcriptomics, venom proteomics and functional assays to characterize the venoms from eight species of the Philodryadini tribe, which includes the genus Philodryas, Chlorosoma and Xenoxybelis. The most abundant components identified in the venoms were snake venom metalloproteinases (SVMPs), cysteine-rich secretory proteins (CRISPs), C-type lectins (CTLs), snake endogenous matrix metalloproteinases type 9 (seMMP-9) and snake venom serinoproteinases (SVSPs). These protein families showed a variable expression profile in each genus. SVMPs were the most abundant components in Philodryas, while seMMP-9 and CRISPs were the most expressed in Chlorosoma and Xenoxybelis, respectively. Lineage-specific differences in venom composition were also observed among Philodryas species, whereas P. olfersii presented the highest amount of SVSPs and P. agassizii was the only species to express significant amounts of 3FTx. The variability observed in venom composition was confirmed by the venom functional assays. Philodryas species presented the highest SVMP activity, whereas Chlorosoma species showed higher levels of gelatin activity, which may correlate to the seMMP-9 enzymes. The variability observed in the composition of these venoms may be related to the tribe phylogeny and influenced by their diets. In the presented study, we expanded the set of venomics studies of the Philodryadini tribe, which paves new roads for further studies on the evolution and ecology of Dipsadidae snakes.
Collapse
Affiliation(s)
- Emilly Campos Tioyama
- Programa de Pós-Graduação em Ciências-Toxinologia, Escola Superior do Instituto Butantan, São Paulo 05508-210, Brazil; (E.C.T.); (J.D.B.-S.)
- Laboratório de Imunopatologia, Instituto Butantan, São Paulo 05503-900, Brazil; (J.A.P.-J.); (A.M.M.-d.-S.)
| | - Juan David Bayona-Serrano
- Programa de Pós-Graduação em Ciências-Toxinologia, Escola Superior do Instituto Butantan, São Paulo 05508-210, Brazil; (E.C.T.); (J.D.B.-S.)
- Laboratório de Toxinologia Aplicada, Instituto Butantan, São Paulo 05503-900, Brazil; (P.G.N.); (V.C.d.S.); (I.L.M.J.-d.-A.)
| | - José A. Portes-Junior
- Laboratório de Imunopatologia, Instituto Butantan, São Paulo 05503-900, Brazil; (J.A.P.-J.); (A.M.M.-d.-S.)
| | - Pedro Gabriel Nachtigall
- Laboratório de Toxinologia Aplicada, Instituto Butantan, São Paulo 05503-900, Brazil; (P.G.N.); (V.C.d.S.); (I.L.M.J.-d.-A.)
| | - Vinicius Carius de Souza
- Laboratório de Toxinologia Aplicada, Instituto Butantan, São Paulo 05503-900, Brazil; (P.G.N.); (V.C.d.S.); (I.L.M.J.-d.-A.)
| | - Emidio Beraldo-Neto
- Laboratório de Bioquímica e Biofísica, Instituto Butantan, São Paulo 05503-900, Brazil;
| | | | | | - Ana Maria Moura-da-Silva
- Laboratório de Imunopatologia, Instituto Butantan, São Paulo 05503-900, Brazil; (J.A.P.-J.); (A.M.M.-d.-S.)
| | | |
Collapse
|
19
|
Heptinstall TC, Strickland JL, Rosales-Garcia RA, Rautsaw RM, Simpson CL, Nystrom GS, Ellsworth SA, Hogan MP, Borja M, Fernandes Campos P, Grazziotin FG, Rokyta DR, Junqueira-de-Azevedo ILM, Parkinson CL. Venom phenotype conservation suggests integrated specialization in a lizard-eating snake. Toxicon 2023; 229:107135. [PMID: 37146732 PMCID: PMC11000244 DOI: 10.1016/j.toxicon.2023.107135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 04/18/2023] [Accepted: 04/24/2023] [Indexed: 05/07/2023]
Abstract
Biological specialization reduces the size of niche space while increasing efficiency in the use of available resources. Specialization often leads to phenotypic changes via natural selection aligning with niche space constraints. Commonly observed changes are in size, shape, behavior, and traits associated with feeding. One often selected trait for dietary specialization is venom, which, in snakes, often shows variation dependent on diet across and within species. The Neotropical Blunt-headed Treesnake (Imantodes cenchoa) is a highly specialized, rear-fanged, arboreal, lizard hunter that displays a long thin body, enlarged eyes, and a large Duvernoy's gland. However, toxin characterization of I. cenchoa has never been completed. Here, we use RNA-seq and mass spectrometry to assemble, annotate, and analyze the venom gland transcriptomes of four I. cenchoa from across their range. We find a lack of significant venom variation at the sequence and expression levels, suggesting venom conservation across the species. We propose this conservation provides evidence of a specialized venom repertoire, adapted to maximize efficiency of capturing and processing lizards. Importantly, this study provides the most complete venom gland transcriptomes of I. cenchoa and evidence of venom specialization in a rear-fanged snake, giving insight into selective pressures of venom across all snake species.
Collapse
Affiliation(s)
| | - Jason L Strickland
- Department of Biological Sciences, Clemson University, Clemson, SC, 29634, USA; Department of Biology, University of South Alabama, Mobile, AL, 36688, USA
| | | | - Rhett M Rautsaw
- Department of Biological Sciences, Clemson University, Clemson, SC, 29634, USA; School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA; Department of Integrative Biology, University of South Florida, Tampa, FL, 33620, USA
| | - Cassandra L Simpson
- Department of Biological Sciences, Clemson University, Clemson, SC, 29634, USA
| | - Gunnar S Nystrom
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA
| | - Schyler A Ellsworth
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA
| | - Michael P Hogan
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA
| | - Miguel Borja
- Facultad de Ciencias Biológicas, Universdad Juárez del Estado de Durango, Av. Universidad s/n. Fracc. Filadelfia, C.P. 35070, Gómez Palacio, Dgo., Mexico
| | | | - Felipe G Grazziotin
- Laboratório Especial de Colecões Zoológicas, Instituto Butantan, São Paulo, São Paulo, Brazil
| | - Darin R Rokyta
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA
| | | | - Christopher L Parkinson
- Department of Biological Sciences, Clemson University, Clemson, SC, 29634, USA; Department of Forestry and Environmental Conservation, Clemson University, Clemson, SC, 29634, USA.
| |
Collapse
|
20
|
Everson KM, Donohue ME, Weisrock DW. A Pervasive History of Gene Flow in Madagascar's True Lemurs (Genus Eulemur). Genes (Basel) 2023; 14:1130. [PMID: 37372308 DOI: 10.3390/genes14061130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/16/2023] [Accepted: 05/19/2023] [Indexed: 06/29/2023] Open
Abstract
In recent years, it has become widely accepted that interspecific gene flow is common across the Tree of Life. Questions remain about how species boundaries can be maintained in the face of high levels of gene flow and how phylogeneticists should account for reticulation in their analyses. The true lemurs of Madagascar (genus Eulemur, 12 species) provide a unique opportunity to explore these questions, as they form a recent radiation with at least five active hybrid zones. Here, we present new analyses of a mitochondrial dataset with hundreds of individuals in the genus Eulemur, as well as a nuclear dataset containing hundreds of genetic loci for a small number of individuals. Traditional coalescent-based phylogenetic analyses of both datasets reveal that not all recognized species are monophyletic. Using network-based approaches, we also find that a species tree containing between one and three ancient reticulations is supported by strong evidence. Together, these results suggest that hybridization has been a prominent feature of the genus Eulemur in both the past and present. We also recommend that greater taxonomic attention should be paid to this group so that geographic boundaries and conservation priorities can be better established.
Collapse
Affiliation(s)
- Kathryn M Everson
- Department of Integrative Biology, Oregon State University, Corvallis, OR 97331, USA
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA
| | - Mariah E Donohue
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA
| | - David W Weisrock
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA
| |
Collapse
|
21
|
Mossop KD, Lemmon AR, Moriarty Lemmon E, Eytan R, Adams M, Unmack PJ, Smith Date K, Morales HE, Hammer MP, Wong BBM, Chapple DG. Phylogenomics and biogeography of arid-adapted Chlamydogobius goby fishes. Mol Phylogenet Evol 2023; 182:107757. [PMID: 36925090 DOI: 10.1016/j.ympev.2023.107757] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 02/01/2023] [Accepted: 03/07/2023] [Indexed: 03/17/2023]
Abstract
The progressive aridification of the Australian continent from ∼ 20 million years ago posed severe challenges for the persistence of its resident biota. A key question involves the role of refugial habitats - specifically, their ability to mediate the effects of habitat loss and fragmentation, and their potential to shape opportunities for allopatric speciation. With freshwater species, for example, the patchiness, or absence, of water will constrain distributions. However, aridity may not necessarily isolate populations if disjunct refugia experience frequent hydrological connections. To investigate this potential dichotomy, we explored the evolutionary history of the Chlamydogobius gobies (Gobiiformes: Gobiidae), an arid-adapted genus of six small, benthic fish species that exploit all types of waterbodies (i.e. desert springs, waterholes and bore-fed wetlands, coastal estuarine creeks and mangroves) across parts of central and northern Australia. We used Anchored Phylogenomics to generate a highly resolved phylogeny of the group from sequence data for 260 nuclear loci. Buttressed by companion allozyme and mtDNA datasets, our molecular findings infer the diversification of Chlamydogobius in arid Australia, and provide a phylogenetic structure that cannot be simply explained by invoking allopatric speciation events reflecting current geographic proximity. Our findings are generally consistent with the existing morphological delimitation of species, with one exception: at the shallowest nodes of phylogenetic reconstruction, the molecular data do not fully support the current dichotomous delineation of C. japalpa from C. eremius in Kati Thanda-Lake Eyre-associated waterbodies. Together these findings illustrate the ability of structural (hydrological) connections to generate patterns of connectivity and isolation for an ecologically moderate disperser in response to ongoing habitat aridification. Finally, we explore the implications of these results for the immediate management of threatened (C. gloveri) and critically endangered (C. micropterus, C. squamigenus) congeners.
Collapse
Affiliation(s)
- Krystina D Mossop
- School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, FL, USA
| | | | - Ron Eytan
- Marine Biology Department, Texas A&M University at Galveston, Galveston, TX 77554, USA; Peabody Museum of Natural History, Yale University, New Haven, CT, USA
| | - Mark Adams
- Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, SA 5000, Australia; School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Peter J Unmack
- School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia; Centre for Applied Water Science, Institute for Applied Ecology, University of Canberra, ACT 2617, Australia
| | - Katie Smith Date
- School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia; Museum Victoria, Sciences Department, GPO Box 666, Melbourne, VIC 3001, Australia
| | - Hernán E Morales
- School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia; Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Michael P Hammer
- Natural Sciences, Museum and Art Gallery of the Northern Territory, Darwin, NT 0801, Australia
| | - Bob B M Wong
- School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia
| | - David G Chapple
- School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia.
| |
Collapse
|
22
|
Benítez-Villaseñor A, Granados Mendoza C, Wanke S, Peñafiel Cevallos M, Freire ME, Lemmon EM, Lemmon AR, Magallón S. The use of Anchored Hybrid Enrichment data to resolve higher-level phylogenetic relationships: A proof-of-concept applied to Asterales (Eudicotyledoneae; Angiosperms). Mol Phylogenet Evol 2023; 181:107714. [PMID: 36708940 DOI: 10.1016/j.ympev.2023.107714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 10/28/2022] [Accepted: 01/18/2023] [Indexed: 01/26/2023]
Abstract
Anchored Hybrid Enrichment (AHE) is a tool for capturing orthologous regions of the nuclear genome shared in low or single copy across lineages. Despite the increasing number of studies using this method, its usefulness to estimate relationships at deeper taxonomic levels in plants has not been fully explored. Here we present a proof of concept about the performance of nuclear loci obtained with AHE to infer phylogenetic relationships and explore the use of gene sampling schemes to estimate divergence times in Asterales. We recovered low-copy nuclear loci using the AHE method from herbarium material and silica-preserved samples. Maximum likelihood, Bayesian inference, and coalescence approaches were used to reconstruct phylogenomic relationships. Dating analyses were conducted under a multispecies coalescent approach by jointly inferring species tree and divergence times with random gene sampling schemes and multiple calibrations. We recovered 403 low-copy nuclear loci for 63 species representing nine out of eleven families of Asterales. Phylogenetic hypotheses were congruent among the applied methods and previously published results. Analyses with concatenated datasets were strongly supported, but coalescence-based analyses showed low support for the phylogenetic position of families Argophyllaceae and Alseuosmiaceae. Estimated family ages were congruent among gene sampling schemes, with the mean age for Asterales around 130 Myr. Our study documents the usefulness of AHE for resolving phylogenetic relationships at deep phylogenetic levels in Asterales. Observed phylogenetic inconsistencies were possibly due to the non-inclusion of families Phellinceae and Pentaphragmataceae. Random gene sampling schemes produced consistent age estimates with coalescence and species tree relaxed clock approaches.
Collapse
Affiliation(s)
- Adriana Benítez-Villaseñor
- Posgrado en Ciencias Biológicas, Instituto de Biología, Universidad Nacional Autónoma de México, A. P. 70-153, C.P.04510 Ciudad de México, Mexico.
| | - Carolina Granados Mendoza
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, 3er Circuito de Ciudad Universitaria, Coyoacán, Mexico City 04510, Mexico; Institut für Botanik, Technische Universität Dresden, Zellescher Weg 20, 01217 Dresden, Germany.
| | - Stefan Wanke
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, 3er Circuito de Ciudad Universitaria, Coyoacán, Mexico City 04510, Mexico; Institut für Botanik, Technische Universität Dresden, Zellescher Weg 20, 01217 Dresden, Germany.
| | - Marcia Peñafiel Cevallos
- Herbario Nacional del Ecuador (QCNE), Instituto Nacional de Biodiversidad, Quito 170135, Ecuador.
| | - M Efraín Freire
- Herbario Nacional del Ecuador (QCNE), Instituto Nacional de Biodiversidad, Quito 170135, Ecuador.
| | - Emily Moriarty Lemmon
- Department of Biology, Florida State University 319 Stadium Drive, P.O. Box 3064295, Tallahassee, FL 32306-4295, United States.
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University 400 Dirac Science Library, Tallahassee, FL 32306-4120, United States.
| | - Susana Magallón
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, 3er Circuito de Ciudad Universitaria, Coyoacán, Mexico City 04510, Mexico.
| |
Collapse
|
23
|
Nystrom GS, Ellsworth SA, Rokyta DR. The remarkably enzyme-rich venom of the Big Bend Scorpion (Diplocentrus whitei). Toxicon 2023; 226:107080. [PMID: 36907567 DOI: 10.1016/j.toxicon.2023.107080] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/06/2023] [Accepted: 03/07/2023] [Indexed: 03/12/2023]
Abstract
Scorpion venoms have long been studied for their peptide discovery potential, with modern high-throughput venom-characterization techniques paving the way for the discovery of thousands of novel putative toxins. Research into these toxins has provided insight into the pathology and treatment of human diseases, even resulting in the development of one compound with Food and Drug Administration (FDA) approval. Although most of this research has focused on the toxins of scorpion species considered medically significant to humans, the venom of harmless scorpion species possess toxins that are homologous to those from medically significant species, indicating that harmless scorpion venoms may also serve as valuable sources of novel peptide variants. Furthermore, as harmless scorpions represent a vast majority of scorpion species diversity, and therefore venom toxin diversity, venoms from these species likely contain entirely new toxin classes. We sequenced the venom-gland transcriptome and venom proteome of two male Big Bend scorpions (Diplocentrus whitei), providing the first high-throughput venom characterization for a member of this genus. We identified a total of 82 toxins in the venom of D. whitei, 25 of which were identified in both the transcriptome and proteome, and 57 of which were only identified in the transcriptome. Furthermore, we identified a unique, enzyme-rich venom dominated by serine proteases and the first arylsulfatase B toxins identified in scorpions.
Collapse
Affiliation(s)
- Gunnar S Nystrom
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA
| | - Schyler A Ellsworth
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA
| | - Darin R Rokyta
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA.
| |
Collapse
|
24
|
Effects of select tannin-free grain sorghum varieties on the performance, carcass traits, intestinal morphology, and gene expression of jejunal mucosa of broiler chickens. APPLIED ANIMAL SCIENCE 2022. [DOI: 10.15232/aas.2022-02329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
25
|
Delgado A, Benedict C, Macrander J, Daly M. Never, Ever Make an Enemy… Out of an Anemone: Transcriptomic Comparison of Clownfish Hosting Sea Anemone Venoms. Mar Drugs 2022; 20:md20120730. [PMID: 36547877 PMCID: PMC9782873 DOI: 10.3390/md20120730] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/15/2022] [Accepted: 11/21/2022] [Indexed: 11/24/2022] Open
Abstract
Sea anemones are predatory marine invertebrates and have diverse venom arsenals. Venom is integral to their biology, and is used in competition, defense, and feeding. Three lineages of sea anemones are known to have independently evolved symbiotic relationships with clownfish, however the evolutionary impact of this relationship on the venom composition of the host is still unknown. Here, we investigate the potential of this symbiotic relationship to shape the venom profiles of the sea anemones that host clownfish. We use transcriptomic data to identify differences and similarities in venom profiles of six sea anemone species, representing the three known clades of clownfish-hosting sea anemones. We recovered 1121 transcripts matching verified toxins across all species, and show that hemolytic and hemorrhagic toxins are consistently the most dominant and diverse toxins across all species examined. These results are consistent with the known biology of sea anemones, provide foundational data on venom diversity of these species, and allow for a review of existing hierarchical structures in venomic studies.
Collapse
Affiliation(s)
- Alonso Delgado
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH 43210, USA
- Correspondence:
| | - Charlotte Benedict
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Jason Macrander
- Department of Biology, Florida Southern College, Lakeland, FL 33815, USA
| | - Marymegan Daly
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH 43210, USA
| |
Collapse
|
26
|
Gonçalves-Machado L, Verçoza BRF, Nogueira FCS, Melani RD, Domont GB, Rodrigues SP, Rodrigues JCF, Zingali RB. Extracellular Vesicles from Bothrops jararaca Venom Are Diverse in Structure and Protein Composition and Interact with Mammalian Cells. Toxins (Basel) 2022; 14:toxins14110806. [PMID: 36422980 PMCID: PMC9698812 DOI: 10.3390/toxins14110806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/14/2022] [Accepted: 11/17/2022] [Indexed: 11/22/2022] Open
Abstract
Snake venoms are complex cocktails of non-toxic and toxic molecules that work synergistically for the envenoming outcome. Alongside the immediate consequences, chronic manifestations and long-term sequelae can occur. Recently, extracellular vesicles (EVs) were found in snake venom. EVs mediate cellular communication through long distances, delivering proteins and nucleic acids that modulate the recipient cell's function. However, the biological roles of snake venom EVs, including possible cross-organism communication, are still unknown. This knowledge may expand the understanding of envenoming mechanisms. In the present study, we isolated and characterized the EVs from Bothrops jararaca venom (Bj-EVs), giving insights into their biological roles. Fresh venom was submitted to differential centrifugation, resulting in two EV populations with typical morphology and size range. Several conserved EV markers and a subset of venom related EV markers, represented mainly by processing enzymes, were identified by proteomic analysis. The most abundant protein family observed in Bj-EVs was 5'-nucleotidase, known to be immunosuppressive and a low abundant and ubiquitous toxin in snake venoms. Additionally, we demonstrated that mammalian cells efficiently internalize Bj-EVs. The commercial antibothropic antivenom partially recognizes Bj-EVs and inhibits cellular EV uptake. Based on the proteomic results and the in vitro interaction assays using macrophages and muscle cells, we propose that Bj-EVs may be involved not only in venom production and processing but also in host immune modulation and long-term effects of envenoming.
Collapse
Affiliation(s)
- Larissa Gonçalves-Machado
- Laboratório de Hemostase e Venenos, Instituto de Bioquímica Médica Leopoldo de Meis (IBqM), Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem (Inbeb), Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
- Instituto Vital Brazil, Gerência de Desenvolvimento Tecnológico, Niterói 24230-410, Brazil
| | - Brunno Renato Farias Verçoza
- Núcleo Multidisciplinar de Pesquisa em Biologia (NUMPEX-Bio), Universidade Federal do Rio de Janeiro, Campus UFRJ Duque de Caxias, Duque de Caxias, Rio de Janeiro 25240-005, Brazil
| | - Fábio César Sousa Nogueira
- Laboratório de Química de Proteínas, Unidade Proteômica, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-909, Brazil
- Laboratório de Proteômica (LabProt)—LADETEC, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-598, Brazil
| | - Rafael Donadélli Melani
- Laboratório de Química de Proteínas, Unidade Proteômica, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-909, Brazil
| | - Gilberto Barbosa Domont
- Laboratório de Química de Proteínas, Unidade Proteômica, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-909, Brazil
| | - Silas Pessini Rodrigues
- Núcleo Multidisciplinar de Pesquisa em Biologia (NUMPEX-Bio), Universidade Federal do Rio de Janeiro, Campus UFRJ Duque de Caxias, Duque de Caxias, Rio de Janeiro 25240-005, Brazil
| | - Juliany Cola Fernandes Rodrigues
- Núcleo Multidisciplinar de Pesquisa em Biologia (NUMPEX-Bio), Universidade Federal do Rio de Janeiro, Campus UFRJ Duque de Caxias, Duque de Caxias, Rio de Janeiro 25240-005, Brazil
| | - Russolina Benedeta Zingali
- Laboratório de Hemostase e Venenos, Instituto de Bioquímica Médica Leopoldo de Meis (IBqM), Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem (Inbeb), Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
- Correspondence: ; Tel.: +55-2139386782
| |
Collapse
|
27
|
Moritz A, Lumpkins B, Mathis G, Bridges W, Wilson S, Blair M, Buresh R, Strickland J, Arguelles-Ramos M. Comparative efficacy of tannin-free grain sorghum varieties for the control of necrotic enteritis caused by Clostridium perfringens in broiler chickens. Poult Sci 2022; 102:102300. [PMID: 36502566 PMCID: PMC9763862 DOI: 10.1016/j.psj.2022.102300] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 10/13/2022] [Accepted: 10/15/2022] [Indexed: 11/09/2022] Open
Abstract
A 28-day battery cage study was conducted to test the efficacy of tannin-free grain sorghum varieties fed to Cobb 500 male broiler chickens (n = 512) and challenged with Eimeria maxima (EM) and Clostridium perfringens (CP). Birds were fed 1 of 8 treatments (corn, red/bronze, white/tan, or U.S. No. 2 sorghum) and were grouped by challenge method (challenged with EM/CP or unchallenged). On d 14, birds in the challenge group were orally inoculated with ∼5,000 oocysts of EM, and on d 19, 20, and 21, birds were given a broth culture of CP with ∼108 CFU/mL once daily. On d 21, three birds were scored for the degree/presence of necrotic enteritis (NE) lesions. Birds and feed were group weighed (d 0, 14, 21, and 28) to calculate average feed intake (FI), body weight gain (BWG), and adjusted feed conversion ratio (AdjFCR). Intestinal integrity was assessed through histological analysis of intestinal tissues, and change in transcriptome was determined using mRNA-sequencing on intestinal mucosa. Relative concentrations of secondary metabolites in grain sorghum were determined by LC-MS/MS analysis. Data were analyzed as a 2-way ANOVA with factors of treatment, challenge and their interaction. Regardless of challenge from 14 to 21 d, birds on the corn, white/tan, and U.S. No. 2 treatments were more efficient than those fed red/bronze treatment (P = 0.0026). From 14 to 28 d, BWG was significantly higher for the white/tan treatment (P = 0.024) compared to the red/bronze treatment. At 21 d, a significant interaction was observed for lesion score (P = 0.0001) in which, challenged birds fed red/bronze and white/tan treatments had reduced intestinal lesions compared to U.S. No. 2 and corn treatments. No differences among treatments were observed in jejunum morphology, but differential expression analysis showed an upregulation in defense response to bacteria and biotic stress in the challenged red/bronze treatment compared to the challenged corn. This study demonstrated improved gut health and minimal impact on growth and efficiency of broilers fed select grain sorghum varieties when challenged with EM/CP.
Collapse
Affiliation(s)
- A.H. Moritz
- Department of Animal and Veterinary Science, Clemson University, Clemson, SC 29634, USA,Corresponding author:
| | - B. Lumpkins
- Southern Poultry Feed and Research, Inc., Athens, GA 30607, USA
| | - G.F. Mathis
- Southern Poultry Feed and Research, Inc., Athens, GA 30607, USA
| | - W.C. Bridges
- Department of Mathematical and Statistical Sciences, Clemson University, Clemson, SC 29634, USA
| | - S. Wilson
- Clemson University Genomics and Bioinformatics Facility, Clemson University, Clemson, SC 29634, USA
| | - M.E. Blair
- United Animal Health, Sheridan, IN 46069, USA
| | - R.E. Buresh
- Novus International, Inc., St. Charles, MO 63304, USA
| | - J.R. Strickland
- Department of Animal and Veterinary Science, Clemson University, Clemson, SC 29634, USA
| | - M. Arguelles-Ramos
- Department of Animal and Veterinary Science, Clemson University, Clemson, SC 29634, USA
| |
Collapse
|
28
|
Bibliometric Analysis of Literature in Snake Venom-Related Research Worldwide (1933–2022). Animals (Basel) 2022; 12:ani12162058. [PMID: 36009648 PMCID: PMC9405337 DOI: 10.3390/ani12162058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/03/2022] [Accepted: 08/09/2022] [Indexed: 11/29/2022] Open
Abstract
Simple Summary Around the world, snake envenomation poses a serious health risk. Proteins with pharmacological effects are present in snake venom. Recent studies elaborate snake venom and its potential application, including as a cancer drug and antibacterial substances. Our study aimed to analyze the global profile of the literature in snake venom research from documents indexed in the Scopus database between 1933 and 2022. In total, 2999 documents were published with Brazil showing the highest productivity. Antivenom, proteomics, and transcriptomics are emerging as hot topics on a global scale. The present study offers a distinctive overview of snake venom research conducted worldwide. Abstract Snake envenomation is a severe economic and health concern affecting countries worldwide. Snake venom carries a wide variety of small peptides and proteins with various immunological and pharmacological properties. A few key research areas related to snake venom, including its applications in treating cancer and eradicating antibiotic-resistant bacteria, have been gaining significant attention in recent years. The goal of the current study was to analyze the global profile of literature in snake venom research. This study presents a bibliometric review of snake venom-related research documents indexed in the Scopus database between 1933 and 2022. The overall number of documents published on a global scale was 2999, with an average annual production of 34 documents. Brazil produced the highest number of documents (n = 729), followed by the United States (n = 548), Australia (n = 240), and Costa Rica (n = 235). Since 1963, the number of publications has been steadily increasing globally. At a worldwide level, antivenom, proteomics, and transcriptomics are growing hot issues for research in this field. The current research provides a unique overview of snake venom research at global level from 1933 through 2022, and it may be beneficial in guiding future research.
Collapse
|
29
|
A strong backbone for an invertebrate group: anchored phylogenomics improves the resolution of genus-level relationships within the Lumbricidae (Annelida, Crassiclitellata). ORG DIVERS EVOL 2022. [DOI: 10.1007/s13127-022-00570-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
|
30
|
Divergent Specialization of Simple Venom Gene Profiles among Rear-Fanged Snake Genera ( Helicops and Leptodeira, Dipsadinae, Colubridae). Toxins (Basel) 2022; 14:toxins14070489. [PMID: 35878227 PMCID: PMC9319703 DOI: 10.3390/toxins14070489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/11/2022] [Accepted: 07/12/2022] [Indexed: 01/27/2023] Open
Abstract
Many venomous animals express toxins that show extraordinary levels of variation both within and among species. In snakes, most studies of venom variation focus on front-fanged species in the families Viperidae and Elapidae, even though rear-fanged snakes in other families vary along the same ecological axes important to venom evolution. Here we characterized venom gland transcriptomes from 19 snakes across two dipsadine rear-fanged genera (Leptodeira and Helicops, Colubridae) and two front-fanged genera (Bothrops, Viperidae; Micrurus, Elapidae). We compared patterns of composition, variation, and diversity in venom transcripts within and among all four genera. Venom gland transcriptomes of rear-fanged Helicops and Leptodeira and front-fanged Micrurus are each dominated by expression of single toxin families (C-type lectins, snake venom metalloproteinase, and phospholipase A2, respectively), unlike highly diverse front-fanged Bothrops venoms. In addition, expression patterns of congeners are much more similar to each other than they are to species from other genera. These results illustrate the repeatability of simple venom profiles in rear-fanged snakes and the potential for relatively constrained venom composition within genera.
Collapse
|
31
|
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] [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.
Collapse
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.
| |
Collapse
|
32
|
Owen CL, Marshall DC, Wade EJ, Meister R, Goemans G, Kunte K, Moulds M, Hill K, Villet M, Pham TH, Kortyna M, Lemmon EM, Lemmon AR, Simon C. Detecting and removing sample contamination in phylogenomic data: an example and its implications for Cicadidae phylogeny (Insecta: Hemiptera). Syst Biol 2022; 71:1504-1523. [PMID: 35708660 DOI: 10.1093/sysbio/syac043] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 05/23/2022] [Accepted: 06/07/2022] [Indexed: 11/13/2022] Open
Abstract
Contamination of a genetic sample with DNA from one or more non-target species is a continuing concern of molecular phylogenetic studies, both Sanger sequencing studies and Next-Generation Sequencing (NGS) studies. We developed an automated pipeline for identifying and excluding likely cross-contaminated loci based on detection of bimodal distributions of patristic distances across gene trees. When the contamination occurs between samples within a dataset, comparisons between a contaminated sample and its contaminant taxon will yield bimodal distributions with one peak close to zero patristic distance. This new method does not rely on a priori knowledge of taxon relatedness nor does it determine the causes(s) of the contamination. Exclusion of putatively contaminated loci from a dataset generated for the insect family Cicadidae showed that these sequences were affecting some topological patterns and branch supports, although the effects were sometimes subtle, with some contamination-influenced relationships exhibiting strong bootstrap support. Long tip branches and outlier values for one anchored phylogenomic pipeline statistic (AvgNHomologs) were correlated with the presence of contamination. While the AHE markers used here, which target hemipteroid taxa, proved effective in resolving deep and shallow level Cicadidae relationships in aggregate, individual markers contained inadequate phylogenetic signal, in part probably due to short length. The cleaned dataset, consisting of 429 loci, from 90 genera representing 44 of 56 current Cicadidae tribes, supported three of the four sampled Cicadidae subfamilies in concatenated-matrix maximum likelihood (ML) and multispecies coalescent-based species tree analyses, with the fourth subfamily weakly supported in the ML trees. No well-supported patterns from previous family-level Sanger sequencing studies of Cicadidae phylogeny were contradicted. One taxon (Aragualna plenalinea) did not fall with its current subfamily in the genetic tree, and this genus and its tribe Aragualnini is reclassified to Tibicininae following morphological re-examination. Only subtle differences were observed in trees after removal of loci for which divergent base frequencies were detected. Greater success may be achieved by increased taxon sampling and developing a probe set targeting a more recent common ancestor and longer loci. Searches for contamination are an essential step in phylogenomic analyses of all kinds and our pipeline is an effective solution.
Collapse
Affiliation(s)
- Christopher L Owen
- Systematic Entomology Laboratory, USDA-ARS, c/o National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - David C Marshall
- Dept. of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Elizabeth J Wade
- Dept. of Natural Science and Mathematics, Curry College, Milton, MA 02186, USA
| | - Russ Meister
- Dept. of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Geert Goemans
- Dept. of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Krushnamegh Kunte
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bellary Road, Bangalore 560 065, India
| | - Max Moulds
- Australian Museum Research Institute, 1 William Street, Sydney N.S.W, Australia. 2010
| | - Kathy Hill
- Dept. of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - M Villet
- Dept. of Biology, Rhodes University, Grahamstown 6140, South Africa
| | - Thai-Hong Pham
- Mientrung Institute for Scientific Research, Vietnam Academy of Science and Technology, Hue, Vietnam.,Vietnam National Museum of Nature and Graduate School of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Michelle Kortyna
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, USA
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University 400 Dirac Science Library, Tallahassee, FL 32306, USA
| | - Chris Simon
- Dept. of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| |
Collapse
|
33
|
Myers EA, Strickland JL, Rautsaw RM, Mason AJ, Schramer TD, Nystrom GS, Hogan MP, Yooseph S, Rokyta DR, Parkinson CL. De Novo Genome Assembly Highlights the Role of Lineage-Specific Duplications in the Evolution of Venom in Fea’s Viper. Genome Biol Evol 2022; 14:6603630. [PMID: 35670514 PMCID: PMC9256536 DOI: 10.1093/gbe/evac082] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2022] [Indexed: 11/12/2022] Open
Abstract
Despite the medical significance to humans and important ecological roles filled by vipers, few high-quality genomic resources exist for these snakes outside of a few genera of pitvipers. Here we sequence, assemble, and annotate the genome of Fea’s Viper (Azemiops feae). This taxon is distributed in East Asia and belongs to a monotypic subfamily, sister to the pitvipers. The newly sequenced genome resulted in a 1.56 Gb assembly, a contig N50 of 1.59 Mb, with 97.6% of the genome assembly in contigs >50 Kb, and a BUSCO completeness of 92.4%. We found that A. feae venom is primarily composed of phospholipase A2 (PLA2) proteins expressed by genes that likely arose from lineage-specific PLA2 gene duplications. Additionally, we show that renin, an enzyme associated with blood pressure regulation in mammals and known from the venoms of two viper species including A. feae, is expressed in the venom gland at comparative levels to known toxins and is present in the venom proteome. The cooption of this gene as a toxin may be more widespread in viperids than currently known. To investigate the historical population demographics of A. feae, we performed coalescent-based analyses and determined that the effective population size has remained stable over the last 100 kyr. This suggests Quaternary glacial cycles likely had minimal influence on the demographic history of A. feae. This newly assembled genome will be an important resource for studying the genomic basis of phenotypic evolution and understanding the diversification of venom toxin gene families.
Collapse
Affiliation(s)
- Edward A. Myers
- Department of Biological Sciences, Clemson University , Clemson, SC 29634, USA
| | - Jason L. Strickland
- Department of Biological Sciences, Clemson University , Clemson, SC 29634, USA
- Department of Biology, University of South Alabama , Mobile, AL 36688, USA
| | - Rhett M. Rautsaw
- Department of Biological Sciences, Clemson University , Clemson, SC 29634, USA
| | - Andrew J. Mason
- Department of Biological Sciences, Clemson University , Clemson, SC 29634, USA
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University , Columbus, OH 43210, USA
| | - Tristan D. Schramer
- Department of Biological Sciences, Clemson University , Clemson, SC 29634, USA
| | - Gunnar S. Nystrom
- Department of Biological Science, Florida State University , Tallahassee, FL 32306, USA
| | - Michael P. Hogan
- Department of Biological Science, Florida State University , Tallahassee, FL 32306, USA
| | - Shibu Yooseph
- Department of Computer Science, Genomics and Bioinformatics Cluster, University of Central Florida, 4000 Central Florida Blvd , Orlando, FL, 32816, USA
| | - Darin R. Rokyta
- Department of Biological Science, Florida State University , Tallahassee, FL 32306, USA
| | - Christopher L. Parkinson
- Department of Biological Sciences, Clemson University , Clemson, SC 29634, USA
- Department of Forestry and Environmental Conservation, Clemson University , Clemson, SC 29634, USA
| |
Collapse
|
34
|
Isomoto A, Shoguchi E, Hisata K, Inoue J, Sun Y, Inaba K, Satoh N, Ogawa T, Shibata H. Active Expression of Genes for Protein Modification Enzymes in Habu Venom Glands. Toxins (Basel) 2022; 14:toxins14050300. [PMID: 35622547 PMCID: PMC9146206 DOI: 10.3390/toxins14050300] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 04/09/2022] [Accepted: 04/16/2022] [Indexed: 01/27/2023] Open
Abstract
Genes encoding snake venom toxins have been studied extensively. However, genes involved in the modification and functioning of venom proteins are little known. Protobothrops is a genus of pit vipers, which are venomous and inhabit the Nansei (Southwest) islands of Japan, Taiwan China, Vietnam, Thailand, Myanmar, Nepal, Bhutan, and India. Our previous study decoded the genome of Protobothrops flavoviridis, a species endemic to the Nansei Islands, Japan, and revealed unique evolutionary processes of some venom genes. In this study, we analyzed genes that are highly expressed in venom glands to survey genes for candidate enzymes or chaperone proteins involved in toxin folding and modification. We found that, in addition to genes that encode venom proteins and ribosomal proteins, genes that encode protein disulfide isomerase (PDI) family members (orthologs of human P4HB and PDIA3), Selenoprotein M (SELENOM), and Calreticulin (CALR) are highly expressed in venom glands. Since these enzymes or chaperones are involved in protein modification and potentially possess protein folding functions, we propose that P4HB, SELENOM, CALR, and PDIA3 encode candidate enzymes or chaperones to confer toxic functions upon the venom transcriptome.
Collapse
Affiliation(s)
- Akiko Isomoto
- Division of Genomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan;
- Department of Biological Chemistry, Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan
- Correspondence: (A.I.); (T.O.); (H.S.)
| | - Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science, Technology Graduate University, Onna 904-0495, Japan; (E.S.); (K.H.); (J.I.); (N.S.)
| | - Kanako Hisata
- Marine Genomics Unit, Okinawa Institute of Science, Technology Graduate University, Onna 904-0495, Japan; (E.S.); (K.H.); (J.I.); (N.S.)
| | - Jun Inoue
- Marine Genomics Unit, Okinawa Institute of Science, Technology Graduate University, Onna 904-0495, Japan; (E.S.); (K.H.); (J.I.); (N.S.)
| | - Yinrui Sun
- Division of Genomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan;
| | - Kenji Inaba
- Institute of Multidisciplinary Research for Advanced Material, Tohoku University, Sendai 980-8577, Japan;
- Department of Biomolecular Science, Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science, Technology Graduate University, Onna 904-0495, Japan; (E.S.); (K.H.); (J.I.); (N.S.)
| | - Tomohisa Ogawa
- Department of Biological Chemistry, Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Japan
- Correspondence: (A.I.); (T.O.); (H.S.)
| | - Hiroki Shibata
- Division of Genomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan;
- Correspondence: (A.I.); (T.O.); (H.S.)
| |
Collapse
|
35
|
Piller KR, Parker E, Lemmon AR, Moriarty Lemmon E. Investigating the utility of Anchored Hybrid Enrichment data to investigate the relationships among the Killifishes (Actinopterygii: Cyprinodontiformes), a globally distributed group of fishes. Mol Phylogenet Evol 2022; 173:107482. [PMID: 35452841 DOI: 10.1016/j.ympev.2022.107482] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 04/06/2022] [Accepted: 04/06/2022] [Indexed: 10/18/2022]
Abstract
The Killifishes (Cyprinodontiformes) are a diverse and well-known group of fishes that contains sixteen families inclusive of Anablepidae, Aphaniidae Aplocheilidae, Cubanichthyidae, Cyprinodontidae, Fluviphylacidae, Fundulidae, Goodeidae, Nothobranchiidae, Orestiidae, Pantanodontidae, Poeciliidae, Procatopodidae, Profundulidae, Rivulidae, and Valenciidae and more than 1,200 species that are globally distributed in tropical and temperate, freshwater and estuarine habitats. The evolutionary relationships among the families within the group, based on different molecular and morphological data sets, have remained uncertain. Therefore, the objective of this study was to use a targeted approach, anchored hybrid enrichment, to investigate the phylogenetic relationships among the families within the Cyprindontiformes. This study included more than 100 individuals, representing all sixteen families within the Cyprinodontiformes, including many recently diagnosed families. We recovered an average of 244 loci per individual. These data were submitted to phylogenetic analyses (RaxML and ASTRAL) and although we recovered many of the same relationships as in previous studies of the group, several novel sets of relationships for other families also were recovered. In addition, two well-established clades (Suborders Cyprinodontoidei and Aplocheilodei) were recovered as monophyletic and are in agreement with most previous studies. We also assessed the degree of gene tree discordance in our dataset to evaluate support for alternative topological hypotheses for interfamilial relationships within the Cyprinodontiformes using a variety of different analyses. The results from this study will provide a robust, historical framework needed to investigate a plethora of biogeographic, taxonomic, ecological, and physiological questions for this group of fishes.
Collapse
Affiliation(s)
- Kyle R Piller
- Department of Biological Science, Southeastern Louisiana University, Hammond, LA 70402, USA.
| | - Elyse Parker
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06511, USA
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, FL, 32306-4120, USA
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, Biomedical Research Facility, Tallahassee, FL, 32306-4295, USA
| |
Collapse
|
36
|
Mason AJ, Holding ML, Rautsaw RM, Rokyta DR, Parkinson CL, Gibbs HL. Venom gene sequence diversity and expression jointly shape diet adaptation in pitvipers. Mol Biol Evol 2022; 39:6567549. [PMID: 35413123 PMCID: PMC9040050 DOI: 10.1093/molbev/msac082] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Understanding the joint roles of protein sequence variation and differential expression during adaptive evolution is a fundamental, yet largely unrealized goal of evolutionary biology. Here, we use phylogenetic path analysis to analyze a comprehensive venom-gland transcriptome dataset spanning three genera of pitvipers to identify the functional genetic basis of a key adaptation (venom complexity) linked to diet breadth (DB). The analysis of gene-family-specific patterns reveals that, for genes encoding two of the most important venom proteins (snake venom metalloproteases and snake venom serine proteases), there are direct, positive relationships between sequence diversity (SD), expression diversity (ED), and increased DB. Further analysis of gene-family diversification for these proteins showed no constraint on how individual lineages achieved toxin gene SD in terms of the patterns of paralog diversification. In contrast, another major venom protein family (PLA2s) showed no relationship between venom molecular diversity and DB. Additional analyses suggest that other molecular mechanisms—such as higher absolute levels of expression—are responsible for diet adaptation involving these venom proteins. Broadly, our findings argue that functional diversity generated through sequence and expression variations jointly determine adaptation in the key components of pitviper venoms, which mediate complex molecular interactions between the snakes and their prey.
Collapse
Affiliation(s)
- Andrew J Mason
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | | | - Rhett M Rautsaw
- Department of Biological Sciences, Clemson University, Clemson, SC, USA
| | - Darin R Rokyta
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Christopher L Parkinson
- Department of Biological Sciences, Clemson University, Clemson, SC, USA.,Department of Forestry and Environmental Conservation, Clemson University, Clemson, SC, USA
| | - H Lisle Gibbs
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
| |
Collapse
|
37
|
Hernández-Gutiérrez R, van den Berg C, Granados Mendoza C, Peñafiel Cevallos M, Freire M. E, Lemmon EM, Lemmon AR, Magallón S. Localized Phylogenetic Discordance Among Nuclear Loci Due to Incomplete Lineage Sorting and Introgression in the Family of Cotton and Cacao (Malvaceae). FRONTIERS IN PLANT SCIENCE 2022; 13:850521. [PMID: 35498660 PMCID: PMC9043901 DOI: 10.3389/fpls.2022.850521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 03/14/2022] [Indexed: 06/14/2023]
Abstract
The economically important cotton and cacao family (Malvaceae sensu lato) have long been recognized as a monophyletic group. However, the relationships among some subfamilies are still unclear as discordant phylogenetic hypotheses keep arising when different sources of molecular data are analyzed. Phylogenetic discordance has previously been hypothesized to be the result of both introgression and incomplete lineage sorting (ILS), but the extent and source of discordance have not yet been evaluated in the context of loci derived from massive sequencing strategies and for a wide representation of the family. Furthermore, no formal methods have been applied to evaluate if the detected phylogenetic discordance among phylogenomic datasets influences phylogenetic dating estimates of the concordant relationships. The objective of this research was to generate a phylogenetic hypothesis of Malvaceae from nuclear genes, specifically we aimed to (1) investigate the presence of major discordance among hundreds of nuclear gene histories of Malvaceae; (2) evaluate the potential source of discordance; and (3) examine whether discordance and loci heterogeneity influence on time estimates of the origin and diversification of subfamilies. Our study is based on a comprehensive dataset representing 96 genera of the nine subfamilies and 268 nuclear loci. Both concatenated and coalescence-based approaches were followed for phylogenetic inference. Using branch lengths and topology, we located the placement of introgression events to directly evaluate whether discordance is due to introgression rather than ILS. To estimate divergence times, concordance and molecular rate were considered. We filtered loci based on congruence with the species tree and then obtained the molecular rate of each locus to distribute them into three different sets corresponding to shared molecular rate ranges. Bayesian dating was performed for each of the different sets of loci with the same parameters and calibrations. Phylogenomic discordance was detected between methods, as well as gene histories. At deep coalescent times, we found discordance in the position of five subclades probably due to ILS and a relatively small proportion of introgression. Divergence time estimation with each set of loci generated overlapping clade ages, indicating that, even with different molecular rate and gene histories, calibrations generally provide a strong prior.
Collapse
Affiliation(s)
- Rebeca Hernández-Gutiérrez
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Cássio van den Berg
- Departamento de Ciencias Biológicas, Universidade Estadual de Feira de Santana, Feira de Santana, Brazil
| | - Carolina Granados Mendoza
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | | | - Efraín Freire M.
- Herbario Nacional del Ecuador (QCNE), Instituto Nacional de Biodiversidad, Quito, Ecuador
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, Tallahassee, FL, United States
| | - Alan R. Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL, United States
| | - Susana Magallón
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| |
Collapse
|
38
|
|
39
|
Snake Venomics: Fundamentals, Recent Updates, and a Look to the Next Decade. Toxins (Basel) 2022; 14:toxins14040247. [PMID: 35448856 PMCID: PMC9028316 DOI: 10.3390/toxins14040247] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 03/18/2022] [Accepted: 03/21/2022] [Indexed: 01/11/2023] Open
Abstract
Venomic research, powered by techniques adapted from proteomics, transcriptomics, and genomics, seeks to unravel the diversity and complexity of venom through which knowledge can be applied in the treatment of envenoming, biodiscovery, and conservation. Snake venom proteomics is most extensively studied, but the methods varied widely, creating a massive amount of information which complicates data comparison and interpretation. Advancement in mass spectrometry technology, accompanied by growing databases and sophisticated bioinformatic tools, has overcome earlier limitations of protein identification. The progress, however, remains challenged by limited accessibility to samples, non-standardized quantitative methods, and biased interpretation of -omic data. Next-generation sequencing (NGS) technologies enable high-throughput venom-gland transcriptomics and genomics, complementing venom proteomics by providing deeper insights into the structural diversity, differential expression, regulation and functional interaction of the toxin genes. Venomic tissue sampling is, however, difficult due to strict regulations on wildlife use and transfer of biological materials in some countries. Limited resources for techniques and funding are among other pertinent issues that impede the progress of venomics, particularly in less developed regions and for neglected species. Genuine collaboration between international researchers, due recognition of regional experts by global organizations (e.g., WHO), and improved distribution of research support, should be embraced.
Collapse
|
40
|
Differences in PLA2 Constitution Distinguish the Venom of Two Endemic Brazilian Mountain Lanceheads, Bothrops cotiara and Bothrops fonsecai. Toxins (Basel) 2022; 14:toxins14040237. [PMID: 35448846 PMCID: PMC9028134 DOI: 10.3390/toxins14040237] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 02/15/2022] [Accepted: 02/23/2022] [Indexed: 02/01/2023] Open
Abstract
Interspecific differences in snake venom compositions can result from distinct regulatory mechanisms acting in each species. However, comparative analyses focusing on identifying regulatory elements and patterns that led to distinct venom composition are still scarce. Among venomous snakes, Bothrops cotiara and Bothrops fonsecai represent ideal models to complement our understanding of the regulatory mechanisms of venom production. These recently diverged species share a similar specialized diet, habitat, and natural history, but each presents a distinct venom phenotype. Here, we integrated data from the venom gland transcriptome and miRNome and the venom proteome of B. fonsecai and B. cotiara to better understand the regulatory mechanisms that may be acting to produce differing venom compositions. We detected not only the presence of similar toxin isoforms in both species but also distinct expression profiles of phospholipases A2 (PLA2) and some snake venom metalloproteinases (SVMPs) and snake venom serine proteinases (SVSPs) isoforms. We found evidence of modular expression regulation of several toxin isoforms implicated in venom divergence and observed correlated expression of several transcription factors. We did not find strong evidence for miRNAs shaping interspecific divergence of the venom phenotypes, but we identified a subset of toxin isoforms whose final expression may be fine-tuned by specific miRNAs. Sequence analysis on orthologous toxins showed a high rate of substitutions between PLA2s, which indicates that these toxins may be under strong positive selection or represent paralogous toxins in these species. Our results support other recent studies in suggesting that gene regulation is a principal mode of venom evolution across recent timescales, especially among species with conserved ecotypes.
Collapse
|
41
|
Dynamic genetic differentiation drives the widespread structural and functional convergent evolution of snake venom proteinaceous toxins. BMC Biol 2022; 20:4. [PMID: 34996434 PMCID: PMC8742412 DOI: 10.1186/s12915-021-01208-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 12/06/2021] [Indexed: 12/25/2022] Open
Abstract
Background The explosive radiation and diversification of the advanced snakes (superfamily Colubroidea) was associated with changes in all aspects of the shared venom system. Morphological changes included the partitioning of the mixed ancestral glands into two discrete glands devoted for production of venom or mucous respectively, as well as changes in the location, size and structural elements of the venom-delivering teeth. Evidence also exists for homology among venom gland toxins expressed across the advanced snakes. However, despite the evolutionary novelty of snake venoms, in-depth toxin molecular evolutionary history reconstructions have been mostly limited to those types present in only two front-fanged snake families, Elapidae and Viperidae. To have a broader understanding of toxins shared among extant snakes, here we first sequenced the transcriptomes of eight taxonomically diverse rear-fanged species and four key viperid species and analysed major toxin types shared across the advanced snakes. Results Transcriptomes were constructed for the following families and species: Colubridae - Helicops leopardinus, Heterodon nasicus, Rhabdophis subminiatus; Homalopsidae – Homalopsis buccata; Lamprophiidae - Malpolon monspessulanus, Psammophis schokari, Psammophis subtaeniatus, Rhamphiophis oxyrhynchus; and Viperidae – Bitis atropos, Pseudocerastes urarachnoides, Tropidolaeumus subannulatus, Vipera transcaucasiana. These sequences were combined with those from available databases of other species in order to facilitate a robust reconstruction of the molecular evolutionary history of the key toxin classes present in the venom of the last common ancestor of the advanced snakes, and thus present across the full diversity of colubroid snake venoms. In addition to differential rates of evolution in toxin classes between the snake lineages, these analyses revealed multiple instances of previously unknown instances of structural and functional convergences. Structural convergences included: the evolution of new cysteines to form heteromeric complexes, such as within kunitz peptides (the beta-bungarotoxin trait evolving on at least two occasions) and within SVMP enzymes (the P-IIId trait evolving on at least three occasions); and the C-terminal tail evolving on two separate occasions within the C-type natriuretic peptides, to create structural and functional analogues of the ANP/BNP tailed condition. Also shown was that the de novo evolution of new post-translationally liberated toxin families within the natriuretic peptide gene propeptide region occurred on at least five occasions, with novel functions ranging from induction of hypotension to post-synaptic neurotoxicity. Functional convergences included the following: multiple occasions of SVMP neofunctionalised in procoagulant venoms into activators of the clotting factors prothrombin and Factor X; multiple instances in procoagulant venoms where kunitz peptides were neofunctionalised into inhibitors of the clot destroying enzyme plasmin, thereby prolonging the half-life of the clots formed by the clotting activating enzymatic toxins; and multiple occasions of kunitz peptides neofunctionalised into neurotoxins acting on presynaptic targets, including twice just within Bungarus venoms. Conclusions We found novel convergences in both structural and functional evolution of snake toxins. These results provide a detailed roadmap for future work to elucidate predator–prey evolutionary arms races, ascertain differential clinical pathologies, as well as documenting rich biodiscovery resources for lead compounds in the drug design and discovery pipeline. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01208-9.
Collapse
|
42
|
Barua A, Koludarov I, Mikheyev AS. Co-option of the same ancestral gene family gave rise to mammalian and reptilian toxins. BMC Biol 2021; 19:268. [PMID: 34949191 PMCID: PMC8705180 DOI: 10.1186/s12915-021-01191-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 11/11/2021] [Indexed: 12/03/2022] Open
Abstract
Background Evolution can occur with surprising predictability when organisms face similar ecological challenges. For most traits, it is difficult to ascertain whether this occurs due to constraints imposed by the number of possible phenotypic solutions or because of parallel responses by shared genetic and regulatory architecture. Exceptionally, oral venoms are a tractable model of trait evolution, being largely composed of proteinaceous toxins that have evolved in many tetrapods, ranging from reptiles to mammals. Given the diversity of venomous lineages, they are believed to have evolved convergently, even though biochemically similar toxins occur in all taxa. Results Here, we investigate whether ancestral genes harbouring similar biochemical activity may have primed venom evolution, focusing on the origins of kallikrein-like serine proteases that form the core of most vertebrate oral venoms. Using syntenic relationships between genes flanking known toxins, we traced the origin of kallikreins to a single locus containing one or more nearby paralogous kallikrein-like clusters. Additionally, phylogenetic analysis of vertebrate serine proteases revealed that kallikrein-like toxins in mammals and reptiles are genetically distinct from non-toxin ones. Conclusions Given the shared regulatory and genetic machinery, these findings suggest that tetrapod venoms evolved by co-option of proteins that were likely already present in saliva. We term such genes ‘toxipotent’—in the case of salivary kallikreins they already had potent vasodilatory activity that was weaponized by venomous lineages. Furthermore, the ubiquitous distribution of kallikreins across vertebrates suggests that the evolution of envenomation may be more common than previously recognized, blurring the line between venomous and non-venomous animals. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01191-1.
Collapse
Affiliation(s)
- Agneesh Barua
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.
| | - Ivan Koludarov
- Animal Venomics Group, Justus Leibig University, Giessen, Germany
| | - Alexander S Mikheyev
- Research School of Biology, Australian National University, Canberra, ACT, Australia.
| |
Collapse
|
43
|
Schramer TD, Rautsaw RM, Bayona-Serrano JD, Nystrom GS, West TR, Ortiz-Medina JA, Sabido-Alpuche B, Meneses-Millán M, Borja M, Junqueira-de-Azevedo ILM, Rokyta DR, Parkinson CL. An integrative view of the toxic potential of Conophis lineatus (Dipsadidae: Xenodontinae), a medically relevant rear-fanged snake. Toxicon 2021; 205:38-52. [PMID: 34793822 DOI: 10.1016/j.toxicon.2021.11.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 10/25/2021] [Accepted: 11/10/2021] [Indexed: 10/19/2022]
Abstract
Most traditional research on snake venoms has focused on front-fanged snake families (Viperidae, Elapidae, and Atractaspididae). However, venom is now generally accepted as being a much more broadly possessed trait within snakes, including species traditionally considered harmless. Unfortunately, due to historical inertia and methodological challenges, the toxin repertoires of non-front-fanged snake families (e.g., Colubridae, Dipsadidae, and Natricidae) have been heavily neglected despite the knowledge of numerous species capable of inflicting medically relevant envenomations. Integrating proteomic data for validation, we perform a de novo assembly and analysis of the Duvernoy's venom gland transcriptome of the Central American Road Guarder (Dipsadidae: Xenodontinae: Conophis lineatus), a species known for its potent bite. We identified 28 putative toxin transcripts from 13 toxin families in the Duvernoy's venom gland transcriptome, comprising 63.7% of total transcriptome expression. In addition to ubiquitous snake toxin families, we proteomically confirmed several atypical venom components. The most highly expressed toxins (55.6% of total toxin expression) were recently described snake venom matrix metalloproteases (svMMPs), with 48.0% of svMMP expression contributable to a novel svMMP isoform. We investigate the evolution of the new svMMP isoform in the context of rear-fanged snakes using phylogenetics. Finally, we examine the morphology of the venom apparatus using μCT and explore how the venom relates to autecology and the highly hemorrhagic effects seen in human envenomations. Importantly, we provide the most complete venom characterization of this medically relevant snake species to date, producing insights into the effects and evolution of its venom, and point to future research directions to better understand the venoms of 'harmless' non-front-fanged snakes.
Collapse
Affiliation(s)
- Tristan D Schramer
- Department of Biological Sciences, Clemson University, Clemson, SC, USA.
| | - Rhett M Rautsaw
- Department of Biological Sciences, Clemson University, Clemson, SC, USA
| | | | - Gunnar S Nystrom
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Taylor R West
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Javier A Ortiz-Medina
- Departamento de Sistemática y Ecología Acuática, El Colegio de La Frontera Sur, Unidad Chetumal, Chetumal, Quintana Roo, Mexico; Unidad de Manejo para La Conservación de La Vida Silvestre, Tsáab Kaan, Baca, Yucatán, Mexico; HERP.MX A.C., Villa de Álvarez, Colima, Mexico
| | - Bianca Sabido-Alpuche
- Unidad de Manejo para La Conservación de La Vida Silvestre, Tsáab Kaan, Baca, Yucatán, Mexico
| | - Marcos Meneses-Millán
- Unidad de Manejo para La Conservación de La Vida Silvestre, Tsáab Kaan, Baca, Yucatán, Mexico
| | - Miguel Borja
- Facultad de Ciencias Biológicas, Universidad Juárez Del Estado de Durango, Gómez Palacio, Durango, Mexico
| | - Inácio L M Junqueira-de-Azevedo
- Laboratório de Toxinologia Aplicada, Instituto Butantan, São Paulo, Brazil; Center of Toxins, Immune-Response and Cell Signaling (CeTICS), São Paulo, Brazil
| | - Darin R Rokyta
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Christopher L Parkinson
- Department of Biological Sciences, Clemson University, Clemson, SC, USA; Department of Forestry and Environmental Conservation, Clemson University, Clemson, SC, USA.
| |
Collapse
|
44
|
Colis-Torres A, Neri-Castro E, Strickland JL, Olvera-Rodríguez A, Borja M, Calvete J, Jones J, Parkinson CL, Bañuelos J, López de León J, Alagón A. Intraspecific venom variation of Mexican West Coast Rattlesnakes (Crotalus basiliscus) and its implications for antivenom production. Biochimie 2021; 192:111-124. [PMID: 34656669 DOI: 10.1016/j.biochi.2021.10.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 09/17/2021] [Accepted: 10/11/2021] [Indexed: 11/02/2022]
Abstract
Intraspecific variation in snake venoms has been widely documented worldwide. However, there are few studies on this subject in Mexico. Venom characterization studies provide important data used to predict clinical syndromes, to evaluate the efficacy of antivenoms and, in some cases, to improve immunogenic mixtures in the production of antivenoms. In the present work, we evaluated the intraspecific venom variation of Crotalus basiliscus, a rattlesnake of medical importance and whose venom is used in the immunization of horses to produce one of the Mexican antivenoms. Our results demonstrate that there is variation in biological and biochemical activities among adult venoms and that there is an ontogenetic change from juvenile to adult venoms. Juvenile venoms were more lethal and had higher percentages of crotamine and crotoxin, while adult venoms had higher percentages of snake venom metalloproteases (SVMPs). Additionally, we documented crotoxin-like PLA2 variation in which specimens from Zacatecas, Sinaloa and Michoacán (except 1) lacked the neurotoxin, while the rest of the venoms had it. Finally, we evaluated the efficacy of three lots of Birmex antivenom and all three were able to neutralize the lethality of four representative venoms but were not able to neutralize crotamine. We also observed significant differences in the LD50 values neutralized per vial among the different lots. Based on these results, we recommend including venoms containing crotamine in the production of antivenom for a better immunogenic mixture and to improve the homogeneity of lots.
Collapse
Affiliation(s)
- Andrea Colis-Torres
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Edgar Neri-Castro
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Jason L Strickland
- Department of Biology, University of South Alabama, 5871 USA Dr. N, Mobile, AL, 36688, USA
| | - Alejandro Olvera-Rodríguez
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Miguel Borja
- Facultad Ciencias Biológicas, Universidad Juárez del Estado de Durango, Av. Universidad s/n. Fracc. Filadelfia, C.P. 35010, Gómez Palacio, Dgo, Mexico
| | - Juan Calvete
- Laboratorio de Venómica Evolutiva y Traslacional, Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas, Jaime Roig 11, 46010, Valencia, Spain
| | - Jason Jones
- Herp.mx A.C, Villa del Álvarez, Colima, Mexico
| | - Christopher L Parkinson
- Department of Biological Sciences and Department of Forestry, and Environmental Conservation, Clemson University, 190 Collings St. Clemson, SC, 29631, USA
| | - Jorge Bañuelos
- Herp.mx A.C, Villa del Álvarez, Colima, Mexico; Unidad Académica de Ciencias Biológicas, Universidad Autónoma de Zacatecas, Edificio de Biología Campus II Ave. Preparatoria S/N, Col. Agronómica, 98066, ZacatecasZacatecas, Mexico
| | - Jorge López de León
- Hospital General Norberto Treviño Zapata, Ciudad Victoria, Tamaulipas, Mexico
| | - Alejandro Alagón
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico.
| |
Collapse
|
45
|
Palasuberniam P, Tan KY, Tan CH. De novo venom gland transcriptomics of Calliophis bivirgata flaviceps: uncovering the complexity of toxins from the Malayan blue coral snake. J Venom Anim Toxins Incl Trop Dis 2021; 27:e20210024. [PMID: 34616441 PMCID: PMC8476087 DOI: 10.1590/1678-9199-jvatitd-2021-0024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 05/12/2021] [Indexed: 03/03/2023] Open
Abstract
Background: The Malayan blue coral snake, Calliophis bivirgata
flaviceps, is a medically important venomous snake in Southeast
Asia. However, the complexity and diversity of its venom genes remain little
explored. Methods: To address this, we applied high-throughput next-generation sequencing to
profile the venom gland cDNA libraries of C. bivirgata
flaviceps. The transcriptome was de novo
assembled, followed by gene annotation, multiple sequence alignment and
analyses of the transcripts. Results: A total of 74 non-redundant toxin-encoding genes from 16 protein families
were identified, with 31 full-length toxin transcripts. Three-finger toxins
(3FTx), primarily delta-neurotoxins and cardiotoxin-like/cytotoxin-like
proteins, were the most diverse and abundantly expressed. The major 3FTx
(Cb_FTX01 and Cb_FTX02) are highly similar to calliotoxin, a
delta-neurotoxin previously reported in the venom of C.
bivirgata. This study also revealed a conserved tyrosine
residue at position 4 of the cardiotoxin-like/cytotoxin-like protein genes
in the species. These variants, proposed as Y-type CTX-like proteins, are
similar to the H-type CTX from cobras. The substitution is conservative
though, preserving a less toxic form of elapid CTX-like protein, as
indicated by the lack of venom cytotoxicity in previous laboratory and
clinical findings. The ecological role of these toxins, however, remains
unclear. The study also uncovered unique transcripts that belong to
phospholipase A2 of Groups IA and IB, and snake venom
metalloproteinases of PIII subclass, which show sequence variations from
those of Asiatic elapids. Conclusion: The venom gland transcriptome of C. bivirgata flaviceps from
Malaysia was de novo assembled and annotated. The diversity
and expression profile of toxin genes provide insights into the biological
and medical importance of the species.
Collapse
Affiliation(s)
- Praneetha Palasuberniam
- Venom Research and Toxicology Laboratory, Department of Pharmacology, Faculty of Medicine, University of Malaya. Kuala Lumpur, Malaysia.,Department of Biomedical Sciences, University Malaysia Sabah, Faculty of Medicine and Health Sciences, Kota Kinabalu, Sabah, Malaysia
| | - Kae Yi Tan
- Protein and Interactomics Laboratory, Department of Molecular Medicine, Faculty of Medicine, University of Malaya. Kuala Lumpur, Malaysia
| | - Choo Hock Tan
- Venom Research and Toxicology Laboratory, Department of Pharmacology, Faculty of Medicine, University of Malaya. Kuala Lumpur, Malaysia
| |
Collapse
|
46
|
Liao X, Guo S, Yin X, Liao B, Li M, Su H, Li Q, Pei J, Gao J, Lei J, Li X, Huang Z, Xu J, Chen S. Hierarchical chromatin features reveal the toxin production in Bungarus multicinctus. Chin Med 2021; 16:90. [PMID: 34535171 PMCID: PMC8447776 DOI: 10.1186/s13020-021-00502-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 09/04/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bungarus multicinctus, from which a classical Chinese medicine is produced, is known as the most venomous land snake in the world, but the chromatin organization and transcription factor activity during venom replenishment progress have not been explored yet. This study aimed to determine the roles of chromatin structure in toxin activity via bioinformatics and experimental validation. METHODS Chromosome conformation capture (Hi-C) analysis was used to examine interactions among chromosomes and identify different scales of chromatin during envenomation in B. multicinctus. Correlations between epigenetic modifications and chromatin structure were verified through ChIP-seq analysis. RNA-seq was used to validate the influence of variation in chromatin structure and gene expression levels on venom production and regulation. RESULTS Our results suggested that intra-chromosomal interactions are more intense than inter-chromosomal interactions among the control group, 3-day group of venom glands and muscles. Through this, we found that compartmental transition was correlated with chromatin interactions. Interestingly, the up-regulated genes in more compartmental switch regions reflect the function of toxin activity. Topologically associated domain (TAD) boundaries enriched with histone modifications are associated with different distributions of genes and the expression levels. Toxin-coding genes in the same loop are highly expressed, implying that the importance of epigenetic regulation during envenomination. On a smaller scale, the epigenetic markers affect transcriptional regulation by controlling the recruitment/inhibition of transcription initiation complexes. CONCLUSIONS Chromatin structure and epigenetic modifications could play a vital status role in the mechanisms of venom regulation in B. multicinctus.
Collapse
Affiliation(s)
- Xuejiao Liao
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Shuai Guo
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Xianmei Yin
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Baosheng Liao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Mingqian Li
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - He Su
- Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, 510006, China
| | - Qiushi Li
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Jin Pei
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Jihai Gao
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Juan Lei
- College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Xiwen Li
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Zhihai Huang
- Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, 510006, China
| | - Jiang Xu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Shilin Chen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| |
Collapse
|
47
|
Evaluation of Signaling Pathways Profiling in Human Dermal Endothelial Cells Treated by Snake Venom Cysteine-Rich Secretory Proteins (svCRiSPs) from North American Snakes Using Reverse Phase Protein Array (RPPA). Toxins (Basel) 2021; 13:toxins13090613. [PMID: 34564617 PMCID: PMC8473428 DOI: 10.3390/toxins13090613] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/25/2021] [Accepted: 08/27/2021] [Indexed: 11/30/2022] Open
Abstract
Cysteine-Rich Secretory Proteins (CRiSPs) are typically found in many snake venoms; however, the role that these toxins play in the pathophysiology of snakebites is still unclear. Herein, we compared the effects of snake venom CRiSPs (svCRiSPs) from the most medically important species of North American snakes on endothelial cell permeability and vascular permeability. We used reverse phase protein array (RPPA) to identify key signaling molecules on human dermal lymphatic (HDLECs) and blood (HDBECs) endothelial cells treated with svCRiSPs. The results showed that Css-CRiSP isolated from Crotalus scutulatus scutulatus and App-CRiSP from Agkistrodon piscivorus piscivorus are the most potent causes of increase vascular and endothelial permeability in comparison with other svCRiSPs used in this study. We examined the protein expression levels and their activated phosphorylation states in HDLECs and HDBECs induced by App-CRiSP and Css-CRiSP using RPPA. Interestingly, both App-CRiSP and Css-CRiSP induced caveolin-1 expression in HDBECs. We also found that stimulating HDBECs with Css-CRiSP and App-CRiSP significantly induced the phosphorylation of mTOR and Src, respectively. In HDLECs, Css-CRiSP significantly downregulated the expression of N-Cadherin and phospholipase C-gamma, while App-CRiSP significantly enhanced Akt and JNK phosphorylation. These results suggest that the increased endothelial permeability in HDLECs and HDBECs by Css-CRiSP and App-CRiSP may occur through different pathways.
Collapse
|
48
|
Gene Flow and Diversification in Himalopsyche martynovi Species Complex (Trichoptera: Rhyacophilidae) in the Hengduan Mountains. BIOLOGY 2021; 10:biology10080816. [PMID: 34440048 PMCID: PMC8389565 DOI: 10.3390/biology10080816] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/16/2021] [Accepted: 08/17/2021] [Indexed: 11/16/2022]
Abstract
The Hengduan Mountains are one of the most species-rich mountainous areas in the world. The origin and evolution of such a remarkable biodiversity are likely to be associated with geological or climatic dynamics, as well as taxon-specific biotic processes (e.g., hybridization, polyploidization, etc.). Here, we investigate the mechanisms fostering the diversification of the endemic Himalopsyche martynovi complex, a poorly known group of aquatic insects. We used multiple allelic datasets generated from 691 AHE loci to reconstruct species and RaxML phylogenetic trees. We selected the most reliable phylogenetic tree to perform network and gene flow analyses. The phylogenetic reconstructions and network analysis identified three clades, including H. epikur, H. martynovi sensu stricto and H. cf. martynovi. Himalopsyche martynovi sensu stricto and H. cf. martynovi present an intermediate morphology between H. epikur and H. viteceki, the closest known relative to the H. martynovi-complex. The gene flow analysis revealed extensive gene flow among these lineages. Our results suggest that H. viteceki and H. epikur are likely to have contributed to the evolution of H. martynovi sensu stricto and H. cf. martynovi via gene flow, and thus, our study provides insights in the diversification process of a lesser-known ecological group, and hints at the potential role of gene flow in the emergence of biological novelty in the Hengduan Mountains.
Collapse
|
49
|
Nicolas V, Mikula O, Lavrenchenko LA, Šumbera R, Bartáková V, Bryjová A, Meheretu Y, Verheyen E, Missoup AD, Lemmon AR, Moriarty Lemmon E, Bryja J. Phylogenomics of African radiation of Praomyini (Muridae: Murinae) rodents: First fully resolved phylogeny, evolutionary history and delimitation of extant genera. Mol Phylogenet Evol 2021; 163:107263. [PMID: 34273505 DOI: 10.1016/j.ympev.2021.107263] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/06/2021] [Accepted: 07/12/2021] [Indexed: 11/25/2022]
Abstract
The tribe Praomyini is a diversified group including 64 species and eight extant rodent genera. They live in a broad spectrum of habitats across whole sub-Saharan Africa. Members of this tribe are often very abundant, they have a key ecological role in ecosystems, they are hosts of many potentially pathogenic microorganisms and comprise numerous agricultural pests. Although this tribe is well supported by both molecular and morphological data, its intergeneric relationships and the species contents of several genera are not yet fully resolved. Recent molecular data suggest that at least three genera in current sense are paraphyletic. However, in these studies the species sampling was sparse and the resolution of relationships among genera was poor, probably due to a fast radiation of the tribe dated to the Miocene and insufficient amount of genetic data. Here we used genomic scale data (395 nuclear loci = 610,965 bp long alignment and mitogenomes = 14,745 bp) and produced the first fully resolved species tree containing most major lineages of the Praomyini tribe (i.e. all but one currently delimited genera and major intrageneric clades). Results of a fossil-based divergence dating analysis suggest that the radiation started during the Messinian stage (ca. 7 Ma) and was likely linked to a fragmentation of the pan-African Miocene forest. Some lineages remained in the rain forests, while many others adapted to a broad spectrum of new open lowland and montane habitats that appeared at the beginning of Pliocene. Our analyses clearly confirmed the presence of three polyphyletic genera (Praomys, Myomyscus and Mastomys). We review current knowledge of these three genera and suggest corresponding taxonomic changes. To keep genera monophyletic, we propose taxonomic re-arrangements and delimit four new genera. Furthermore, we discovered a new highly divergent genetic lineage of Praomyini in southwestern Ethiopia, which is described as a new species and genus.
Collapse
Affiliation(s)
- Violaine Nicolas
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, CP51, 75005 Paris, France
| | - Ondřej Mikula
- Institute of Vertebrate Biology of the Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic
| | - Leonid A Lavrenchenko
- A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences, Leninskii pr. 33, Moscow 119071, Russia
| | - Radim Šumbera
- Department of Zoology, Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic
| | - Veronika Bartáková
- Institute of Vertebrate Biology of the Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic
| | - Anna Bryjová
- Institute of Vertebrate Biology of the Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic
| | - Yonas Meheretu
- Institute of Vertebrate Biology of the Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic; Department of Biology and Institute of Mountain Research and Development, Mekelle University, Mekelle, Tigray, Ethiopia
| | - Erik Verheyen
- Royal Belgian Institute for Natural Sciences, Operational Direction Taxonomy and Phylogeny, 1000 Brussels, Belgium; Evolutionary Ecology Group, Biology Department, University of Antwerp, 2020 Antwerp, Belgium
| | - Alain Didier Missoup
- Zoology Unit, Laboratory of Biology and Physiology of Animal Organisms, Faculty of Science, University of Douala, Douala, Cameroon
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, FL 32306-4295, United States
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, 319 Stadium Drive, PO Box 3064295, Tallahassee, FL 32306-4295, United States
| | - Josef Bryja
- Institute of Vertebrate Biology of the Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic; Department of Botany and Zoology, Faculty of Science, Masaryk University, 611 37, Brno, Czech Republic.
| |
Collapse
|
50
|
Gene flow in phylogenomics: Sequence capture resolves species limits and biogeography of Afromontane forest endemic frogs from the Cameroon Highlands. Mol Phylogenet Evol 2021; 163:107258. [PMID: 34252546 DOI: 10.1016/j.ympev.2021.107258] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 06/28/2021] [Accepted: 07/07/2021] [Indexed: 11/21/2022]
Abstract
Puddle frogs of the Phrynobatrachus steindachneri species complex are a useful group for investigating speciation and phylogeography in Afromontane forests of the Cameroon Volcanic Line, western Central Africa. The species complex is represented by six morphologically relatively cryptic mitochondrial DNA lineages, only two of which are distinguished at the species level - southern P. jimzimkusi and Lake Oku endemic P. njiomock, leaving the remaining four lineages identified as 'P. steindachneri'. In this study, the six mtDNA lineages are subjected to genomic sequence capture analyses and morphological examination to delimit species and to study biogeography. The nuclear DNA data (387 loci; 571,936 aligned base pairs) distinguished all six mtDNA lineages, but the topological pattern and divergence depths supported only four main clades: P. jimzimkusi, P. njiomock, and only two divergent evolutionary lineages within the four 'P. steindachneri' mtDNA lineages. One of the two lineages is herein described as a new species, P. amieti sp. nov. Reticulate evolution (hybridization) was detected within the species complex with morphologically intermediate hybrid individuals placed between the parental species in phylogenomic analyses, forming a ladder-like phylogenetic pattern. The presence of hybrids is undesirable in standard phylogenetic analyses but is essential and beneficial in the network multispecies coalescent. This latter approach provided insight into the reticulate evolutionary history of these endemic frogs. Introgressions likely occurred during the Middle and Late Pleistocene climatic oscillations, due to the cyclic connections (likely dominating during cold glacials) and separations (during warm interglacials) of montane forests. The genomic phylogeographic pattern supports the separation of the southern (Mt. Manengouba to Mt. Oku) and northern mountains at the onset of the Pleistocene. Further subdivisions occurred in the Early Pleistocene, separating populations from the northernmost (Tchabal Mbabo, Gotel Mts.) and middle mountains (Mt. Mbam, Mt. Oku, Mambilla Plateau), as well as the microendemic lineage restricted to Lake Oku (Mt. Oku). This unique model system is highly threatened as all the species within the complex have exhibited severe population declines in the past decade, placing them on the brink of extinction. In addition, Mount Oku is identified to be of particular conservation importance because it harbors three species of this complex. We, therefore, urge for conservation actions in the Cameroon Highlands to preserve their diversity before it is too late.
Collapse
|