1
|
Favre F, Jourda C, Grisoni M, Chiroleu F, Dijoux JB, Jade K, Rivallan R, Besse P, Charron C. First Vanilla planifolia High-Density Genetic Linkage Map Provides Quantitative Trait Loci for Resistance to Fusarium oxysporum. PLANT DISEASE 2023; 107:2997-3006. [PMID: 36856646 DOI: 10.1094/pdis-10-22-2386-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Fusarium oxysporum f. sp. radicis-vanillae (Forv), the causal agent of root and stem rot disease, is the main pathogen affecting vanilla production. Sources of resistance have been reported in Vanilla planifolia G. Jackson ex Andrews, the main cultivated vanilla species. In this study, we developed the first high-density genetic map in this species with 1,804 genotyping-by-sequencing (GBS)-generated single nucleotide polymorphism (SNP) markers using 125 selfed progenies of the CR0040 traditional vanilla cultivar. Sixteen linkage groups (LG) were successfully constructed, with a mean of 113 SNPs and an average length of 207 cM per LG. The map had a high density with an average of 5.45 SNP every 10 cM and an average distance of 1.85 cM between adjacent markers. The first three LG were aligned against the first assembled chromosome of CR0040, and the other 13 LG were correctly associated with the other 13 assembled chromosomes. The population was challenged with the highly pathogenic Forv strain Fo072 using the root-dip inoculation method. Five traits were mapped, and 20 QTLs were associated with resistance to Fo072. Among the genes retrieved in the CR0040 physical regions associated with QTLs, genes potentially involved in biotic resistance mechanisms, coding for kinases, E3 ubiquitin ligases, pentatricopeptide repeat-containing proteins, and one leucine-rich repeat receptor underlying the qFo72_08.1 QTL have been highlighted. This study should provide useful resources for marker-assisted selection in V. planifolia.
Collapse
Affiliation(s)
- Félicien Favre
- University of Reunion Island, UMR PVBMT, F-97410 St. Pierre, Reunion Island, France
| | - Cyril Jourda
- CIRAD, UMR PVBMT, F-97410 St Pierre, Reunion Island, France
| | | | | | | | - Katia Jade
- CIRAD, UMR PVBMT, F-97410 St Pierre, Reunion Island, France
| | - Ronan Rivallan
- CIRAD, UMR AGAP, F-34398 Montpellier, France
- AGAP, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Pascale Besse
- University of Reunion Island, UMR PVBMT, F-97410 St. Pierre, Reunion Island, France
| | - Carine Charron
- CIRAD, UMR PVBMT, F-97410 St Pierre, Reunion Island, France
| |
Collapse
|
2
|
Zhang M, Qiu X. Genetic basis of genome size variation of wheat. Funct Integr Genomics 2023; 23:285. [PMID: 37648783 DOI: 10.1007/s10142-023-01194-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/22/2023] [Accepted: 07/29/2023] [Indexed: 09/01/2023]
Abstract
Research on various species has revealed a connection between genome size variation and the physiological and ecological characteristics of the species, suggesting that it could be a crucial factor influencing a species' adaptability to different environments. Wheat, being one of the world's three primary grains, holds significance in this regard. Investigating the genome size of wheat and analyzing the genetic factors contributing to its variation could offer valuable insights for enhancing wheat agronomic traits. This project has developed a conservative site ratio calculation approach to determine the size of the wheat genome. Additionally, it employs flow cytometry and k-mer distribution analysis to validate this method. Furthermore, the researchers use re-sequencing data to investigate the impact of environmental selection pressure and transposon dynamics on the variation in the size of the wheat genome. The findings from this study demonstrate a strong relationship between the size of the wheat genome and several environmental factors. These results serve as a valuable reference for understanding the development of variation in the size of the hetero-hexaploid wheat genome. Moreover, they contribute to advancing fundamental research on the genetic mechanisms underlying wheat characteristics. Additionally, the study paves the way for exploring new research directions in wheat breeding, which holds promise for future advancements in this field.
Collapse
Affiliation(s)
- Ming Zhang
- University of Chinese Academy of Sciences, Beijing, 100101, China.
| | - Xuebing Qiu
- University of Chinese Academy of Sciences, Beijing, 100101, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| |
Collapse
|
3
|
Kołodziejczyk I, Tomczyk P, Kaźmierczak A. Endoreplication-Why Are We Not Using Its Full Application Potential? Int J Mol Sci 2023; 24:11859. [PMID: 37511616 PMCID: PMC10380914 DOI: 10.3390/ijms241411859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/17/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
Endoreplication-a process that is common in plants and also accompanies changes in the development of animal organisms-has been seen from a new perspective in recent years. In the paper, we not only shed light on this view, but we would also like to promote an understanding of the application potential of this phenomenon in plant cultivation. Endoreplication is a pathway for cell development, slightly different from the classical somatic cell cycle, which ends with mitosis. Since many rounds of DNA synthesis take place within its course, endoreplication is a kind of evolutionary compensation for the relatively small amount of genetic material that plants possess. It allows for its multiplication and active use through transcription and translation. The presence of endoreplication in plants has many positive consequences. In this case, repeatedly produced copies of genes, through the corresponding transcripts, help the plant acquire the favorable properties for which proteins are responsible directly or indirectly. These include features that are desirable in terms of cultivation and marketing: a greater saturation of fruit and flower colors, a stronger aroma, a sweeter fruit taste, an accumulation of nutrients, an increased resistance to biotic and abiotic stress, superior tolerance to adverse environmental conditions, and faster organ growth (and consequently the faster growth of the whole plant and its biomass). The two last features are related to the nuclear-cytoplasmic ratio-the greater the content of DNA in the nucleus, the higher the volume of cytoplasm, and thus the larger the cell size. Endoreplication not only allows cells to reach larger sizes but also to save the materials used to build organelles, which are then passed on to daughter cells after division, thus ending the classic cell cycle. However, the content of genetic material in the cell nucleus determines the number of corresponding organelles. The article also draws attention to the potential practical applications of the phenomenon and the factors currently limiting its use.
Collapse
Affiliation(s)
- Izabela Kołodziejczyk
- Department of Geobotany and Plant Ecology, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 12/14, 90237 Lodz, Poland
| | - Przemysław Tomczyk
- The National Institute of Horticultural Research, Konstytucji 3 Maja 1/3, 96100 Skierniewice, Poland
| | - Andrzej Kaźmierczak
- Department of Cytophysiology, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90237 Lodz, Poland
| |
Collapse
|
4
|
Weinstein AM, Bohman B, Linde CC, Phillips RD. Conservation assessment of the Drakaea livida (Orchidaceae) ecotypes and an evaluation of methods for their identification. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.1004177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Morphologically cryptic taxa must be accounted for when quantifying biodiversity and implementing effective conservation measures. Some orchids pollinated by sexual deception of male insects contain morphologically cryptic ecotypes, such as the warty hammer orchid Drakaea livida (Orchidaceae). This species is comprised of three cryptic pollination ecotypes, which can be distinguished based on differences in pollinator species and floral volatiles. The present study aims were: (a) to investigate the geographic range of the three D. livida ecotypes, enabling assessment of their conservation status; and (b) to test the efficacy of different methods of identifying the D. livida ecotypes. Three methods of ecotype identification were assessed: morphometric analysis, genome size comparison, and analysis of chemical volatile composition of labellum extracts from pollinated flowers. MaxEnt species distribution models revealed that each ecotype has a different predicted geographic range, with small areas of overlap at the range margins. One ecotype is known from just ten populations over a limited geographic area, the majority of which has been cleared for agriculture, and urban development. While there was broad overlap between the ecotypes in individual morphological traits, multivariate analysis of morphological traits provided correct assignment to ecotype in 87% of individuals. Using the labellum of pollinated flowers, screening for volatile chemical compounds associated with particular ecotypes returned an even higher correct assignment rate, of 96.5%. As such, we advocate that the use of volatiles from the labellum of recently pollinated flowers is an effective way to determine the ecotype of unknown individuals of D. livida, with minimal impact on the flowering plant.
Collapse
|
5
|
Kondo H, Deguchi A, Kikuchi S, Miyoshi K. Two pathways of 2n gamete formation and differences in the frequencies of 2n gametes between wild species and interspecific hybrids. PLANT CELL REPORTS 2022; 41:2187-2200. [PMID: 35984498 DOI: 10.1007/s00299-022-02915-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 07/26/2022] [Indexed: 06/15/2023]
Abstract
Epidendrum produces 2n gametes with high frequency. This paper is the first to report on multiple pathways for forming 2n gametes, meiotic defeats, and pre-meiotic chromosome doubling. Unreduced 2n reproductive cells are predominantly involved in pathways that lead to polyploid plants. Although one of the most common pathways for inducing 2n gametes is through meiotic defects, a small set of isolated species alternatively generates 2n gametes from tetraploid pollen mother cells in the pre-meiotic phase. Hence, determining the mechanisms underlying 2n gamete formation is critical to improving breeding programmes and understanding plant evolution. We investigated sporads to reveal the pathway(s) accounting for the formation and frequencies of 2n gametes in wild species and interspecific hybrids in the genus Epidendrum. We investigated different types of sporads with varying frequencies, sizes, and viability in the wild species and hybrids of the genus Epidendrum. Large tetrad-estimated pre-meiotic chromosome doubling was observed in wild species. The Epidendrum is unique in that it forms 2n pollens via two pathways, namely, meiotic defects and pre-meiotic chromosome doubling. These two pathways of 2n pollen formation could influence the high diversity generation of polyploidy with different degrees of heterozygosity and genetic backgrounds in the genus Epidendrum. Therefore, these findings are proposed to influence polyploid breeding of Epidendrum via 2n pollen, helping us understand evolution and speciation via unreduced 2n gamete formation in Orchidaceae.
Collapse
Affiliation(s)
- Haruka Kondo
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba, 271-8510, Japan
| | - Ayumi Deguchi
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba, 271-8510, Japan
| | - Shinji Kikuchi
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba, 271-8510, Japan
| | - Kazumitsu Miyoshi
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba, 271-8510, Japan.
| |
Collapse
|
6
|
Koprivý L, Fráková V, Kolarčik V, Mártonfiová L, Dudáš M, Mártonfi P. Genome size and endoreplication in two pairs of cytogenetically contrasting species of Pulmonaria (Boraginaceae) in Central Europe. AOB PLANTS 2022; 14:plac036. [PMID: 36128515 PMCID: PMC9476981 DOI: 10.1093/aobpla/plac036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 08/16/2022] [Indexed: 06/13/2023]
Abstract
Genome size is species-specific feature and commonly constant in an organism. In various plants, DNA content in cell nucleus is commonly increased in process of endoreplication, cellular-specific multiplication of DNA content without mitosis. This leads to the endopolyploidy, the presence of multiplied chromosome sets in a subset of cells. The relationship of endopolyploidy to species-specific genome size is rarely analysed and is not fully understood. While negative correlation between genome size and endopolyploidy level is supposed, this is species- and lineage-specific. In the present study, we shed light on this topic, exploring both genome size and endoreplication-induced DNA content variation in two pairs of morphologically similar species of Pulmonaria, P. obscura-P. officinalis and P. mollis-P. murinii. We aim (i) to characterize genome size and chromosome numbers in these species using cytogenetic, root-tip squashing and flow cytometry (FCM) techniques; (ii) to investigate the degree of endopolyploidy in various plant organs, including the root, stem, leaf, calyx and corolla using FCM; and (iii) to comprehensively characterize and compare the level of endopolyploidy and DNA content in various organs of all four species in relation to species systematic relationships and genome size variation. We have confirmed the diploid-dysploid nature of chromosome complements, and divergent genome sizes for Pulmonaria species: P. murinii with 2n = 2x = 14, 2.31 pg/2C, P. obscura 2n = 2x = 14, 2.69 pg/2C, P. officinalis 2n = 2x = 16, 2.96 pg/2C and P. mollis 2n = 2x = 18, 3.18 pg/2C. Endopolyploidy varies between species and organs, and we have documented 4C-8C in all four organs and up to 32C (64C) endopolyploid nuclei in stems at least in some species. Two species with lower genome sizes tend to have higher endopolyploidy levels than their closest relatives. Endoreplication-generated tissue-specific mean DNA content is increased and more balanced among species in all four organs compared to genome size. Our results argue for the narrow relationship between genome size and endopolyploidy in the present plant group within the genus Pulmonaria, and endopolyploidization seems to play a compensatory developmental role in organs of related morphologically similar species.
Collapse
Affiliation(s)
- Lukáš Koprivý
- Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University, Mánesova 23, SK-041 54 Košice, Slovak Republic
- Botanical Garden, Pavol Jozef Šafárik University, Mánesova 23, SK-043 52 Košice, Slovak Republic
| | - Viera Fráková
- Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University, Mánesova 23, SK-041 54 Košice, Slovak Republic
| | | | - Lenka Mártonfiová
- Botanical Garden, Pavol Jozef Šafárik University, Mánesova 23, SK-043 52 Košice, Slovak Republic
| | - Matej Dudáš
- Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University, Mánesova 23, SK-041 54 Košice, Slovak Republic
| | - Pavol Mártonfi
- Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University, Mánesova 23, SK-041 54 Košice, Slovak Republic
- Botanical Garden, Pavol Jozef Šafárik University, Mánesova 23, SK-043 52 Košice, Slovak Republic
| |
Collapse
|
7
|
Song C, Wang Y, Manzoor MA, Mao D, Wei P, Cao Y, Zhu F. In-depth analysis of genomes and functional genomics of orchid using cutting-edge high-throughput sequencing. FRONTIERS IN PLANT SCIENCE 2022; 13:1018029. [PMID: 36212315 PMCID: PMC9539832 DOI: 10.3389/fpls.2022.1018029] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 09/05/2022] [Indexed: 06/01/2023]
Abstract
High-throughput sequencing technology has been facilitated the development of new methodologies and approaches for studying the origin and evolution of plant genomes and subgenomes, population domestication, and functional genomics. Orchids have tens of thousands of members in nature. Many of them have promising application potential in the extension and conservation of the ecological chain, the horticultural use of ornamental blossoms, and the utilization of botanical medicines. However, a large-scale gene knockout mutant library and a sophisticated genetic transformation system are still lacking in the improvement of orchid germplasm resources. New gene editing tools, such as the favored CRISPR-Cas9 or some base editors, have not yet been widely applied in orchids. In addition to a large variety of orchid cultivars, the high-precision, high-throughput genome sequencing technology is also required for the mining of trait-related functional genes. Nowadays, the focus of orchid genomics research has been directed to the origin and classification of species, genome evolution and deletion, gene duplication and chromosomal polyploidy, and flower morphogenesis-related regulation. Here, the progressing achieved in orchid molecular biology and genomics over the past few decades have been discussed, including the evolution of genome size and polyploidization. The frequent incorporation of LTR retrotransposons play important role in the expansion and structural variation of the orchid genome. The large-scale gene duplication event of the nuclear genome generated plenty of recently tandem duplicated genes, which drove the evolution and functional divergency of new genes. The evolution and loss of the plastid genome, which mostly affected genes related to photosynthesis and autotrophy, demonstrated that orchids have experienced more separate transitions to heterotrophy than any other terrestrial plant. Moreover, large-scale resequencing provide useful SNP markers for constructing genetic maps, which will facilitate the breeding of novel orchid varieties. The significance of high-throughput sequencing and gene editing technologies in the identification and molecular breeding of the trait-related genes in orchids provides us with a representative trait-improving gene as well as some mechanisms worthy of further investigation. In addition, gene editing has promise for the improvement of orchid genetic transformation and the investigation of gene function. This knowledge may provide a scientific reference and theoretical basis for orchid genome studies.
Collapse
Affiliation(s)
- Cheng Song
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
| | - Yan Wang
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
| | | | - Di Mao
- Albrecht Daniel Thaer Institute for Agricultural and Horticultural Sciences, Humboldt University of Berlin, Berlin, Germany
| | - Peipei Wei
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
| | - Yunpeng Cao
- Chinese Academy of Sciences (CAS) Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Fucheng Zhu
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
| |
Collapse
|
8
|
Piet Q, Droc G, Marande W, Sarah G, Bocs S, Klopp C, Bourge M, Siljak-Yakovlev S, Bouchez O, Lopez-Roques C, Lepers-Andrzejewski S, Bourgois L, Zucca J, Dron M, Besse P, Grisoni M, Jourda C, Charron C. A chromosome-level, haplotype-phased Vanilla planifolia genome highlights the challenge of partial endoreplication for accurate whole-genome assembly. PLANT COMMUNICATIONS 2022; 3:100330. [PMID: 35617961 PMCID: PMC9482989 DOI: 10.1016/j.xplc.2022.100330] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 04/10/2022] [Accepted: 04/27/2022] [Indexed: 06/02/2023]
Abstract
Vanilla planifolia, the species cultivated to produce one of the world's most popular flavors, is highly prone to partial genome endoreplication, which leads to highly unbalanced DNA content in cells. We report here the first molecular evidence of partial endoreplication at the chromosome scale by the assembly and annotation of an accurate haplotype-phased genome of V. planifolia. Cytogenetic data demonstrated that the diploid genome size is 4.09 Gb, with 16 chromosome pairs, although aneuploid cells are frequently observed. Using PacBio HiFi and optical mapping, we assembled and phased a diploid genome of 3.4 Gb with a scaffold N50 of 1.2 Mb and 59 128 predicted protein-coding genes. The atypical k-mer frequencies and the uneven sequencing depth observed agreed with our expectation of unbalanced genome representation. Sixty-seven percent of the genes were scattered over only 30% of the genome, putatively linking gene-rich regions and the endoreplication phenomenon. By contrast, low-coverage regions (non-endoreplicated) were rich in repeated elements but also contained 33% of the annotated genes. Furthermore, this assembly showed distinct haplotype-specific sequencing depth variation patterns, suggesting complex molecular regulation of endoreplication along the chromosomes. This high-quality, anchored assembly represents 83% of the estimated V. planifolia genome. It provides a significant step toward the elucidation of this complex genome. To support post-genomics efforts, we developed the Vanilla Genome Hub, a user-friendly integrated web portal that enables centralized access to high-throughput genomic and other omics data and interoperable use of bioinformatics tools.
Collapse
Affiliation(s)
- Quentin Piet
- CIRAD, UMR PVBMT, 97410 Saint-Pierre, La Réunion, France
| | - Gaetan Droc
- CIRAD, UMR AGAP Institut, 34398 Montpellier, France; UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France; French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, 34398 Montpellier, France.
| | | | - Gautier Sarah
- French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, 34398 Montpellier, France; AGAP, Univ. Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France
| | - Stéphanie Bocs
- CIRAD, UMR AGAP Institut, 34398 Montpellier, France; UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France; French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, 34398 Montpellier, France
| | - Christophe Klopp
- Plateforme Bioinformatique, Genotoul, BioinfoMics, UR875 Biométrie et Intelligence Artificielle, INRAE, Castanet-Tolosan, France
| | - Mickael Bourge
- Cytometry Facility, Imagerie-Gif, Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Sonja Siljak-Yakovlev
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique Evolution (ESE), 91190 Gif-sur-Yvette, France
| | | | | | | | | | - Joseph Zucca
- Département Biotechnologie, V. Mane Fils, 06620 Le Bar Sur Loup, France
| | - Michel Dron
- Université Paris-Saclay, CNRS, INRAE, Univ. Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405 Orsay, France
| | - Pascale Besse
- Université de la Réunion, UMR PVBMT, Saint-Pierre, La Réunion, France
| | | | - Cyril Jourda
- CIRAD, UMR PVBMT, 97410 Saint-Pierre, La Réunion, France.
| | - Carine Charron
- CIRAD, UMR PVBMT, 97410 Saint-Pierre, La Réunion, France
| |
Collapse
|
9
|
Sliwinska E, Loureiro J, Leitch IJ, Šmarda P, Bainard J, Bureš P, Chumová Z, Horová L, Koutecký P, Lučanová M, Trávníček P, Galbraith DW. Application-based guidelines for best practices in plant flow cytometry. Cytometry A 2021; 101:749-781. [PMID: 34585818 DOI: 10.1002/cyto.a.24499] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 08/10/2021] [Accepted: 08/26/2021] [Indexed: 12/15/2022]
Abstract
Flow cytometry (FCM) is currently the most widely-used method to establish nuclear DNA content in plants. Since simple, 1-3-parameter, flow cytometers, which are sufficient for most plant applications, are commercially available at a reasonable price, the number of laboratories equipped with these instruments, and consequently new FCM users, has greatly increased over the last decade. This paper meets an urgent need for comprehensive recommendations for best practices in FCM for different plant science applications. We discuss advantages and limitations of establishing plant ploidy, genome size, DNA base composition, cell cycle activity, and level of endoreduplication. Applications of such measurements in plant systematics, ecology, molecular biology research, reproduction biology, tissue cultures, plant breeding, and seed sciences are described. Advice is included on how to obtain accurate and reliable results, as well as how to manage troubleshooting that may occur during sample preparation, cytometric measurements, and data handling. Each section is followed by best practice recommendations; tips as to what specific information should be provided in FCM papers are also provided.
Collapse
Affiliation(s)
- Elwira Sliwinska
- Laboratory of Molecular Biology and Cytometry, Department of Agricultural Biotechnology, UTP University of Science and Technology, Bydgoszcz, Poland
| | - João Loureiro
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Ilia J Leitch
- Kew Science Directorate, Royal Botanic Gardens, Kew, Richmond, Surrey, UK
| | - Petr Šmarda
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Jillian Bainard
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, Saskatchewan, Canada
| | - Petr Bureš
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Zuzana Chumová
- Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic.,Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
| | - Lucie Horová
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Petr Koutecký
- Department of Botany, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Magdalena Lučanová
- Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic.,Department of Botany, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Pavel Trávníček
- Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic
| | - David W Galbraith
- School of Plant Sciences, BIO5 Institute, Arizona Cancer Center, Department of Biomedical Engineering, University of Arizona, Tucson, Arizona, USA.,Henan University, School of Life Sciences, State Key Laboratory of Crop Stress Adaptation and Improvement, State Key Laboratory of Cotton Biology, Key Laboratory of Plant Stress Biology, Kaifeng, China
| |
Collapse
|
10
|
Galbraith DW. Validation of crowd-sourced plant genome size measurements. Cytometry A 2021; 101:703-706. [PMID: 34363316 DOI: 10.1002/cyto.a.24493] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/21/2021] [Accepted: 07/23/2021] [Indexed: 11/11/2022]
Affiliation(s)
- David W Galbraith
- BIO5 Institute, Arizona Cancer Center, and Department of Biomedical Engineering, University of Arizona, School of Plant Sciences, Tucson, Arizona, USA
| |
Collapse
|
11
|
Čertner M, Lučanová M, Sliwinska E, Kolář F, Loureiro J. Plant material selection, collection, preservation, and storage for nuclear DNA content estimation. Cytometry A 2021; 101:737-748. [PMID: 34254737 DOI: 10.1002/cyto.a.24482] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 06/30/2021] [Accepted: 07/01/2021] [Indexed: 01/23/2023]
Abstract
In theory, any plant tissue providing intact nuclei in sufficient quantity is suitable for nuclear DNA content estimation using flow cytometry (FCM). While this certainly opens a wide variety of possible applications of FCM, especially when compared to classical karyological techniques restricted to tissues with active cell division, tissue selection and quality may directly affect the precision (and sometimes even reliability) of FCM measurements. It is usually convenient to first consider the goals of the study to either aim for the highest possible accuracy of estimates (e.g., for inferring genome size, detecting homoploid intraspecific genome size variation, aneuploidy, among others), or to decide that histograms of reasonable resolution provide sufficient information (e.g., ploidy level screening within a single model species). Here, a set of best practices guidelines for selecting the optimal plant tissue for FCM analysis, sampling of material, and material preservation and storage are provided. In addition, factors potentially compromising the quality of FCM estimates of nuclear DNA content and data interpretation are discussed.
Collapse
Affiliation(s)
- Martin Čertner
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic.,Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic
| | - Magdalena Lučanová
- Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic.,Department of Botany, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Elwira Sliwinska
- Laboratory of Molecular Biology and Cytometry, Department of Agricultural Biotechnology, UTP University of Science and Technology, Bydgoszcz, Poland
| | - Filip Kolář
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic.,Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic
| | - João Loureiro
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| |
Collapse
|
12
|
Chumová Z, Záveská E, Hloušková P, Ponert J, Schmidt PA, Čertner M, Mandáková T, Trávníček P. Repeat proliferation and partial endoreplication jointly shape the patterns of genome size evolution in orchids. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:511-524. [PMID: 33960537 DOI: 10.1111/tpj.15306] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 04/27/2021] [Accepted: 05/03/2021] [Indexed: 05/21/2023]
Abstract
Although the evolutionary drivers of genome size change are known, the general patterns and mechanisms of plant genome size evolution are yet to be established. Here we aim to assess the relative importance of proliferation of repetitive DNA, chromosomal variation (including polyploidy), and the type of endoreplication for genome size evolution of the Pleurothallidinae, the most species-rich orchid lineage. Phylogenetic relationships between 341 Pleurothallidinae representatives were refined using a target enrichment hybrid capture combined with high-throughput sequencing approach. Genome size and the type of endoreplication were assessed using flow cytometry supplemented with karyological analysis and low-coverage Illumina sequencing for repeatome analysis on a subset of samples. Data were analyzed using phylogeny-based models. Genome size diversity (0.2-5.1 Gbp) was mostly independent of profound chromosome count variation (2n = 12-90) but tightly linked with the overall content of repetitive DNA elements. Species with partial endoreplication (PE) had significantly greater genome sizes, and genomic repeat content was tightly correlated with the size of the non-endoreplicated part of the genome. In PE species, repetitive DNA is preferentially accumulated in the non-endoreplicated parts of their genomes. Our results demonstrate that proliferation of repetitive DNA elements and PE together shape the patterns of genome size diversity in orchids.
Collapse
Affiliation(s)
- Zuzana Chumová
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, Průhonice, CZ-25243, Czech Republic
- Department of Botany, Faculty of Science, Charles University, Benátská 2, Prague, CZ-12800, Czech Republic
| | - Eliška Záveská
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, Průhonice, CZ-25243, Czech Republic
- Department of Botany, University of Innsbruck, Sternwartestraße 15, Innsbruck, 6020, Austria
| | | | - Jan Ponert
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, Průhonice, CZ-25243, Czech Republic
- Prague Botanical Garden, Trojská 800/196, Prague, CZ-17100, Czech Republic
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, Prague, CZ-12844, Czech Republic
| | - Philipp-André Schmidt
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, Průhonice, CZ-25243, Czech Republic
| | - Martin Čertner
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, Průhonice, CZ-25243, Czech Republic
- Department of Botany, Faculty of Science, Charles University, Benátská 2, Prague, CZ-12800, Czech Republic
| | - Terezie Mandáková
- CEITEC, Masaryk University, Brno, CZ-62500, Czech Republic
- Faculty of Science, Masaryk University, Brno, CZ-62500, Czech Republic
| | - Pavel Trávníček
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, Průhonice, CZ-25243, Czech Republic
| |
Collapse
|
13
|
Evaluation of endopolyploidy patterns in selected Capsicum and Nicotiana species (Solanaceae). Biologia (Bratisl) 2021. [DOI: 10.1007/s11756-021-00704-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
14
|
Chumová Z, Mandáková T, Trávníček P. On the Origin of Tetraploid Vernal Grasses ( Anthoxanthum) in Europe. Genes (Basel) 2021; 12:966. [PMID: 34202779 PMCID: PMC8308110 DOI: 10.3390/genes12070966] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/19/2021] [Accepted: 06/23/2021] [Indexed: 11/16/2022] Open
Abstract
Polyploidy has played a crucial role in the evolution of many plant taxa, namely in higher latitudinal zones. Surprisingly, after several decades of an intensive research on polyploids, there are still common polyploid species whose evolutionary history is virtually unknown. Here, we addressed the origin of sweet vernal grass (Anthoxanthum odoratum) using flow cytometry, DNA sequencing, and in situ hybridization-based cytogenetic techniques. An allotetraploid and polytopic origin of the species has been verified. The chromosome study reveals an extensive variation between the European populations. In contrast, an autopolyploid origin of the rarer tetraploid vernal grass species, A. alpinum, has been corroborated. Diploid A. alpinum played an essential role in the polyploidization of both European tetraploids studied.
Collapse
Affiliation(s)
- Zuzana Chumová
- Czech Academy of Sciences, Institute of Botany, CZ-242 53 Průhonice, Czech Republic;
- Department of Botany, Faculty of Science, Charles University, Benátská 2, CZ-128 00 Prague, Czech Republic
| | - Terezie Mandáková
- CEITEC, Masaryk University, CZ-625 00 Brno, Czech Republic;
- Department of Experimental Biology, Faculty of Science, Masaryk University, CZ-625 00 Brno, Czech Republic
| | - Pavel Trávníček
- Czech Academy of Sciences, Institute of Botany, CZ-242 53 Průhonice, Czech Republic;
| |
Collapse
|
15
|
Kron P, Loureiro J, Castro S, Čertner M. Flow cytometric analysis of pollen and spores: An overview of applications and methodology. Cytometry A 2021; 99:348-358. [PMID: 33625767 DOI: 10.1002/cyto.a.24330] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 01/21/2021] [Accepted: 02/16/2021] [Indexed: 01/01/2023]
Abstract
Pollen grains are the male gametophytes in a seed-plant life cycle. Their small, particulate nature and crucial role in plant reproduction have made them an attractive object of study using flow cytometry (FCM), with a wide range of applications existing in the literature. While methodological considerations for many of these overlap with those for other tissue types (e.g., general considerations for the measurement of nuclear DNA content), the relative complexity of pollen compared to single cells presents some unique challenges. We consider these here in the context of both the identification and isolation of pollen and its subunits, and the types of research applications. While the discussion here mostly concerns pollen, the general principles described here can be extended to apply to spores in ferns, lycophytes, and bryophytes. In addition to recommendations provided in more general studies, some recurring and notable issues related specifically to pollen and spores are highlighted.
Collapse
Affiliation(s)
- Paul Kron
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - João Loureiro
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Sílvia Castro
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Martin Čertner
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic.,Department of Evolutionary Plant Biology, Institute of Botany of the Czech Academy of Sciences, Průhonice, Czech Republic
| |
Collapse
|
16
|
Farminhão JNM, Verlynde S, Kaymak E, Droissart V, Simo-Droissart M, Collobert G, Martos F, Stévart T. Rapid radiation of angraecoids (Orchidaceae, Angraecinae) in tropical Africa characterised by multiple karyotypic shifts under major environmental instability. Mol Phylogenet Evol 2021; 159:107105. [PMID: 33601026 DOI: 10.1016/j.ympev.2021.107105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 01/13/2021] [Accepted: 02/03/2021] [Indexed: 10/22/2022]
Abstract
Angraecoid orchids present a remarkable diversity of chromosome numbers, which makes them a highly suitable system for exploring the impact of karyotypic changes on cladogenesis, diversification and morphological differentiation. We compiled an annotated cytotaxonomic checklist for 126 species of Angraecinae, which was utilised to reconstruct chromosomal evolution using a newly-produced, near-comprehensive phylogenetic tree that includes 245 angraecoid taxa. In tandem with this improved phylogenetic framework, using combined Bayesian, maximum likelihood and parsimony approaches on ITS-1 and five plastid markers, we propose a new cladistic nomenclature for the angraecoids, and we estimate a new timeframe for angraecoid radiation based on a secondary calibration, and calculate diversification rates using a Bayesian approach. Coincident divergence dates between clades with identical geographical distributions in the angraecoids and the pantropical orchid genus Bulbophyllum suggest that the same events may have intervened in the dispersal of these two epiphytic groups between Asia, continental Africa, Madagascar and the Neotropics. The major angraecoid lineages probably began to differentiate in the Middle Miocene, and most genera and species emerged respectively around the Late Miocene-Pliocene boundary and the Pleistocene. Ancestral state reconstruction using maximum likelihood estimation revealed an eventful karyotypic history dominated by descending dysploidy. Karyotypic shifts seem to have paralleled cladogenesis in continental tropical Africa, where approximately 90% of the species have descended from at least one inferred transition from n = 17-18 to n = 25 during the Middle Miocene Climatic Transition, followed by some clade-specific descending and ascending dysploidy from the Late Miocene to the Pleistocene. Conversely, detected polyploidy is restricted to a few species lineages mostly originating during the Pleistocene. No increases in net diversification could be related to chromosome number changes, and the apparent net diversification was found to be highest in Madagascar, where karyotypic stasis predominates. Finally, shifts in chromosome number appear to have paralleled the evolution of rostellum structure, leaflessness, and conspicuous changes in floral colour.
Collapse
Affiliation(s)
- João N M Farminhão
- Herbarium and Library of African Botany, C.P. 265, Université Libre de Bruxelles, Campus de la Plaine, Boulevard du Triomphe 1050, Brussels, Belgium; Plant Ecology and Biogeochemistry, C.P. 244, Université Libre de Bruxelles, Campus de la Plaine, Boulevard du Triomphe, 1050, Brussels, Belgium.
| | - Simon Verlynde
- Cullman Program for Molecular Systematics, New York Botanical Garden, Bronx, NY 10458-5126, USA; PhD Program in Biology, Graduate Center, City University of New York, 365 5th Ave., New York, NY 10016, USA
| | - Esra Kaymak
- Evolutionary Biology and Ecology, Faculté des Sciences, C.P. 160/12, Université Libre de Bruxelles, 50 Avenue F. Roosevelt, BE-1050 Brussels, Belgium
| | - Vincent Droissart
- Herbarium and Library of African Botany, C.P. 265, Université Libre de Bruxelles, Campus de la Plaine, Boulevard du Triomphe 1050, Brussels, Belgium; AMAP Lab, Univ Montpellier, IRD, CNRS, INRAE, CIRAD, Montpellier, France; Missouri Botanical Garden, Africa and Madagascar Department, 4344 Shaw Blvd., St. Louis, MO 63110, USA; Plant Systematics and Ecology Laboratory, Higher Teachers' Training College, University of Yaoundé I, P. O. Box 047, Yaoundé, Cameroon
| | - Murielle Simo-Droissart
- Plant Systematics and Ecology Laboratory, Higher Teachers' Training College, University of Yaoundé I, P. O. Box 047, Yaoundé, Cameroon
| | - Géromine Collobert
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, CP 39, 57 rue Cuvier, 75005 Paris, France
| | - Florent Martos
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, CP 39, 57 rue Cuvier, 75005 Paris, France
| | - Tariq Stévart
- Herbarium and Library of African Botany, C.P. 265, Université Libre de Bruxelles, Campus de la Plaine, Boulevard du Triomphe 1050, Brussels, Belgium; Missouri Botanical Garden, Africa and Madagascar Department, 4344 Shaw Blvd., St. Louis, MO 63110, USA; Meise Botanic Garden, Domein van Bouchout, Nieuwelaan 38, B-1860 Meise, Belgium
| |
Collapse
|
17
|
Trávníček P, Chumová Z, Záveská E, Hanzlíčková J, Kupková (Jankolová) L, Kučera J, Gbúrová Štubňová E, Rejlová L, Mandáková T, Ponert J. Integrative Study of Genotypic and Phenotypic Diversity in the Eurasian Orchid Genus Neotinea. FRONTIERS IN PLANT SCIENCE 2021; 12:734240. [PMID: 34745168 PMCID: PMC8570840 DOI: 10.3389/fpls.2021.734240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 09/20/2021] [Indexed: 05/04/2023]
Abstract
Knowledge of population variation across species' ranges is a prerequisite for correctly assessing the overall variability of any group of organisms and provides an invaluable basis for unraveling evolutionary history, optimizing taxonomy and devising effective conservation strategies. Here, we examine the genus Neotinea, which represents a relatively recently delimited monophyletic genus of orchids, for which a detailed study of its overall variability was lacking. We applied a suite of biosystematic methods, consisting of flow cytometry, multivariate and geometric morphometrics, and analysis of genomic SNP data, to identify phylogenetic lineages within the genus, to delineate phenotypic variation relevant to these lineages, and to identify potential cryptic taxa within lineages. We found clear differentiation into four major lineages corresponding to the groups usually recognized within the genus: Neotinea maculata as a distinct and separate taxon, the Neotinea lactea group comprising two Mediterranean taxa N. lactea and Neotinea conica, the Neotinea ustulata group comprising two phenologically distinct varieties, and the rather complex Neotinea tridentata group comprising two major lineages and various minor lineages of unclear taxonomic value. N. conica constitutes both a monophyletic group within N. lactea and a distinct phenotype within the genus and merits its proposed subspecies-level recognition. By contrast, the spring and summer flowering forms of N. ustulata (var. ustulata and var. aestivalis) were confirmed to be distinct only morphologically, not phylogenetically. The most complex pattern emerged in the N. tridentata group, which splits into two main clades, one containing lineages from the Balkans and eastern Mediterranean and the other consisting of plants from Central Europe and the central Mediterranean. These individual lineages differ in genome size and show moderate degrees of morphological divergence. The tetraploid Neotinea commutata is closely related to the N. tridentata group, but our evidence points to an auto- rather than an allopolyploid origin. Our broad methodological approach proved effective in recognizing cryptic lineages among the orchids, and we propose the joint analysis of flow cytometric data on genome size and endopolyploidy as a useful and beneficial marker for delineating orchid species with partial endoreplication.
Collapse
Affiliation(s)
- Pavel Trávníček
- Institute of Botany, Czech Academy of Sciences, Průhonice, Czechia
- *Correspondence: Pavel Trávníček,
| | - Zuzana Chumová
- Institute of Botany, Czech Academy of Sciences, Průhonice, Czechia
- Department of Botany, Faculty of Science, Charles University, Prague, Czechia
- Zuzana Chumová,
| | - Eliška Záveská
- Institute of Botany, Czech Academy of Sciences, Průhonice, Czechia
| | - Johana Hanzlíčková
- Institute of Botany, Czech Academy of Sciences, Průhonice, Czechia
- Department of Botany, Faculty of Science, Charles University, Prague, Czechia
| | | | - Jaromír Kučera
- Institute of Botany, Plant Science and Biodiversity Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Eliška Gbúrová Štubňová
- Institute of Botany, Plant Science and Biodiversity Center, Slovak Academy of Sciences, Bratislava, Slovakia
- Slovak National Museum, Bratislava, Slovakia
| | - Ludmila Rejlová
- Institute of Botany, Czech Academy of Sciences, Průhonice, Czechia
- Department of Botany, Faculty of Science, Charles University, Prague, Czechia
| | - Terezie Mandáková
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czechia
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Jan Ponert
- Institute of Botany, Czech Academy of Sciences, Průhonice, Czechia
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Prague, Czechia
- Prague Botanical Garden, Prague, Czechia
- Jan Ponert,
| |
Collapse
|
18
|
The Application of Flow Cytometry for Estimating Genome Size, Ploidy Level Endopolyploidy, and Reproductive Modes in Plants. Methods Mol Biol 2021; 2222:325-361. [PMID: 33301101 DOI: 10.1007/978-1-0716-0997-2_17] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Over the years, the amount of DNA in a nucleus (genome size) has been estimated using a variety of methods, but increasingly, flow cytometry (FCM) has become the method of choice. The popularity of this technique lies in the ease of sample preparation and in the large number of particles (i.e., nuclei) that can be analyzed in a very short period of time. This chapter presents a step-by-step guide to estimating the nuclear DNA content of plant nuclei using FCM. Attempting to serve as a tool for daily laboratory practice, we list, in detail, the equipment required, specific reagents and buffers needed, as well as the most frequently used protocols to carry out nuclei isolation. In addition, solutions to the most common problems that users may encounter when working with plant material and troubleshooting advice are provided. Finally, information about the correct terminology to use and the importance of obtaining chromosome counts to avoid cytological misinterpretations of the FCM data are discussed.
Collapse
|
19
|
Veselý P, Šmarda P, Bureš P, Stirton C, Muasya AM, Mucina L, Horová L, Veselá K, Šilerová A, Šmerda J, Knápek O. Environmental pressures on stomatal size may drive plant genome size evolution: evidence from a natural experiment with Cape geophytes. ANNALS OF BOTANY 2020; 126:323-330. [PMID: 32474609 PMCID: PMC7380457 DOI: 10.1093/aob/mcaa095] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 05/21/2020] [Indexed: 05/02/2023]
Abstract
BACKGROUND AND AIMS The idea that genome (size) evolution in eukaryotes could be driven by environmental factors is still vigorously debated. In extant plants, genome size correlates positively with stomatal size, leading to the idea that conditions enabling the existence of large stomata in fossil plants also supported growth of their genome size. We test this inductive assumption in drought-adapted, prostrate-leaved Cape (South Africa) geophytes where, compared with their upright-leaved geophytic ancestors, stomata develop in a favourably humid microclimate formed underneath their leaves. METHODS Stomatal parameters (leaf cuticle imprints) and genome size (flow cytometry) were measured in 16 closely related geophytic species pairs from seven plant families. In each pair, representing a different genus, we contrasted a prostrate-leaved species with its upright-leaved phylogenetic relative, the latter whose stomata are exposed to the ambient arid climate. KEY RESULTS Except for one, all prostrate-leaves species had larger stomata, and in 13 of 16 pairs they also had larger genomes than their upright-leaved relatives. Stomatal density and theoretical maximum conductance were less in prostrate-leaved species with small guard cells (<1 pL) but showed no systematic difference in species pairs with larger guard cells (>1 pL). Giant stomata were observed in the prostrate-leaved Satyrium bicorne (89-137 µm long), despite its relatively small genome (2C = 9 Gbp). CONCLUSIONS Our results imply that climate, through selection on stomatal size, might be able to drive genome size evolution in plants. The data support the idea that plants from 'greenhouse' geological periods with large stomata might have generally had larger genome sizes when compared with extant plants, though this might not have been solely due to higher atmospheric CO2 in these periods but could also have been due to humid conditions prevailing at fossil deposit sites.
Collapse
Affiliation(s)
- Pavel Veselý
- Department of Botany and Zoology, Masaryk University, Kotlářská, Brno, Czech Republic
| | - Petr Šmarda
- Department of Botany and Zoology, Masaryk University, Kotlářská, Brno, Czech Republic
- For correspondence. E-mail
| | - Petr Bureš
- Department of Botany and Zoology, Masaryk University, Kotlářská, Brno, Czech Republic
| | - Charles Stirton
- Bolus Herbarium, Department of Biological Sciences, University of Cape Town, Rondebosch, Cape Town, South Africa
| | - A Muthama Muasya
- Bolus Herbarium, Department of Biological Sciences, University of Cape Town, Rondebosch, Cape Town, South Africa
| | - Ladislav Mucina
- Iluka Chair in Vegetation Science and Biogeography, Harry Butler Institute, Murdoch University, Murdoch, Perth, Australia
- Department of Geography and Environmental Studies, Stellenbosch University, Matieland, Stellenbosch, South Africa
| | - Lucie Horová
- Department of Botany and Zoology, Masaryk University, Kotlářská, Brno, Czech Republic
| | - Kristýna Veselá
- Department of Botany and Zoology, Masaryk University, Kotlářská, Brno, Czech Republic
| | - Alexandra Šilerová
- Department of Botany and Zoology, Masaryk University, Kotlářská, Brno, Czech Republic
| | - Jakub Šmerda
- Department of Botany and Zoology, Masaryk University, Kotlářská, Brno, Czech Republic
| | - Ondřej Knápek
- Department of Botany and Zoology, Masaryk University, Kotlářská, Brno, Czech Republic
| |
Collapse
|
20
|
Trávníček P, Čertner M, Ponert J, Chumová Z, Jersáková J, Suda J. Diversity in genome size and GC content shows adaptive potential in orchids and is closely linked to partial endoreplication, plant life-history traits and climatic conditions. THE NEW PHYTOLOGIST 2019; 224:1642-1656. [PMID: 31215648 DOI: 10.1111/nph.15996] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 06/07/2019] [Indexed: 05/21/2023]
Abstract
In angiosperms, genome size and nucleobase composition (GC content) exhibit pronounced variation with possible adaptive consequences. The hyperdiverse orchid family possessing the unique phenomenon of partial endoreplication (PE) provides a great opportunity to search for interactions of both genomic traits with the evolutionary history of the family. Using flow cytometry, we report values of both genomic traits and the type of endoreplication for 149 orchid species and compare these with a suite of life-history traits and climatic niche data using phylogeny-based statistics. The evolution of genomic traits was further studied using the Brownian motion (BM) and Ornstein-Uhlenbeck (OU) models to access their adaptive potential. Pronounced variation in genome size (341-54 878 Mb), and especially in GC content (23.9-50.5%), was detected among orchids. Diversity in both genomic traits was closely related to the type of endoreplication, plant growth form and climatic conditions. GC content was also associated with the type of dormancy. In all tested scenarios, OU models always outperformed BM models. Unparalleled GC content variation was discovered in orchids, setting new limits for plants. Our study indicates that diversity in both genome size and GC content has adaptive consequences and is tightly linked with evolutionary transitions to PE.
Collapse
Affiliation(s)
- Pavel Trávníček
- Institute of Botany, Czech Academy of Sciences, Zámek 1, Průhonice, CZ-25243, Czech Republic
| | - Martin Čertner
- Institute of Botany, Czech Academy of Sciences, Zámek 1, Průhonice, CZ-25243, Czech Republic
- Department of Botany, Faculty of Science, Charles University, Benátská 2, Prague, CZ-12801, Czech Republic
| | - Jan Ponert
- Institute of Botany, Czech Academy of Sciences, Zámek 1, Průhonice, CZ-25243, Czech Republic
- Prague Botanical Garden, Trojská 800/196, Prague, CZ-17100, Czech Republic
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, Prague, CZ-12844, Czech Republic
| | - Zuzana Chumová
- Institute of Botany, Czech Academy of Sciences, Zámek 1, Průhonice, CZ-25243, Czech Republic
- Department of Botany, Faculty of Science, Charles University, Benátská 2, Prague, CZ-12801, Czech Republic
| | - Jana Jersáková
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, Branišovská 1760, České Budějovice, CZ-37005, Czech Republic
| | | |
Collapse
|
21
|
Hloušková P, Mandáková T, Pouch M, Trávníček P, Lysak MA. The large genome size variation in the Hesperis clade was shaped by the prevalent proliferation of DNA repeats and rarer genome downsizing. ANNALS OF BOTANY 2019; 124:103-120. [PMID: 31220201 PMCID: PMC6676390 DOI: 10.1093/aob/mcz036] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 02/28/2019] [Indexed: 05/13/2023]
Abstract
BACKGROUND AND AIMS Most crucifer species (Brassicaceae) have small nuclear genomes (mean 1C-value 617 Mb). The species with the largest genomes occur within the monophyletic Hesperis clade (Mandáková et al., Plant Physiology174: 2062-2071; also known as Clade E or Lineage III). Whereas most chromosome numbers in the clade are 6 or 7, monoploid genome sizes vary 16-fold (256-4264 Mb). To get an insight into genome size evolution in the Hesperis clade (~350 species in ~48 genera), we aimed to identify, quantify and localize in situ the repeats from which these genomes are built. We analysed nuclear repeatomes in seven species, covering the phylogenetic and genome size breadth of the clade, by low-pass whole-genome sequencing. METHODS Genome size was estimated by flow cytometry. Genomic DNA was sequenced on an Illumina sequencer and DNA repeats were identified and quantified using RepeatExplorer; the most abundant repeats were localized on chromosomes by fluorescence in situ hybridization. To evaluate the feasibility of bacterial artificial chromosome (BAC)-based comparative chromosome painting in Hesperis-clade species, BACs of arabidopsis were used as painting probes. KEY RESULTS Most biennial and perennial species of the Hesperis clade possess unusually large nuclear genomes due to the proliferation of long terminal repeat retrotransposons. The prevalent genome expansion was rarely, but repeatedly, counteracted by purging of transposable elements in ephemeral and annual species. CONCLUSIONS The most common ancestor of the Hesperis clade has experienced genome upsizing due to transposable element amplification. Further genome size increases, dominating diversification of all Hesperis-clade tribes, contrast with the overall stability of chromosome numbers. In some subclades and species genome downsizing occurred, presumably as an adaptive transition to an annual life cycle. The amplification versus purging of transposable elements and tandem repeats impacted the chromosomal architecture of the Hesperis-clade species.
Collapse
Affiliation(s)
- Petra Hloušková
- CEITEC - Central European Institute of Technology, and Faculty of Science, Masaryk University, Kamenice, Brno, Czech Republic
| | - Terezie Mandáková
- CEITEC - Central European Institute of Technology, and Faculty of Science, Masaryk University, Kamenice, Brno, Czech Republic
| | - Milan Pouch
- CEITEC - Central European Institute of Technology, and Faculty of Science, Masaryk University, Kamenice, Brno, Czech Republic
| | - Pavel Trávníček
- Institute of Botany, Czech Academy of Sciences, Zámek 1, 252 43 Průhonice, Czech Republic
| | - Martin A Lysak
- CEITEC - Central European Institute of Technology, and Faculty of Science, Masaryk University, Kamenice, Brno, Czech Republic
| |
Collapse
|
22
|
Tyagi A, Sandhya, Sharma P, Saxena S, Sharma R, Amitha Mithra SV, Solanke AU, Singh NK, Sharma TR, Gaikwad K. The genome size of clusterbean (Cyamopsis tetragonoloba) is significantly smaller compared to its wild relatives as estimated by flow cytometry. Gene 2019; 707:205-211. [PMID: 30898697 DOI: 10.1016/j.gene.2019.02.090] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 02/04/2019] [Accepted: 02/28/2019] [Indexed: 02/06/2023]
Abstract
Clusterbean (C. tetragonoloba) is an important, leguminous vegetable and industrial crop with vast genetic diversity but meager genetic, cytological and genomic information. In the present study, an optimized procedure of flow cytometry was used to estimate the genome size of three clusterbean species, represented by C. tetragonoloba (cv. RGC-936) and two wild relatives (C. serreta and C. senegalensis). For accurate estimation of genomic content, singlet G0/G1 populations of multiple tissues such as leaves, hypocotyl, and matured seeds were determined and used along with three different plant species viz. Pisum sativum (as primary), Oryza sativa, and Glycine max (secondary), as external and internal reference standards. Seed tissue of the test sample and G. max provided the best estimate of nuclear DNA content in comparison to other sample tissues and reference standards. The genome size of C. tetragonoloba was detemined at 580.9±0.02Mbp (1C), while that of C. serreta and C. senegalensis was estimated at 979.6±0.02Mbp (1C) and 943.4±0.03Mbp (1C), respectively. Thus, the wild relatives harbor, nearly double the genome content of the cultivated cluster bean. Findings of this study will enrich genomic database of the legume family and can serve as the starting point for clusterbean evolutionary and genomics studies.
Collapse
Affiliation(s)
- Anshika Tyagi
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
| | - Sandhya
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
| | - Priya Sharma
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
| | - Swati Saxena
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
| | - Ramavtar Sharma
- ICAR-Central Arid Zone Research Institute (CAZRI), Jodhpur, India
| | - S V Amitha Mithra
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
| | | | | | - Tilak Raj Sharma
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India
| | - Kishor Gaikwad
- ICAR-National Research Centre on Plant Biotechnology, New Delhi, India.
| |
Collapse
|
23
|
Hu Y, Resende MFR, Bombarely A, Brym M, Bassil E, Chambers AH. Genomics-based diversity analysis of Vanilla species using a Vanilla planifolia draft genome and Genotyping-By-Sequencing. Sci Rep 2019; 9:3416. [PMID: 30833623 PMCID: PMC6399343 DOI: 10.1038/s41598-019-40144-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 02/11/2019] [Indexed: 11/09/2022] Open
Abstract
Demand for all-natural vanilla flavor is increasing, but its botanical source, Vanilla planifolia, faces critical challenges arising from a narrow germplasm base and supply limitations. Genomics tools are the key to overcoming these limitations by enabling advanced genetics and plant breeding for new cultivars with improved yield and quality. The objective of this work was to establish the genomic resources needed to facilitate analysis of diversity among Vanilla accessions and to provide a resource to analyze other Vanilla collections. A V. planifolia draft genome was assembled and used to identify 521,732 single nucleotide polymorphism (SNP) markers using Genotyping-By-Sequencing (GBS). The draft genome had a size of 2.20 Gb representing 97% of the estimated genome size. A filtered set of 5,082 SNPs was used to genotype a living collection of 112 Vanilla accessions from 23 species including native Florida species. Principal component analysis of the genetic distances, population structure, and the maternally inherited rbcL gene identified putative hybrids, misidentified accessions, significant diversity within V. planifolia, and evidence for 12 clusters that separate accessions by species. These results validate the efficiency of genomics-based tools to characterize and identify genetic diversity in Vanilla and provide a significant tool for genomics-assisted plant breeding.
Collapse
Affiliation(s)
- Ying Hu
- Horticultural Sciences Department, University of Florida, Gainesville, FL, USA
| | - Marcio F R Resende
- Horticultural Sciences Department, University of Florida, Gainesville, FL, USA
| | - Aureliano Bombarely
- School of Plant and Environmental Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA.,Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Maria Brym
- Tropical Research and Education Center, Horticultural Sciences Department, Homestead, FL, USA
| | - Elias Bassil
- Tropical Research and Education Center, Horticultural Sciences Department, Homestead, FL, USA.
| | - Alan H Chambers
- Tropical Research and Education Center, Horticultural Sciences Department, Homestead, FL, USA.
| |
Collapse
|
24
|
Zhang S, Gu S, Ni X, Li X. Genome Size Reversely Correlates With Host Plant Range in Helicoverpa Species. Front Physiol 2019; 10:29. [PMID: 30761014 PMCID: PMC6363812 DOI: 10.3389/fphys.2019.00029] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 01/11/2019] [Indexed: 12/02/2022] Open
Abstract
In organisms with very low percentages of transposable elements (TEs), genome size may positively or negatively correlate with host range, depending on whether host adaptation or host modification is the main route to host generalism. To test if this holds true for insect herbivores with greater percentages of TEs, we conducted flow cytometry to measure the endopolyploidy levels and C-values of the host modification (salivary gland and mandibular gland in head), host adaptation (midgut), and host use-independent tissues (male gonad, hemolymph, and Malpighian tubules) of the generalist Helicoverpa armigera and the head of its older specialist sister H. assulta. Larval salivary gland displayed a consecutive chain of endopolyploidy particles from 8Cx to higher than 32Cx and larval head and midgut had endopolyploidy nuclei clusters of 16Cx and 32Cx, whereas larval male gonad, hemolymph, and Malpighian tubules possessed no endopolyploidy nuclei of higher than 8Cx. The estimated genome size of the Solanaceae plant specialist H. assulta is 430 Mb, significantly larger than that of its older generalist sister Heliothis virescens (408 Mb) and those of its two generalist descendants H. armigera (394 Mb) and H. zea (363 Mb). These data not only reveal a negative correlation between host plant range and genome size in this terminal lineage, but also imply that Helicoverpa species appear to depend more on host modification than on host adaptation to achieve polyphagy.
Collapse
Affiliation(s)
- Shen Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shaohua Gu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xinzhi Ni
- USDA-ARS Crop Genetics and Breeding Research Unit, Tifton, GA, United States
| | - Xianchun Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.,Department of Entomology and BIO5 Institute, University of Arizona, Tucson, AZ, United States
| |
Collapse
|
25
|
Lee YI, Yap JW, Izan S, Leitch IJ, Fay MF, Lee YC, Hidalgo O, Dodsworth S, Smulders MJM, Gravendeel B, Leitch AR. Satellite DNA in Paphiopedilum subgenus Parvisepalum as revealed by high-throughput sequencing and fluorescent in situ hybridization. BMC Genomics 2018; 19:578. [PMID: 30068293 PMCID: PMC6090851 DOI: 10.1186/s12864-018-4956-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 07/23/2018] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Satellite DNA is a rapidly diverging, largely repetitive DNA component of many eukaryotic genomes. Here we analyse the evolutionary dynamics of a satellite DNA repeat in the genomes of a group of Asian subtropical lady slipper orchids (Paphiopedilum subgenus Parvisepalum and representative species in the other subgenera/sections across the genus). A new satellite repeat in Paphiopedilum subgenus Parvisepalum, SatA, was identified and characterized using the RepeatExplorer pipeline in HiSeq Illumina reads from P. armeniacum (2n = 26). Reconstructed monomers were used to design a satellite-specific fluorescent in situ hybridization (FISH) probe. The data were also analysed within a phylogenetic framework built using the internal transcribed spacer (ITS) sequences of 45S nuclear ribosomal DNA. RESULTS SatA comprises c. 14.5% of the P. armeniacum genome and is specific to subgenus Parvisepalum. It is composed of four primary monomers that range from 230 to 359 bp and contains multiple inverted repeat regions with hairpin-loop motifs. A new karyotype of P. vietnamense (2n = 28) is presented and shows that the chromosome number in subgenus Parvisepalum is not conserved at 2n = 26, as previously reported. The physical locations of SatA sequences were visualised on the chromosomes of all seven Paphiopedilum species of subgenus Parvisepalum (2n = 26-28), together with the 5S and 45S rDNA loci using FISH. The SatA repeats were predominantly localisedin the centromeric, peri-centromeric and sub-telocentric chromosome regions, but the exact distribution pattern was species-specific. CONCLUSIONS We conclude that the newly discovered, highly abundant and rapidly evolving satellite sequence SatA is specific to Paphiopedilum subgenus Parvisepalum. SatA and rDNA chromosomal distributions are characteristic of species, and comparisons between species reveal that the distribution patterns generate a strong phylogenetic signal. We also conclude that the ancestral chromosome number of subgenus Parvisepalum and indeed of all Paphiopedilum could be either 2n = 26 or 28, if P. vietnamense is sister to all species in the subgenus as suggested by the ITS data.
Collapse
Affiliation(s)
- Yung-I Lee
- Biology Department, National Museum of Natural Science, No 1, Kuan-Chien Rd, 40453 Taichung, Taiwan, Republic of China
- Department of Life Sciences, National Chung Hsing University, 40227 Taichung, Taiwan, Republic of China
| | - Jing Wei Yap
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS UK
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB UK
- Forest Research Institute Malaysia (FRIM), 52109 Kepong, Selangor Darul Ehsan Malaysia
| | - Shairul Izan
- Plant Breeding, Wageningen University & Research, P.O. Box 386, NL-6700 AJ Wageningen, The Netherlands
- Department of Crop Science, Faculty of Agriculture, University Putra Malaysia (UPM) Serdang, Serdang, Selangor Malaysia
| | - Ilia J. Leitch
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB UK
| | - Michael F. Fay
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB UK
- School of Plant Biology, University of Western Australia, Crawley, WA 6009 Australia
| | - Yi-Ching Lee
- Biology Department, National Museum of Natural Science, No 1, Kuan-Chien Rd, 40453 Taichung, Taiwan, Republic of China
| | - Oriane Hidalgo
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB UK
| | - Steven Dodsworth
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB UK
| | - Marinus J. M. Smulders
- Plant Breeding, Wageningen University & Research, P.O. Box 386, NL-6700 AJ Wageningen, The Netherlands
| | - Barbara Gravendeel
- Endless Forms Group, Naturalis Biodiversity Center, Vondellaan 55, 2332 AA Leiden, The Netherlands
- Faculty of Science and Technology, University of Applied Sciences Leiden, Zernikedreef 11, 2333 CK Leiden, The Netherlands
- Institute Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Andrew R. Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS UK
| |
Collapse
|
26
|
Kolarčik V, Kocová V, Vašková D. Flow cytometric seed screen data are consistent with models of chromosome inheritance in asymmetrically compensating allopolyploids. Cytometry A 2018; 93:737-748. [PMID: 30071155 DOI: 10.1002/cyto.a.23511] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 05/10/2018] [Accepted: 06/04/2018] [Indexed: 12/19/2022]
Abstract
Angiosperms have evolved a mechanism of double fertilization, which results in the production of a separate embryo (new individual) and endosperm (nutritive tissue). The flow cytometric seed screen (FCSS) was developed to infer plant reproduction modes based on endosperm-to-embryo DNA content ratio (Pind ). A ratio of 1.5 indicates sexual reproduction, whereas higher values of ≥2.0 are consistent with apomixis. Although FCSS has been successfully applied to the study of sexual and asexual plants, the limits of FCSS and particularly its potential for determination of reproduction modes in hemisexual plants have not been explored. Here, we evaluated the application of FCSS to the study of reproduction modes in two asymmetrically compensating allopolyploids (ACAs), Onosma arenaria and Rosa canina. These two species are characterized by the presence of asexually inherited univalent-forming and sexually inherited bivalent-forming chromosome sets. They both use asymmetric meiosis, which eliminates univalent-forming chromosome sets from the male gamete and retains them in the female gamete. Different chromosomal behavior in male and female meiosis in these plants is reflected in different theoretically derived Pind values, which deviate from a sexual 1.5 value. Here, we determined Pind FCSS-based values in seeds of ACAs, and compared the results to sexual species. As expected, we determined that the mean Pind is 1.51, 1.52, and 1.52 in the sexual plants, that is, Capsella bursa-pastoris, Crataegus monogyna, and O. pseudoarenaria, respectively. In the ACAs, different mean Pind values were determined for O. arenaria (1.61) and R. canina (1.82). These values are consistent with the theoretical Pind values determined based on models of chromosome inheritance. This study highlights the precision of flow cytometry in determining DNA content and it's utility in screening reproduction modes. Additionally, it advocates for more in-depth investigations into rapid screening of accessions where the Pind ratio has deviated from the 1.5 value typical of sexual species, which may indicate meiotic irregularities.
Collapse
Affiliation(s)
- V Kolarčik
- Department of Botany, Institute of Biology and Ecology, Faculty of Science, P. J. Šafárik University, Mánesova 23, SK-041 54, Košice, Slovak Republic
| | - V Kocová
- Department of Botany, Institute of Biology and Ecology, Faculty of Science, P. J. Šafárik University, Mánesova 23, SK-041 54, Košice, Slovak Republic
| | - D Vašková
- Department of Botany, Institute of Biology and Ecology, Faculty of Science, P. J. Šafárik University, Mánesova 23, SK-041 54, Košice, Slovak Republic
| |
Collapse
|
27
|
Bateman RM, Guy JJ, Rudall PJ, Leitch IJ, Pellicer J, Leitch AR. Evolutionary and functional potential of ploidy increase within individual plants: somatic ploidy mapping of the complex labellum of sexually deceptive bee orchids. ANNALS OF BOTANY 2018; 122:133-150. [PMID: 29672665 PMCID: PMC6025197 DOI: 10.1093/aob/mcy048] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 03/15/2018] [Indexed: 05/07/2023]
Abstract
Background and Aims Recent tissue-level observations made indirectly via flow cytometry suggest that endoreplication (duplication of the nuclear genome within the nuclear envelope in the absence of subsequent cell division) is widespread within the plant kingdom. Here, we also directly observe ploidy variation among cells within individual petals, relating size of nucleus to cell micromorphology and (more speculatively) to function. Methods We compared the labella (specialized pollinator-attracting petals) of two European orchid genera: Dactylorhiza has a known predisposition to organismal polyploidy, whereas Ophrys exhibits exceptionally complex epidermal patterning that aids pseudocopulatory pollination. Confocal microscopy using multiple staining techniques allowed us to observe directly both the sizes and the internal structures of individual nuclei across each labellum, while flow cytometry was used to test for progressively partial endoreplication. Key Results In Dactylorhiza, endoreplication was comparatively infrequent, reached only low levels, and appeared randomly located across the labellum, whereas in Ophrys endoreplication was commonplace, being most frequent in large peripheral trichomes. Endoreplicated nuclei reflected both endomitosis and endocycling, the latter reaching the third round of genome doubling (16C) to generate polytene nuclei. All Ophrys individuals studied exhibited progressively partial endoreplication. Conclusions Comparison of the two genera failed to demonstrate the hypothesized pattern of frequent polyploid speciation in genera showing extensive endoreplication. Endoreplication in Ophrys appears more strongly positively correlated with cell size/complexity than with cell location or secretory role. Epigenetic control of gene overexpression by localized induction of endoreplication within individual plant organs may represent a significant component of a plant's developmental programme, contributing substantially to organ plasticity.
Collapse
Affiliation(s)
| | - Jessica J Guy
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
- School of Biological Sciences, University of Reading, Reading, UK
| | - Paula J Rudall
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, UK
| | - Ilia J Leitch
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, UK
| | - Jaume Pellicer
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, UK
| | - Andrew R Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| |
Collapse
|
28
|
Bateman RM, Sramkó G, Paun O. Integrating restriction site-associated DNA sequencing (RAD-seq) with morphological cladistic analysis clarifies evolutionary relationships among major species groups of bee orchids. ANNALS OF BOTANY 2018; 121:85-105. [PMID: 29325077 PMCID: PMC5786241 DOI: 10.1093/aob/mcx129] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Accepted: 10/02/2017] [Indexed: 05/03/2023]
Abstract
BACKGROUND AND AIMS Bee orchids (Ophrys) have become the most popular model system for studying reproduction via insect-mediated pseudo-copulation and for exploring the consequent, putatively adaptive, evolutionary radiations. However, despite intensive past research, both the phylogenetic structure and species diversity within the genus remain highly contentious. Here, we integrate next-generation sequencing and morphological cladistic techniques to clarify the phylogeny of the genus. METHODS At least two accessions of each of the ten species groups previously circumscribed from large-scale cloned nuclear ribosomal internal transcibed spacer (nrITS) sequencing were subjected to restriction site-associated sequencing (RAD-seq). The resulting matrix of 4159 single nucleotide polymorphisms (SNPs) for 34 accessions was used to construct an unrooted network and a rooted maximum likelihood phylogeny. A parallel morphological cladistic matrix of 43 characters generated both polymorphic and non-polymorphic sets of parsimony trees before being mapped across the RAD-seq topology. KEY RESULTS RAD-seq data strongly support the monophyly of nine out of ten groups previously circumscribed using nrITS and resolve three major clades; in contrast, supposed microspecies are barely distinguishable. Strong incongruence separated the RAD-seq trees from both the morphological trees and traditional classifications; mapping of the morphological characters across the RAD-seq topology rendered them far more homoplastic. CONCLUSIONS The comparatively high level of morphological homoplasy reflects extensive convergence, whereas the derived placement of the fusca group is attributed to paedomorphic simplification. The phenotype of the most recent common ancestor of the extant lineages is inferred, but it post-dates the majority of the character-state changes that typify the genus. RAD-seq may represent the high-water mark of the contribution of molecular phylogenetics to understanding evolution within Ophrys; further progress will require large-scale population-level studies that integrate phenotypic and genotypic data in a cogent conceptual framework.
Collapse
Affiliation(s)
- Richard M Bateman
- Jodrell Laboratory, Royal Botanic Gardens Kew, Richmond, Surrey, UK
- For correspondence. E-mail
| | - Gábor Sramkó
- Department of Botany, University of Debrecen, Egyetem, Debrecen, Hungary
- MTA-DE ‘Lendület’ Evolutionary Phylogenomics Research Group, Egyetem, Debrecen, Hungary
| | - Ovidiu Paun
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg, Vienna, Austria
| |
Collapse
|
29
|
Abreu JA, Hawkins JA, Cotrim H, Fay MF, Hidalgo O, Pellicer J. Ophrys fusca and Ophrys dyris (Orchidaceae) – constancy of tetraploidy amongst populations in Central Portugal. ACTA ACUST UNITED AC 2017. [DOI: 10.1080/20423489.2017.1408185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- J. A. Abreu
- Centre for Ecology, Evolution and Evironmental Changes (CE3C), Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal
- Conservation Science, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3DS, UK
- School of Biological Sciences, University of Reading, Whiteknights, Reading, Berkshire RG6 6BX, UK
| | - J. A. Hawkins
- School of Biological Sciences, University of Reading, Whiteknights, Reading, Berkshire RG6 6BX, UK
| | - H. Cotrim
- Centre for Ecology, Evolution and Evironmental Changes (CE3C), Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal
| | - M. F. Fay
- Conservation Science, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3DS, UK
- School of Plant Biology, University of Western Australia, Crawley, WA 6009, Australia
| | - O. Hidalgo
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey, TW3 3DS, UK
| | - J. Pellicer
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey, TW3 3DS, UK
| |
Collapse
|
30
|
Brown SC, Bourge M, Maunoury N, Wong M, Wolfe Bianchi M, Lepers-Andrzejewski S, Besse P, Siljak-Yakovlev S, Dron M, Satiat-Jeunemaître B. DNA Remodeling by Strict Partial Endoreplication in Orchids, an Original Process in the Plant Kingdom. Genome Biol Evol 2017; 9:1051-1071. [PMID: 28419219 PMCID: PMC5546068 DOI: 10.1093/gbe/evx063] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2017] [Indexed: 12/12/2022] Open
Abstract
DNA remodeling during endoreplication appears to be a strong developmental characteristic in orchids. In this study, we analyzed DNA content and nuclei in 41 species of orchids to further map the genome evolution in this plant family. We demonstrate that the DNA remodeling observed in 36 out of 41 orchids studied corresponds to strict partial endoreplication. Such process is developmentally regulated in each wild species studied. Cytometry data analyses allowed us to propose a model where nuclear states 2C, 4E, 8E, etc. form a series comprising a fixed proportion, the euploid genome 2C, plus 2-32 additional copies of a complementary part of the genome. The fixed proportion ranged from 89% of the genome in Vanilla mexicana down to 19% in V. pompona, the lowest value for all 148 orchids reported. Insterspecific hybridization did not suppress this phenomenon. Interestingly, this process was not observed in mass-produced epiphytes. Nucleolar volumes grow with the number of endocopies present, coherent with high transcription activity in endoreplicated nuclei. Our analyses suggest species-specific chromatin rearrangement. Towards understanding endoreplication, V. planifolia constitutes a tractable system for isolating the genomic sequences that confer an advantage via endoreplication from those that apparently suffice at diploid level.
Collapse
Affiliation(s)
- Spencer C. Brown
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université
Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette Cedex, France
| | - Mickaël Bourge
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université
Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette Cedex, France
| | - Nicolas Maunoury
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université
Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette Cedex, France
| | - Maurice Wong
- Service du Développement Rural, Papeete Tahiti, French Polynesia,
France
| | - Michele Wolfe Bianchi
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université
Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette Cedex, France
| | | | - Pascale Besse
- UMR 53, PVBMT Université de la Réunion – Cirad, Pôle de Protection des
Plantes, St Pierre, France
| | - Sonja Siljak-Yakovlev
- Ecologie Systématique Evolution, Université Paris-Sud, CNRS, AgroParisTech,
Université Paris-Saclay, Orsay Cedex, France
| | - Michel Dron
- Institute of Plant Sciences Paris Saclay IPS2, Université Paris-Sud, CNRS,
INRA, Université Evry, Université Paris Diderot, Sorbonne Paris-Cité, Université
Paris-Saclay, Orsay, France
| | - Béatrice Satiat-Jeunemaître
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université
Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette Cedex, France
| |
Collapse
|
31
|
Moraes AP, Koehler S, Cabral JS, Gomes SSL, Viccini LF, Barros F, Felix LP, Guerra M, Forni-Martins ER. Karyotype diversity and genome size variation in Neotropical Maxillariinae orchids. PLANT BIOLOGY (STUTTGART, GERMANY) 2017; 19:298-308. [PMID: 27917576 DOI: 10.1111/plb.12527] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 11/28/2016] [Indexed: 06/06/2023]
Abstract
Orchidaceae is a widely distributed plant family with very diverse vegetative and floral morphology, and such variability is also reflected in their karyotypes. However, since only a low proportion of Orchidaceae has been analysed for chromosome data, greater diversity may await to be unveiled. Here we analyse both genome size (GS) and karyotype in two subtribes recently included in the broadened Maxillariinea to detect how much chromosome and GS variation there is in these groups and to evaluate which genome rearrangements are involved in the species evolution. To do so, the GS (14 species), the karyotype - based on chromosome number, heterochromatic banding and 5S and 45S rDNA localisation (18 species) - was characterised and analysed along with published data using phylogenetic approaches. The GS presented a high phylogenetic correlation and it was related to morphological groups in Bifrenaria (larger plants - higher GS). The two largest GS found among genera were caused by different mechanisms: polyploidy in Bifrenaria tyrianthina and accumulation of repetitive DNA in Scuticaria hadwenii. The chromosome number variability was caused mainly through descending dysploidy, and x=20 was estimated as the base chromosome number. Combining GS and karyotype data with molecular phylogeny, our data provide a more complete scenario of the karyotype evolution in Maxillariinae orchids, allowing us to suggest, besides dysploidy, that inversions and transposable elements as two mechanisms involved in the karyotype evolution. Such karyotype modifications could be associated with niche changes that occurred during species evolution.
Collapse
Affiliation(s)
- A P Moraes
- Departamento de Biologia Vegetal, Instituto de Biociências, Universidade Estadual de Campinas, Campinas, Brazil
- Departamento de Genética, Instituto de Biociências, Universidade Estadual Paulista Julio de Mesquita Filho, Botucatu, Brazil
- Instituto de Ciências e Tecnologia, Universidade Federal de São Paulo, São José dos Campos, Brazil
| | - S Koehler
- Departamento de Biologia Vegetal, Instituto de Biociências, Universidade Estadual de Campinas, Campinas, Brazil
| | - J S Cabral
- Departamento de Botânica, Centro de Ciências Biológicas, Cidade Universitária, Universidade Federal de Pernambuco, Recife, Brazil
- Synthesis Centre, German Centre for Integrative Biodiversity Research, Leipzig, Germany
- Center for Computational and Theoretical Biology, Ecosystem Modeling, University of Würzburg, Würzburg, Germany
| | - S S L Gomes
- Departamento de Biologia, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Juiz de Fora, Brazil
| | - L F Viccini
- Departamento de Biologia, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Juiz de Fora, Brazil
| | - F Barros
- Instituto de Botânica, Núcleo de Pesquisa Orquidário do Estado de São Paulo, São Paulo, Brazil
| | - L P Felix
- Departamento de Ciências Biológicas, Centro de Ciências Agrárias, Universidade Federal da Paraíba, Rodovia, Areias, Brazil
| | - M Guerra
- Departamento de Botânica, Centro de Ciências Biológicas, Cidade Universitária, Universidade Federal de Pernambuco, Recife, Brazil
| | - E R Forni-Martins
- Departamento de Biologia Vegetal, Instituto de Biociências, Universidade Estadual de Campinas, Campinas, Brazil
| |
Collapse
|
32
|
Kocová V, Straková N, Kolarčik V, Rákai A, Mártonfi P. Endoreduplication as a part of flower ontogeny in Trifolium pratense cultivars. BOTANICAL STUDIES 2016; 57:34. [PMID: 28597444 PMCID: PMC5430558 DOI: 10.1186/s40529-016-0150-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2016] [Accepted: 10/22/2016] [Indexed: 05/13/2023]
Abstract
BACKGROUND Endoreduplication appears in numerous plant species and plays a vital role during ontogeny. The presence of polyploid cells in an otherwise diploid organism is tied specifically to the taxonomy, ecology and physiology of the studied specimen. Little is known about the changes in endopolyploidy levels of floral organs during their development. In order to uncover the workings of endoreduplication in polysomatic species, our study examines flowers of T. pratense in three ontogenetic stages by means of flow cytometry. RESULTS Cultivar 'Manuela' is characterized by the presence of 2C-8C and 'Dajana' 2C-16C nuclei. In general, the frequencies of nuclei only slightly changed during development. Endopolyploidy levels represented by endoreduplication index (EI) in the 'Manuela' sepals and stamens showed statistical differences between young and old stages, other organs of both cultivars between stages are not statistically different. Significant differences between 'Manuela' and 'Dajana' cultivars were found only in sepals of I. stage, and in petals and carpels of III. stage. Cultivars showed a similar pattern of endopolyploidy. However, a considerable decrease in EI 'Manuela' petals and carpels at III. stage was detected as opposed to 'Dajana'. Overall, a higher endoreduplication index is distinctive for organs of the 'Dajana' cultivar. CONCLUSIONS In this study we prove the permanent presence of endopolyploid cells in the floral organs of T. pratense throughout their development.
Collapse
Affiliation(s)
- Valéria Kocová
- Department of Botany, Faculty of Science, Institute of Biology and Ecology, P.J. Šafárik University, Mánesova 23, 04154 Košice, Slovakia
| | | | - Vladislav Kolarčik
- Department of Botany, Faculty of Science, Institute of Biology and Ecology, P.J. Šafárik University, Mánesova 23, 04154 Košice, Slovakia
| | - Albert Rákai
- Department of Botany, Faculty of Science, Institute of Biology and Ecology, P.J. Šafárik University, Mánesova 23, 04154 Košice, Slovakia
| | - Pavol Mártonfi
- Department of Botany, Faculty of Science, Institute of Biology and Ecology, P.J. Šafárik University, Mánesova 23, 04154 Košice, Slovakia
| |
Collapse
|
33
|
Hřibová E, Holušová K, Trávníček P, Petrovská B, Ponert J, Šimková H, Kubátová B, Jersáková J, Čurn V, Suda J, Doležel J, Vrána J. The Enigma of Progressively Partial Endoreplication: New Insights Provided by Flow Cytometry and Next-Generation Sequencing. Genome Biol Evol 2016; 8:1996-2005. [PMID: 27324917 PMCID: PMC4943206 DOI: 10.1093/gbe/evw141] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
In many plant species, somatic cell differentiation is accompanied by endoreduplication, a process during which cells undergo one or more rounds of DNA replication cycles in the absence of mitosis, resulting in nuclei with multiples of 2C DNA amounts (4C, 8C, 16C, etc.). In some orchids, a disproportionate increase in nuclear DNA contents has been observed, where successive endoreduplication cycles result in DNA amounts 2C + P, 2C + 3P, 2C + 7P, etc., where P is the DNA content of the replicated part of the 2C nuclear genome. This unique phenomenon was termed "progressively partial endoreplication" (PPE). We investigated processes behind the PPE in Ludisia discolor using flow cytometry (FCM) and Illumina sequencing. In particular, we wanted to determine whether chromatin elimination or incomplete genome duplication was involved, and to identify types of DNA sequences that were affected. Cell cycle analysis of root tip cell nuclei pulse-labeled with EdU revealed two cell cycles, one ending above the population of nuclei with 2C + P content, and the other with a typical "horseshoe" pattern of S-phase nuclei ranging from 2C to 4C DNA contents. The process leading to nuclei with 2C + P amounts therefore involves incomplete genome replication. Subsequent Illumina sequencing of flow-sorted 2C and 2C + P nuclei showed that all types of repetitive DNA sequences were affected during PPE; a complete elimination of any specific type of repetitive DNA was not observed. We hypothesize that PPE is part of a highly controlled transition mechanism from proliferation phase to differentiation phase of plant tissue development.
Collapse
Affiliation(s)
- Eva Hřibová
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Olomouc, Czech Republic
| | - Kateřina Holušová
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Olomouc, Czech Republic
| | - Pavel Trávníček
- Institute of Botany, the Czech Academy of Sciences, Průhonice, Czech Republic Department of Botany, Faculty of Science, Charles University in Prague, Czech Republic Biotechnological Centre, Faculty of Agriculture, University of South Bohemia in České Budějovice, Czech Republic
| | - Beáta Petrovská
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Olomouc, Czech Republic
| | - Jan Ponert
- Department of Experimental Plant Biology, Faculty of Science, Charles University in Prague, Czech Republic Prague Botanical Garden, Prague, Czech Republic
| | - Hana Šimková
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Olomouc, Czech Republic
| | - Barbora Kubátová
- Biotechnological Centre, Faculty of Agriculture, University of South Bohemia in České Budějovice, Czech Republic
| | - Jana Jersáková
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia in České Budějovice, Czech Republic
| | - Vladislav Čurn
- Biotechnological Centre, Faculty of Agriculture, University of South Bohemia in České Budějovice, Czech Republic
| | - Jan Suda
- Institute of Botany, the Czech Academy of Sciences, Průhonice, Czech Republic Department of Botany, Faculty of Science, Charles University in Prague, Czech Republic
| | - Jaroslav Doležel
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Olomouc, Czech Republic
| | - Jan Vrána
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Olomouc, Czech Republic
| |
Collapse
|