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Hewett AM, Sánchez Vilas J, Hailer F. Two novel PCR-based assays for sexing of Silene latifolia and Silene dioica plants. MethodsX 2024; 12:102708. [PMID: 38651001 PMCID: PMC11033195 DOI: 10.1016/j.mex.2024.102708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 04/09/2024] [Indexed: 04/25/2024] Open
Abstract
Silene latifolia and S. dioica are model systems in studies of plant reproduction, chromosome evolution and sexual dimorphism, but sexing of plants based on morphology is only possible from flowering stage onwards. Both species show homogametic females (XX) and heterogametic males (XY).•Here we developed two assays (primer pairs ss816 and ss441) for molecular sexing of S. latifolia and S. dioica, targeting length polymorphisms between the X and Y-linked copies of the spermidine synthase gene.The two assays were successful in identifying known (flowering-stage) males and females from UK and Spanish populations, with an error rate of 3.1% (ss816; successful for both species) and 0% (ss441, only successful for S. latifolia). Our assays therefore represent novel tools for rapid, robust and simple determination of the genotypic sex of S. latifolia and S. dioica.
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Affiliation(s)
- Anna M. Hewett
- School of Biosciences, Sir Martin Evans Building, Cardiff University, Cardiff CF10 3AX, UK
- Department of Ecology and Evolution, University of Lausanne (UNIL), Lausanne 1015, Switzerland
| | - Julia Sánchez Vilas
- School of Biosciences, Sir Martin Evans Building, Cardiff University, Cardiff CF10 3AX, UK
- Departamento de Bioloxía Funcional (Área de Ecoloxía) Facultade de Bioloxía, Universidade de Santiago de Compostelac/ Lope Gómez de Marzoa, s/n15782 Santiago de Compostela, Spain
| | - Frank Hailer
- School of Biosciences, Sir Martin Evans Building, Cardiff University, Cardiff CF10 3AX, UK
- Cardiff University-Institute of Zoology Joint Laboratory for Biocomplexity Research, Beijing, China
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Marcel H, Javier MGJ, Emilio C, Roman H, Jose Luis RL. Seed shape and size of Silene latifolia, differences between sexes, and influence of the parental genome in hybrids with Silene dioica. FRONTIERS IN PLANT SCIENCE 2024; 15:1297676. [PMID: 38529065 PMCID: PMC10961389 DOI: 10.3389/fpls.2024.1297676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 02/21/2024] [Indexed: 03/27/2024]
Abstract
Introduction Plants undergo various natural changes that dramatically modify their genomes. One is polyploidization and the second is hybridization. Both are regarded as key factors in plant evolution and result in phenotypic differences in different plant organs. In Silene, we can find both examples in nature, and this genus has a seed shape diversity that has long been recognized as a valuable source of information for infrageneric classification. Methods Morphometric analysis is a statistical study of shape and size and their covariations with other variables. Traditionally, seed shape description was limited to an approximate comparison with geometric figures (rounded, globular, reniform, or heart-shaped). Seed shape quantification has been based on direct measurements, such as area, perimeter, length, and width, narrowing statistical analysis. We used seed images and processed them to obtain silhouettes. We performed geometric morphometric analyses, such as similarity to geometric models and elliptic Fourier analysis, to study the hybrid offspring of S. latifolia and S. dioica. Results We generated synthetic tetraploids of Silene latifolia and performed controlled crosses between diploid S. latifolia and Silene dioica to analyze seed morphology. After imaging capture and post-processing, statistical analysis revealed differences in seed size, but not in shape, between S. latifolia diploids and tetraploids, as well as some differences in shape among the parentals and hybrids. A detailed inspection using fluorescence microscopy allowed for the identification of shape differences in the cells of the seed coat. In the case of hybrids, differences were found in circularity and solidity. Overal seed shape is maternally regulated for both species, whereas cell shape cannot be associated with any of the sexes. Discussion Our results provide additional tools useful for the combination of morphology with genetics, ecology or taxonomy. Seed shape is a robust indicator that can be used as a complementary tool for the genetic and phylogenetic analyses of Silene hybrid populations.
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Affiliation(s)
- Hubinský Marcel
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czechia
- National Centre for Biomolecular Research (NCBR), Faculty of Science, Masaryk University, Brno, Czechia
| | | | - Cervantes Emilio
- Instituto de Recursos Naturales y Agrobiología de Salamanca (IRNASA)-CSIC, Salamanca, Spain
| | - Hobza Roman
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czechia
| | - Rodríguez Lorenzo Jose Luis
- Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czechia
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Veltsos P, Delph LF. The X chromosome is necessary for ovule production in Silene latifolia. PLoS One 2019; 14:e0217558. [PMID: 31121002 PMCID: PMC6533010 DOI: 10.1371/journal.pone.0217558] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 05/14/2019] [Indexed: 12/28/2022] Open
Abstract
Sex chromosomes stop recombining and accumulate differences over time. In particular, genes on the chromosome restricted to the heterogametic sex degenerate and become non-functional. Here, we investigated whether or not the degeneration of a plant Y chromosome was sufficient to cause ovules containing a Y to fail to develop, thereby eliminating the possibility of YY individuals. We used two genotypic assays to determine the genotype-XX, XY, or YY-of offspring from a single fruit of an otherwise normal male XY plant of Silene latifolia. The fruit contained fewer ovules than normal pistillate flowers, produced an equal offspring sex ratio, and generated no YY offspring. The results indicate that ovaries must contain an X chromosome to develop properly. While haploid selection has slowed down Y-chromosome degeneration in S. latifolia, we find that it has progressed sufficiently to prevent the proper development of ovules, and hence prevent the presence of YY individuals.
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Affiliation(s)
- Paris Veltsos
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
- * E-mail:
| | - Lynda F. Delph
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
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Hernández-Fernández J, Pinzón A, Mariño-Ramírez L. De novo transcriptome assembly of loggerhead sea turtle nesting of the Colombian Caribbean. GENOMICS DATA 2017; 13:18-20. [PMID: 28649496 PMCID: PMC5472237 DOI: 10.1016/j.gdata.2017.06.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 05/31/2017] [Accepted: 06/07/2017] [Indexed: 11/23/2022]
Abstract
Loggerhead sea turtle Caretta caretta is widely distributed in the oceans of tropical and subtropical latitude. This turtle is an endangered species due to anthropic and natural factors that have decreased their population levels. In this study, RNA sequencing and de-novo assembly of genes expressed in blood were performed. The raw FASTQ files have been deposited on NCBI's SRA database with accession number SRX2629512. A total of 5.4 Gb raw sequence data were obtained, corresponding to 48,257,019 raw reads. Trinity pipeline was used to perform a de-novo assembly, we were able to identify 64,930 transcripts for female loggerhead turtle transcriptome with an N50 of 1131 bp. The obtained transcriptome data will be useful for further studies of the physiology, biochemistry and evolution in this species.
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Affiliation(s)
- Javier Hernández-Fernández
- Genetics, Molecular Biology and Bioinformatics Lab, Department of Natural and Environmental Sciences, Universidad Jorge Tadeo Lozano, Cra. 4 N° 22-61 modulo 7 Piso 6, Bogotá D. C., Colombia
- Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Andrés Pinzón
- Bioinformatics and Systems Biology Group, National University of Colombia, Bogotá, Colombia
| | - Leonardo Mariño-Ramírez
- NCBI, NLM, NIH Computational Biology Branch, Building 38A, Room 6S614M 8600 Rockville Pike, MSC 6075 Bethesda, MD 20894-6075, United States
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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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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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Soukupova M, Nevrtalova E, Cížková J, Vogel I, Cegan R, Hobza R, Vyskot B. The X chromosome is necessary for somatic development in the dioecious Silene latifolia: cytogenetic and molecular evidence and sequencing of a haploid genome. Cytogenet Genome Res 2014; 143:96-103. [PMID: 24993893 DOI: 10.1159/000363431] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Silene latifolia (or white campion) possesses a well-established sex determination system with a dominant Y chromosome in males (the mammalian type). The heteromorphic sex chromosomes X and Y in S. latifolia largely stopped recombination; thus, we can expect a gradual genetic degeneration of the Y chromosome. It is well proven that neither diploid nor polyploid S. latifolia sporophytes can survive without at least one X, so the only life stage possessing the Y as the sole sex chromosome is the male gametophyte (pollen tube), while the female gametophyte seems to be X-dependent. Previous studies on anther-derived plants of this species showed that the obtained plants (largely haploid or dihaploid) were phenotypically and cytologically female. In this paper, we provide molecular evidence for the inviability of plants lacking the X chromosome. Using sex-specific PCR primers, we show that all plantlets and plants derived from anther cultures are female. In studying anther-derived diploid females by sequencing of X-linked markers, we demonstrate that these plants are really homozygous dihaploids. A haploid regenerant plant was sequenced (8× genome coverage) using Illumina technology. Genome data are disposable in the EMBL database as a standard for full genome and X chromosome assembly in this model species. Homozygous dihaploids were back-crossed with males to yield a progeny useful for the study of the evolution of the Y chromosome.
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Affiliation(s)
- Magda Soukupova
- Department of Plant Developmental Genetics, Institute of Biophysics ASCR, Brno, Czech Republic
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