Abstracts
Abstracts
17 May 2022 – Session 1
Pangenomes as a new tool for studying ecology and evolution of natural populations
Scott Edwards
Chromosome-scale assembly of the Silene latifolia genome.
Carol Moraga1,2, Corinne Cruaud3, Jerôme Briolay4, Karine Labadie3, Caroline Menguy3, Adil El Filali1, Radim Cegan5, Roman Hobza5, Amin Madoui3, Alex di Genova2, Gabriel AB Marais1,6.
1 Laboratoire Biométrie et Biologie Evolutive, CNRS / Univ. Lyon 1, Villeurbanne, France.
2 Instituto de Ciencias de la Ingeniería, Universidad de O'Higgins, Rancagua, Chile.
3 Genoscope, CEA, Evry, France.
4 DTAMB, Univ. Lyon 1, Villeurbanne, France.
5 IBP, Czech Academy of Science, Brno, Czech Republic.
6 CIBIO, Biopolis / Univ. Porto, Vairao, Portugal.
Silene latifolia is an ideal plant model to study and uncover the evolution of sex chromosomes.
The S.latifolia genome is complex with an estimated genome size of 2.6-3.2 Gb of which 0.5-0.6 correspond to the Y chromosome sequence, one of the largest Y chromosomes of plant species. Additionally, it has been described that the X and Y chromosomes shares an undifferentiated genomic region of more than 100Mb called PAR (Partial Autosomal Region) resulting in a very challenging genome to assemble.
Here, we tackled the genome complexity of S. latifolia by generating a highly homozygous male individual (17 generations of brother-sister crosses); which was sequenced using a hybrid sequencing strategy at more than 400X genome coverage including Illumina, Oxford Nanopore, bionano and Hi-C technologies. We generated an assembly that has a total size of 2.6Gb (N50=17Mb) with a maximum contig size of 33Mb that represent an improvement in contiguity of at least 1,400X with respect to the current draft genome. Additionally, after further refining using HI-C data we reach chromosome arm level scaffolds with an N50 of 84Mb. Finally, genetic map integration allows the elucidation almost all autosome sequences. Ongoing analysis using bionano data may further improve the quality of our assembly to achieve chromosome level sequences of the complex Y chromosome S. latifolia, therefore, our genome allowed for the first time to complete the gene catalog for S.latifolia and permit a fine-scale study of the sex chromosomes.
A chromosomal assembly of Silene conica
Peter Fields
Colorado State University, U.S.A
Our ability to resolve high-quality, whole chromosomal assemblies continues to improve. Here we report a chromosomal assembly of the species Silene conica. The combination of PacBio High Fidelity (HiFi) sequencing, Bionano optimal map, and Hi-C scaffolding allowed for the construction of one of the most complete assemblies of a Silene species to date. By directly comparing our assembly of S. conica to chromosomal assemblies of S. uniflora and S. vulgaris via recently developed whole-genome alignment methods, we describe the likely chromosomal rearrangements that led to a reduced karyotype of S. conica. Finally, we use a set of transcriptomes from across the S. conica species range to infer the efficacy of positive selection across the genome, including direct comparisons amongst individual gene classes to infer how selection strength varies across the genome. In addition to continued advances in sequencing and bioinformatics algorithms, the described approaches will allow for a tremendous expansion of genomic resources in Silene while also enhancing biological insights available in the genus.
Laying a foundation for Silene research - From transcriptomes to target capture
Patrik Cangren
University of Gothenburg, Sweden
With increasing sequencing output at decreasing costs, the possibility of large data collection is greater than ever before. Target capture remains a cost-efficient and practical solution to data collection compared to other techniques such as whole genome sequencing or radSeq. By using a specific set of reference markers, the assembly process becomes less complex and time consuming, while also lowering the cost per sample through collection of a specific set of markers and exclusion of unused data.
To further enable the use of target capture and high throughput sequencing for Sileneae we developed a set of markers to use in target capture. Starting from a few nuclear loci developed by traditional PCR/Sanger methods and a set of 40 transcriptomes sampled across the taxonomic diversity of the tribe, we developed an initial set of 142 markers. We complemented and improved these, for example by adding intron sequence information, through repeated sequencing runs. Finally we selected a set of 48 markers with good sequencing results and phylogenetic usefulness for an array of taxa.
By developing a transcriptome database and a common set of markers tested for Sileneae we strive to support cooperation and data sharing between among researchers working on different sections of Sileneae.
17 May 2022 – Session 2
Differential distribution and regulation of transposable elements in Silene latifolia
José Luis Rodríguez Lorenzo, Marcel Hubinský, Zdenek Kubat, Eduard Keinovský, Roman Hobza
Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65 Brno, Czech Republic
Silene latifolia is a model organism for studying sex chromosome evolution in plants. Repetitive DNA is a driven force in plant genome size evolution, because the largest fraction of plant genomes belongs to transposable elements (TEs). Several families of retrotransposons have contributed to genome size variation in S. latifolia, however they are not responsible for Y chromosome size. Interestingly, some TEs proliferate preferentially either in the male or in the female germline, which can be connected with specific circumstances affecting TE management and activity in male and female plants. To explain this phenomenon, sex-specific silencing of TEs by RNAi based mechanisms have been proposed to be the most likely to happen. A model was described based on the fact that in a typical population the probability of autosomes being present in male or female is ½. For X chromosomes the probability is ⅓ in male and ⅔ in female and for Y chromosomes it is 1 in male and 0 in female. This model was followed by most of TEs and work on their regulation is on progress. This regulation includes epigenetics, given that transposable elements are often epigenetically regulated, being DNA methylation and heterochromatinization the mechanisms proposed as responsible for the evolution of sex chromosomes. The process of evolutionary diversification of sex chromosomes is also connected with specific chromatin modifications of both histones and cytosines. The recent identification of several cytosine modifications such as 5-hmC, 5-fC and 5-caC with a significant biological value in plants, suggested an additional epigenetic regulatory pathway of TEs evolution in the sex chromosomes. According to this, we found out differential regulation of specific sex-biased TEs. This regulation is sex specific in males and females and provides new evidence about TE epigenetic regulatory dynamics.
Organellar genomes of Silene nutans: two genomes, two tales
Zoé Postel1, Sloan D.2, Gallina S.1, Varré J. S.3, Godé C.1, Schmitt E.1, Mangenot S.4, Maréchal-Drouard L.5, Touzet P.1
¹ Univ. Lille, EEP- Ecologie, Evolution, Paléontologie, UMR CNRS 8198, Université de Lille, F-59655 Villeneuve d’Ascq, France
² Colorado State University, Fort Collins, CO, USA
3 Univ. Lille, Inria, UMR CNRS 9189 - CRIStAL Centre de Recherche en Informatique Signal et Automatique de Lille F-59000 Lille, France
4 DSV/IG/Genoscope/LF, CEA, Evry, France
5 Institut de Biologie Moléculaire des Plantes-CNRS, Université de Strasbourg, Strasbourg, France
Silene nutans is a Caryophyllaceae species composed of four genetic lineages present in France. A diallel cross revealed strong reproductive isolation between them, the intensity of which depends on the cytoplasm of the hybrid. By analyzing plastid genes and the set of nuclear genes that encode proteins targeted to the plastid, we found strong plastid-nuclear non-synonymous divergence between these lineages, potentially involved in their reproductive isolation (Postel et al. 2022). The organellar genomes (i.e. mitochondrial and
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plastid) are commonly assumed to be co-transmitted and in strong linkage disequilibrium, thus sharing a common evolutionary history. We therefore wanted to test to what extent the mitochondrial genome might also be involved in reproductive isolation and to what extent plastid and mitochondrial genomes exhibited similar evolutionary patterns. We analyzed mitochondrial genomic data acquired by gene capture on a representative sample of the four lineages. We show that contrary to our initial hypothesis, the histories of these two are largely uncoupled, with no signature of involvement of the mitochondrial genome in the reproductive isolation of the Silene nutans lineages.
Genetic assimilation during rapid adaptation in Silene uniflora
Alexander Papadopulos
Bangor University, UK
Phenotypic plasticity in ancestral populations may facilitate adaptation in descendent populations, but its influence on parallel adaptive changes has not been explored. Generally, the majority of ancestral plasticity in gene expression reverses during the adaptive process; but this pattern is often examined transcriptome-wide rather than assessed solely in those genes that are involved in adaptation. Silene uniflora has independently evolved tolerance to zinc contaminated soils at abandoned mines and we used this replication to quantify experimentally the contribution of ancestral plasticity to adaptive gene expression evolution. The generally observed pattern of transcriptome wide reversion is driven by the absence of a widespread stress response in zinc-tolerant populations compared to the zinc-sensitive populations. A third of the constitutive differences between tolerant and sensitive ecotypes have resulted from genetic assimilation of pre-existing ancestral plasticity. The chance that genes are recruited across parallel instances of adaptation is also increased if plasticity is present in the ancestral populations. These experiments indicate that parallel evolution is indeed impacted by ancestral plasticity.
18 May 2022 – Session 3
Life-history of the short-lived perennial Silene virginica in a mature eastern deciduous forest
Diane V. Roeder1, Charles B. Fenster2, Michele R. Dudash1
1 South Dakota State University, Department of Natural Resource Management, U.S.A.
2 South Dakota State University, Oak Lake Field Station, U.S.A.
We followed hundreds of S. virginica plants over 20 years at a site near the Mountain Lake Biological Station (Giles County, Virginia) at one site (elev∼1100 m, 80°3314W, 37°2120N) from 1992-2012. The site is located in a mixed oak-hickory forest with heterogeneous light environment due to tree falls and gaps in the canopy, and it is on a steep grade on Bean Field Mountain, adjacent to Salt Pond Mountain. In natural populations, seeds germinate in the early spring, and plants overwinter as rosettes of basal leaves, growing a minimum of 2 years prior to flowering. In April–May of the following year plants may produce one to several reproductive stems each holding one to several flowers, which bloom from late May to early July. The flowers are typical of hummingbird pollinated plants, with long red "tubular" flowers containing copious nectar. Here we report on a subset of our study, a series of experimental plots with plants grown from seed in the greenhouse and planted either several months old in the spring or 5 months old in the fall, all in the rosette stage. The majority of plants lived 1-5 years and flowered only once, but some plants flowered multiple times. Major causes of overwinter mortality included flowering the previous year and indications of possible viral infection found on the leaves. We discuss our finding in the context of life-history evolution.
Comprehensive analysis of floral scent and fatty acids in nectar of Silene nutans through modern analytical gas chromatography techniques
Damien Eggermont1, Veronika Křešťáková2, Steven Mascrez1, Natasha Spadafora3, Fabienne Van Rossum4, Giorgia Purcaro1
1 Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés, 2, Gembloux, B-5030, Belgium.
2 Department of Biochemistry, Faculty of Science, Masaryk University, Kamenice, 753/5, Brno, 62500, Czech Republic
3 Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, via Ludovico Ariosto, 35 - 44121 Ferrara, Italy
4 Meise Botanic Garden, Nieuwelaan 38, B-1860, Meise, Belgium
Silene is one of the largest genera of the world’s flora, including around 700 species. Among them, the nocturnal moth-pollinated Silene nutans appeared to be a species complex comprising at least seven genetically differentiated lineages.
In the present study floral scent and fatty acid composition of nectar of four reproductively isolated genetic lineages of S. nutans from different regions of Western Europe were evaluated to highlight differences among them. Comprehensive bidimensional gas chromatography (GC×GC) was used to allow enhanced separation of these complex samples. Floral scents were collected by trapping volatile organic compounds (VOCs) from flowering plants grown in a controlled chamber, onto sorbent-packed thermal desorption (TD) tubes placed near flowers prior separation through GC×GC and detection by mass spectrometry (MS). This analytical workflow provided a comprehensive chemical fingerprint in a single analytical run. The differences among lineages were revealed by a novel data mining and chemometrics software that enabled the extraction of useful information through powerful multivariate statistical analysis. Fatty acid (FA) profile of nectar, a very poorly investigated topic, was also evaluated. FAs, from crude nectar collected with microcapillary tubes from flowers grown under controlled conditions, were extracted and derivatised into methyl esters (FAMEs) before analysis by GC×GC and Flame Ionisation Detector. Statistical analysis was performed on FAMEs profiles to underline differences between lineages.
Chemical genetics in Silene latifolia elucidate regulatory pathways involved in gynoecium development
Radim Čegan1, Václav Bačovský1, Lubomír Smrža1, Vojtěch Hudzieczek1, Tomáš Janíček1, Eva Tihlaříková2, Vilém Neděla2, Vladimír Beneš3, Roman Hobza1
1 Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65 Brno, Czech Republic
2 Environmental Electron Microscopy Group, Institute of Scientific Instruments of the Czech Academy of Sciences, Kralovopolska 147, 612 64 Brno, Czech Republic
3 EMBL Genomics Core Facility, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
Silene latifolia, a dioecious plant with stable dimorphism in floral traits and heteromorphic sex chromosomes, is a well established model to study sex determination and sex chromosomes evolution. However, little is still known how sex-linked genes regulate the floral developmental differences between sexes. To identify these regulators we used zebularine (DNA-methyltransferase inhibitor) and sodium butyrate (a histone deacetylase inhibitor) to turn S. latifolia males to androhermaphrodites. We characterized obtained androhermaphrodites by combination of several approaches including classical genetics, fine phenotyping, transcriptome profiling and advanced bioinformatic tools. We found rapid transcriptional changes in two subsequent generations and eight candidates which were found to have a positive role in gynoecium promotion, floral organ size, whorl boundary, and affect the expression of class B MADS-box flowering genes. We show that the expression profiles for the candidate genes are transmitted into subsequent generations if androhermaphrodites are used as a pollen donors. Our results reveal the regulatory pathways involved in sex-specific flower development and answer one of the most fundamental questions in Silene sex chromosome biology. The strongest candidate GATA18 transcription factor is now being tested by amiRNA down-regulation in males and females. This work was supported by the Czech Science Foundation no. 19-02476Y.
18 May 2022 – Session 4
How does the Silene latifolia XY system compare to XY systems in other flowering plants?
Susanne S. Renner
Washington University, U.S.A.
Few species of land plants have heteromorphic sex chromosomes studied under light microscopy or with genomic methods, and most of these have XY systems. Based on published and ongoing work on the evolution and function of heteromorphic sex chromosomes, I will assess current understanding of the general and the specific features of the Silene latifolia sex chromosomes.
Cytogenetic studies on the sex chromosomes in Silene latifolia: historical insights and recent advances
Pavla Novotná, Bohuslav Janoušek, Roman Hobza, Václav Bačovský
Institute of Biophysics ASCR, Czech Republic
Silene latifolia, a dioecious plant, is a well-established model to study sex determination, Y chromosome degeneration, and dosage compensation. The use of this model for cytogenetic experiments dates to 1940s, and since then many research groups continued to develop protocols for efficient chromosome preparation (hairy-root cultures, air-dropping) and chromosome labelling (M-FISH, oligo-painting, BAC-derived probes). During the last decades, several important advances have been made to understand sex-specific regulation of various transposable elements and sex chromosome origin with combination of FISH-based methods. Thus, the cytogenetics became necessary in Silene genomics and essential for fundamental questions of Silene sex chromosome research. Recent progress in click-based chemistry and molecular biology opens new important questions regarding the sex chromosome functionality and chromatin organization. Here, we present the click method adapted to Silene and show how cytogenetics tools may identify chromosomal rearrangements, screening various ecotypes in S. latifolia and S. dioica. Newly, we characterized centromeric variant of H3 (CENH3) in genus Silene which is important to understand centromere satellite divergence, in subgenus Behenantha and Silene. This work was supported by Czech Science Foundation (project 22-00364S).
Evidence of novel epigenetic marks within Silene latifolia genome
Marcel Hubinský1, Jose Luis Rodríguez Lorenzo1, Daniel Gackowski2, Tomáš Janíček1 and Roman Hobza1
1 Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65 Brno, Czech Republic
2 Department of Clinical Biochemistry, Collegium Medicum, Nicolaus Copernicus University, ul. Karlowicza 24, PO-85-092, Bydgoszcz, Poland
Silene latifolia is a model organism for the study of sex chromosome evolution in plants. Its sex chromosomes include large regions in which recombination became gradually suppressed (Hobza et al., 2018). These non-recombining regions are represented by
18 May 2022 – Session 4
accumulation of repetitive elements and degeneration of genes (Hobza et al., 2017). Epigenetics play a crucial role in S. latifolia sex chromosome evolution (Li et al., 2017; Rodríguez Lorenzo et al., 2020). In particular DNA methylation, which is involved in gene and repetitive element silencing (Kubat et al., 2014; Rodríguez Lorenzo, Hobza and Vyskot, 2018). Additionally, three recent cytosine modifications, 5-hydroxymethylcytosine (5-hmC), 5-formylcytosine (5-fC) and 5-carboxycytosine (5-caC) have become relevant in plants (Mahmood and Dunwell, 2019). Global quantification of cytosine modifications revealed no significant differences between male and female plants. However, cytogenetics showed differences in metaphasic chromosomes. By DNA immunoprecipitation coupled with qPCR we found differential regulation in genes of Y alleles by 5-hmC and X alleles by 5-fC. Transposable elements showed similar sex-dependent regulation, especially those with biased distribution in the sex chromosomes.
What can we learn from plant sex chromosomes?
Judith Mank
19 May 2022 – Session 5
An overview of online taxonomic resources
Nadja Korotkova
Botanic Garden Berlin, Freie Universität Berlin, Germany
This overview of online taxonomic resources is especially intended for non-taxonomists. There are many helpful online resources nowadays, but they are compiled and maintained differently, resulting in different data quality. Whereas some databases are a mere aggregation of data from elsewhere, other are carefully curated by experts and this is important to consider when using information from these resources.
Examples will include IPNI, Tropicos, Plants of the World Online, World Flora Online, the Euro+Med PlantBase, and others. The databases will be compared in terms of content, taxonomic coverage, curation, updates and general reliability.
For the Caryophyllaceae specifically, I will focus on the Global Caryophyllales Initiative which is working towards an expert-based dynamic online taxonomic backbone for the Caryophyllales; a family-level checklist of the Caryophyllaceae is currently in preparation. I will explain the rationale behind the approach and how it differs from the previously mentioned taxonomic resources.
Floral color and morphological evolution in North American Silene
Andrea E. Berardi
Harvard University, U.S.A.
Determining how and why reproductive traits evolve between and within species is key to understanding patterns of speciation. In plants, floral traits such as color are major drivers of diversification. Flower color and morphology are key reproductive traits in the North American species of Silene (Caryophyllaceae). In this genus there appears to be an intriguing interaction between ploidy and flower color evolution, with red flower color arising almost exclusively in North American polyploids. Insights into the phylogeny of North American Silene are made from target capture of herbarium specimens, gene silencing, and character mapping of floral pigments, floral UV patterns, and morphology are combined to answer the following main questions: What is the most likely driver of floral color evolution in Silene - pollinator shifts, sympatric competition, abiotic factors, or polyploidy? Are red flowers transgressive phenotypes? Do all red species use the same pigments to create red? And last, do the existing red species represent independent origins?
What makes Silene in Asia difficult?
Farzaneh Jafari*1, Maryam Keshavarzi1, Richard K. Rabeler2
1 Department of Plant Sciences, Faculty of Biological Sciences, Alzahra University, Vanak, Tehran, Iran
2 University of Michigan Herbarium-EEB, 3600 Varsity Drive, Ann Arbor, Michigan 48108-2228, U.S.A.
Silene L. consisting of c. 870 spp. often grows in dry habitats including rocky or gravelly places, sandy soils in steppes, chalky soil, and deserts, with little competition from other plants. The country of Iran, as one of the diversity centers of the genus, houses 120 species including 35 endemics which mainly belong to S. sect. Auriculatae (Boiss.) Schischk. Flora Iranica is one of the main resources for floristic studies in western Asia; Flora of Turkey and Flora of Iraq are others. Investigation of herbarium specimens of Silene in western Asia sometimes indicates that species listed in the local floras need to be revised. We present examples of different types of revisions that may be involved. Sometimes revisions of identification are needed; e.g., S. atocioides Boiss., which was listed in Flora Iranica from Iran has been revised as S. pendula L. which had not been reported in Iran. A nomenclatural revision may be needed; e.g. S. simsii F.Jafari, Rabeler & Oxelman was proposed as a replacement name for transferring Cucubalus multifidus Adams to Silene. Phylogenetic studies can show changes in species delimitation may be needed; e.g., S. arenosa K. Koch. and S. villosa Forssk. Errors of identification and species delimitation lead to considerable confusion. In this situation, the description of taxa in local floras are not as helpful as one might expect.
The genus Silene s.l. (Caryophyllaceae) in Armenia
Anush Nersesyan
A. Takhtajyan Institute of Botany NAS Armenia
The first treatment of the genus Silene was published 1956 in the Flora of Armenia, and revised in the PhD thesis “Representatives of the genus Silene L.s.l. (Caryophyllaceae) from Southern Transcaucasia”. Later, S. chustupica Nersesian was described and S. manissadjiani Freyn has been revealed as new for the country. Armenian taxa were included in the revision of the genus for the Caucasian Flora Conspectus. In recent phylogenetic studies, DNA sequence data has been used to revise the infrageneric taxonomy of 36 of the species occurring in Armenia. The majority of the species are distributed in W Asia. Silene araxina, S. chustupica, S. depressa, S. eremitica, S. caucasica, S. raddeana are endemic to the Caucasus Ecoregion.
Taxonomic ambiguities on Silene section Silene (Caryophyllaceae).: The case of Silene nocturna group
Melilia Mesbah1, Mohamed Sahnoune1, Errol Vela2, Bengt Oxelman3
1 UAM Bejaia, Algeria
2 INRAE, UMR AMAP,Montpellier, France
3 GGBC, GU Gothenburg, Sweden
Insights from molecular phylogenetics have significantly changed the taxonomy of the genus Silene by far the most diverse in the family of Caryophyllaceae, with approximately 870 currently accepted taxonomic species. An overview of a recent outcomes revising the infra-generic classification of North African taxa with phylogenetic relationships is given. In addition, some outstanding problems are highlighted to determine the correct application of the Linnaean names Silene pertaining to the S. nocturna group (S. nocturna, S. mutabilis and Cucubalus reflexus).
To improve the phylogenetic relationships and evolution within the S. nocturna group, a representative sampling including 84 populations from the Mediterranean is carried out. Work based on biometrical analysis have been initiated to determine how morphological traits evolve. This is key to understanding patterns of speciation and will potentially resolve the taxonomic confusion currently present in the Silene nocturna group.
Keywords: Silene nocturna, Morphometry, application of the Linnaeus names.