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Abstract
The successful interaction between pathogen/parasite and host requires a delicate balance between fitness of the former and survival of the latter. To optimize fitness a parasite/pathogen must effectively create an environment conducive to reproductive success, while simultaneously avoiding or minimizing detrimental host defense response. The association between Microbotryum lychnidis-dioicae and its host Silene latifolia serves as an excellent model to examine such interactions. This fungus is part of a species complex that infects species of the Caryophyllaceae, replacing pollen with the fungal spores. In the current study, transcriptome analyses of the fungus and its host were conducted during discrete stages of bud development so as to identify changes in fungal gene expression that lead to spore development and to identify changes associated with infection in the host plant. In contrast to early biotrophic phase stages of infection for the fungus, the latter stages involve tissue necrosis and in the case of infected female flowers, further changes in the developmental program in which the ovary aborts and a pseudoanther is produced. Transcriptome analysis via Illumina RNA sequencing revealed enrichment of fungal genes encoding small secreted proteins, with hallmarks of effectors and genes found to be relatively unique to the Microbotryum species complex. Host gene expression analyses also identified interesting sets of genes up-regulated, including those involving stress response, host defense response, and several agamous-like MADS-box genes (AGL61 and AGL80), predicted to interact and be involved in male gametophyte development.
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52
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Varga S, Soulsbury CD. Paternal arbuscular mycorrhizal fungal status affects DNA methylation in seeds. Biol Lett 2017; 13:rsbl.2017.0407. [PMID: 28931731 DOI: 10.1098/rsbl.2017.0407] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 08/29/2017] [Indexed: 11/12/2022] Open
Abstract
Most land plants grow in association with arbuscular mycorrhizal fungi (AMF) in their roots and these fungi can cause transgenerational effects on plants' offspring. These may be caused by changes in DNA methylation of the offspring. In this study, we compared the amount of global DNA methylation in seeds of the gynodioecious plant Geranium sylvaticum in relation to the gender and the AMF status of the parents producing the seeds. The amount of DNA methylated was positively related to seed mass. Seeds produced by females had a similar proportion of methylated DNA regardless of the AMF status of the father siring the seed. By contrast, seeds from hermaphrodites had higher DNA methylation when sired by AMF fathers. We show to the best of our knowledge for the first time, that the AMF status of fathers can affect DNA methylation in seeds and that these changes in DNA methylation are further dependent on the gender of the mother producing the seeds.
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Affiliation(s)
- Sandra Varga
- School of Life Sciences, University of Lincoln, Joseph Banks Laboratories, Lincoln LN6 7TS, UK
| | - Carl D Soulsbury
- School of Life Sciences, University of Lincoln, Joseph Banks Laboratories, Lincoln LN6 7TS, UK
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53
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Antonovics J. Transmission dynamics: critical questions and challenges. Philos Trans R Soc Lond B Biol Sci 2017; 372:rstb.2016.0087. [PMID: 28289255 DOI: 10.1098/rstb.2016.0087] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/25/2016] [Indexed: 11/12/2022] Open
Abstract
This article overviews the dynamics of disease transmission in one-host-one-parasite systems. Transmission is the result of interacting host and pathogen processes, encapsulated with the environment in a 'transmission triangle'. Multiple transmission modes and their epidemiological consequences are often not understood because the direct measurement of transmission is difficult. However, its different components can be analysed using nonlinear transmission functions, contact matrices and networks. A particular challenge is to develop such functions for spatially extended systems. This is illustrated for vector transmission where a 'perception kernel' approach is developed that incorporates vector behaviour in response to host spacing. A major challenge is understanding the relative merits of the large number of approaches to quantifying transmission. The evolution of transmission mode itself has been a rather neglected topic, but is important in the context of understanding disease emergence and genetic variation in pathogens. Disease impacts many biological processes such as community stability, the evolution of sex and speciation, yet the importance of different transmission modes in these processes is not understood. Broader approaches and ideas to disease transmission are important in the public health realm for combating newly emerging infections.This article is part of the themed issue 'Opening the black box: re-examining the ecology and evolution of parasite transmission'.
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Affiliation(s)
- Janis Antonovics
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
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54
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Muyle A, Shearn R, Marais GA. The Evolution of Sex Chromosomes and Dosage Compensation in Plants. Genome Biol Evol 2017; 9:627-645. [PMID: 28391324 PMCID: PMC5629387 DOI: 10.1093/gbe/evw282] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/13/2017] [Indexed: 12/17/2022] Open
Abstract
Plant sex chromosomes can be vastly different from those of the few historical animal model organisms from which most of our understanding of sex chromosome evolution is derived. Recently, we have seen several advancements from studies on green algae, brown algae, and land plants that are providing a broader understanding of the variable ways in which sex chromosomes can evolve in distant eukaryotic groups. Plant sex-determining genes are being identified and, as expected, are completely different from those in animals. Species with varying levels of differentiation between the X and Y have been found in plants, and these are hypothesized to be representing different stages of sex chromosome evolution. However, we are also finding that sex chromosomes can remain morphologically unchanged over extended periods of time. Where degeneration of the Y occurs, it appears to proceed similarly in plants and animals. Dosage compensation (a phenomenon that compensates for the consequent loss of expression from the Y) has now been documented in a plant system, its mechanism, however, remains unknown. Research has also begun on the role of sex chromosomes in sexual conflict resolution, and it appears that sex-biased genes evolve similarly in plants and animals, although the functions of these genes remain poorly studied. Because the difficulty in obtaining sex chromosome sequences is increasingly being overcome by methodological developments, there is great potential for further discovery within the field of plant sex chromosome evolution.
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Affiliation(s)
- Aline Muyle
- Laboratoire de Biométrie et Biologie Evolutive (UMR 5558), CNRS/Université Lyon 1, Villeurbanne, France
| | - Rylan Shearn
- Laboratoire de Biométrie et Biologie Evolutive (UMR 5558), CNRS/Université Lyon 1, Villeurbanne, France
| | - Gabriel Ab Marais
- Laboratoire de Biométrie et Biologie Evolutive (UMR 5558), CNRS/Université Lyon 1, Villeurbanne, France
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55
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Antonova EV, Korchagina OS. Microsatellite loci variability in the ural population of Silene latifolia (caryophyllaceae). BIOL BULL+ 2017. [DOI: 10.1134/s1062359017050028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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56
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Evaluation of reference genes for reverse transcription quantitative real-time PCR (RT-qPCR) studies in Silene vulgaris considering the method of cDNA preparation. PLoS One 2017; 12:e0183470. [PMID: 28817728 PMCID: PMC5560574 DOI: 10.1371/journal.pone.0183470] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 08/04/2017] [Indexed: 01/05/2023] Open
Abstract
Accurate gene expression measurements are essential in studies of both crop and wild plants. Reverse transcription quantitative real-time PCR (RT-qPCR) has become a preferred tool for gene expression estimation. A selection of suitable reference genes for the normalization of transcript levels is an essential prerequisite of accurate RT-qPCR results. We evaluated the expression stability of eight candidate reference genes across roots, leaves, flower buds and pollen of Silene vulgaris (bladder campion), a model plant for the study of gynodioecy. As random priming of cDNA is recommended for the study of organellar transcripts and poly(A) selection is indicated for nuclear transcripts, we estimated gene expression with both random-primed and oligo(dT)-primed cDNA. Accordingly, we determined reference genes that perform well with oligo(dT)- and random-primed cDNA, making it possible to estimate levels of nucleus-derived transcripts in the same cDNA samples as used for organellar transcripts, a key benefit in studies of cyto-nuclear interactions. Gene expression variance was estimated by RefFinder, which integrates four different analytical tools. The SvACT and SvGAPDH genes were the most stable candidates across various organs of S. vulgaris, regardless of whether pollen was included or not.
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57
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Coelho MA, Bakkeren G, Sun S, Hood ME, Giraud T. Fungal Sex: The Basidiomycota. Microbiol Spectr 2017; 5:10.1128/microbiolspec.FUNK-0046-2016. [PMID: 28597825 PMCID: PMC5467461 DOI: 10.1128/microbiolspec.funk-0046-2016] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Indexed: 12/29/2022] Open
Abstract
Fungi of the Basidiomycota, representing major pathogen lineages and mushroom-forming species, exhibit diverse means to achieve sexual reproduction, with particularly varied mechanisms to determine compatibilities of haploid mating partners. For species that require mating between distinct genotypes, discrimination is usually based on both the reciprocal exchange of diffusible mating pheromones, rather than sexes, and the interactions of homeodomain protein signals after cell fusion. Both compatibility factors must be heterozygous in the product of mating, and genetic linkage relationships of the mating pheromone/receptor and homeodomain genes largely determine the complex patterns of mating-type variation. Independent segregation of the two compatibility factors can create four haploid mating genotypes from meiosis, referred to as tetrapolarity. This condition is thought to be ancestral to the basidiomycetes. Alternatively, cosegregation by linkage of the two mating factors, or in some cases the absence of the pheromone-based discrimination, yields only two mating types from meiosis, referred to as bipolarity. Several species are now known to have large and highly rearranged chromosomal regions linked to mating-type genes. At the population level, polymorphism of the mating-type genes is an exceptional aspect of some basidiomycete fungi, where selection under outcrossing for rare, intercompatible allelic variants is thought to be responsible for numbers of mating types that may reach several thousand. Advances in genome sequencing and assembly are yielding new insights by comparative approaches among and within basidiomycete species, with the promise to resolve the evolutionary origins and dynamics of mating compatibility genetics in this major eukaryotic lineage.
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Affiliation(s)
- Marco A. Coelho
- UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Guus Bakkeren
- Agriculture and Agri-Food Canada, Summerland Research and Development Centre Summerland, BC, V0H 1Z0, Canada
| | - Sheng Sun
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Michael E. Hood
- Department of Biology, Amherst College, 01002-5000 Amherst, Massachusetts, USA
| | - Tatiana Giraud
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France
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58
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Brothers AN, Delph LF. Divergence in style length and pollen size leads to a postmating-prezygotic reproductive barrier among populations of Silene latifolia. Evolution 2017; 71:1532-1540. [PMID: 28394403 DOI: 10.1111/evo.13248] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2016] [Accepted: 03/27/2017] [Indexed: 12/25/2022]
Abstract
A central tenet of speciation research is the need to identify reproductive isolating barriers. One approach to this line of research is to identify the phenotypes that lead to reproductive isolation. Several studies on flowering plants have shown that differences in style length contribute to reproductive isolation between species, leading us to consider whether style length could act as a reproductive barrier among populations of a single species. This could occur if style length varied sufficiently and pollen size covaried with style length. Populations of Silene latifolia exhibit variation in flower size, including style length, that is negatively correlated with annual precipitation. We show that this divergence in style length has a genetic basis and acts as a reproductive barrier: males from small-flowered populations produced relatively small pollen grains that were poor at fertilizing ovules when crossed to females from large-flowered populations, leading to a significant reduction in seed production. Manipulating the distance pollen tubes had to travel revealed that this failure was purely mechanical and not the result of other incompatibilities. These results show that style length acts as a postmating-prezygotic reproductive barrier and indicate a potential link between ecotypic differentiation and reproductive isolation within a species.
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Affiliation(s)
- Amanda N Brothers
- Department of Biology, Indiana University, Bloomington, Indiana, 47405
| | - Lynda F Delph
- Department of Biology, Indiana University, Bloomington, Indiana, 47405
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59
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Petit E, Silver C, Cornille A, Gladieux P, Rosenthal L, Bruns E, Yee S, Antonovics J, Giraud T, Hood ME. Co-occurrence and hybridization of anther-smut pathogens specialized on Dianthus hosts. Mol Ecol 2017; 26:1877-1890. [PMID: 28231407 DOI: 10.1111/mec.14073] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 01/13/2017] [Accepted: 02/09/2017] [Indexed: 01/05/2023]
Abstract
Host specialization has important consequences for the diversification and ecological interactions of obligate pathogens. The anther-smut disease of natural plant populations, caused by Microbotryum fungi, has been characterized by specialized host-pathogen interactions, which contribute in part to the isolation among these numerous fungal species. This study investigated the molecular variation of Microbotryum pathogens within the geographic and host-specific distributions on wild Dianthus species in southern European Alps. In contrast to prior studies on this pathogen genus, a range of overlapping host specificities was observed for four delineated Microbotryum lineages on Dianthus hosts, and their frequent co-occurrence within single-host populations was quantified at local and regional scales. In addition to potential consequences for direct pathogen competition, the sympatry of Microbotryum lineages led to hybridization between them in many populations, and these admixed genotypes suffered significant meiotic sterility. Therefore, this investigation of the anther-smut fungi reveals how variation in the degrees of host specificity can have major implications for ecological interactions and genetic integrity of differentiated pathogen lineages.
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Affiliation(s)
- Elsa Petit
- Stockbridge School of Agriculture, University of Massachusetts, Amherst, MA, USA
| | - Casey Silver
- Biology Department, Amherst College, Amherst, MA, 01002, USA
| | - Amandine Cornille
- Center for Adaptation to a Changing Environment, ETH Zürich, 8092, Zürich, Switzerland
| | - Pierre Gladieux
- UMR BGPI, INRA, Campus International de Baillarguet, 34398, Montpellier, France
| | - Lisa Rosenthal
- Biology Department, Amherst College, Amherst, MA, 01002, USA
| | - Emily Bruns
- Department of Biology, University of Virginia, Charlottesville, VA, 22903, USA
| | - Sarah Yee
- Biology Department, Amherst College, Amherst, MA, 01002, USA
| | - Janis Antonovics
- Department of Biology, University of Virginia, Charlottesville, VA, 22903, USA
| | - Tatiana Giraud
- Ecologie Systematique Evolution, CNRS, University of Paris-Sud, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France
| | - Michael E Hood
- Biology Department, Amherst College, Amherst, MA, 01002, USA
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60
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Stone JD, Koloušková P, Sloan DB, Štorchová H. Non-coding RNA may be associated with cytoplasmic male sterility in Silene vulgaris. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:1599-1612. [PMID: 28369520 PMCID: PMC5444436 DOI: 10.1093/jxb/erx057] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Cytoplasmic male sterility (CMS) is a widespread phenomenon in flowering plants caused by mitochondrial (mt) genes. CMS genes typically encode novel proteins that interfere with mt functions and can be silenced by nuclear fertility-restorer genes. Although the molecular basis of CMS is well established in a number of crop systems, our understanding of it in natural populations is far more limited. To identify CMS genes in a gynodioecious plant, Silene vulgaris, we constructed mt transcriptomes and compared transcript levels and RNA editing patterns in floral bud tissue from female and hermaphrodite full siblings. The transcriptomes from female and hermaphrodite individuals were very similar overall with respect to variation in levels of transcript abundance across the genome, the extent of RNA editing, and the order in which RNA editing and intron splicing events occurred. We found only a single genomic region that was highly overexpressed and differentially edited in females relative to hermaphrodites. This region is not located near any other transcribed elements and lacks an open-reading frame (ORF) of even moderate size. To our knowledge, this transcript would represent the first non-coding mt RNA associated with CMS in plants and is, therefore, an important target for future functional validation studies.
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Affiliation(s)
- James D Stone
- Institute of Experimental Botany v.v.i, Academy of Sciences of the Czech Republic, Rozvojová 263, Prague, 16502 Czech Republic
- Institute of Botany v.v.i, Academy of Sciences of the Czech Republic, Průhonice, Central Bohemia, 25243 Czech Republic
| | - Pavla Koloušková
- Institute of Experimental Botany v.v.i, Academy of Sciences of the Czech Republic, Rozvojová 263, Prague, 16502Czech Republic
| | - Daniel B Sloan
- Colorado State University, Department of Biology, Fort Collins, CO 80523, USA
| | - Helena Štorchová
- Institute of Experimental Botany v.v.i, Academy of Sciences of the Czech Republic, Rozvojová 263, Prague, 16502Czech Republic
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61
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Cegan R, Hudzieczek V, Hobza R. De novo transcriptome assembly of heavy metal tolerant Silene dioica. GENOMICS DATA 2017; 11:118-119. [PMID: 28180085 PMCID: PMC5279694 DOI: 10.1016/j.gdata.2017.01.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 01/25/2017] [Indexed: 11/26/2022]
Abstract
Silene dioica is a dioecious plant of the family Caryophyllaceae. In the present study, we used Illumina sequencing technology (MiSeq) to sequence, de novo assembly and annotate the transcriptomes of male and female copper tolerant S. dioica individuals. We sequenced the normalized mRNA of roots, shoots, flower buds and flowers for each sex. Raw reads of the transcriptome assembly project for S. dioica male and female individual have been deposited in NCBI's Sequence Read Archive (SRA) database with the accession number SRP094611. The Trinity and Detonate program was used to de novo assembly 92,347 transcripts for male and 94,757 transcripts for female transcriptome. The assembled transcriptome sequences for S. dioica male and female individuals can be accessed at NCBI with the following accession numbers: GFCG00000000 (male); GFCH00000000 (female). The obtained transcriptomic data will be useful for further studies focusing on copper tolerance, comparative transcriptome analysis with other Silene species and sex chromosomes evolution.
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Affiliation(s)
- Radim Cegan
- Department of Plant Developmental Genetics, Institute of Biophysics of the CAS, v.v.i., Kralovopolska 135, CZ-612 00 Brno, Czech Republic
| | - Vojtech Hudzieczek
- Department of Plant Developmental Genetics, Institute of Biophysics of the CAS, v.v.i., Kralovopolska 135, CZ-612 00 Brno, Czech Republic
| | - Roman Hobza
- Department of Plant Developmental Genetics, Institute of Biophysics of the CAS, v.v.i., Kralovopolska 135, CZ-612 00 Brno, Czech Republic; Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the CAS, v.v.i., Slechtitelu 31, CZ-78371 Olomouc-Holice, Czech Republic
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62
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Favre A, Widmer A, Karrenberg S. Differential adaptation drives ecological speciation in campions (Silene): evidence from a multi-site transplant experiment. THE NEW PHYTOLOGIST 2017; 213:1487-1499. [PMID: 27775172 DOI: 10.1111/nph.14202] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 08/12/2016] [Indexed: 06/06/2023]
Abstract
In order to investigate the role of differential adaptation for the evolution of reproductive barriers, we conducted a multi-site transplant experiment with the dioecious sister species Silene dioica and S. latifolia and their hybrids. Crosses within species as well as reciprocal first-generation (F1 ) and second-generation (F2 ) interspecific hybrids were transplanted into six sites, three within each species' habitat. Survival and flowering were recorded over 4 yr. At all transplant sites, the local species outperformed the foreign species, reciprocal F1 hybrids performed intermediately and F2 hybrids underperformed in comparison to F1 hybrids (hybrid breakdown). Females generally had slightly higher cumulative fitness than males in both within- and between-species crosses and we thus found little evidence for Haldane's rule acting on field performance. The strength of selection against F1 and F2 hybrids as well as hybrid breakdown increased with increasing strength of habitat adaptation (i.e. the relative fitness difference between the local and the foreign species) across sites. Our results suggest that differential habitat adaptation led to ecologically dependent post-zygotic reproductive barriers and drives divergence and speciation in this Silene system.
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Affiliation(s)
- Adrien Favre
- Plant Ecological Genetics, ETH Zurich, Institute of Integrative Biology, Universitätstrasse 16, 8092, Zurich, Switzerland
- Department of Molecular Evolution and Plant Systematics & Herbarium (LZ), Institute of Biology, University of Leipzig, Johannisallee 21-23, 04103, Leipzig, Germany
| | - Alex Widmer
- Plant Ecological Genetics, ETH Zurich, Institute of Integrative Biology, Universitätstrasse 16, 8092, Zurich, Switzerland
| | - Sophie Karrenberg
- Plant Ecological Genetics, ETH Zurich, Institute of Integrative Biology, Universitätstrasse 16, 8092, Zurich, Switzerland
- Department of Ecology and Genetics, Plant Ecology and Evolution, Uppsala University, Norbyvägen 18 D, 752 36, Uppsala, Sweden
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63
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Badouin H, Gladieux P, Gouzy J, Siguenza S, Aguileta G, Snirc A, Le Prieur S, Jeziorski C, Branca A, Giraud T. Widespread selective sweeps throughout the genome of model plant pathogenic fungi and identification of effector candidates. Mol Ecol 2017; 26:2041-2062. [DOI: 10.1111/mec.13976] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Revised: 12/15/2016] [Accepted: 12/19/2016] [Indexed: 12/11/2022]
Affiliation(s)
- H. Badouin
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech; Université Paris-Saclay; 91400 Orsay France
| | - P. Gladieux
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech; Université Paris-Saclay; 91400 Orsay France
- UMR BGPI; Campus International de Baillarguet; INRA; 34398 Montpellier France
| | - J. Gouzy
- Laboratoire des Interactions Plantes-Microorganismes (LIPM); UMR441; INRA; 31326 Castanet-Tolosan France
- Laboratoire des Interactions Plantes-Microorganismes (LIPM); UMR2594; CNRS; 31326 Castanet-Tolosan France
| | - S. Siguenza
- Laboratoire des Interactions Plantes-Microorganismes (LIPM); UMR441; INRA; 31326 Castanet-Tolosan France
- Laboratoire des Interactions Plantes-Microorganismes (LIPM); UMR2594; CNRS; 31326 Castanet-Tolosan France
| | - G. Aguileta
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech; Université Paris-Saclay; 91400 Orsay France
| | - A. Snirc
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech; Université Paris-Saclay; 91400 Orsay France
| | - S. Le Prieur
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech; Université Paris-Saclay; 91400 Orsay France
| | - C. Jeziorski
- Genotoul; GeT-PlaGe; INRA Auzeville 31326 Castanet-Tolosan France
- UAR1209; INRA Auzeville 31326 Castanet-Tolosan France
| | - A. Branca
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech; Université Paris-Saclay; 91400 Orsay France
| | - T. Giraud
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech; Université Paris-Saclay; 91400 Orsay France
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64
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Zhou J, Dudash MR, Fenster CB, Zimmer EA. Development of highly variable microsatellite markers for the tetraploid Silene stellata (Caryophyllaceae). APPLICATIONS IN PLANT SCIENCES 2016; 4:apps1600117. [PMID: 28101439 PMCID: PMC5238704 DOI: 10.3732/apps.1600117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 10/27/2016] [Indexed: 05/14/2023]
Abstract
PREMISE OF THE STUDY We designed and tested microsatellite markers for the North American native species Silene stellata (Caryophyllaceae) to investigate its population genetic structure and identify selection on floral design through male reproductive success. METHODS AND RESULTS A total of 153 candidate microsatellite loci were isolated based on next-generation sequencing. We identified 18 polymorphic microsatellite loci in three populations of S. stellata, with di- or trinucleotide repeats. Genotyping results showed the number of alleles per locus ranged from six to 45 and expected heterozygosity ranged from 0.511 to 0.951. Five of these loci were successfully amplified in S. virginica and S. caroliniana and were also polymorphic. CONCLUSIONS The microsatellite markers reported here provide a valuable tool for paternity analysis in S. stellata. They will also be useful for investigating the population genetic structures of S. stellata and related species.
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Affiliation(s)
- Juannan Zhou
- Behavior, Ecology, Evolution and Systematics Graduate Program, University of Maryland, College Park, Maryland 20742 USA
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC 20013-7012 USA
- Author for correspondence:
| | - Michele R. Dudash
- Department of Natural Resource Management, South Dakota State University, Brookings, South Dakota 57007 USA
| | - Charles B. Fenster
- Department of Biology and Microbiology, South Dakota State University, Brookings, South Dakota 57007 USA
| | - Elizabeth A. Zimmer
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC 20013-7012 USA
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65
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Zemp N, Tavares R, Muyle A, Charlesworth D, Marais GAB, Widmer A. Evolution of sex-biased gene expression in a dioecious plant. NATURE PLANTS 2016; 2:16168. [PMID: 27808231 DOI: 10.1038/nplants.2016.168] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 09/29/2016] [Indexed: 05/25/2023]
Abstract
Separate sexes and sex-biased gene expression have repeatedly evolved in animals and plants, but the underlying changes in gene expression remain unknown. Here, we studied a pair of plant species, one in which separate sexes and sex chromosomes evolved recently and one which maintained hermaphrodite flowers resembling the ancestral state, to reconstruct expression changes associated with the evolution of dioecy. We found that sex-biased gene expression has evolved in autosomal and sex-linked genes in the dioecious species. Most expression changes relative to hermaphrodite flowers occurred in females rather than males, with higher and lower expression in females leading to female-biased and male-biased expression, respectively. Expression changes were more common in genes located on the sex chromosomes than the autosomes and led to feminization of the X chromosome and masculinization of the Y chromosome. Our results support a scenario in which sex-biased gene expression evolved during the evolution of dioecy to resolve intralocus sexual conflicts over the allocation of resources.
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Affiliation(s)
- Niklaus Zemp
- ETH Zurich, Institute of Integrative Biology, Universitätstrasse 16, 8092 Zürich, Switzerland
| | - Raquel Tavares
- Université Lyon 1, CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622 Villeurbanne, France
| | - Aline Muyle
- Université Lyon 1, CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622 Villeurbanne, France
| | - Deborah Charlesworth
- University of Edinburgh, Institute of Evolutionary Biology, Edinburgh EH9 3JT, UK
| | - Gabriel A B Marais
- Université Lyon 1, CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622 Villeurbanne, France
| | - Alex Widmer
- ETH Zurich, Institute of Integrative Biology, Universitätstrasse 16, 8092 Zürich, Switzerland
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66
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Feurtey A, Gladieux P, Hood ME, Snirc A, Cornille A, Rosenthal L, Giraud T. Strong phylogeographic co-structure between the anther-smut fungus and its white campion host. THE NEW PHYTOLOGIST 2016; 212:668-679. [PMID: 27500396 DOI: 10.1111/nph.14125] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 06/18/2016] [Indexed: 06/06/2023]
Abstract
Although congruence between host and pathogen phylogenies has been extensively investigated, the congruence between host and pathogen genetic structures at the within-species level has received little attention. Using an unprecedented and comprehensive collection of associated plant-pathogen samples, we investigated the degree of congruence between the genetic structures across Europe of two evolutionary and ecological model organisms, the anther-smut pathogen Microbotryum lychnidis-dioicae and its host plant Silene latifolia. We demonstrated a significant and particularly strong level of host-pathogen co-structure, with three main genetic clusters displaying highly similar spatial ranges in Western Europe, Eastern Europe and Italy, respectively. Correcting for the geographical component of genetic variation, significant correlations were still found between the genetic distances of anther-smut and host populations. Inoculation experiments suggested plant local adaptation, at the cluster level, for resistance to pathogens. These findings indicate that the pathogen remained isolated in the same fragmented southern refugia as its host plant during the last glaciation, and that little long-distance dispersal has occurred since the recolonization of Europe for either the plant or the pathogen, despite their known ability to travel across continents. This, together with the inoculation results, suggests that coevolutionary and competitive processes may be drivers of host-pathogen co-structure.
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Affiliation(s)
- Alice Feurtey
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Orsay, 91400, France
| | - Pierre Gladieux
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Orsay, 91400, France
- UMR BGPI, INRA, Montpellier, 34398, France
| | - Michael E Hood
- Department of Biology, Amherst College, Amherst, MA, 01002, USA
| | - Alodie Snirc
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Orsay, 91400, France
| | - Amandine Cornille
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Orsay, 91400, France
| | - Lisa Rosenthal
- Department of Biology, Amherst College, Amherst, MA, 01002, USA
| | - Tatiana Giraud
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Orsay, 91400, France.
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67
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Karimullina E, Antonova EV, Pozolotina VN. Genetic variation in natural Melandrium album populations exposed to chronic ionizing radiation. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:21565-21576. [PMID: 27515527 DOI: 10.1007/s11356-016-7355-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 08/01/2016] [Indexed: 06/06/2023]
Abstract
The effect of radiation pollution on genetic variation in natural populations of Melandrium album was investigated at the head part of the East-Ural Radioactive Trace (EURT) and background areas. The highest genetic differentiation estimated using F ST was revealed between compared pairs of the background and impact samples in populations of M. album. The highest rate of polymorphism was observed at the closest to nuclear accident, Impact-1 site. The unique alleles (Mdh-3104, Pgi-2106, Lap 105, Mdh-296, and Dia 94) were discovered at the EURT. Individuals from chronically low-level irradiated sites were genetically closer than to plants from background sites using Nadhdh locus. The increase of the frequency of unique homozygous and heterozygous genotypes was identified in populations of M. album growing under chronic radiation exposure conditions. The largest contribution to the group of unique heterozygous genotypes at the EURT was made by three loci - Lap, Pgi-2, and Nadhdh; the main role in interpopulation differentiation of samples was made by the alleles Sod-2115, Skdh 100, and Nadhdh 100. Our results provide evidence for the correlation between the increase of genetic variation other than the «genetic erosion» and chronic radiation exposure factor in natural plant populations.
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Affiliation(s)
- Elina Karimullina
- Laboratory of Population Radiobiology, Institute of Plant and Animal Ecology, Ural Branch of the Russian Academy of Sciences, 8 Marta St., 202, Ekaterinburg, Russian Federation, 620144.
| | - Elena V Antonova
- Laboratory of Population Radiobiology, Institute of Plant and Animal Ecology, Ural Branch of the Russian Academy of Sciences, 8 Marta St., 202, Ekaterinburg, Russian Federation, 620144
| | - Vera N Pozolotina
- Laboratory of Population Radiobiology, Institute of Plant and Animal Ecology, Ural Branch of the Russian Academy of Sciences, 8 Marta St., 202, Ekaterinburg, Russian Federation, 620144
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68
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Croll D, Laine AL. What the population genetic structures of host and pathogen tell us about disease evolution. THE NEW PHYTOLOGIST 2016; 212:537-539. [PMID: 27735071 DOI: 10.1111/nph.14203] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Affiliation(s)
- Daniel Croll
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Universitätsstrasse 2, Zürich, CH-8092, Switzerland.
| | - Anna-Liisa Laine
- Metapopulation Research Centre, Plant Biology, Department of Biosciences, University of Helsinki, PO Box 65 (Viikinkaari 1), Helsinki, FI-00014, Finland.
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69
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Prieto-Benítez S, Dötterl S, Giménez-Benavides L. Circadian rhythm of a Silene species favours nocturnal pollination and constrains diurnal visitation. ANNALS OF BOTANY 2016; 118:907-918. [PMID: 27451986 PMCID: PMC5055817 DOI: 10.1093/aob/mcw136] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 04/24/2016] [Accepted: 05/31/2016] [Indexed: 05/24/2023]
Abstract
Background and Aims Traits related to flower advertisement and reward sometimes vary in a circadian way, reflecting phenotypic specialization. However, specialized flowers are not necessarily restricted to specialized pollinators. This is the case of most Silene species, typically associated with diurnal or nocturnal syndromes of pollination but usually showing complex suites of pollinators. Methods A Silene species with mixed floral features between diurnal and nocturnal syndromes was used to test how petal opening, nectar production, scent emission and pollination success correlate in a circadian rhythm, and whether this is influenced by environmental conditions. The effect of diurnal and nocturnal visitation rates on plant reproductive success is also explored in three populations, including the effect of the pollinating seed predator Hadena sancta. Key Results The result showed that repeated petal opening at dusk was correlated with nectar secretion and higher scent production during the night. However, depending on environmental conditions, petals remain opened for a while in the morning, when nectar and pollen still were available. Pollen deposition was similarly effective at night and in the morning, but less effective in the afternoon. These results were consistent with field studies. Conclusions The circadian rhythm regulating floral attractiveness and reward in S. colorata is predominantly adapted to nocturnal flower visitors. However, favourable environmental conditions lengthen the optimal daily period of flower attraction and pollination towards morning. This allows the complementarity of day and night pollination. Diurnal pollination may help to compensate the plant reproductive success when nocturnal pollinators are scarce and when the net outcome of H. sancta shifts from mutualism to parasitism. These results suggest a functional mechanism explaining why the supposed nocturnal syndrome of many Silene species does not successfully predict their pollinator guilds.
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Affiliation(s)
- Samuel Prieto-Benítez
- Departamento de Biología y Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos-ESCET, C/ Tulipán, s/n. 28933-Móstoles, Madrid, Spain
| | - Stefan Dötterl
- Department of Ecology & Evolution, Plant Ecology, University of Salzburg, Hellbrunnerstr. 34, 5020 Salzburg, Austria
| | - Luis Giménez-Benavides
- Departamento de Biología y Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos-ESCET, C/ Tulipán, s/n. 28933-Móstoles, Madrid, Spain
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70
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Aguileta G, Badouin H, Hood ME, Møller AP, Le Prieur S, Snirc A, Siguenza S, Mousseau TA, Shykoff JA, Cuomo CA, Giraud T. Lower prevalence but similar fitness in a parasitic fungus at higher radiation levels near Chernobyl. Mol Ecol 2016; 25:3370-83. [PMID: 27136128 DOI: 10.1111/mec.13675] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 04/04/2016] [Accepted: 04/15/2016] [Indexed: 12/24/2022]
Abstract
Nuclear disasters at Chernobyl and Fukushima provide examples of effects of acute ionizing radiation on mutations that can affect the fitness and distribution of species. Here, we investigated the prevalence of Microbotryum lychnidis-dioicae, a pollinator-transmitted fungal pathogen of plants causing anther-smut disease in Chernobyl, its viability, fertility and karyotype variation, and the accumulation of nonsynonymous mutations in its genome. We collected diseased flowers of Silene latifolia from locations ranging by more than two orders of magnitude in background radiation, from 0.05 to 21.03 μGy/h. Disease prevalence decreased significantly with increasing radiation level, possibly due to lower pollinator abundance and altered pollinator behaviour. Viability and fertility, measured as the budding rate of haploid sporidia following meiosis from the diploid teliospores, did not vary with increasing radiation levels and neither did karyotype overall structure and level of chromosomal size heterozygosity. We sequenced the genomes of twelve samples from Chernobyl and of four samples collected from uncontaminated areas and analysed alignments of 6068 predicted genes, corresponding to 1.04 × 10(7) base pairs. We found no dose-dependent differences in substitution rates (neither dN, dS, nor dN/dS). Thus, we found no significant evidence of increased deleterious mutation rates at higher levels of background radiation in this plant pathogen. We even found lower levels of nonsynonymous substitution rates in contaminated areas compared to control regions, suggesting that purifying selection was stronger in contaminated than uncontaminated areas. We briefly discuss the possibilities for a mechanistic basis of radio resistance in this nonmelanized fungus.
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Affiliation(s)
- Gabriela Aguileta
- Ecologie Systématique Evolution, CNRS, Univ. Paris-Sud, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France
| | - Helene Badouin
- Ecologie Systématique Evolution, CNRS, Univ. Paris-Sud, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France
| | - Michael E Hood
- Biology Department, Amherst College, Amherst, MA 01002, USA
| | - Anders P Møller
- Ecologie Systématique Evolution, CNRS, Univ. Paris-Sud, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France
| | - Stephanie Le Prieur
- Ecologie Systématique Evolution, CNRS, Univ. Paris-Sud, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France
| | - Alodie Snirc
- Ecologie Systématique Evolution, CNRS, Univ. Paris-Sud, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France
| | - Sophie Siguenza
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, F-31326, France.,CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, F-31326, France
| | - Timothy A Mousseau
- Department of Biological Sciences, University of South Carolina, Columbia, SC, 29208, USA
| | - Jacqui A Shykoff
- Ecologie Systématique Evolution, CNRS, Univ. Paris-Sud, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France
| | | | - Tatiana Giraud
- Ecologie Systématique Evolution, CNRS, Univ. Paris-Sud, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France
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71
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Casimiro-Soriguer I, Narbona E, Buide ML, del Valle JC, Whittall JB. Transcriptome and Biochemical Analysis of a Flower Color Polymorphism in Silene littorea (Caryophyllaceae). FRONTIERS IN PLANT SCIENCE 2016; 7:204. [PMID: 26973662 PMCID: PMC4770042 DOI: 10.3389/fpls.2016.00204] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 02/06/2016] [Indexed: 05/23/2023]
Abstract
Flower color polymorphisms are widely used as model traits from genetics to ecology, yet determining the biochemical and molecular basis can be challenging. Anthocyanin-based flower color variations can be caused by at least 12 structural and three regulatory genes in the anthocyanin biosynthetic pathway (ABP). We use mRNA-Seq to simultaneously sequence and estimate expression of these candidate genes in nine samples of Silene littorea representing three color morphs (dark pink, light pink and white) across three developmental stages in hopes of identifying the cause of flower color variation. We identified 29 putative paralogs for the 15 candidate genes in the ABP. We assembled complete coding sequences for 16 structural loci and nine of ten regulatory loci. Among these 29 putative paralogs, we identified 622 SNPs, yet only nine synonymous SNPs in Ans had allele frequencies that differentiated pigmented petals (dark pink and light pink) from white petals. These Ans allele frequency differences were further investigated with an expanded sequencing survey of 38 individuals, yet no SNPs consistently differentiated the color morphs. We also found one locus, F3h1, with strong differential expression between pigmented and white samples (>42x). This may be caused by decreased expression of Myb1a in white petal buds. Myb1a in S. littorea is a regulatory locus closely related to Subgroup 7 Mybs known to regulate F3h and other loci in the first half of the ABP in model species. We then compare the mRNA-Seq results with petal biochemistry which revealed cyanidin as the primary anthocyanin and five flavonoid intermediates. Concentrations of three of the flavonoid intermediates were significantly lower in white petals than in pigmented petals (rutin, quercetin and isovitexin). The biochemistry results for rutin, quercetin, luteolin and apigenin are consistent with the transcriptome results suggesting a blockage at F3h, possibly caused by downregulation of Myb1a.
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Affiliation(s)
- Inés Casimiro-Soriguer
- Department of Molecular Biology and Biochemical Engineering, Pablo de Olavide UniversitySeville, Spain
- Department of Plant Biology and Ecology, University of SevilleSeville, Spain
| | - Eduardo Narbona
- Department of Molecular Biology and Biochemical Engineering, Pablo de Olavide UniversitySeville, Spain
| | - M. L. Buide
- Department of Molecular Biology and Biochemical Engineering, Pablo de Olavide UniversitySeville, Spain
| | - José C. del Valle
- Department of Molecular Biology and Biochemical Engineering, Pablo de Olavide UniversitySeville, Spain
| | - Justen B. Whittall
- Department of Biology, Santa Clara University, College of Arts and SciencesSanta Clara, CA, USA
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72
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Hu XS, Filatov DA. The large-X effect in plants: increased species divergence and reduced gene flow on the Silene X-chromosome. Mol Ecol 2016; 25:2609-19. [PMID: 26479725 DOI: 10.1111/mec.13427] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 10/12/2015] [Accepted: 10/15/2015] [Indexed: 12/25/2022]
Abstract
The disproportionately large involvement of the X-chromosome in the isolation of closely related species (the large-X effect) has been reported for many animals, where X-linked genes are mostly hemizygous in the heterogametic sex. The expression of deleterious recessive mutations is thought to drive the frequent involvement of the X-chromosome in hybrid sterility, as well as to reduce interspecific gene flow for X-linked genes. Here, we evaluate the role of the X-chromosome in the speciation of two closely related plant species - the white and red campions (Silene latifolia and S. dioica) - that hybridize widely across Europe. The two species evolved separate sexes and sex chromosomes relatively recently (~10(7) years), and unlike most animal species, most X-linked genes have intact Y-linked homologs. We demonstrate that the X-linked genes show a very small and insignificant amount of interspecific gene flow, while gene flow involving autosomal loci is significant and sufficient to homogenize the gene pools of the two species. These findings are consistent with the hypothesis of the large-X effect in Silene and comprise the first report of this effect in plants. Nonhemizygosity of many X-linked genes in Silene males indicates that exposure of recessive mutations to selection may not be essential for the occurrence of the large-X effect. Several possible causes of the large-X effect in Silene are discussed.
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Affiliation(s)
- Xin-Sheng Hu
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX13RB, UK
| | - Dmitry A Filatov
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX13RB, UK
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73
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Zhang JJ, Montgomery BR, Huang SQ. Evidence for asymmetrical hybridization despite pre- and post-pollination reproductive barriers between two Silene species. AOB PLANTS 2016; 8:plw032. [PMID: 27178066 PMCID: PMC4940505 DOI: 10.1093/aobpla/plw032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 04/27/2016] [Indexed: 05/14/2023]
Abstract
Interspecific hybridization is widespread among plants; nevertheless, pre- and post-zygotic isolating mechanisms may maintain species integrity for interfertile species in sympatry despite some gene flow. Interspecific hybridization and potential isolating barriers were evaluated between co-flowering Silene asclepiadea and Silene yunnanensis in an alpine community in southwest China. We investigated morphological and molecular (nuclear microsatellites and chloroplast gene sequence) variation in sympatric populations of S. asclepiadea and S. yunnanensis. Additionally, we analyzed pollinator behaviour and compared reproductive success between the putative hybrids and their parental species. Both the molecular and morphological data indicate that there were putative natural hybrids in the field, with S. asclepiadae the ovule parent and S. yunnanensis the pollen parent. Bumblebees were the primary visitors to S. asclepiadae and putative hybrids, while butterflies were the primary visitors to S. yunnanensis Pollen production and viability were significantly lower in putative hybrids than the parental species. The direction of hybridization is quite asymmetric from S. yunnanensis to S. asclepiadea Protandry combined with later peak flowering of S. yunnanensis, and pollinator preference may have contributed to the asymmetric pattern of hybridization, but putative hybrids were rare. Our results thus suggest that despite gene flow, S. asclepiadea and S. yunnanensis can maintain species boundaries, perhaps as a result of floral isolation and low fecundity of the hybrids.
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Affiliation(s)
- Jin-Ju Zhang
- School of Life Sciences, Central China Normal University, Wuhan 430079, China State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Benjamin R Montgomery
- Division of Natural Sciences & Engineering, University of South Carolina Upstate, Spartanburg, SC 29303, USA
| | - Shuang-Quan Huang
- School of Life Sciences, Central China Normal University, Wuhan 430079, China
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74
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Wu Z, Tembrock LR. Two complete chloroplast genomes of white campion (Silene latifolia) from male and female individuals. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 28:375-376. [PMID: 26714215 DOI: 10.3109/19401736.2015.1126829] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In this study, we assembled two individuals' complete chloroplast genomes with one male and one female from the dioecious plant species white campion (Silene latifolia). The two chloroplast genomes have an identical composition with each other as a circular molecule of 150 931 bp in length, with an overall GC content of 36.4%. The genomes consist of a pair of inverted repeats (IRs) of 25 503 bp, separated by a large single-copy (LSC) region and a small single-copy (SSC) region of 82 708 and 17 217 bp, respectively. The genomes contain 111 single copy genes, including 77 protein-coding genes, 4 ribosomal RNA genes and 30 transfer RNA genes. In these protein-coding genes, eight genes (rpl16, rpoC1, rps16, petD, petB, ndhB, ndhA and atpF) contain a single intron and three genes (rps12, clpP and ycf3) contain two introns. The two newly sequenced chloroplast genomes provide valuable information for detecting polymorphisms within species and between sexes.
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Affiliation(s)
- Zhiqiang Wu
- a Department of Biology , Colorado State University , Fort Collins , CO , USA
| | - Luke R Tembrock
- a Department of Biology , Colorado State University , Fort Collins , CO , USA
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75
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Zemp N, Tavares R, Widmer A. Fungal Infection Induces Sex-Specific Transcriptional Changes and Alters Sexual Dimorphism in the Dioecious Plant Silene latifolia. PLoS Genet 2015; 11:e1005536. [PMID: 26448481 PMCID: PMC4598173 DOI: 10.1371/journal.pgen.1005536] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 08/27/2015] [Indexed: 01/27/2023] Open
Abstract
Sexual dimorphism, including differences in morphology, behavior and physiology between females and males, is widespread in animals and plants and is shaped by gene expression differences between the sexes. Such expression differences may also underlie sex-specific responses of hosts to pathogen infections, most notably when pathogens induce partial sex reversal in infected hosts. The genetic changes associated with sex-specific responses to pathogen infections on the one hand, and sexual dimorphism on the other hand, remain poorly understood. The dioecious White Campion (Silene latifolia) displays sexual dimorphism in floral traits and infection with the smut fungus Micobrotryum lychnidis-dioicae induces a partial sex reversal in females. We find strong sex-specific responses to pathogen infection and reduced sexual dimorphism in infected S. latifolia. This provides a direct link between pathogen-mediated changes in sex-biased gene expression and altered sexual dimorphism in the host. Expression changes following infection affected mainly genes with male-biased expression in healthy plants. In females, these genes were up-regulated, leading to a masculinization of the transcriptome. In contrast, infection in males was associated with down-regulation of these genes, leading to a demasculinization of the transcriptome. To a lesser extent, genes with female-biased expression in healthy plants were also affected in opposite directions in the two sexes. These genes were overall down-regulated in females and up-regulated in males, causing, respectively, a defeminization in infected females and a feminization of the transcriptome in infected males. Our results reveal strong sex-specific responses to pathogen infection in a dioecious plant and provide a link between pathogen-induced changes in sex-biased gene expression and sexual dimorphism. Females and males differ from each other in many traits, including morphology, behavior and physiology. Differences in gene expression between the sexes, known as sex-biased gene expression, contribute to such sexual dimorphism. Here we characterize the responses of females and males of the dioecious plant Silene latifolia to infection with the anther smut fungus Micobrotryum lychnidis-dioicae. This fungus sterilizes the plant and induces a partial sex reversal in female hosts that form rudimentary stamens, thus allowing the fungus to transmit its spores via pollinators. Our comparisons of gene expression in healthy and infected plants reveal strong sex-specific responses to anther smut infection. Expression changes in females and males are in opposite directions and are associated with reduced sexual dimorphism between infected females and males. Our study reveals that infection with the anther smut fungus alters the extent of sex-biased gene expression in S. latifolia in a sex-specific manner and highlights how transcriptomic changes in females and males shape sexual dimorphism.
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Affiliation(s)
- Niklaus Zemp
- Institute of Integrative Biology (IBZ), ETH Zurich, Zürich, Switzerland
| | - Raquel Tavares
- Laboratoire de Biométrie et Biologie Evolutive (UMR 5558), CNRS / Université Lyon 1, Villeurbanne, France
| | - Alex Widmer
- Institute of Integrative Biology (IBZ), ETH Zurich, Zürich, Switzerland
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76
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Abstract
The nonrecombining regions of animal Y chromosomes are known to undergo genetic degeneration, but previous work has failed to reveal large-scale gene degeneration on plant Y chromosomes. Here, we uncover rapid and extensive degeneration of Y-linked genes in a plant species, Silene latifolia, that evolved sex chromosomes de novo in the last 10 million years. Previous transcriptome-based studies of this species missed unexpressed, degenerate Y-linked genes. To identify sex-linked genes, regardless of their expression, we sequenced male and female genomes of S. latifolia and integrated the genomic contigs with a high-density genetic map. This revealed that 45% of Y-linked genes are not expressed, and 23% are interrupted by premature stop codons. This contrasts with X-linked genes, in which only 1.3% of genes contained stop codons and 4.3% of genes were not expressed in males. Loss of functional Y-linked genes is partly compensated for by gene-specific up-regulation of X-linked genes. Our results demonstrate that the rate of genetic degeneration of Y-linked genes in S. latifolia is as fast as in animals, and that the evolutionary trajectories of sex chromosomes are similar in the two kingdoms.
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77
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Müller E, Hlaváčková I, Svoen ME, Alsos IG, Eidesen PB. Characterization of 14 microsatellite markers for Silene acaulis (Caryophyllaceae)(1). APPLICATIONS IN PLANT SCIENCES 2015; 3:apps1500036. [PMID: 26421249 PMCID: PMC4578374 DOI: 10.3732/apps.1500036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 04/14/2015] [Indexed: 05/15/2023]
Abstract
PREMISE OF THE STUDY Fifty candidate microsatellite markers, generated using 454 shotgun sequencing, were tested for the widespread arctic/alpine herb Silene acaulis (Caryophyllaceae). METHODS AND RESULTS Fourteen out of 50 markers resulted in polymorphic products with profiles that enabled interpretation. The numbers of alleles per locus ranged from two to six, and the expected heterozygosity per locus ranged from 0.06 to 0.68. Analysis of F0 and F1 samples proved that one allele was always inherited maternally. Four multiplex mixes have been developed. CONCLUSIONS Microsatellite markers for this species will be a valuable tool to study detailed small-scale genetic patterns in an arctic/alpine herb and to relate them to demographic parameters.
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Affiliation(s)
- Eike Müller
- University Centre in Svalbard, Postboks 156, NO-9170 Longyearbyen, Norway
| | - Iva Hlaváčková
- Institute of Chemical Technology, University of Chemistry and Technology (UCT) Prague, Technická 5, 16628 Prague, Czech Republic
| | - Mildrid Elvik Svoen
- University Centre in Svalbard, Postboks 156, NO-9170 Longyearbyen, Norway
- University of Oslo, Postboks 1072 Blindern, NO-0316 Oslo, Norway
| | - Inger Greve Alsos
- University Centre in Svalbard, Postboks 156, NO-9170 Longyearbyen, Norway
- Tromsø Museum, University of Tromsø, Postboks 6050 Langnes, NO-9037 Tromsø, Norway
| | - Pernille Bronken Eidesen
- University Centre in Svalbard, Postboks 156, NO-9170 Longyearbyen, Norway
- Author for correspondence:
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78
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Kyrkou I, Iriondo JM, García-Fernández A. A glacial survivor of the alpine Mediterranean region: phylogenetic and phylogeographic insights into Silene ciliata Pourr. (Caryophyllaceae). PeerJ 2015; 3:e1193. [PMID: 26312184 PMCID: PMC4548490 DOI: 10.7717/peerj.1193] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 07/26/2015] [Indexed: 11/20/2022] Open
Abstract
Silene ciliata Pourr. (Caryophyllaceae) is a species with a highly disjunct distribution which inhabits the alpine mountains of the Mediterranean Basin. We investigated the phylogeny and phylogeography of the species to (a) clarify the long-suggested division of S. ciliata into two subspecies, (b) evaluate its phylogenetic origin and (c) assess whether the species' diversification patterns were affected by the Mediterranean relief. For this purpose, we collected DNA from 25 populations of the species that inhabit the mountains of Portugal, Spain, France, Italy, former Yugoslav Republic of Macedonia, Bulgaria and Greece and studied the plastid regions rbcL, rps16 and trnL. Major intraspecific variation was supported by all analyses, while the possibility of the existence of more varieties or subspecies was not favoured. Plastid DNA (cpDNA) evidence was in accordance with the division of S. ciliata into the two subspecies, one spreading west (Iberian Peninsula and Central Massif) and the other east of the Alps region (Italian and Balkan Peninsula). This study proposes that the species' geographically disconnected distribution has probably derived from vicariance processes and from the Alps acting as a barrier to the species' dispersal. The monophyletic origin of the species is highly supported. cpDNA patterns were shown independent of the chromosome evolution in the populations and could have resulted from a combination of geographic factors providing links and barriers, climatic adversities and evolutionary processes that took place during Quaternary glaciations.
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Affiliation(s)
- Ifigeneia Kyrkou
- Department of Biotechnology, Agricultural University of Athens , Athens , Greece ; Area de Biodiversidad y Conservación, Universidad Rey Juan Carlos , Móstoles, Madrid , Spain
| | - José María Iriondo
- Area de Biodiversidad y Conservación, Universidad Rey Juan Carlos , Móstoles, Madrid , Spain
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79
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Ferreira V, Castro I, Rocha J, Crespí AL, Pinto-Carnide O, Amich F, Almeida R, Carnide V. Chloroplast and nuclear DNA studies in Iberian Peninsula endemic Silene scabriflora subspecies using cpSSR and ISSR markers: Genetic diversity and phylogenetic relationships. BIOCHEM SYST ECOL 2015. [DOI: 10.1016/j.bse.2015.06.029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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80
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Abstract
Background Silene latifolia represents one of the best-studied plant sex chromosome systems. A new approach using RNA-seq data has recently identified hundreds of new sex-linked genes in this species. However, this approach is expected to miss genes that are either not expressed or are expressed at low levels in the tissue(s) used for RNA-seq. Therefore other independent approaches are needed to discover such sex-linked genes. Results Here we used 10 well-characterized S. latifolia sex-linked genes and their homologs in Silene vulgaris, a species without sex chromosomes, to screen BAC libraries of both species. We isolated and sequenced 4 Mb of BAC clones of S. latifolia X and Y and S. vulgaris genomic regions, which yielded 59 new sex-linked genes (with S. vulgaris homologs for some of them). We assembled sequences that we believe represent the tip of the Xq arm. These sequences are clearly not pseudoautosomal, so we infer that the S. latifolia X has a single pseudoautosomal region (PAR) on the Xp arm. The estimated mean gene density in X BACs is 2.2 times lower than that in S. vulgaris BACs, agreeing with the genome size difference between these species. Gene density was estimated to be extremely low in the Y BAC clones. We compared our BAC-located genes with the sex-linked genes identified in previous RNA-seq studies, and found that about half of them (those with low expression in flower buds) were not identified as sex-linked in previous RNA-seq studies. We compiled a set of ~70 validated X/Y genes and X-hemizygous genes (without Y copies) from the literature, and used these genes to show that X-hemizygous genes have a higher probability of being undetected by the RNA-seq approach, compared with X/Y genes; we used this to estimate that about 30 % of our BAC-located genes must be X-hemizygous. The estimate is similar when we use BAC-located genes that have S. vulgaris homologs, which excludes genes that were gained by the X chromosome. Conclusions Our BAC sequencing identified 59 new sex-linked genes, and our analysis of these BAC-located genes, in combination with RNA-seq data suggests that gene losses from the S. latifolia Y chromosome could be as high as 30 %, higher than previous estimates of 10-20 %. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1698-7) contains supplementary material, which is available to authorized users.
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81
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Twyford AD, Streisfeld MA, Lowry DB, Friedman J. Genomic studies on the nature of species: adaptation and speciation inMimulus. Mol Ecol 2015; 24:2601-9. [DOI: 10.1111/mec.13190] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Revised: 03/25/2015] [Accepted: 03/27/2015] [Indexed: 12/27/2022]
Affiliation(s)
- Alex D. Twyford
- Ashworth Laboratories; Institute of Evolutionary Biology; The University of Edinburgh; Charlotte Auerbach Road Edinburgh EH9 3FL UK
- Department of Biology; Syracuse University; 107 College Place Syracuse NY 13244 USA
| | | | - David B. Lowry
- Plant Biology Laboratories; Department of Plant Biology; Michigan State University; 612 Wilson Road Room 166 East Lansing MI 48824 USA
| | - Jannice Friedman
- Department of Biology; Syracuse University; 107 College Place Syracuse NY 13244 USA
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82
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Casimiro-Soriguer I, Buide ML, Narbona E. Diversity of sexual systems within different lineages of the genus Silene. AOB PLANTS 2015; 7:plv037. [PMID: 25862920 PMCID: PMC4433491 DOI: 10.1093/aobpla/plv037] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 03/26/2015] [Indexed: 05/15/2023]
Abstract
Species and populations can be categorized by their sexual systems, depending on the spatial distribution of female and male reproductive structures within and among plants. Although a high diversity of sexual systems exists in Silene, their relative frequency at the genus and infrageneric level is unknown. Here, we carried out an extensive literature search for direct or indirect descriptions of sexual systems in Silene species. We found descriptions of sexual systems for 98 Silene species, where 63 and 35 correspond to the phylogenetically supported subgenera Silene and Behenantha, respectively. Hermaphroditism was the commonest sexual system (58.2 %), followed by dioecy (14.3 %), gynodioecy (13.3 %) and gynodioecy-gynomonoecy (i.e. hermaphroditic, female and gynomonoecious plants coexisting in the same population; 12.2 %). The presence of these sexual systems in both subgenera suggests their multiple origins. In 17 species, the description of sexual systems varied, and in most cases these differences corresponded to variations within or among populations. Interestingly, the poorly studied gynodioecy-gynomonoecy sexual system showed similar frequency to dioecy and gynodioecy in both subgenera. In addition, the incidence of gynodioecy-gynomonoecy was analysed in the species of section Psammophilae (Silene littorea, S. psammitis, S. adscendens and S. cambessedesii), in a survey of 26 populations across the distribution area of the species. The four species showed gynomonoecy-gynodioecy in most populations. Hermaphrodites were the most frequent morph, with a low number of females and gynomonoecious plants in all populations. The frequency of sexual morphs varied significantly among the studied populations but not among species. Female plants generally produced smaller numbers of flowers than hermaphroditic or gynomonoecious plants, and the percentages of female flowers per population were low. All these findings suggest that the gynodioecious-gynomonoecious sexual system in section Psammophilae is closer to hermaphroditism or gynomonoecy than gynodioecy.
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Affiliation(s)
- Inés Casimiro-Soriguer
- Área de Botánica, Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Ctra. de Utrera, km 1, 41013 Sevilla, Spain Área de Botánica, Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Avenida Reina Mercedes s/n, 41012 Sevilla, Spain
| | - Maria L Buide
- Área de Botánica, Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Ctra. de Utrera, km 1, 41013 Sevilla, Spain
| | - Eduardo Narbona
- Área de Botánica, Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Ctra. de Utrera, km 1, 41013 Sevilla, Spain
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83
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Carlsson-Granér U, Thrall PH. Host resistance and pathogen infectivity in host populations with varying connectivity. Evolution 2015; 69:926-38. [DOI: 10.1111/evo.12631] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 02/18/2015] [Indexed: 01/28/2023]
Affiliation(s)
- Ulla Carlsson-Granér
- Department of Ecology and Environmental Sciences; University of Umeå; S-90187 Umeå Sweden
| | - Peter H. Thrall
- CSIRO Agriculture Flagship GPO Box 1600; Canberra ACT 2601 Australia
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84
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Abstract
Dioecy (separate male and female individuals) ensures outcrossing and is more prevalent in animals than in plants. Although it is common in bryophytes and gymnosperms, only 5% of angiosperms are dioecious. In dioecious higher plants, flowers borne on male and female individuals are, respectively deficient in functional gynoecium and androecium. Dioecy is inherited via three sex chromosome systems: XX/XY, XX/X0 and WZ/ZZ, such that XX or WZ is female and XY, X0 or ZZ are males. The XX/XY system generates the rarer XX/X0 and WZ/ZZ systems. An autosome pair begets XY chromosomes. A recessive loss-of-androecium mutation (ana) creates X chromosome and a dominant gynoecium-suppressing (GYS) mutation creates Y chromosome. The ana/ANA and gys/GYS loci are in the sex-determining region (SDR) of the XY pair. Accumulation of inversions, deleterious mutations and repeat elements, especially transposons, in the SDR of Y suppresses recombination between X and Y in SDR, making Y labile and increasingly degenerate and heteromorphic from X. Continued recombination between X and Y in their pseudoautosomal region located at the ends of chromosomal arms allows survival of the degenerated Y and of the species. Dioecy is presumably a component of the evolutionary cycle for the origin of new species. Inbred hermaphrodite species assume dioecy. Later they suffer degenerate-Y-led population regression. Cross-hybridization between such extinguishing species and heterologous species, followed by genome duplication of segregants from hybrids, give rise to new species.
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85
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Recent and massive expansion of the mating-type-specific region in the smut fungus Microbotryum. Genetics 2015; 199:809-16. [PMID: 25567990 DOI: 10.1534/genetics.114.171702] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The presence of large genomic regions with suppressed recombination (SR) is a key shared property of some sex- and mating-type determining (mat) chromosomes identified to date in animals, plants, and fungi. Why such regions form and how they evolve remain central questions in evolutionary genetics. The smut fungus Microbotryum lychnis-dioicae is a basidiomycete fungus in which dimorphic mat chromosomes have been reported, but the size, age, and evolutionary dynamics of the SR region remains unresolved. To identify the SR region in M. lychnis-dioicae and to study its evolution, we sequenced 12 genomes (6 per mating type) of this species and identified the genomic contigs that show fixed sequence differences between the mating types. We report that the SR region spans more than half of the mat chromosome (>2.3 Mbp) and that it is of very recent origin (∼2 × 10(6) years) as the average sequence divergence between mating types was only 2% in the SR region. This contrasts with a much higher divergence in and around the mating-type determining pheromone receptor locus in the SR, suggesting a recent and massive expansion of the SR region. Our results comprise the first reported case of recent massive SR expansion documented in a basidiomycete fungus.
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86
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Gladieux P, Feurtey A, Hood ME, Snirc A, Clavel J, Dutech C, Roy M, Giraud T. The population biology of fungal invasions. Mol Ecol 2015; 24:1969-86. [DOI: 10.1111/mec.13028] [Citation(s) in RCA: 142] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 11/24/2014] [Accepted: 11/28/2014] [Indexed: 12/16/2022]
Affiliation(s)
- P. Gladieux
- Ecologie; Systématique et Evolution; Université Paris-Sud; Bâtiment 360 F-91405 Orsay France
- CNRS; 91405 Orsay France
| | - A. Feurtey
- Ecologie; Systématique et Evolution; Université Paris-Sud; Bâtiment 360 F-91405 Orsay France
- CNRS; 91405 Orsay France
| | - M. E. Hood
- Department of Biology; Amherst College; Amherst Massachusetts 01002 USA
| | - A. Snirc
- Ecologie; Systématique et Evolution; Université Paris-Sud; Bâtiment 360 F-91405 Orsay France
- CNRS; 91405 Orsay France
| | - J. Clavel
- Conservation des Espèces; Restauration et Suivi des Populations - CRBPO; Muséum National d'Histoire Naturelle-CNRS-Université Pierre et Marie Curie; 55 rue Buffon 75005 Paris France
| | - C. Dutech
- Biodiversité Gènes et Communautés; INRA-Université Bordeaux 1; Site de Pierroton 33610 Cestas France
| | - M. Roy
- Evolution et Diversité Biologique; Université Toulouse Paul Sabatier-Ecole Nationale de Formation Agronomique-CNRS; 118 route de Narbonne 31062 Toulouse France
| | - T. Giraud
- Ecologie; Systématique et Evolution; Université Paris-Sud; Bâtiment 360 F-91405 Orsay France
- CNRS; 91405 Orsay France
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87
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Liston A, Cronn R, Ashman TL. Fragaria: a genus with deep historical roots and ripe for evolutionary and ecological insights. AMERICAN JOURNAL OF BOTANY 2014; 101:1686-99. [PMID: 25326614 DOI: 10.3732/ajb.1400140] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The cultivated strawberry, Fragaria ×ananassa, is one of the youngest domesticated plants. Its 18th century origin via hybridization in Europe between the North American F. virginiana and the South American F. chiloensis was documented by the botanist Antoine Nicolas Duchesne. His 1766 "Natural History of Strawberries" is an extraordinary work that integrates fundamental discoveries on the biology, ecology, and phylogeny of Fragaria with applied information on cultivation and ethnobotanical uses, serving as an inspiration for current research in the genus. Fragaria species exhibit the full range of sexual systems in the gynodioecy pathway from hermaphroditism to dioecy (and back again), as well as variation in self-compatibility, and evidence of sex chromosomes with female heterogamety. The genus is also characterized by interspecific hybridization and polyploidy, with a natural range of ploidy levels from diploids to decaploids. This biological diversity, combined with the availability of genomic resources and the ease of growing and experimenting with the plants, makes Fragaria a very attractive system for ecological and evolutionary genomics. The goal of this review is to introduce Fragaria as a model genus and to provide a roadmap for future integrative research. These research directions will deepen our understanding of the ecological and evolutionary context that shaped the ancestors of the cultivated strawberry, not only providing information that can be applied to efforts to shape the future of this important fruit crop but also our understanding of key transitions in plant evolution.
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Affiliation(s)
- Aaron Liston
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331 USA
| | - Richard Cronn
- Pacific Northwest Research Station, USDA Forest Service, Corvallis, Oregon 97331 USA
| | - Tia-Lynn Ashman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260 USA
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88
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Aydin Z, Marcussen T, Ertekin AS, Oxelman B. Marginal likelihood estimate comparisons to obtain optimal species delimitations in Silene sect. Cryptoneurae (Caryophyllaceae). PLoS One 2014; 9:e106990. [PMID: 25216034 PMCID: PMC4162574 DOI: 10.1371/journal.pone.0106990] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 07/28/2014] [Indexed: 11/27/2022] Open
Abstract
Coalescent-based inference of phylogenetic relationships among species takes into account gene tree incongruence due to incomplete lineage sorting, but for such methods to make sense species have to be correctly delimited. Because alternative assignments of individuals to species result in different parametric models, model selection methods can be applied to optimise model of species classification. In a Bayesian framework, Bayes factors (BF), based on marginal likelihood estimates, can be used to test a range of possible classifications for the group under study. Here, we explore BF and the Akaike Information Criterion (AIC) to discriminate between different species classifications in the flowering plant lineage Silene sect. Cryptoneurae (Caryophyllaceae). We estimated marginal likelihoods for different species classification models via the Path Sampling (PS), Stepping Stone sampling (SS), and Harmonic Mean Estimator (HME) methods implemented in BEAST. To select among alternative species classification models a posterior simulation-based analog of the AIC through Markov chain Monte Carlo analysis (AICM) was also performed. The results are compared to outcomes from the software BP&P. Our results agree with another recent study that marginal likelihood estimates from PS and SS methods are useful for comparing different species classifications, and strongly support the recognition of the newly described species S. ertekinii.
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Affiliation(s)
- Zeynep Aydin
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Department of Biology, Faculty of Sciences, University of Dicle, Diyarbakir, Turkey
- * E-mail:
| | - Thomas Marcussen
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
| | | | - Bengt Oxelman
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
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89
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Determinants of genetic structure in a nonequilibrium metapopulation of the plant Silene latifolia. PLoS One 2014; 9:e104575. [PMID: 25198341 PMCID: PMC4157773 DOI: 10.1371/journal.pone.0104575] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 07/15/2014] [Indexed: 11/19/2022] Open
Abstract
Population genetic differentiation will be influenced by the demographic history of populations, opportunities for migration among neighboring demes and founder effects associated with repeated extinction and recolonization. In natural populations, these factors are expected to interact with each other and their magnitudes will vary depending on the spatial distribution and age structure of local demes. Although each of these effects has been individually identified as important in structuring genetic variance, their relative magnitude is seldom estimated in nature. We conducted a population genetic analysis in a metapopulation of the angiosperm, Silene latifolia, from which we had more than 20 years of data on the spatial distribution, demographic history, and extinction and colonization of demes. We used hierarchical Bayesian methods to disentangle which features of the populations contributed to among population variation in allele frequencies, including the magnitude and direction of their effects. We show that population age, long-term size and degree of connectivity all combine to affect the distribution of genetic variance; small, recently-founded, isolated populations contributed most to increase FST in the metapopulation. However, the effects of population size and population age are best understood as being modulated through the effects of connectivity to other extant populations, i.e. FST diminishes as populations age, but at a rate that depends how isolated the population is. These spatial and temporal correlates of population structure give insight into how migration, founder effect and within-deme genetic drift have combined to enhance and restrict genetic divergence in a natural metapopulation.
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90
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Schuck S, Weinhold A, Luu VT, Baldwin IT. Isolating fungal pathogens from a dynamic disease outbreak in a native plant population to establish plant-pathogen bioassays for the ecological model plant Nicotiana attenuata. PLoS One 2014; 9:e102915. [PMID: 25036191 PMCID: PMC4103856 DOI: 10.1371/journal.pone.0102915] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 06/25/2014] [Indexed: 11/19/2022] Open
Abstract
The wild tobacco species Nicotiana attenuata has been intensively used as a model plant to study its interaction with insect herbivores and pollinators in nature, however very little is known about its native pathogen community. We describe a fungal disease outbreak in a native N. attenuata population comprising 873 plants growing in an area of about 1500 m2. The population was divided into 14 subpopulations and disease symptom development in the subpopulations was monitored for 16 days, revealing a waxing and waning of visible disease symptoms with some diseased plants recovering fully. Native fungal N. attenuata pathogens were isolated from diseased plants, characterized genetically, chemotaxonomically and morphologically, revealing several isolates of the ascomycete genera Fusarium and Alternaria, that differed in the type and strength of the disease symptoms they caused in bioassays on either detached leaves or intact soil-grown plants. These isolates and the bioassays will empower the study of N. attenuata-pathogen interactions in a realistic ecological context.
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Affiliation(s)
- Stefan Schuck
- Max Planck Institute for Chemical Ecology, Department of Molecular Ecology, Jena, Germany
| | - Arne Weinhold
- Max Planck Institute for Chemical Ecology, Department of Molecular Ecology, Jena, Germany
| | - Van Thi Luu
- Max Planck Institute for Chemical Ecology, Department of Molecular Ecology, Jena, Germany
| | - Ian T. Baldwin
- Max Planck Institute for Chemical Ecology, Department of Molecular Ecology, Jena, Germany
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91
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Diversity of Secondary Metabolites in the Genus Silene L. (Caryophyllaceae)—Structures, Distribution, and Biological Properties. DIVERSITY-BASEL 2014. [DOI: 10.3390/d6030415] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The genus Silene (family Caryophyllaceae) comprises more than 700 species, which are widely distributed in temperate zones of the Northern Hemisphere, but are also present in Africa and have been introduced in other continents. Silene produces a high diversity of secondary metabolites and many of them show interesting biological and pharmacological activities. More than 450 compounds have been isolated; important classes include phytoecdysteroids (which mimic insect molting hormones), triterpene saponins (with detergent properties), volatiles, other terpenoids and phenolics. This review focusses on the phytochemical diversity, distribution of Silene secondary metabolites and their biological activities.
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92
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Kula AAR, Castillo DM, Dudash MR, Fenster CB. Interactions between a pollinating seed predator and its host plant: the role of environmental context within a population. Ecol Evol 2014; 4:2901-12. [PMID: 25165527 PMCID: PMC4130447 DOI: 10.1002/ece3.1134] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 04/30/2014] [Indexed: 11/09/2022] Open
Abstract
Plant-insect interactions often are important for plant reproduction, but the outcome of these interactions may vary with environmental context. Pollinating seed predators have positive and negative effects on host plant reproduction, and the interaction outcome is predicted to vary with density or abundance of the partners. We studied the interaction between Silene stellata, an herbaceous perennial, and Hadena ectypa, its specialized pollinating seed predator. Silene stellata is only facultatively dependent upon H. ectypa for pollination because other nocturnal moth co-pollinators are equally effective at pollen transfer. We hypothesized that for plants without conspecific neighbors, H. ectypa would have higher visitation rates compared to co-pollinators, and the plants would experience lower levels of H. ectypa pollen deposition. We predicted similar oviposition throughout the study site but greater H. ectypa predation in the area without conspecific neighbors compared to plants embedded in a naturally high density area. We found that H. ectypa had consistently higher visitation than moth co-pollinators in all host plant contexts. However, H. ectypa pollinator importance declined in areas with low conspecific density because of reduced pollen deposition, resulting in lower seed set. Conversely, oviposition was similar across the study site independent of host plant density. Greater likelihood of very high fruit predation combined with lower pollination by H. ectypa resulted in reduced S. stellata female reproductive success in areas with low conspecific density. Our results demonstrate local context dependency of the outcomes of pollinating seed predator interactions with conspecific host plant density within a population.
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Affiliation(s)
- Abigail A R Kula
- Department of Biology, University of Maryland College Park, Maryland, 20742 ; Mountain Lake Biological Station Pembroke, Virginia, 24136
| | - Dean M Castillo
- Mountain Lake Biological Station Pembroke, Virginia, 24136 ; Department of Biology, Indiana University Bloomington, Indiana, 47405
| | - Michele R Dudash
- Department of Biology, University of Maryland College Park, Maryland, 20742 ; Mountain Lake Biological Station Pembroke, Virginia, 24136
| | - Charles B Fenster
- Department of Biology, University of Maryland College Park, Maryland, 20742 ; Mountain Lake Biological Station Pembroke, Virginia, 24136
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93
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Abbate JL, Antonovics J. Elevational disease distribution in a natural plant-pathogen system: insights from changes across host populations and climate. OIKOS 2014. [DOI: 10.1111/oik.01001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jessica L. Abbate
- Centre d'Écologie Fonctionelle et Évolutive (CEFE); UMR 5175, CNRS, 1919 route de Mende FR-34293 Montpellier France
| | - Janis Antonovics
- Dept of Biology; Univ. of Virginia; Charlottesville VA 22904 USA
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94
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Page P, Favre A, Schiestl FP, Karrenberg S. Do flower color and floral scent of silene species affect host preference of Hadena bicruris, a seed-eating pollinator, under field conditions? PLoS One 2014; 9:e98755. [PMID: 24905986 PMCID: PMC4048206 DOI: 10.1371/journal.pone.0098755] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 05/06/2014] [Indexed: 01/19/2023] Open
Abstract
Specialization in plant–insect interactions is an important driver of evolutionary divergence; yet, plant traits mediating such interactions are poorly understood. In this study, we investigated how flower color and floral scent are related to seed predation by a seed-eating pollinator. We used field-transplanted recombinant F2 hybrids between Silene latifolia and S. dioica that are the preferred and alternative hosts of the moth Hadena bicruris and crosses within these species for comparison. We scored seed predation and flower color and analyzed floral scent. Pinker S. dioica-like flowers and emission of α-pinene decreased the odds of seed predation while emission of benzyl acetate and 6-methyl-5-hepten-2-one increased the odds of seed predation. Emission of these compounds did not differ significantly between the two Silene species. Our results suggest that flower color plays an important role in the specific interaction of H. bicruris with its preferred host S. latifolia. The compounds α-pinene, benzyl acetate and 6-methyl-5-hepten-2-one could represent non-specific deterrents and attractants to ovipositing moths. Alternatively, emission of these compounds could be related to herbivory or pathogen attack and act as a signal for host quality. This would weaken the predictability of the plant's costs and benefits of the interaction and act to maintain an imperfect degree of specialization.
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Affiliation(s)
- Paul Page
- ETH Zurich, Institute of Integrative Biology (IBZ), Zurich, Switzerland
| | - Adrien Favre
- ETH Zurich, Institute of Integrative Biology (IBZ), Zurich, Switzerland
- Department of Molecular Evolution and Systematics of Plants, Institute of Biology, University of Leipzig, Leipzig, Germany
| | - Florian P. Schiestl
- ETH Zurich, Institute of Integrative Biology (IBZ), Zurich, Switzerland
- Institute of Systematic Botany, University of Zurich, Zurich, Switzerland
| | - Sophie Karrenberg
- ETH Zurich, Institute of Integrative Biology (IBZ), Zurich, Switzerland
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
- * E-mail:
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95
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Magalhaes IS, Bernasconi G. Phenotypic divergence and inter-specific trait correlation in a plant-pollinator/seed predator mutualism. Evol Ecol 2014. [DOI: 10.1007/s10682-014-9713-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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96
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Weingartner LA, Delph LF. Neo-sex chromosome inheritance across species in Silene
hybrids. J Evol Biol 2014; 27:1491-9. [DOI: 10.1111/jeb.12371] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 03/05/2014] [Accepted: 03/10/2014] [Indexed: 10/25/2022]
Affiliation(s)
| | - L. F. Delph
- Department of Biology; Indiana University; Bloomington IN USA
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97
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Zemp N, Minder A, Widmer A. Identification of internal reference genes for gene expression normalization between the two sexes in dioecious white Campion. PLoS One 2014; 9:e92893. [PMID: 24675788 PMCID: PMC3968030 DOI: 10.1371/journal.pone.0092893] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Accepted: 02/26/2014] [Indexed: 11/29/2022] Open
Abstract
Quantitative real time (qRT)-PCR is a precise and efficient method for studying gene expression changes between two states of interest, and is frequently used for validating interesting gene expression patterns in candidate genes initially identified in genome-wide expression analyses, such as RNA-seq experiments. For an adequate normalisation of qRT-PCR data, it is essential to have reference genes available whose expression intensities are constant among the different states of interest. In this study we present and validate a catalogue of traditional and newly identified reference genes that were selected from RNA-seq data from multiple individuals from the dioecious plant Silene latifolia with the aim of studying gene expression differences between the two sexes in both reproductive and vegetative tissues. The catalogue contains more than 15 reference genes with both stable expression intensities and a range of expression intensities in flower buds and leaf tissues. These reference genes were used to normalize expression differences between reproductive and vegetative tissues in eight candidate genes with sex-biased expression. Our results suggest a trend towards a reduced sex-bias in sex-linked gene expression in vegetative tissues. In this study, we report on the systematic identification and validation of internal reference genes for adequate normalization of qRT-PCR-based analyses of gene expression differences between the two sexes in S. latifolia. We also show how RNA-seq data can be used efficiently to identify suitable reference genes in a wide diversity of species.
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Affiliation(s)
- Niklaus Zemp
- ETH Zurich, Institute of Integrative Biology (IBZ), Zürich, Switzerland
| | - Aria Minder
- ETH Zurich, Genetic Diversity Centre (GDC), Zürich, Switzerland
| | - Alex Widmer
- ETH Zurich, Institute of Integrative Biology (IBZ), Zürich, Switzerland
- * E-mail:
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98
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A quantitative genetic signature of senescence in a short-lived perennial plant. Curr Biol 2014; 24:744-7. [PMID: 24631239 DOI: 10.1016/j.cub.2014.02.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 12/17/2013] [Accepted: 02/04/2014] [Indexed: 12/31/2022]
Abstract
The evolution of senescence (the physiological decline of organisms with age) poses an apparent paradox because it represents a failure of natural selection to increase the survival and reproductive performance of organisms. The paradox can be resolved if natural selection becomes less effective with age, because the death of postreproductive individuals should have diminished effects on Darwinian fitness [1, 2]. A substantial body of empirical work is consistent with this prediction for animals, which transmit their genes to progeny via an immortal germline. However, such evidence is still lacking in plants, which lack a germline and whose reproduction is diffuse and modular across the soma. Here, we provide experimental evidence for a genetic basis of senescence in the short-lived perennial plant Silene latifolia. Our pedigree-based analysis revealed a marked increase with age in the additive genetic variance of traits closely associated with fitness. This result thus extends to plants the quantitative genetic support for the evolutionary theory of senescence.
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99
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Casimiro-Soriguer I, Buide ML, Narbona E. The roles of female and hermaphroditic flowers in the gynodioecious-gynomonoecious Silene littorea: insights into the phenology of sex expression. PLANT BIOLOGY (STUTTGART, GERMANY) 2013; 15:941-7. [PMID: 23174011 DOI: 10.1111/j.1438-8677.2012.00697.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Accepted: 09/28/2012] [Indexed: 05/23/2023]
Abstract
Some gynodioecious species have intermediate individuals that bear both female and hermaphroditic flowers. This phenomenon is known as a gynodioecious-gynomonoecious sexual system. Gender expression in such species has received little attention in the past, and the phenologies of male and female functions have also yet to be explored. In this study, we examined variations in gender patterns, their effects on female reproductive success and sex expression in depth throughout the flowering period in two populations. The studied populations of Silene littorea contained mostly gynomonoecious plants and the number of pure females was very low. The gynomonoecious plants showed high variability in the total proportion of female flowers. In addition, the proportion of female flowers in each plant varied widely across the flowering season. Although there was a trend towards maleness, our measures of functional gender suggested that most plants transmit their genes via both pollen and ovules. Fruit set and seed set were not significantly different among populations; in contrast, flower production significantly varied between the two populations - and among plants - with consequent variation in total seed production. Conversely, gender and sex expression were similar in both populations. Plants with higher phenotypic femaleness did not have higher fruit set, seed set or total female fecundity. The mating environment fluctuated little across the flowering period, but fluctuations were higher in the population with low flower production. We therefore conclude that the high proportion of gynomonoecious individuals in our studied populations of S. littorea may be advantageous for the species, providing the benefits of both hermaphroditic and female flowers.
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Affiliation(s)
- I Casimiro-Soriguer
- Área de Botánica, Dpto. Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Sevilla, Spain; Área de Botánica, Dpto. de Biología Vegetal y Ecología, Universidad de Sevilla, Sevilla, Spain
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100
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Patterns of cyto-nuclear linkage disequilibrium in Silene latifolia: genomic heterogeneity and temporal stability. Heredity (Edinb) 2013; 112:99-104. [PMID: 24002238 DOI: 10.1038/hdy.2013.79] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2012] [Revised: 06/21/2013] [Accepted: 07/01/2013] [Indexed: 12/16/2022] Open
Abstract
Non-random association of alleles in the nucleus and cytoplasmic organelles, or cyto-nuclear linkage disequilibrium (LD), is both an important component of a number of evolutionary processes and a statistical indicator of others. The evolutionary significance of cyto-nuclear LD will depend on both its magnitude and how stable those associations are through time. Here, we use a longitudinal population genetic data set to explore the magnitude and temporal dynamics of cyto-nuclear disequilibria through time. We genotyped 135 and 170 individuals from 16 and 17 patches of the plant species Silene latifolia in Southwestern VA, sampled in 1993 and 2008, respectively. Individuals were genotyped at 14 highly polymorphic microsatellite markers and a single-nucleotide polymorphism (SNP) in the mitochondrial gene, atp1. Normalized LD (D') between nuclear and cytoplasmic loci varied considerably depending on which nuclear locus was considered (ranging from 0.005-0.632). Four of the 14 cyto-nuclear associations showed a statistically significant shift over approximately seven generations. However, the overall magnitude of this disequilibrium was largely stable over time. The observed origin and stability of cyto-nuclear LD is most likely caused by the slow admixture between anciently diverged lineages within the species' newly invaded range, and the local spatial structure and metapopulation dynamics that are known to structure genetic variation in this system.
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