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Macrander J, Broe M, Daly M. Multi-copy venom genes hidden in de novo transcriptome assemblies, a cautionary tale with the snakelocks sea anemone Anemonia sulcata (Pennant, 1977). Toxicon 2015; 108:184-8. [PMID: 26464059 DOI: 10.1016/j.toxicon.2015.09.038] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 09/29/2015] [Indexed: 12/20/2022]
Abstract
Using a partial transcriptome of the snakelocks anemone (Anemonia sulcata) we identify toxin gene candidates that were incorrectly assembled into several Trinity components. Our approach recovers hidden diversity found within some toxin gene families that would otherwise go undetected when using Trinity, a widely used program for venom-focused transcriptome reconstructions. Unidentified hidden transcripts may significantly impact conclusions made regarding venom composition (or other multi-copy conserved genes) when using Trinity or other de novo assembly programs.
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Affiliation(s)
- Jason Macrander
- The Ohio State University, Department of Evolution, Ecology, and Organismal Biology, 1315 Kinnear Road, Columbus, OH 43215, USA.
| | - Michael Broe
- The Ohio State University, Department of Evolution, Ecology, and Organismal Biology, 1315 Kinnear Road, Columbus, OH 43215, USA
| | - Marymegan Daly
- The Ohio State University, Department of Evolution, Ecology, and Organismal Biology, 1315 Kinnear Road, Columbus, OH 43215, USA
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52
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Sebastian A, Herdegen M, Migalska M, Radwan J. amplisas: a web server for multilocus genotyping using next-generation amplicon sequencing data. Mol Ecol Resour 2015; 16:498-510. [DOI: 10.1111/1755-0998.12453] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Revised: 07/16/2015] [Accepted: 08/04/2015] [Indexed: 12/30/2022]
Affiliation(s)
- Alvaro Sebastian
- Evolutionary Biology Group; Faculty of Biology; Adam Mickiewicz University; ul. Umultowska 89 61-614 Poznan Poland
| | - Magdalena Herdegen
- Evolutionary Biology Group; Faculty of Biology; Adam Mickiewicz University; ul. Umultowska 89 61-614 Poznan Poland
| | - Magdalena Migalska
- Evolutionary Biology Group; Faculty of Biology; Adam Mickiewicz University; ul. Umultowska 89 61-614 Poznan Poland
| | - Jacek Radwan
- Evolutionary Biology Group; Faculty of Biology; Adam Mickiewicz University; ul. Umultowska 89 61-614 Poznan Poland
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53
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Fijarczyk A, Babik W. Detecting balancing selection in genomes: limits and prospects. Mol Ecol 2015; 24:3529-45. [DOI: 10.1111/mec.13226] [Citation(s) in RCA: 144] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 04/27/2015] [Accepted: 04/30/2015] [Indexed: 12/17/2022]
Affiliation(s)
- Anna Fijarczyk
- Institute of Environmental Sciences; Jagiellonian University; Gronostajowa 7 30-387 Kraków Poland
| | - Wiesław Babik
- Institute of Environmental Sciences; Jagiellonian University; Gronostajowa 7 30-387 Kraków Poland
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54
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Macrander J, Brugler MR, Daly M. A RNA-seq approach to identify putative toxins from acrorhagi in aggressive and non-aggressive Anthopleura elegantissima polyps. BMC Genomics 2015; 16:221. [PMID: 25886045 PMCID: PMC4397815 DOI: 10.1186/s12864-015-1417-4] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 02/28/2015] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND The use of venom in intraspecific aggression is uncommon and venom-transmitting structures specifically used for intraspecific competition are found in few lineages of venomous taxa. Next-generation transcriptome sequencing allows robust characterization of venom diversity and exploration of functionally unique tissues. Using a tissue-specific RNA-seq approach, we investigate the venom composition and gene ontology diversity of acrorhagi, specialized structures used in intraspecific competition, in aggressive and non-aggressive polyps of the aggregating sea anemone Anthopleura elegantissima (Cnidaria: Anthozoa: Hexacorallia: Actiniaria: Actiniidae). RESULTS Collectively, we generated approximately 450,000 transcripts from acrorhagi of aggressive and non-aggressive polyps. For both transcriptomes we identified 65 candidate sea anemone toxin genes, representing phospholipase A2s, cytolysins, neurotoxins, and acrorhagins. When compared to previously characterized sea anemone toxin assemblages, each transcriptome revealed greater within-species sequence divergence across all toxin types. The transcriptome of the aggressive polyp had a higher abundance of type II voltage gated potassium channel toxins/Kunitz-type protease inhibitors and type II acrorhagins. Using toxin-like proteins from other venomous taxa, we also identified 612 candidate toxin-like transcripts with signaling regions, potentially unidentified secretory toxin-like proteins. Among these, metallopeptidases and cysteine rich (CRISP) candidate transcripts were in high abundance. Furthermore, our gene ontology analyses identified a high prevalence of genes associated with "blood coagulation" and "positive regulation of apoptosis", as well as "nucleoside: sodium symporter activity" and "ion channel binding". The resulting assemblage of expressed genes may represent synergistic proteins associated with toxins or proteins related to the morphology and behavior exhibited by the aggressive polyp. CONCLUSION We implement a multifaceted approach to investigate the assemblage of expressed genes specifically within acrorhagi, specialized structures used only for intraspecific competition. By combining differential expression, phylogenetic, and gene ontology analyses, we identify several candidate toxins and other potentially important proteins in acrorhagi of A. elegantissima. Although not all of the toxins identified are used in intraspecific competition, our analysis highlights some candidates that may play a vital role in intraspecific competition. Our findings provide a framework for further investigation into components of venom used exclusively for intraspecific competition in acrorhagi-bearing sea anemones and potentially other venomous animals.
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Affiliation(s)
- Jason Macrander
- The Ohio State University, Evolution, Ecology, and Organismal Biology, 318 W. 12th Avenue, Columbus, OH, 43210-1293, USA.
| | - Mercer R Brugler
- Sackler Institute for Comparative Genomics, Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA. .,Biological Sciences Department, NYC College of Technology (CUNY), 300 Jay Street, Brooklyn, NY, 11201, USA.
| | - Marymegan Daly
- The Ohio State University, Evolution, Ecology, and Organismal Biology, 318 W. 12th Avenue, Columbus, OH, 43210-1293, USA.
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55
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Ferrandiz-Rovira M, Bigot T, Allainé D, Callait-Cardinal MP, Cohas A. Large-scale genotyping of highly polymorphic loci by next-generation sequencing: how to overcome the challenges to reliably genotype individuals? Heredity (Edinb) 2015; 114:485-93. [PMID: 25757407 DOI: 10.1038/hdy.2015.13] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 01/19/2015] [Accepted: 01/23/2015] [Indexed: 11/10/2022] Open
Abstract
Studying the different roles of adaptive genes is still a challenge in evolutionary ecology and requires reliable genotyping of large numbers of individuals. Next-generation sequencing (NGS) techniques enable such large-scale sequencing, but stringent data processing is required. Here, we develop an easy to use methodology to process amplicon-based NGS data and we apply this methodology to reliably genotype four major histocompatibility complex (MHC) loci belonging to MHC class I and II of Alpine marmots (Marmota marmota). Our post-processing methodology allowed us to increase the number of retained reads. The quality of genotype assignment was further assessed using three independent validation procedures. A total of 3069 high-quality MHC genotypes were obtained at four MHC loci for 863 Alpine marmots with a genotype assignment error rate estimated as 0.21%. The proposed methodology could be applied to any genetic system and any organism, except when extensive copy-number variation occurs (that is, genes with a variable number of copies in the genotype of an individual). Our results highlight the potential of amplicon-based NGS techniques combined with adequate post-processing to obtain the large-scale highly reliable genotypes needed to understand the evolution of highly polymorphic functional genes.
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Affiliation(s)
- M Ferrandiz-Rovira
- 1] Laboratoire Biométrie et Biologie Evolutive, Université de Lyon, CNRS, UMR5558, Université Lyon 1, F-69622, Villeurbanne, F-69000 Lyon, France [2] Université Lyon, VetAgro Sup Campus Vet, Marcy-L'Étoile, France
| | - T Bigot
- Laboratoire Biométrie et Biologie Evolutive, Université de Lyon, CNRS, UMR5558, Université Lyon 1, F-69622, Villeurbanne, F-69000 Lyon, France
| | - D Allainé
- Laboratoire Biométrie et Biologie Evolutive, Université de Lyon, CNRS, UMR5558, Université Lyon 1, F-69622, Villeurbanne, F-69000 Lyon, France
| | - M-P Callait-Cardinal
- 1] Laboratoire Biométrie et Biologie Evolutive, Université de Lyon, CNRS, UMR5558, Université Lyon 1, F-69622, Villeurbanne, F-69000 Lyon, France [2] Université Lyon, VetAgro Sup Campus Vet, Marcy-L'Étoile, France
| | - A Cohas
- Laboratoire Biométrie et Biologie Evolutive, Université de Lyon, CNRS, UMR5558, Université Lyon 1, F-69622, Villeurbanne, F-69000 Lyon, France
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56
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Pechouskova E, Dammhahn M, Brameier M, Fichtel C, Kappeler PM, Huchard E. MHC class II variation in a rare and ecological specialist mouse lemur reveals lower allelic richness and contrasting selection patterns compared to a generalist and widespread sympatric congener. Immunogenetics 2015; 67:229-45. [PMID: 25687337 PMCID: PMC4357647 DOI: 10.1007/s00251-015-0827-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 01/30/2015] [Indexed: 11/20/2022]
Abstract
The polymorphism of immunogenes of the major histocompatibility complex (MHC) is thought to influence the functional plasticity of immune responses and, consequently, the fitness of populations facing heterogeneous pathogenic pressures. Here, we evaluated MHC variation (allelic richness and divergence) and patterns of selection acting on the two highly polymorphic MHC class II loci (DRB and DQB) in the endangered primate Madame Berthe’s mouse lemur (Microcebus berthae). Using 454 pyrosequencing, we examined MHC variation in a total of 100 individuals sampled over 9 years in Kirindy Forest, Western Madagascar, and compared our findings with data obtained previously for its sympatric congener, the grey mouse lemur (Microcebus murinus). These species exhibit a contrasting ecology and demography that were expected to affect MHC variation and molecular signatures of selection. We found a lower allelic richness concordant with its low population density, but a similar level of allelic divergence and signals of historical selection in the rare feeding specialist M. berthae compared to the widespread generalist M. murinus. These findings suggest that demographic factors may exert a stronger influence than pathogen-driven selection on current levels of allelic richness in M. berthae. Despite a high sequence similarity between the two congeners, contrasting selection patterns detected at DQB suggest its potential functional divergence. This study represents a first step toward unravelling factors influencing the adaptive divergence of MHC genes between closely related but ecologically differentiated sympatric lemurs and opens new questions regarding potential functional discrepancy that would explain contrasting selection patterns detected at DQB.
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Affiliation(s)
- Eva Pechouskova
- Behavioral Ecology and Sociobiology Unit, German Primate Center, Kellnerweg 4, Göttingen, Germany,
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57
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Rieseberg L, Vines T, Gow J, Geraldes A. Editorial 2015. Mol Ecol 2015; 24:1-17. [DOI: 10.1111/mec.12997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 11/10/2014] [Indexed: 11/30/2022]
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58
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Wilson AB, Whittington CM, Bahr A. High intralocus variability and interlocus recombination promote immunological diversity in a minimal major histocompatibility system. BMC Evol Biol 2014; 14:273. [PMID: 25526691 PMCID: PMC4302578 DOI: 10.1186/s12862-014-0273-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 12/12/2014] [Indexed: 12/03/2022] Open
Abstract
Background The genes of the major histocompatibility complex (MHC/MH) have attracted considerable scientific interest due to their exceptional levels of variability and important function as part of the adaptive immune system. Despite a large number of studies on MH class II diversity of both model and non-model organisms, most research has focused on patterns of genetic variability at individual loci, failing to capture the functional diversity of the biologically active dimeric molecule. Here, we take a systematic approach to the study of MH variation, analyzing patterns of genetic variation at MH class IIα and IIβ loci of the seahorse, which together form the immunologically active peptide binding cleft of the MH class II molecule. Results The seahorse carries a minimal class II system, consisting of single copies of both MH class IIα and IIβ, which are physically linked and inherited in a Mendelian fashion. Both genes are ubiquitously expressed and detectible in the brood pouch of male seahorses throughout pregnancy. Genetic variability of the two genes is high, dominated by non-synonymous variation concentrated in their peptide-binding regions. Coding variation outside these regions is negligible, a pattern thought to be driven by intra- and interlocus recombination. Despite the tight physical linkage of MH IIα and IIβ loci, recombination has produced novel composite alleles, increasing functional diversity at sites responsible for antigen recognition. Conclusions Antigen recognition by the adaptive immune system of the seahorse is enhanced by high variability at both MH class IIα and IIβ loci. Strong positive selection on sites involved in pathogen recognition, coupled with high levels of intra- and interlocus recombination, produce a patchwork pattern of genetic variation driven by genetic hitchhiking. Studies focusing on variation at individual MH loci may unintentionally overlook an important component of ecologically relevant variation.
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Affiliation(s)
- Anthony B Wilson
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland. .,Department of Biology, Brooklyn College and The Graduate Center, City University of New York, 2900 Bedford Avenue, Brooklyn, New York, 11210, USA. .,Department of Biology, Brooklyn College, 2900 Bedford Avenue, Brooklyn, New York, 11210, USA.
| | - Camilla M Whittington
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland. .,School of Biological Sciences, University of Sydney, Heydon-Laurence Building A08, Sydney, NSW, 2006, Australia.
| | - Angela Bahr
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland. .,Institute of Medical Molecular Genetics, University of Zurich, Wagistrasse 12, 8952, Schlieren, Switzerland.
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454 screening of individual MHC variation in an endemic island passerine. Immunogenetics 2014; 67:149-62. [PMID: 25515684 PMCID: PMC4325181 DOI: 10.1007/s00251-014-0822-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 11/28/2014] [Indexed: 11/03/2022]
Abstract
Genes of the major histocompatibility complex (MHC) code for receptors that are central to the adaptive immune response of vertebrates. These genes are therefore important genetic markers with which to study adaptive genetic variation in the wild. Next-generation sequencing (NGS) has increasingly been used in the last decade to genotype the MHC. However, NGS methods are highly prone to sequencing errors, and although several methodologies have been proposed to deal with this, until recently there have been no standard guidelines for the validation of putative MHC alleles. In this study, we used the 454 NGS platform to screen MHC class I exon 3 variation in a population of the island endemic Berthelot's pipit (Anthus berthelotii). We were able to characterise MHC genotypes across 309 individuals with high levels of repeatability. We were also able to determine alleles that had low amplification efficiencies, whose identification within individuals may thus be less reliable. At the population level we found lower levels of MHC diversity in Berthelot's pipit than in its widespread continental sister species the tawny pipit (Anthus campestris), and observed trans-species polymorphism. Using the sequence data, we identified signatures of gene conversion and evidence of maintenance of functionally divergent alleles in Berthelot's pipit. We also detected positive selection at 10 codons. The present study therefore shows that we have an efficient method for screening individual MHC variation across large datasets in Berthelot's pipit, and provides data that can be used in future studies investigating spatio-temporal patterns and scales of selection on the MHC.
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