2b-RAD Genotyping of the Seagrass Cymodocea nodosa Along a Latitudinal Cline Identifies Candidate Genes for Environmental Adaptation

Plant populations distributed along broad latitudinal gradients often show patterns of clinal variation in genotype and phenotype. Differences in photoperiod and temperature cues across latitudes influence major phenological events, such as timing of flowering or seed dormancy. Here, we used an array of 4,941 SNPs derived from 2b-RAD genotyping to characterize population differentiation and levels of genetic and genotypic diversity of three populations of the seagrass Cymodocea nodosa along a latitudinal gradient extending across the Atlantic-Mediterranean boundary (i.e., Gran Canaria-Canary Islands, Faro-Portugal, and Ebro Delta-Spain). Our main goal was to search for potential outlier loci that could underlie adaptive differentiation of populations across the latitudinal distribution of the species. We hypothesized that such polymorphisms could be related to variation in photoperiod-temperature regime occurring across latitudes. The three populations were clearly differentiated and exhibited diverse levels of clonality and genetic diversity. Cymodocea nodosa from the Mediterranean displayed the highest genotypic richness, while the Portuguese population had the highest clonality values. Gran Canaria exhibited the lowest genetic diversity (as observed heterozygosity). Nine SNPs were reliably identified as outliers across the three sites by two different methods (i.e., BayeScan and pcadapt), and three SNPs could be associated to specific protein-coding genes by screening available C. nodosa transcriptomes. Two SNPs-carrying contigs encoded for transcription factors, while the other one encoded for an enzyme specifically involved in the regulation of flowering time, namely Lysine-specific histone demethylase 1 homolog 2. When analyzing biological processes enriched within the whole dataset of outlier SNPs identified by at least one method, "regulation of transcription" and "signalling" were among the most represented. Our results highlight the fundamental importance signal integration and gene-regulatory networks, as well as epigenetic regulation via DNA (de)methylation, could have for enabling adaptation of seagrass populations along environmental gradients.info:eu-repo/semantics/publishedVersio

What is at stake for scientists when communicating ecology? Insight from the informal communication initiative “Cammini LTER”

What is at stake for scientists when communicating ecology? This is the basic question tackled in this paper, that we explored through reflections about an initiative of informal communication of ecological research called “Cammini LTER”: itineraries connecting a number of sites belonging to the Italian Long-Term Ecological Research network (LTER-Italy). LTER-Italy ecologists walked and cycled together with citizens creating a physical and visible movement of researchers ‘towards’ and ‘with’ citizens, aiming at providing the public with the opportunity to get familiar with Italian ecosystems, from the sea to alpine tundra. We address here the debates and the critical considerations among researchers themselves, stimulated by the overall experience, with focus on some relevant issues pertaining science communication, and even research production, evidencing the need for a cultural shift, which go far beyond the national context and the LTER – Italy network. Using a participant observations approach, through researchers’ words used to describe - formally and informally - the experience, we report and comment here the main narratives emerged, showing different attitudes of LTER researchers in Cammini towards the society and the role of ecology in it. Relationship and knowledge exchange appear crucial for communicating ecology, which can thus become an opportunity for building new qualities of knowledge and for creating a shared civic culture, able to make all players feel mutual responsible and contribute to the solution of particular socio-ecological challenges

m6A RNA Methylation in marine plants: first insights and relevance for biological rhythms

Circadian regulations are essential for enabling organisms to synchronize physiology with environmental light-dark cycles. Post-transcriptional RNA modifications still represent an understudied level of gene expression regulation in plants, although they could play crucial roles in environmental adaptation. N6-methyl-adenosine (m6A) is the most prevalent mRNA modification, established by "writer" and "eraser" proteins. It influences the clockwork in several taxa, but only few studies have been conducted in plants and none in marine plants. Here, we provided a first inventory of m6A-related genes in seagrasses and investigated daily changes in the global RNA methylation and transcript levels of writers and erasers in Cymodocea nodosa and Zostera marina. Both species showed methylation peaks during the dark period under the same photoperiod, despite exhibiting asynchronous changes in the m6A profile and related gene expression during a 24-h cycle. At contrasting latitudes, Z. marina populations displayed overlapping daily patterns of the m6A level and related gene expression. The observed rhythms are characteristic for each species and similar in populations of the same species with different photoperiods, suggesting the existence of an endogenous circadian control. Globally, our results indicate that m6A RNA methylation could widely contribute to circadian regulation in seagrasses, potentially affecting the photo-biological behaviour of these plants.FCT: UIDB/04326/2020info:eu-repo/semantics/publishedVersio

Transcriptome characterisation and SSR markers development in the seagrass Posidonia oceanica

Posidonia oceanica is an endemic seagrass in the Mediterranean Sea, where it provides important ecosystem services and sustains a rich and diverse ecosystem. P. oceanica meadows extend from the surface to 40 meters depth. With the aim of boosting research in this iconic species, we generated a comprehensive RNA-Seq data set for P. oceanica by sequencing specimens collected at two depths and two times during the day. With this approach we attempted to capture the transcriptional diversity associated with change in light and other depth-related environmental factors. Using this extensive data set we generated gene predictions and identified an extensive catalogue of potential Simple Sequence Repeats (SSR) markers. The data generated here will open new avenues for the analysis of population genetic features and functional variation in P. oceanica. In total, 79,235 contigs were obtained by the assembly of 70,453,120 paired end reads. 43,711 contigs were successfully annotated. A total of 17,436 SSR were identified within 13,912 contigs

A trait-based framework for seagrass ecology: Trends and prospects

In the last three decades, quantitative approaches that rely on organism traits instead of taxonomy have advanced different fields of ecological research through establishing the mechanistic links between environmental drivers, functional traits, and ecosystem functions. A research subfield where trait-based approaches have been frequently used but poorly synthesized is the ecology of seagrasses; marine angiosperms that colonized the ocean 100M YA and today make up productive yet threatened coastal ecosystems globally. Here, we compiled a comprehensive trait-based response-effect framework (TBF) which builds on previous concepts and ideas, including the use of traits for the study of community assembly processes, from dispersal and response to abiotic and biotic factors, to ecosystem function and service provision. We then apply this framework to the global seagrass literature, using a systematic review to identify the strengths, gaps, and opportunities of the field. Seagrass trait research has mostly focused on the effect of environmental drivers on traits, i.e., “environmental filtering” (72%), whereas links between traits and functions are less common (26.9%). Despite the richness of trait-based data available, concepts related to TBFs are rare in the seagrass literature (15% of studies), including the relative importance of neutral and niche assembly processes, or the influence of trait dominance or complementarity in ecosystem function provision. These knowledge gaps indicate ample potential for further research, highlighting the need to understand the links between the unique traits of seagrasses and the ecosystem services they provide

The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea

Seagrasses colonized the sea(1) on at least three independent occasions to form the basis of one of the most productive and widespread coastal ecosystems on the planet(2). Here we report the genome of Zostera marina (L.), the first, to our knowledge, marine angiosperm to be fully sequenced. This reveals unique insights into the genomic losses and gains involved in achieving the structural and physiological adaptations required for its marine lifestyle, arguably the most severe habitat shift ever accomplished by flowering plants. Key angiosperm innovations that were lost include the entire repertoire of stomatal genes(3), genes involved in the synthesis of terpenoids and ethylene signalling, and genes for ultraviolet protection and phytochromes for far-red sensing. Seagrasses have also regained functions enabling them to adjust to full salinity. Their cell walls contain all of the polysaccharides typical of land plants, but also contain polyanionic, low-methylated pectins and sulfated galactans, a feature shared with the cell walls of all macroalgae(4) and that is important for ion homoeostasis, nutrient uptake and O-2/CO2 exchange through leaf epidermal cells. The Z. marina genome resource will markedly advance a wide range of functional ecological studies from adaptation of marine ecosystems under climate warming(5,6), to unravelling the mechanisms of osmoregulation under high salinities that may further inform our understanding of the evolution of salt tolerance in crop plants(7)

Genetic diversity and connectivity in the Mediterranean seagrass Posidonia oceanica: state of art and future directions

Seagrasses are marine flowering plants providing key ecological services and functions in coastal zones and estuaries all across the globe. Posidonia oceanica is endemic to the Mediterranean Sea, where it forms highly productive meadows that enhance biodiversity of nearshore waters, prevent coastal erosion and contribute to climate change mitigation. Here, we aim to provide a comprehensive review on the status of the genetic knowledge of P. oceanica, with a special focus on the genetic structure of the species throughout the basin, the genetic and clonal diversities of studied populations and their potential and realized connectivity. We start providing basic information on the role of genetic and non-genetic diversity on supporting ecosystem functioning and resistance to environmental changes, in seagrasses and P. oceanica in particular. We further discuss drivers of population structure, connectivity and dispersal, and evidences of local adaptation of populations along environmental clines. An insight box is included to review the importance of sexual reproduction in P. oceanica and discuss recent massive flowering events in relation to ongoing seawater warming. We finally highlight the need and discuss the strategies to integrate current genetic knowledge with management actions to support and improve conservation of P. oceanica meadows

Dynamics of DNA methylation in Posidonia oceanica (L.) Delile from different environments

The dynamics of DNA methylation play important roles in the regulation of gene expression and genome stability. These epigenetic modifications are regulated by environmental factors through the activation of different writers/erasers that can be at the basis of the appearance of different phenotypic responses to environmental stresses. In the context of climate change, understanding the impact of ocean warming in combination with local pressures is fundamental for exploring resilience capacity of marine organisms. Seagrasses, which are marine angiosperms particularly vulnerable to environmental changes, display high degree of phenotypic plasticity colonizing heterogeneous environments. Here we explore, for the first time, the dynamics of DNA-methylation in Posidonia oceanica shoots from meadows experiencing different nutrient conditions (oligotrophic, Ol; eutrophic, Eu). The expression of key genes involved in the de novo DNA methylation, maintenance, demethylation and histone modifications were selected and analysed after one, two and five weeks of exposure to single (temperature and nutrients) and combined stressors (nutrients + temperature). Global DNA methylation levels were also measured in both Ol and Eu plants at the same time points. Our results revealed that the global DNA methylation and the expression dynamics of selected genes were influenced by both plants origin and the duration of the imposed stresses. Temperature was the main driver modulating gene expression during the experiment. These findings suggest that DNA methylation in marine plants is a dynamic process that could potentially regulate phenotypic responses to environmental changes