Publications by authors named "Oriane Hidalgo"

29 Publications

  • Page 1 of 1

Low dispersal and ploidy differences in a grass maintain photosynthetic diversity despite gene flow and habitat overlap.

Mol Ecol 2021 Mar 7. Epub 2021 Mar 7.

Department of Animal and Plant Science, University of Sheffield, Sheffield, UK.

Geographical isolation facilitates the emergence of distinct phenotypes within a single species, but reproductive barriers or selection are needed to maintain the polymorphism after secondary contact. Here, we explore the processes that maintain intraspecific variation of C photosynthesis, a complex trait that results from the combined action of multiple genes. The grass Alloteropsis semialata includes C and non-C populations, which have coexisted as a polyploid series for more than 1 million years in the miombo woodlands of Africa. Using population genomics, we show that there is genome-wide divergence for the photosynthetic types, but the current geographical distribution does not reflect a simple habitat displacement scenario as the genetic clusters overlap, being occasionally mixed within a given habitat. Despite evidence of recurrent introgression between non-C and C groups, in both diploids and polyploids, the distinct genetic lineages retain their identity, potentially because of selection against hybrids. Coupled with strong isolation by distance within each genetic group, this selection created a geographical mosaic of photosynthetic types. Diploid C and non-C types never grew together, and the C type from mixed populations constantly belonged to the hexaploid lineage. By limiting reproductive interactions between photosynthetic types, the ploidy difference probably allows their co-occurrence, reinforcing the functional diversity within this species. Together, these factors enabled the persistence of divergent physiological traits of ecological importance within a single species despite gene flow and habitat overlap.
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http://dx.doi.org/10.1111/mec.15871DOI Listing
March 2021

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

Ann Bot 2021 Apr;127(5):681-695

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
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8052921PMC
April 2021

The Role of Botanical Families in Medicinal Ethnobotany: A Phylogenetic Perspective.

Plants (Basel) 2021 Jan 15;10(1). Epub 2021 Jan 15.

Laboratori de Botànica (UB)-Unitat associada al CSIC, Institut de Recerca de la Biodiversitat-IRBio, Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de Barcelona, Av. Joan XXIII 27-31, 08028 Barcelona, Catalonia, Spain.

Studies suggesting that medicinal plants are not chosen at random are becoming more common. The goal of this work is to shed light on the role of botanical families in ethnobotany, depicting in a molecular phylogenetic frame the relationships between families and medicinal uses of vascular plants in several Catalan-speaking territories. The simple quantitative analyses for ailments categories and the construction of families and disorders matrix were carried out in this study. A Bayesian approach was used to estimate the over- and underused families in the medicinal flora. Phylogenetically informed analyses were carried out to identify lineages in which there is an overrepresentation of families in a given category of use, i.e., hot nodes. The ethnobotanicity index, at a specific level, was calculated and also adapted to the family level. Two diversity indices to measure the richness of reported taxa within each family were calculated. A total of 47,630 use reports were analysed. These uses are grouped in 120 botanical families. The ethnobotanicity index for this area is 14.44% and the ethnobotanicity index at the family level is 68.21%. The most-reported families are Lamiaceae and Asteraceae and the most reported troubles are disorders of the digestive and nutritional system. Based on the meta-analytic results, indicating hot nodes of useful plants at the phylogenetic level, specific ethnopharmacological research may be suggested, including a phytochemical approach of particularly interesting taxa.
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http://dx.doi.org/10.3390/plants10010163DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7830233PMC
January 2021

Genome Size Evolution and Dynamics in , with Special Focus on the Section .

Plants (Basel) 2020 Dec 1;9(12). Epub 2020 Dec 1.

Laboratoire Biodiversité et Génomique Fonctionnelle, Faculté des Sciences, Campus Sciences et Technologies, Université Saint-Joseph, Mar Roukos, Mkalles, BP: 1514 Riad el Solh, Beirut 1107 2050, Lebanon.

Insights into genome size dynamics and its evolutionary impact remain limited by the lack of data for many plant groups. One of these is the genus , of which only 53 out of c. 260 species have available genome sizes. In this study, we estimated the C-values for 41 species and subspecies of mainly from the Eastern Mediterranean region. We constructed a phylogenetic framework to shed light on the distribution of genome sizes across subgenera and sections of . Finally, we tested evolutionary models to explore the mode and tempo of genome size evolution during the radiation of section . as a whole displayed a great variety of C-values; however, they were unequally distributed across the subgenera and sections, suggesting that lineage-specific patterns of genome size diversification have taken place within the genus. The evolutionary model that best fitted our data was the speciational model, as changes in genome size appeared to be mainly associated with speciation events. These results suggest that genome size dynamics may have contributed to the radiation of irises. In addition, our phylogenetic analysis provided evidence that supports the segregation of the Lebanese population currently attributed to as a distinct species.
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http://dx.doi.org/10.3390/plants9121687DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7760388PMC
December 2020

Contrasted histories of organelle and nuclear genomes underlying physiological diversification in a grass species.

Proc Biol Sci 2020 11 11;287(1938):20201960. Epub 2020 Nov 11.

Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK.

C photosynthesis evolved multiple times independently in angiosperms, but most origins are relatively old so that the early events linked to photosynthetic diversification are blurred. The grass is an exception, as this species encompasses C and non-C populations. Using phylogenomics and population genomics, we infer the history of dispersal and secondary gene flow before, during and after photosynthetic divergence in . We further analyse the genome composition of individuals with varied ploidy levels to establish the origins of polyploids in this species. Detailed organelle phylogenies indicate limited seed dispersal within the mountainous region of origin and the emergence of a C lineage after dispersal to warmer areas of lower elevation. Nuclear genome analyses highlight repeated secondary gene flow. In particular, the nuclear genome associated with the C phenotype was swept into a distantly related maternal lineage probably via unidirectional pollen flow. Multiple intraspecific allopolyploidy events mediated additional secondary genetic exchanges between photosynthetic types. Overall, our results show that limited dispersal and isolation allowed lineage divergence, with photosynthetic innovation happening after migration to new environments, and pollen-mediated gene flow led to the rapid spread of the derived C physiology away from its region of origin.
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http://dx.doi.org/10.1098/rspb.2020.1960DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7735283PMC
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

A Target Capture-Based Method to Estimate Ploidy From Herbarium Specimens.

Front Plant Sci 2019 24;10:937. Epub 2019 Jul 24.

Royal Botanic Gardens, Kew, Richmond, United Kingdom.

Whole genome duplication (WGD) events are common in many plant lineages, but the ploidy status and possible occurrence of intraspecific ploidy variation are unknown for most species. Standard methods for ploidy determination are chromosome counting and flow cytometry approaches. While flow cytometry approaches typically use fresh tissue, an increasing number of studies have shown that recently dried specimens can be used to yield ploidy data. Recent studies have started to explore whether high-throughput sequencing (HTS) data can be used to assess ploidy levels by analyzing allelic frequencies from single copy nuclear genes. Here, we compare different approaches using a range of yam () tissues of varying ages, drying methods and quality, including herbarium tissue. Our aims were to: (1) explore the limits of flow cytometry in estimating ploidy level from dried samples, including herbarium vouchers collected between 1831 and 2011, and (2) optimize a HTS-based method to estimate ploidy by considering allelic frequencies from nuclear genes obtained using a target-capture method. We show that, although flow cytometry can be used to estimate ploidy levels from herbarium specimens collected up to fifteen years ago, success rate is low (5.9%). We validated our HTS-based estimates of ploidy using 260 genes by benchmarking with dried samples of species of known ploidy (, , and ). Subsequently, we successfully applied the method to the 85 herbarium samples analyzed with flow cytometry, and successfully provided results for 91.7% of them, comprising species across the phylogenetic tree of . We also explored the limits of using this HTS-based approach for identifying high ploidy levels in herbarium material and the effects of heterozygosity and sequence coverage. Overall, we demonstrated that ploidy diversity within and between species may be ascertained from historical collections, allowing the determination of polyploidization events from samples collected up to two centuries ago. This approach has the potential to provide insights into the drivers and dynamics of ploidy level changes during plant evolution and crop domestication.
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http://dx.doi.org/10.3389/fpls.2019.00937DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6667659PMC
July 2019

Polyploidy in the Conifer Genus : An Unexpectedly High Rate.

Front Plant Sci 2019 22;10:676. Epub 2019 May 22.

Laboratoire Biodiversité et Génomique Fonctionnelle, Faculté des Sciences, Université Saint-Joseph, Campus Sciences et Technologies, Beirut, Lebanon.

Recent research suggests that the frequency of polyploidy may have been underestimated in gymnosperms. One notable example is in the conifer genus , where there are already a few reports of polyploids although data are still missing for most species. In this study, we evaluated the extent of polyploidy in by conducting the first comprehensive screen across nearly all of the genus. Genome size data from fresh material, together with chromosome counts, were used to demonstrate that genome sizes estimated from dried material could be used as reliable proxies to uncover the extent of ploidy diversity across the genus. Our analysis revealed that 16 taxa were polyploid, with tetraploids and one hexaploid being reported. Furthermore, by analyzing the genome size and chromosome data within a phylogenetic framework we provide the first evidence of possible lineage-specific polyploidizations within the genus. Genome downsizing following polyploidization is moderate, suggesting limited genome restructuring. This study highlights the importance of polyploidy in , making it the first conifer genus and only the second genus in gymnosperms where polyploidy is frequent. In this sense, represents an interesting model for investigating the genomic and ecological consequences of polyploidy in conifers.
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http://dx.doi.org/10.3389/fpls.2019.00676DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6541006PMC
May 2019

Satellite DNA in Paphiopedilum subgenus Parvisepalum as revealed by high-throughput sequencing and fluorescent in situ hybridization.

BMC Genomics 2018 Aug 2;19(1):578. Epub 2018 Aug 2.

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

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.
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http://dx.doi.org/10.1186/s12864-018-4956-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6090851PMC
August 2018

Evolutionary diversification of CYC/TB1-like TCP homologs and their recruitment for the control of branching and floral morphology in Papaveraceae (basal eudicots).

New Phytol 2018 10 27;220(1):317-331. Epub 2018 Jun 27.

Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, 00014, Finland.

Angiosperms possess enormous morphological variation in plant architectures and floral forms. Previous studies in Pentapetalae and monocots have demonstrated the involvement of TCP domain CYCLOIDEA/TEOSINTE BRANCHED1-like (CYC/TB1) genes in the control of floral symmetry and shoot branching. However, how TCP/CYC-like (CYL) genes originated, evolved and functionally diversified remain unclear. We conducted a comparative functional study in Ranunculales, the sister lineage to all other eudicots, between Eschscholzia californica and Cysticapnos vesicaria, two species of Papaveraceae with actinomorphic and zygomorphic flowers, respectively. Phylogenetic analysis indicates that CYL genes in Papaveraceae form two paralogous lineages, PapaCYL1 and PapaCYL2. Papaveraceae CYL genes show highly diversified expression patterns as well as functions. Enhanced branching by silencing of EscaCYL1 suggests that the role of CYC/TB1-like genes in branching control is conserved in Papaveraceae. In contrast to the arrest of stamen development in Pentapetalae, PapaCYL genes promote stamen initiation and growth. In addition, we demonstrate that CyveCYLs are involved in perianth development, specifying sepal and petal identity in Cysticapnos by regulating the B-class floral organ identity genes. Our data also suggest the involvement of CyveCYL genes in the regulation of flower symmetry in Cysticapnos. Our work provides evidence of the importance of TCP/CYC-like genes in the promotion of morphological diversity across angiosperms.
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http://dx.doi.org/10.1111/nph.15289DOI Listing
October 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

Evolutionary implications of heterochromatin and rDNA in chromosome number and genome size changes during dysploidy: A case study in Reichardia genus.

PLoS One 2017 9;12(8):e0182318. Epub 2017 Aug 9.

Comparative Plant & Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey, United Kingdom.

In this study we showed that constitutive heterochromatin, GC-rich DNA and rDNA are implicated in chromosomal rearrangements during the basic chromosome number changing (dysploidy) in Reichardia genus. This small Mediterranean genus comprises 8-10 species and presents three basic chromosome numbers (x = 9, 8 and 7). To assess genome evolution and differentiation processes, studies were conducted in a dysploid series of six species: R. dichotoma, R. macrophylla and R. albanica (2n = 18), R. tingitana and R. gaditana (2n = 16), and R. picroides (2n = 14). The molecular phylogeny reconstruction comprised three additional species (R. crystallina and R. ligulata, 2n = 16 and R. intermedia, 2n = 14). Our results indicate that the way of dysploidy is descending. During this process, a positive correlation was observed between chromosome number and genome size, rDNA loci number and pollen size, although only the correlation between chromosome number and genome size is still recovered significant once considering the phylogenetic effect. Fluorescent in situ hybridisation also evidenced changes in number, position and organisation of two rDNA families (35S and 5S), including the reduction of loci number and, consequently, reduction in the number of secondary constrictions and nuclear organising regions from three to one per diploid genome. The potential mechanisms of chromosomal and genome evolution, strongly implicating heterochromatin, are proposed and discussed, with particular consideration for Reichardia genus.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0182318PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5549912PMC
October 2017

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

Genome biogeography reveals the intraspecific spread of adaptive mutations for a complex trait.

Mol Ecol 2016 Dec 30;25(24):6107-6123. Epub 2016 Nov 30.

Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK.

Physiological novelties are often studied at macro-evolutionary scales such that their micro-evolutionary origins remain poorly understood. Here, we test the hypothesis that key components of a complex trait can evolve in isolation and later be combined by gene flow. We use C photosynthesis as a study system, a derived physiology that increases plant productivity in warm, dry conditions. The grass Alloteropsis semialata includes C and non-C genotypes, with some populations using laterally acquired C -adaptive loci, providing an outstanding system to track the spread of novel adaptive mutations. Using genome data from C and non-C A. semialata individuals spanning the species' range, we infer and date past migrations of different parts of the genome. Our results show that photosynthetic types initially diverged in isolated populations, where key C components were acquired. However, rare but recurrent subsequent gene flow allowed the spread of adaptive loci across genetic pools. Indeed, laterally acquired genes for key C functions were rapidly passed between populations with otherwise distinct genomic backgrounds. Thus, our intraspecific study of C -related genomic variation indicates that components of adaptive traits can evolve separately and later be combined through secondary gene flow, leading to the assembly and optimization of evolutionary innovations.
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http://dx.doi.org/10.1111/mec.13914DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6849575PMC
December 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

Unlocking the Karyological and Cytogenetic Diversity of Iris from Lebanon: Oncocyclus Section Shows a Distinctive Profile and Relative Stasis during Its Continental Radiation.

PLoS One 2016 15;11(8):e0160816. Epub 2016 Aug 15.

Ecologie, Systématique, Evolution, UMR 8079 Univ. Paris-Sud, AgroParisTech, Université Paris-Saclay, Bat. 360, 91405 Orsay, France.

Despite being an important target of conservation concern and horticultural interest, Lebanese irises yet have a confusing taxonomic history and species' delimitation is often considered problematic, more especially among royal irises (Iris section Oncocyclus). Indeed, these irises of exceptionally large and spectacular flowers have radiated across Caucasus and eastern Mediterranean giving rise to a number of strict endemic taxa, many of them being considered under threat. Whilst efforts have mostly focused on clarifying the evolutionary relationships in the group based on morphological and molecular data, karyological and cytogenetic characters have been comparatively overlooked. In this study, we established for the first time the physical mapping of 35S rDNA loci and heterochromatin, and obtained karyo-morphological data for ten Lebanese Iris species belonging to four sections (Iris, Limniris, Oncocyclus and Scorpiris). Our results evidenced distinctive genomic profiles for each one of the sections, where Oncocyclus irises, while having the lowest chromosome numbers, exhibit both the highest number of 35S loci and CMA3+ sites. The continental radiation of royal irises has been accompanied by a relative karyological and cytogenetic stasis, even though some changes were observed regarding karyotype formula and asymmetry indexes. In addition to that, our results enabled taxonomic differentiation between I. germanica and I. mesopotamica-two taxa currently considered as synonyms-and highlighted the need for further studies on populations of I. persica and I. wallasiae in the Eastern Mediterranean Region.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0160816PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4985135PMC
July 2017

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

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

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

Assessing duplication and loss of APETALA1/FRUITFULL homologs in Ranunculales.

Front Plant Sci 2013 17;4:358. Epub 2013 Sep 17.

Grupo de Biotecnología, Instituto de Biología, Universidad de Antioquia Medellín, Colombia ; The New York Botanical Garden Bronx, NY, USA.

Gene duplication and loss provide raw material for evolutionary change within organismal lineages as functional diversification of gene copies provide a mechanism for phenotypic variation. Here we focus on the APETALA1/FRUITFULL MADS-box gene lineage evolution. AP1/FUL genes are angiosperm-specific and have undergone several duplications. By far the most significant one is the core-eudicot duplication resulting in the euAP1 and euFUL clades. Functional characterization of several euAP1 and euFUL genes has shown that both function in proper floral meristem identity, and axillary meristem repression. Independently, euAP1 genes function in floral meristem and sepal identity, whereas euFUL genes control phase transition, cauline leaf growth, compound leaf morphogenesis and fruit development. Significant functional variation has been detected in the function of pre-duplication basal-eudicot FUL-like genes, but the underlying mechanisms for change have not been identified. FUL-like genes in the Papaveraceae encode all functions reported for euAP1 and euFUL genes, whereas FUL-like genes in Aquilegia (Ranunculaceae) function in inflorescence development and leaf complexity, but not in flower or fruit development. Here we isolated FUL-like genes across the Ranunculales and used phylogenetic approaches to analyze their evolutionary history. We identified an early duplication resulting in the RanFL1 and RanFL2 clades. RanFL1 genes were present in all the families sampled and are mostly under strong negative selection in the MADS, I and K domains. RanFL2 genes were only identified from Eupteleaceae, Papaveraceae s.l., Menispermaceae and Ranunculaceae and show relaxed purifying selection at the I and K domains. We discuss how asymmetric sequence diversification, new motifs, differences in codon substitutions and likely protein-protein interactions resulting from this Ranunculiid-specific duplication can help explain the functional differences among basal-eudicot FUL-like genes.
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http://dx.doi.org/10.3389/fpls.2013.00358DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3775002PMC
September 2013

Virus-induced gene silencing (VIGS) in Cysticapnos vesicaria, a zygomorphic-flowered Papaveraceae (Ranunculales, basal eudicots).

Ann Bot 2012 Apr 2;109(5):911-20. Epub 2012 Feb 2.

Department of Environmental and Plant Biology, Ohio University, Athens, OH 45701, USA.

Background And Aims: Studies of evolutionary diversification in the basal eudicot family Papaveraceae, such as the transition from actinomorphy to zygomorphy, are hampered by the lack of comparative functional studies. So far, gene silencing methods are only available in the actinomorphic species Eschscholzia californica and Papaver somniferum. This study addresses the amenability of Cysticapnos vesicaria, a derived fumitory with zygomorphic flowers, to virus-induced gene silencing (VIGS), and describes vegetative and reproductive traits in this species.

Methods: VIGS-mediated downregulation of the C. vesicaria PHYTOENE DESATURASE gene (CvPDS) and of the FLORICAULA gene CvFLO was carried out using Agrobacterium tumefaciens transfer of Tobacco rattle virus (TRV)-based vectors. Wild-type and vector-treated plants were characterized using reverse transcription-PCR (RT-PCR), in situ hybridization, and macroscopic and scanning electron microscopic imaging.

Key Results: Cysticapnos vesicaria germinates rapidly, can be grown at high density, has a short life cycle and is self-compatible. Inoculation of C. vesicaria with a CvPDS-VIGS vector resulted in strong photobleaching of green parts and reduction of endogenous CvPDS transcript levels. Gene silencing persisted during inflorescence development until fruit set. Inoculation of plants with CvFLO-VIGS affected floral phyllotaxis, symmetry and floral organ identities.

Conclusions: The high penetrance, severity and stability of pTRV-mediated silencing, including the induction of meristem-related phenotypes, make C. vesicaria a very promising new focus species for evolutionary-developmental (evo-devo) studies in the Papaveraceae. This now enables comparative studies of flower symmetry, inflorescence determinacy and other traits that diversified in the Papaveraceae.
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http://dx.doi.org/10.1093/aob/mcs008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3310490PMC
April 2012

Phylogeny of Rhaponticum (Asteraceae, Cardueae-Centaureinae) and related genera inferred from nuclear and chloroplast DNA sequence data: taxonomic and biogeographic implications.

Ann Bot 2006 May 22;97(5):705-14. Epub 2006 Feb 22.

Institut Botànic de Barcelona (CSIC-Ajuntament de Barcelona), Passeig del Migdia s. n., Parc de Montjuïc, 08038 Barcelona, Catalonia, Spain.

Background And Aims: The precise generic delimitation of the Rhaponticum group is not totally resolved. The lack of knowledge of the relationships between the basal genera of Centaureinae could imply that genera whose position is as yet unresolved could belong to the Rhaponticum group. On the other hand, the affinities among the genera that are considered as members of this group are not well known. The aim of the study is to contribute to the phylogenetic and generic delineation of the Rhaponticum group on the basis of molecular data.

Methods: Parsimony and Bayesian analyses of the combined sequences of one plastid (trnL-trnF) and two nuclear (ITS region and ETS) molecular markers were carried out. The results of these analyses are discussed in the light of the biogeographic history.

Key Results: The Rhaponticum group appears as monophyletic, and closely related to the genus Klasea. The results confirm the preliminary generic delimitation of the Rhaponticum group, with the new incorporation of the genus Centaurothamnus. Ochrocephala is supported as a separate genus from Rhaponticum and, contrary to this, Acroptilon and Leuzea appear as merged into the genus Rhaponticum. Several nomenclatural rearrangements are made in Klasea and Rhaponticum.

Conclusions: The new molecular evidence is consistent with the morphological and karyological data, and suggests particularly coherent biogeographic routes of migration and speciation processes for the genus Rhaponticum. The biogeographic inference proposes a Near East and/or Caucasian origin for the genus. Furthermore, representatives of Rhaponticum could have reached Europe in two different ways: (1) expansion across central Asia to eastern Europe, and (2) expansion through the Near East, North Africa and then to the Iberian Peninsula and the Alps.
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http://dx.doi.org/10.1093/aob/mcl029DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2803413PMC
May 2006

Genome size in Echinops L. and related genera (Asteraceae, Cardueae): karyological, ecological and phylogenetic implications.

Biol Cell 2004 Mar;96(2):117-24

Institut Botànic de Barcelona (CSIC-Ajuntament de Barcelona). Passeig del Migdia s.n. Parc de Montjuïc, Catalonia, Spain.

Genome size was assessed by flow cytometry in 33 species belonging to seven genera of the tribe Cardueae (Asteraceae), which can be grouped in three taxonomic complexes. 2C nuclear DNA content ranged from 1.49 to 16.98 pg, which is more than elevenfold variation. Genome size correlated well with some karyological traits. Nuclear DNA amount variations also have systematic and evolutionary implications and/or are linked to adaptations to ecological conditions.
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http://dx.doi.org/10.1016/j.biolcel.2003.11.005DOI Listing
March 2004

Phylogeny of Valerianaceae based on matK and ITS markers, with reference to matK individual polymorphism.

Ann Bot 2004 Mar;93(3):283-93

Botanical Institute of Barcelona (CSIC-Ajuntament de Barcelona), Av. Muntanyans, s.n., E-08038 Barcelona, Spain.

Background And Aims: The monophyly of Valerianaceae and the precise delimitation of the family are not totally resolved. Our knowledge on the phylogeny of the group is only partial: on a morphological basis, some contradicting taxonomic proposals have been published, which demonstrates the difficulties in establishing a natural classification of the family and especially in proposing a relevant treatment of the large genus Valeriana. The aims of this study are to contribute to the phylogeny and generic delineation of the Valerianaceae on the basis of molecular data.

Methods: A cladistic analysis of the sequences of one plastid (matK) and one nuclear (ITS) molecular marker was carried out, both individually and in combination.

Key Results: The results of the analyses of both regions confirm that the family is monophyletic, with the exclusion of Triplostegia. The tribe Patrinieae is monophyletic, and the tribe Valerianeae is also a natural group. Two of the subtribes of Valerianeae, Fediinae and Centranthinae, are also monophyletic, with the exclusion of the genus Plectritis from Fediinae. The subtribe Valerianinae, on the other hand, is paraphyletic.

Conclusions: Our results confirm, for the first time on a molecular basis, the suggested paraphyly of Valeriana in its present circumscription, with profound nomenclatural and taxonomic implications. The correlation between molecular phylogeny and biogeography is close. In the course of the plastid DNA sequencing, a polymorphism concerning the matK gene was found, a fact that should be carefully evaluated in phylogenetic analyses.
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http://dx.doi.org/10.1093/aob/mch042DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4242203PMC
March 2004