Publications by authors named "Jaume Pellicer"

35 Publications

Biogeography and genome size evolution of the oldest extant vascular plant genus, Equisetum (Equisetaceae).

Ann Bot 2021 Feb 18. Epub 2021 Feb 18.

Royal Botanic Gardens, Kew, Richmond, UK.

Background And Aims: Extant plant groups with a long fossil history are key elements in understanding vascular plant evolution. Horsetails (Equisetum, Equisetaceae) have a nearly continuous fossil record dating back to the Carboniferous, but their phylogenetic and biogeographic patterns are still poorly understood. We use here the most extensive phylogenetic analysis to date as a framework to evaluate their age, biogeography and genome size evolution.

Methods: DNA sequences of four plastid loci were used to estimate divergence times and investigate the biogeographic history of all extant species of Equisetum. Flow cytometry was used to study genome size evolution against the framework of phylogenetic relationships in Equisetum.

Key Results: On a well-supported phylogenetic tree including all extant Equisetum species, a molecular clock calibrated with multiple fossils places the node at which the outgroup and Equisetum diverged at 343 Mya (Early Carboniferous), with the first major split among extant species occurring 170 Mya (Middle Jurassic). These dates are older than those reported in some other recent molecular clock studies but are largely in agreement with a timeline established by fossil appearance in the geological record. Representatives of evergreen subgenus Hippochaete have much larger genome sizes than those of deciduous subgenus Equisetum, despite their shared conserved chromosome number. Subgenus Paramochaete has an intermediate genome size and maintains the same number of chromosomes.

Conclusions: The first divergences among extant members of the genus coincided with the break-up of Pangaea and the resulting more humid, warmer climate. Subsequent tectonic activity most likely involved vicariance events that led to species divergences combined with some more recent, long-distance dispersal events. We hypothesize that differences in genome size between subgenera may be related to the number of sperm flagellae.
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http://dx.doi.org/10.1093/aob/mcab005DOI Listing
February 2021

The Application of Flow Cytometry for Estimating Genome Size, Ploidy Level Endopolyploidy, and Reproductive Modes in Plants.

Methods Mol Biol 2021 ;2222:325-361

Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey, UK.

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.
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http://dx.doi.org/10.1007/978-1-0716-0997-2_17DOI Listing
March 2021

Genome Size Versus Genome Assemblies: Are the Genomes Truly Expanded in Polyploid Fungal Symbionts?

Genome Biol Evol 2020 12;12(12):2384-2390

Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, United Kingdom.

Each day, as the amount of genomic data and bioinformatics resources grows, researchers are increasingly challenged with selecting the most appropriate approach to analyze their data. In addition, the opportunity to undertake comparative genomic analyses is growing rapidly. This is especially true for fungi due to their small genome sizes (i.e., mean 1C = 44.2 Mb). Given these opportunities and aiming to gain novel insights into the evolution of mutualisms, we focus on comparing the quality of whole genome assemblies for fungus-growing ants cultivars (Hymenoptera: Formicidae: Attini) and a free-living relative. Our analyses reveal that currently available methodologies and pipelines for analyzing whole-genome sequence data need refining. By using different genome assemblers, we show that the genome assembly size depends on what software is used. This, in turn, impacts gene number predictions, with higher gene numbers correlating positively with genome assembly size. Furthermore, the majority of fungal genome size data currently available are based on estimates derived from whole-genome assemblies generated from short-read genome data, rather than from the more accurate technique of flow cytometry. Here, we estimated the haploid genome sizes of three ant fungal symbionts by flow cytometry using the fungus Pleurotus ostreatus (Jacq.) P. Kumm. (1871) as a calibration standard. We found that published genome sizes based on genome assemblies are 2.5- to 3-fold larger than our estimates based on flow cytometry. We, therefore, recommend that flow cytometry is used to precalibrate genome assembly pipelines, to avoid incorrect estimates of genome sizes and ensure robust assemblies.
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http://dx.doi.org/10.1093/gbe/evaa217DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7719231PMC
December 2020

Repeat-sequence turnover shifts fundamentally in species with large genomes.

Nat Plants 2020 11 19;6(11):1325-1329. Epub 2020 Oct 19.

School of Biological and Chemical Sciences, Queen Mary University of London, London, UK.

Given the 2,400-fold range of genome sizes (0.06-148.9 Gbp (gigabase pair)) of seed plants (angiosperms and gymnosperms) with a broadly similar gene content (amounting to approximately 0.03 Gbp), the repeat-sequence content of the genome might be expected to increase with genome size, resulting in the largest genomes consisting almost entirely of repetitive sequences. Here we test this prediction, using the same bioinformatic approach for 101 species to ensure consistency in what constitutes a repeat. We reveal a fundamental change in repeat turnover in genomes above around 10 Gbp, such that species with the largest genomes are only about 55% repetitive. Given that genome size influences many plant traits, habits and life strategies, this fundamental shift in repeat dynamics is likely to affect the evolutionary trajectory of species lineages.
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http://dx.doi.org/10.1038/s41477-020-00785-xDOI Listing
November 2020

Automated video monitoring of insect pollinators in the field.

Emerg Top Life Sci 2020 07;4(1):87-97

Red Butte Garden and Arboretum, University of Utah, Salt Lake City, UT 84108, U.S.A.

Ecosystems are at increasing risk from the global pollination crisis. Gaining better knowledge about pollinators and their interactions with plants is an urgent need. However, conventional methods of manually recording pollinator activity in the field can be time- and cost-consuming in terms of labour. Field-deployable video recording systems have become more common in ecological studies as they enable the capture of plant-insect interactions in fine detail. Standard video recording can be effective, although there are issues with hardware reliability under field-conditions (e.g. weatherproofing), and reviewing raw video manually is a time-consuming task. Automated video monitoring systems based on motion detection partly overcome these issues by only recording when activity occurs hence reducing the time needed to review footage during post-processing. Another advantage of these systems is that the hardware has relatively low power requirements. A few systems have been tested in the field which permit the collection of large datasets. Compared with other systems, automated monitoring allows vast increases in sampling at broad spatiotemporal scales. Some tools such as post-recording computer vision software and data-import scripts exist, further reducing users' time spent processing and analysing the data. Integrated computer vision and automated species recognition using machine learning models have great potential to further the study of pollinators in the field. Together, it is predicted that future advances in technology-based field monitoring methods will contribute significantly to understanding the causes underpinning pollinator declines and, hence, developing effective solutions for dealing with this global challenge.
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http://dx.doi.org/10.1042/ETLS20190074DOI Listing
July 2020

Polyploidy in gymnosperms - Insights into the genomic and evolutionary consequences of polyploidy in Ephedra.

Mol Phylogenet Evol 2020 06 2;147:106786. Epub 2020 Mar 2.

Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, United Kingdom.

While polyploidization is recognized as a major evolutionary driver for ferns and angiosperms, little is known about its impact in gymnosperms, where polyploidy is much less frequent. We explore Ephedra to evaluate (i) the extent of genome size diversity in the genus and the influence polyploidy has had on the evolution of nuclear DNA contents, and (ii) identify where shifts in genome size and polyploidy have occurred both temporally and spatially. A phylogenetic framework of all Ephedra species together with genome sizes and karyotypes for 87% and 67% of them respectively, were used to explore ploidy evolution and its global distribution patterns. Polyploidy was shown to be extremely common, with 41 species (83%) being polyploid (up to 8×) or having polyploid cytotypes - the highest frequency and level reported for any gymnosperm. Genome size was also diverse, with values ranging ~5-fold (8.09-38.34 pg/1C) - the largest range for any gymnosperm family - and increasing in proportion to ploidy level (i.e. no genome downsizing). Our findings provide novel data which support the view that gymnosperms have a more conserved mode of genomic evolution compared with angiosperms.
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http://dx.doi.org/10.1016/j.ympev.2020.106786DOI Listing
June 2020

Genome size variation at constant chromosome number is not correlated with repetitive DNA dynamism in Anacyclus (Asteraceae).

Ann Bot 2020 03;125(4):611-623

Institut Botànic de Barcelona (IBB, CSIC-ICUB), Passeig del Migdia sn, 08038 Barcelona, Catalonia, Spain.

Background And Aims: Changes in the amount of repetitive DNA (dispersed and tandem repeats) are considered the main contributors to genome size variation across plant species in the absence of polyploidy. However, the study of repeatome dynamism in groups showing contrasting genomic features and complex evolutionary histories is needed to determine whether other processes underlying genome size variation may have been overlooked. The main aim here was to elucidate which mechanism best explains genome size evolution in Anacyclus (Asteraceae).

Methods: Using data from Illumina sequencing, we analysed the repetitive DNA in all species of Anacyclus, a genus with a reticulate evolutionary history, which displays significant genome size and karyotype diversity albeit presenting a stable chromosome number.

Key Results: By reconstructing ancestral genome size values, we inferred independent episodes of genome size expansions and contractions during the evolution of the genus. However, analysis of the repeatome revealed a similar DNA repeat composition across species, both qualitative and quantitative. Using comparative methods to study repeatome dynamics in the genus, we found no evidence for repeat activity causing genome size variation among species.

Conclusions: Our results, combined with previous cytogenetic data, suggest that genome size differences in Anacyclus are probably related to chromosome rearrangements involving losses or gains of chromosome fragments, possibly associated with homoploid hybridization. These could represent balanced rearrangements that do not disrupt gene dosage in merged genomes, for example via chromosome segment exchanges.
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http://dx.doi.org/10.1093/aob/mcz183DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7103019PMC
March 2020

The Plant DNA C-values database (release 7.1): an updated online repository of plant genome size data for comparative studies.

New Phytol 2020 04 8;226(2):301-305. Epub 2019 Nov 8.

Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, TW9 3DS, UK.

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http://dx.doi.org/10.1111/nph.16261DOI Listing
April 2020

Ecological speciation in sympatric palms: 3. Genetic map reveals genomic islands underlying species divergence in Howea.

Evolution 2019 09 24;73(9):1986-1995. Epub 2019 Jul 24.

Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, SL5 7PY, United Kingdom.

Although it is now widely accepted that speciation can occur in the face of continuous gene flow, with little or no spatial separation, the mechanisms and genomic architectures that permit such divergence are still debated. Here, we examined speciation in the face of gene flow in the Howea palms of Lord Howe Island, Australia. We built a genetic map using a novel method applicable to long-lived tree species, combining it with double digest restriction site-associated DNA sequencing of multiple individuals. Based upon various metrics, we detected 46 highly differentiated regions throughout the genome, four of which contained genes with functions that are particularly relevant to the speciation scenario for Howea, specifically salt and drought tolerance.
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http://dx.doi.org/10.1111/evo.13796DOI Listing
September 2019

Apomixis and Hybridization Drives Reticulate Evolution and Phyletic Differentiation in L.: Implications for Conservation.

Front Plant Sci 2018 13;9:1796. Epub 2018 Dec 13.

Molecular Ecology and Evolution Group, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom.

Hybridization and polyploidy are major forces in the evolution of plant diversity and the study of these processes is of particular interest to understand how novel taxa are formed and how they maintain genetic integrity. is an example of a genus where active diversification and speciation are ongoing and, as such, represents an ideal model to investigate the roles of hybridization, polyploidy and apomixis in a reticulate evolutionary process. To elucidate breeding systems and evolutionary origins of a complex of closely related taxa, we assessed genotypic diversity and population structure within and among taxa, combining data from nuclear DNA microsatellite markers and flow cytometry. Clonal analysis and low genotypic diversity within the polyploid taxa suggest apomixis is obligate. However, genetic variation has led to groups of 'clone-mates' within apomictic taxa that strongly suggest mutation is responsible for the genotypic diversity of these apomictic lineages. In addition, microsatellite profiles and site demographics suggest hybridization events among apomictic polyploid may have contributed to the extant diversity of recognized taxa in this region. This research demonstrates that both macro- and micro-evolutionary processes are active within this reticulate complex. Conservation measures should be aimed at maintaining this process and should therefore be prioritized for those areas of species richness where the potential for interspecific gene flow is greatest.
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http://dx.doi.org/10.3389/fpls.2018.01796DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6300497PMC
December 2018

Functional and evolutionary genomic inferences in through genome and population sequencing of American and European aspen.

Proc Natl Acad Sci U S A 2018 11 29;115(46):E10970-E10978. Epub 2018 Oct 29.

Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87 Umeå, Sweden;

The genus is one of the major plant model systems, but genomic resources have thus far primarily been available for poplar species, and primarily (Torr. & Gray), which was the first tree with a whole-genome assembly. To further advance evolutionary and functional genomic analyses in , we produced genome assemblies and population genetics resources of two aspen species, L. and Michx. The two aspen species have distributions spanning the Northern Hemisphere, where they are keystone species supporting a wide variety of dependent communities and produce a diverse array of secondary metabolites. Our analyses show that the two aspens share a similar genome structure and a highly conserved gene content with but display substantially higher levels of heterozygosity. Based on population resequencing data, we observed widespread positive and negative selection acting on both coding and noncoding regions. Furthermore, patterns of genetic diversity and molecular evolution in aspen are influenced by a number of features, such as expression level, coexpression network connectivity, and regulatory variation. To maximize the community utility of these resources, we have integrated all presented data within the PopGenIE web resource (PopGenIE.org).
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http://dx.doi.org/10.1073/pnas.1801437115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6243237PMC
November 2018

A phylogenetic road map to antimalarial Artemisia species.

J Ethnopharmacol 2018 Oct 22;225:1-9. Epub 2018 Jun 22.

Natural History Museum of Denmark, Faculty of Science, University of Copenhagen, Øster Farimagsgade 5A, Copenhagen 1353, Denmark. Electronic address:

Ethnopharmacological Relevance: The discovery of the antimalarial agent artemisinin is considered one of the most significant success stories of ethnopharmacological research in recent times. The isolation of artemisinin was inspired by the use of Artemisia annua in traditional Chinese medicine (TCM) and was awarded a Nobel Prize in 2015. Antimalarial activity has since been demonstrated for a range of other Artemisia species, suggesting that the genus could provide alternative sources of antimalarial treatments. Given the stunning diversity of the genus (c. 500 species), a prioritisation of taxa to be investigated for their likely antimalarial properties is required.

Materials And Methods: Here we use a phylogenetic approach to explore the potential for identifying species more likely to possess antimalarial properties. Ethnobotanical data from literature reports is recorded for 117 species. Subsequent phylogenetically informed analysis was used to identify lineages in which there is an overrepresentation of species used to treat malarial symptoms, and which could therefore be high priority for further investigation of antimalarial activity.

Results: We show that these lineages indeed include several species with documented antimalarial activity. To further inform our approach, we use LC-MS/MS analysis to explore artemisinin content in fifteen species from both highlighted and not highlighted lineages. We detected artemisinin in nine species, in eight of them for the first time, doubling the number of Artemisia taxa known to content this molecule.

Conclusions: Our findings indicate that artemisinin may be widespread across the genus, providing an accessible local resource outside the distribution area of Artemisia annua.
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http://dx.doi.org/10.1016/j.jep.2018.06.030DOI Listing
October 2018

Evolutionary and functional potential of ploidy increase within individual plants: somatic ploidy mapping of the complex labellum of sexually deceptive bee orchids.

Ann Bot 2018 06;122(1):133-150

School of Biological and Chemical Sciences, Queen Mary University of London, London, UK.

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.
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http://dx.doi.org/10.1093/aob/mcy048DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6025197PMC
June 2018

Genome Size Diversity and Its Impact on the Evolution of Land Plants.

Genes (Basel) 2018 Feb 14;9(2). Epub 2018 Feb 14.

Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew TW9 3DS, UK.

Genome size is a biodiversity trait that shows staggering diversity across eukaryotes, varying over 64,000-fold. Of all major taxonomic groups, land plants stand out due to their staggering genome size diversity, ranging ca. 2400-fold. As our understanding of the implications and significance of this remarkable genome size diversity in land plants grows, it is becoming increasingly evident that this trait plays not only an important role in shaping the evolution of plant genomes, but also in influencing plant community assemblages at the ecosystem level. Recent advances and improvements in novel sequencing technologies, as well as analytical tools, make it possible to gain critical insights into the genomic and epigenetic mechanisms underpinning genome size changes. In this review we provide an overview of our current understanding of genome size diversity across the different land plant groups, its implications on the biology of the genome and what future directions need to be addressed to fill key knowledge gaps.
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http://dx.doi.org/10.3390/genes9020088DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5852584PMC
February 2018

Is There an Upper Limit to Genome Size?

Trends Plant Sci 2017 07 12;22(7):567-573. Epub 2017 May 12.

Royal Botanic Gardens, Kew, Richmond TW9 3DS, UK. Electronic address:

At 50-fold the size of the human genome (3 Gb), the staggeringly huge genome of 147.3 Gb recently discovered in the fern Tmesipteris obliqua is comparable in size to those of the other plant and animal record-holders (i.e., Paris japonica, a flowering plant with a genome size of 148.8 Gb, and Protopterus aethiopicus, a lungfish with a genome of 130 Gb). The synthesis of available information on giant genomes suggests that the biological limit to genome size expansion in eukaryotes may have been reached. We propose several explanations for why the genomes of ferns, flowering plants, and lungfish, all of which have independently undergone dramatic increases in genome size through a variety of mechanisms, do not exceed 150 Gb.
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http://dx.doi.org/10.1016/j.tplants.2017.04.005DOI Listing
July 2017

transect of Europe: variation in ploidy and genome size in willow-associated common nettle, L. , from Greece to arctic Norway.

Biodivers Data J 2016 27(4):e10003. Epub 2016 Sep 27.

Royal Botanic Gardens, Kew, United Kingdom.

Background: The common stinging nettle, L. sensu lato, is an invertebrate "superhost", its clonal patches maintaining large populations of insects and molluscs. It is extremely widespread in Europe and highly variable, and two ploidy levels (diploid and tetraploid) are known. However, geographical patterns in cytotype variation require further study.

New Information: We assembled a collection of nettles in conjunction with a transect of Europe from the Aegean to Arctic Norway (primarily conducted to examine the diversity of and -associated insects). Using flow cytometry to measure genome size, our sample of 29 plants reveals 5 diploids and 24 tetraploids. Two diploids were found in SE Europe (Bulgaria and Romania) and three diploids in S. Finland. More detailed cytotype surveys in these regions are suggested. The tetraploid genome size (2C value) varied between accessions from 2.36 to 2.59 pg. The diploids varied from 1.31 to 1.35 pg per 2C nucleus, equivalent to a haploid genome size of c. 650 Mbp. Within the tetraploids, we find that the most northerly samples (from N. Finland and arctic Norway) have a generally higher genome size. This is possibly indicative of a distinct population in this region.
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http://dx.doi.org/10.3897/BDJ.4.e10003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5136675PMC
September 2016

Salamanders' slow slither into genomic gigantism.

Evolution 2016 12;70(12):2915-2916

Royal Botanic Gardens, Kew-Comparative Plant and Fungal Biology, Kew, Richmond, TW9 3DS, United Kingdom.

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http://dx.doi.org/10.1111/evo.13112DOI Listing
December 2016

Genome evolution of ferns: evidence for relative stasis of genome size across the fern phylogeny.

New Phytol 2016 May 12;210(3):1072-82. Epub 2016 Jan 12.

Department of Life Sciences, Natural History Museum, London, SW7 5BD, UK.

The genome evolution of ferns has been considered to be relatively static compared with angiosperms. In this study, we analyse genome size data and chromosome numbers in a phylogenetic framework to explore three hypotheses: the correlation of genome size and chromosome number, the origin of modern ferns from ancestors with high chromosome numbers, and the occurrence of several whole-genome duplications during the evolution of ferns. To achieve this, we generated new genome size data, increasing the percentage of fern species with genome sizes estimated to 2.8% of extant diversity, and ensuring a comprehensive phylogenetic coverage including at least three species from each fern order. Genome size was correlated with chromosome number across all ferns despite some substantial variation in both traits. We observed a trend towards conservation of the amount of DNA per chromosome, although Osmundaceae and Psilotaceae have substantially larger chromosomes. Reconstruction of the ancestral genome traits suggested that the earliest ferns were already characterized by possessing high chromosome numbers and that the earliest divergences in ferns were correlated with substantial karyological changes. Evidence for repeated whole-genome duplications was found across the phylogeny. Fern genomes tend to evolve slowly, albeit genome rearrangements occur in some clades.
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http://dx.doi.org/10.1111/nph.13833DOI Listing
May 2016

In Depth Characterization of Repetitive DNA in 23 Plant Genomes Reveals Sources of Genome Size Variation in the Legume Tribe Fabeae.

PLoS One 2015 25;10(11):e0143424. Epub 2015 Nov 25.

Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, United Kingdom.

The differential accumulation and elimination of repetitive DNA are key drivers of genome size variation in flowering plants, yet there have been few studies which have analysed how different types of repeats in related species contribute to genome size evolution within a phylogenetic context. This question is addressed here by conducting large-scale comparative analysis of repeats in 23 species from four genera of the monophyletic legume tribe Fabeae, representing a 7.6-fold variation in genome size. Phylogenetic analysis and genome size reconstruction revealed that this diversity arose from genome size expansions and contractions in different lineages during the evolution of Fabeae. Employing a combination of low-pass genome sequencing with novel bioinformatic approaches resulted in identification and quantification of repeats making up 55-83% of the investigated genomes. In turn, this enabled an analysis of how each major repeat type contributed to the genome size variation encountered. Differential accumulation of repetitive DNA was found to account for 85% of the genome size differences between the species, and most (57%) of this variation was found to be driven by a single lineage of Ty3/gypsy LTR-retrotransposons, the Ogre elements. Although the amounts of several other lineages of LTR-retrotransposons and the total amount of satellite DNA were also positively correlated with genome size, their contributions to genome size variation were much smaller (up to 6%). Repeat analysis within a phylogenetic framework also revealed profound differences in the extent of sequence conservation between different repeat types across Fabeae. In addition to these findings, the study has provided a proof of concept for the approach combining recent developments in sequencing and bioinformatics to perform comparative analyses of repetitive DNAs in a large number of non-model species without the need to assemble their genomes.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0143424PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4659654PMC
June 2016

250 years of hybridization between two biennial herb species without speciation.

AoB Plants 2015 Jul 17;7. Epub 2015 Jul 17.

School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK

Hybridization between plant species can generate novel morphological diversity and lead to speciation at homoploid or polyploid levels. Hybrids between biennial herbs Tragopogon pratensis and T. porrifolius have been studied in experimental and natural populations for over 250 years. Here we examine their current status in natural populations in southeast England. All hybrids found were diploid; they tended to grow taller and with more buds than their parental species; many showed partial fertility; a few showed evidence of backcrossing. However, we found no evidence to suggest that the hybrids are establishing as a new species, nor can we find literature documenting speciation of these hybrids elsewhere. This lack of speciation despite at least 250 years of hybridization contrasts with the fact that both parental species have formed new allopolyploid species through hybridization with another diploid, T. dubius. Understanding why hybrids often do not speciate, despite repeated opportunities, would enhance our understanding of both the evolutionary process and risk assessments of invasive species.
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http://dx.doi.org/10.1093/aobpla/plv081DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4571729PMC
July 2015

Analysis of the giant genomes of Fritillaria (Liliaceae) indicates that a lack of DNA removal characterizes extreme expansions in genome size.

New Phytol 2015 Oct 8;208(2):596-607. Epub 2015 Jun 8.

Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, TW9 3DS, UK.

Plants exhibit an extraordinary range of genome sizes, varying by > 2000-fold between the smallest and largest recorded values. In the absence of polyploidy, changes in the amount of repetitive DNA (transposable elements and tandem repeats) are primarily responsible for genome size differences between species. However, there is ongoing debate regarding the relative importance of amplification of repetitive DNA versus its deletion in governing genome size. Using data from 454 sequencing, we analysed the most repetitive fraction of some of the largest known genomes for diploid plant species, from members of Fritillaria. We revealed that genomic expansion has not resulted from the recent massive amplification of just a handful of repeat families, as shown in species with smaller genomes. Instead, the bulk of these immense genomes is composed of highly heterogeneous, relatively low-abundance repeat-derived DNA, supporting a scenario where amplified repeats continually accumulate due to infrequent DNA removal. Our results indicate that a lack of deletion and low turnover of repetitive DNA are major contributors to the evolution of extremely large genomes and show that their size cannot simply be accounted for by the activity of a small number of high-abundance repeat families.
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http://dx.doi.org/10.1111/nph.13471DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4744688PMC
October 2015

Key processes for Cheirolophus (Asteraceae) diversification on oceanic islands inferred from AFLP data.

PLoS One 2014 20;9(11):e113207. Epub 2014 Nov 20.

Institut Botànic de Barcelona (IBB-CSIC-ICUB), Barcelona, Catalonia, Spain.

The radiation of the genus Cheirolophus (Asteraceae) in Macaronesia constitutes a spectacular case of rapid diversification on oceanic islands. Twenty species - nine of them included in the IUCN Red List of Threatened Species - have been described to date inhabiting the Madeiran and Canarian archipelagos. A previous phylogenetic study revealed that the diversification of Cheirolophus in Macaronesia started less than 2 Ma. As a result of such an explosive speciation process, limited phylogenetic resolution was reported, mainly due to the low variability of the employed molecular markers. In the present study, we used highly polymorphic AFLP markers to i) evaluate species' boundaries, ii) infer their evolutionary relationships and iii) investigate the patterns of genetic diversity in relation to the potential processes likely involved in the radiation of Cheirolophus. One hundred and seventy-two individuals representing all Macaronesian Cheirolophus species were analysed using 249 AFLP loci. Our results suggest that geographic isolation played an important role in this radiation process. This was likely driven by the combination of poor gene flow capacity and a good ability for sporadic long-distance colonisations. In addition, we also found some traces of introgression and incipient ecological adaptation, which could have further enhanced the extraordinary diversification of Cheirolophus in Macaronesia. Last, we hypothesize that current threat categories assigned to Macaronesian Cheirolophus species do not reflect their respective evolutionary relevance, so future evaluations of their conservation status should take into account the results presented here.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0113207PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4239036PMC
January 2016

Chromosome behavior at the base of the angiosperm radiation: karyology of Trithuria submersa (Hydatellaceae, Nymphaeales).

Am J Bot 2014 Sep 17;101(9):1447-55. Epub 2014 Sep 17.

Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK.

Unlabelled: •

Premise Of The Study: Hydatellaceae are minute annual herbs with potential as a model system for studying early angiosperm evolution, but their karyology and ploidy levels are almost unknown. We investigated these aspects of Trithuria submersa, a widespread species that we show to be amenable to extended vegetative propagation.•

Methods: We cultivated plants of T. submersa in vitro after developing and optimizing culture conditions. We estimated genome size using flow cytometry, counted chromosome numbers using root-meristem squashes after Feulgen staining, and examined meiotic chromosome behavior using microsporocytes.•

Key Results: We developed methods to reliably germinate seeds of T. submersa and to propagate them vegetatively in critical thermo- and photoperiod regimes on 1/2 Murashige-Skoog (MS) medium with vitamins and 2% sucrose solidified with 0.7% agar-agar. Seedling growth requires the medium be supplemented with activated charcoal. The mean nuclear DNA content of T. submersa sporophytes is 2C = 2.74 pg (∼2.68 Gbp). The sporophytic chromosome number is 2n = 56 with a bimodal complement, which may suggest an allopolyploid origin. Some of the largest chromosomes lack a recognizable constriction, which relates to a highly unusual and irregular chromosome behavior. Microsporocytes undergo reduced and asynchronous meioses that show a modified intermediate cell division with a nucleus division by fractional postreduction, indicating partially inverted microsporogenesis.•

Conclusions: In vitro cultivation and karyological assessment of T. submersa open new opportunities for investigating early-divergent angiosperms. The remarkably different meiotic behavior exhibits new insights into a potentially ancestral microsporogenesis.
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http://dx.doi.org/10.3732/ajb.1400050DOI Listing
September 2014

The explosive radiation of Cheirolophus (Asteraceae, Cardueae) in Macaronesia.

BMC Evol Biol 2014 Jun 2;14:118. Epub 2014 Jun 2.

Laboratori de Botànica - Unitat associada CSIC, Facultat de Farmàcia, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain.

Background: Considered a biodiversity hotspot, the Canary Islands have been the key subjects of numerous evolutionary studies concerning a large variety of organisms. The genus Cheirolophus (Asteraceae) represents one of the largest plant radiations in the Canarian archipelago. In contrast, only a few species occur in the Mediterranean region, the putative ancestral area of the genus. Here, our main aim was to reconstruct the phylogenetic and biogeographic history of Cheirolophus with special focus on explaining the origin of the large Canarian radiation.

Results: We found significant incongruence in phylogenetic relationships between nuclear and plastid markers. Each dataset provided resolution at different levels in Cheirolophus: the nuclear markers resolved the backbone of the phylogeny while the plastid data provided better resolution within the Canarian clade. The origin of Cheirolophus was dated in the Mid-Late Miocene, followed by rapid diversification into the three main Mediterranean lineages and the Macaronesian clade. A decrease in diversification rates was inferred at the end of the Miocene, with a new increase in the Late Pliocene concurrent with the onset of the Mediterranean climate. Diversification within the Macaronesian clade started in the Early-Mid Pleistocene, with unusually high speciation rates giving rise to the extant insular diversity.

Conclusions: Climate-driven diversification likely explains the early evolutionary history of Cheirolophus in the Mediterranean region. It appears that the exceptionally high diversification rate in the Canarian clade was mainly driven by allopatric speciation (including intra- and interisland diversification). Several intrinsic (e.g. breeding system, polyploid origin, seed dispersal syndrome) and extrinsic (e.g. fragmented landscape, isolated habitats, climatic and geological changes) factors probably contributed to the progressive differentiation of populations resulting in numerous microendemisms. Finally, hybridization events and emerging ecological adaptation may have also reinforced the diversification process.
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http://dx.doi.org/10.1186/1471-2148-14-118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4048045PMC
June 2014

The application of flow cytometry for estimating genome size and ploidy level in plants.

Methods Mol Biol 2014 ;1115:279-307

Jodrell Laboratory, Royal Botanic Gardens, Surrey, UK.

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.
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http://dx.doi.org/10.1007/978-1-62703-767-9_14DOI Listing
August 2014

Genome size expansion and the relationship between nuclear DNA content and spore size in the Asplenium monanthes fern complex (Aspleniaceae).

BMC Plant Biol 2013 Dec 20;13:219. Epub 2013 Dec 20.

Department of Botany, Natural History Museum, London SW7 5BD, UK.

Background: Homosporous ferns are distinctive amongst the land plant lineages for their high chromosome numbers and enigmatic genomes. Genome size measurements are an under exploited tool in homosporous ferns and show great potential to provide an overview of the mechanisms that define genome evolution in these ferns. The aim of this study is to investigate the evolution of genome size and the relationship between genome size and spore size within the apomictic Asplenium monanthes fern complex and related lineages.

Results: Comparative analyses to test for a relationship between spore size and genome size show that they are not correlated. The data do however provide evidence for marked genome size variation between species in this group. These results indicate that Asplenium monanthes has undergone a two-fold expansion in genome size.

Conclusions: Our findings challenge the widely held assumption that spore size can be used to infer ploidy levels within apomictic fern complexes. We argue that the observed genome size variation is likely to have arisen via increases in both chromosome number due to polyploidy and chromosome size due to amplification of repetitive DNA (e.g. transposable elements, especially retrotransposons). However, to date the latter has not been considered to be an important process of genome evolution within homosporous ferns. We infer that genome evolution, at least in some homosporous fern lineages, is a more dynamic process than existing studies would suggest.
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http://dx.doi.org/10.1186/1471-2229-13-219DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3930065PMC
December 2013

A universe of dwarfs and giants: genome size and chromosome evolution in the monocot family Melanthiaceae.

New Phytol 2014 Mar 2;201(4):1484-97. Epub 2013 Dec 2.

Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK.

• Since the occurrence of giant genomes in angiosperms is restricted to just a few lineages, identifying where shifts towards genome obesity have occurred is essential for understanding the evolutionary mechanisms triggering this process. • Genome sizes were assessed using flow cytometry in 79 species and new chromosome numbers were obtained. Phylogenetically based statistical methods were applied to infer ancestral character reconstructions of chromosome numbers and nuclear DNA contents. • Melanthiaceae are the most diverse family in terms of genome size, with C-values ranging more than 230-fold. Our data confirmed that giant genomes are restricted to tribe Parideae, with most extant species in the family characterized by small genomes. Ancestral genome size reconstruction revealed that the most recent common ancestor (MRCA) for the family had a relatively small genome (1C = 5.37 pg). Chromosome losses and polyploidy are recovered as the main evolutionary mechanisms generating chromosome number change. • Genome evolution in Melanthiaceae has been characterized by a trend towards genome size reduction, with just one episode of dramatic DNA accumulation in Parideae. Such extreme contrasting profiles of genome size evolution illustrate the key role of transposable elements and chromosome rearrangements in driving the evolution of plant genomes.
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http://dx.doi.org/10.1111/nph.12617DOI Listing
March 2014

Recent updates and developments to plant genome size databases.

Nucleic Acids Res 2014 Jan 27;42(Database issue):D1159-66. Epub 2013 Nov 27.

Laboratori de Botànica-Unitat Associada CSIC, Facultat de Farmàcia, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain, Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK, Departament de Biologia Vegetal, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain, Department of Managerial Decision Sciences, IESE Business School, Universidad de Navarra, 08032 Barcelona, Catalonia, Spain, BioScripts - Centro de Investigación y Desarrollo de Recursos Científicos, 41012 Sevilla, Andalusia, Spain, Institut Botànic de Barcelona (IBB-CSIC-ICUB), 08038 Barcelona, Catalonia, Spain and Laboratoire d'Evolution et Systématique, Université Paris Sud, UMR8079 CNRS-UPS-AgroParis-Tech, 91405 Orsay Cedex, France.

Two plant genome size databases have been recently updated and/or extended: the Plant DNA C-values database (http://data.kew.org/cvalues), and GSAD, the Genome Size in Asteraceae database (http://www.asteraceaegenomesize.com). While the first provides information on nuclear DNA contents across land plants and some algal groups, the second is focused on one of the largest and most economically important angiosperm families, Asteraceae. Genome size data have numerous applications: they can be used in comparative studies on genome evolution, or as a tool to appraise the cost of whole-genome sequencing programs. The growing interest in genome size and increasing rate of data accumulation has necessitated the continued update of these databases. Currently, the Plant DNA C-values database (Release 6.0, Dec. 2012) contains data for 8510 species, while GSAD has 1219 species (Release 2.0, June 2013), representing increases of 17 and 51%, respectively, in the number of species with genome size data, compared with previous releases. Here we provide overviews of the most recent releases of each database, and outline new features of GSAD. The latter include (i) a tool to visually compare genome size data between species, (ii) the option to export data and (iii) a webpage containing information about flow cytometry protocols.
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http://dx.doi.org/10.1093/nar/gkt1195DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965065PMC
January 2014

Genome sequence of dwarf birch (Betula nana) and cross-species RAD markers.

Mol Ecol 2013 Jun 21;22(11):3098-111. Epub 2012 Nov 21.

School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK.

New sequencing technologies allow development of genome-wide markers for any genus of ecological interest, including plant genera such as Betula (birch) that have previously proved difficult to study due to widespread polyploidy and hybridization. We present a de novo reference genome sequence assembly, from 66× short read coverage, of Betula nana (dwarf birch) - a diploid that is the keystone woody species of subarctic scrub communities but of conservation concern in Britain. We also present 100 bp PstI RAD markers for B. nana and closely related Betula tree species. Assembly of RAD markers in 15 individuals by alignment to the reference B. nana genome yielded 44-86k RAD loci per individual, whereas de novo RAD assembly yielded 64-121k loci per individual. Of the loci assembled by the de novo method, 3k homologous loci were found in all 15 individuals studied, and 35k in 10 or more individuals. Matching of RAD loci to RAD locus catalogues from the B. nana individual used for the reference genome showed similar numbers of matches from both methods of RAD locus assembly but indicated that the de novo RAD assembly method may overassemble some paralogous loci. In 12 individuals hetero-specific to B. nana 37-47k RAD loci matched a catalogue of RAD loci from the B. nana individual used for the reference genome, whereas 44-60k RAD loci aligned to the B. nana reference genome itself. We present a preliminary study of allele sharing among species, demonstrating the utility of the data for introgression studies and for the identification of species-specific alleles.
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http://dx.doi.org/10.1111/mec.12131DOI Listing
June 2013