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Angiosperm genome sizes (GS) range ~2400-fold and comprise genes and their regulatory regions, repeats, semi-degraded repeats, and ‘dark matter’. The latter represents repeats so degraded that they can no longer be recognised as repetitive. In exploring whether the histone modifications associated with chromatin packaging of these contrasting genomic components are conserved across the diversity of GS in angiosperms, we compared immunocytochemistry data for two species whose GS differ ~286-fold. We compared published data for Arabidopsis thaliana with a small genome (GS = 157 Mbp/1C) with newly generated data from Fritillaria imperialis, which has a giant genome (GS = 45,000 Mbp/1C). We compared the distributions of the following histone marks: H3K4me1, H3K4me2, H3K9me1, H3K9me2, H3K9me3, H3K27me1, H3K27me2, and H3K27me3. Assuming these histone marks are associated with the same genomic features across all species, irrespective of GS, our comparative analysis enables us to suggest that while H3K4me1 and H3K4me2 methylation identifies genic DNA, H3K9me3 and H3K27me3 marks are associated with ‘dark matter’, H3K9me1 and H3K27me1 mark highly homogeneous repeats, and H3K9me2 and H3K27me2 mark semi-degraded repeats. The results have implications for our understanding of epigenetic profiles, chromatin packaging and the divergence of genomes, and highlight contrasting organizations of the chromatin within the nucleus depending on GS itself.

Background Preparatory, written plans for mass casualty incidents are designed to help hospitals deliver an effective response. However, addressing the frequently observed mismatch between planning and delivery of effective responses to mass casualty incidents is a key challenge. We aimed to use simulation-based iterative learning to bridge this gap. Methods We used Normalisation Process Theory as the framework for iterative learning from mass casualty incident simulations. Five small-scale ‘focused response' simulations generated learning points that were fed into two large-scale whole-hospital response simulations. Debrief notes were used to improve the written plans iteratively. Anonymised individual online staff surveys tracked learning. The primary outcome was system safety and latent errors identified from group debriefs. The secondary outcomes were the proportion of completed surveys, confirmation of reporting location, and respective roles for mass casualty incidents. Results Seven simulation exercises involving more than 700 staff and multidisciplinary responses were completed with debriefs. Usual emergency care was not affected by simulations. Each simulation identified latent errors and system safety issues, including overly complex processes, utilisation of space, and the need for clarifying roles. After the second whole hospital simulation, participants were more likely to return completed surveys (odds ratio=2.7; 95% confidence interval [CI], 1.7–4.3). Repeated exercises resulted in respondents being more likely to know where to report (odds ratio=4.3; 95% CI, 2.5–7.3) and their respective roles (odds ratio=3.7; 95% CI, 2.2–6.1) after a simulated mass casualty incident was declared. Conclusion Simulation exercises are a useful tool to improve mass casualty incident plans iteratively and continuously through hospital-wide engagement of staff.

Simple telomeric repeats composed of six to seven iterating nucleotide units are important sequences typically found at the ends of chromosomes. Here we analyzed their abundance and homogeneity in 42 gymnosperm (29 newly sequenced), 29 angiosperm (one newly sequenced), and eight bryophytes using bioinformatics, conventional cytogenetic and molecular biology approaches to explore their diversity across land plants. We found more than 10 000-fold variation in the amounts of telomeric repeats among the investigated taxa. Repeat abundance was positively correlated with increasing intragenomic sequence heterogeneity and occurrence at non-telomeric positions, but there was no correlation with genome size. The highest abundance/heterogeneity was found in the gymnosperm genus Cycas (Cycadaceae), in which megabase-sized blocks of telomeric repeats (i.e., billions of copies) were identified. Fluorescent in situ hybridization experiments using variant-specific probes revealed canonical Arabidopsis-type telomeric TTTAGGG repeats at chromosome ends, while pericentromeric blocks comprised at least four major telomeric variants with decreasing abundance: TTTAGGG>TTCAGGG >TTTAAGG>TTCAAGG. Such a diversity of repeats was not found in the sister cycad family Zamiaceae or in any other species analyzed. Using immunocytochemistry, we showed that the pericentromeric blocks of telomeric repeats overlapped with histone H3 serine 10 phosphorylation signals. We show that species of Cycas have amplified their telomeric repeats in centromeric and telomeric positions on telocentric chromosomes to extraordinary high levels. The ancestral chromosome number reconstruction suggests their occurrence is unlikely to be the product of ancient Robertsonian chromosome fusions. We speculate as to how the observed chromosome dynamics may be associated with the diversification of cycads., This project was supported by the Czech Academy of Science, Czech Science Foundation (22-16826S), Czech National Infrastructure for Biological data (ELIXIR CZ, LM2018131), NERC and China Scholarship Council (CSC). JP benefited from a Ramón y Cajal grant Ref: RYC-2017-2274 funded by MCIN/AEI/, INTRODUCTION RESULTS Identification and quantification of telomeric repeats in high-throughput reads In silico identification of telomeric repeat variants Southern blot hybridization analysis of telomeric variants Identification of cycad centromeres by immunostaining of chromatin FISH analysis of telomeric variants Evolution of chromosome numbers and genome sizes across cycads DISCUSSION Variable abundance of telomeric repeats in plant genomes Origin of telomeric repeat variants in cycad genomes Epigenetic modification of telomeric repeats Chromosome evolution in cycads CONCLUSION EXPERIMENTAL PROCEDURES Plant material DNA isolation and Illumina sequencing Estimation of telomeric repeats abundance and diversity from high-throughput sequencing data Ancestral chromosome and genome size reconstruction Southern blot hybridization and DNA methylation analysis DNA probe preparation for FISH and southern blotting FISH Immunohistochemical staining of chromosomes ACKNOWLEDGEMENTS Author CONTRIBUTIONS

An analysis of over 10 000 plant genome sizes (GSs) indicates that most species have smaller genomes than expected given the incidence of polyploidy in their ancestries, suggesting selection for genome downsizing. However, comparing ancestral GS with the incidence of ancestral polyploidy suggests that the rate of DNA loss following polyploidy is likely to have been very low (4-70 Mb/million years, 4-482 bp/generation). This poses a problem. How might such small DNA losses be visible to selection, overcome the power of genetic drift and drive genome downsizing? Here we explore that problem, focussing on the role that double-strand break (DSB) repair pathways (non-homologous end joining and homologous recombination) may have played. We also explore two hypotheses that could explain how selection might favour genome downsizing following polyploidy: to reduce (i) nitrogen (N) and phosphate (P) costs associated with nucleic acid synthesis in the nucleus and the transcriptome and (ii) the impact of scaling effects of GS on cell size, which influences CO2 uptake and water loss. We explore the hypothesis that losses of DNA must be fastest in early polyploid generations. Alternatively, if DNA loss is a more continuous process over evolutionary time, then we propose it is a byproduct of selection elsewhere, such as limiting the damaging activity of repetitive DNA. If so, then the impact of GS on photosynthesis, water use efficiency and/or nutrient costs at the nucleus level may be emergent properties, which have advantages, but not ones that could have been selected for over generational timescales., XW is funded by the China Scholarship Council (CSC, Grant 201908370151) from the Ministry of Education of the P.R. China. JP is supported by a Ramón y Cajal Fellowship (2017-RYC-2274) funded by the Ministry of Science and Technology (Government of Spain)., INTRODUCTION IMPACT OF WHOLE-GENOME DUPLICATIONS ON GENOME SIZE DIVERSITY IN ANGIOSPERMS MECHANISMS UNDERPINNING GENOME SIZE DIVERGENCE PREDICTING RATES OF GENOME SIZE CHANGE FOLLOWING WHOLE-GENOME DUPLICATIONS POTENTIAL SOURCES OF SELECTION ACTING ON GENOME SIZE FOLLOWING WHOLE-GENOME DUPLICATIONS Selection for small genomes generated by the nutrient costs of nucleic acids Selection for small genomes to maximise photosynthesis and/or water use efficiency HOW MIGHT GENOME DOWNSIZING ARISE? Genome downsizing arises through selection against genome upsizing Genome downsizing is selected for in early-generation polyploids Genome downsizing is a byproduct of high recombination frequencies in polyploids Genome downsizing is a byproduct of selection for a nutrient-efficient transcriptome CONCLUDING REMARKS AND FUTURE PERSPECTIVES ACKNOWLEDGEMENTS CONFLICT OF INTEREST

Grassland ecosystems cover c. 40% of global land area and contain c. 40% of soil organic carbon. Understanding the effects of adding nutrients to grasslands is essential because they provide much of our food, support diverse ecosystem services and harbor rich biodiversity. Using the meadow steppe (grassland) study site of Inner Mongolia, we manipulated seven key nutrients and a cocktail of micronutrients to examine their effects on grassland biomass productivity and diversity. The results, explained in structural equation models, link two previously disparate hypotheses in grassland ecology: (1) the light asymmetry competition hypothesis and (2) the genome size-nutrient interaction hypothesis. We show that aboveground net primary productivity increases predominantly from species with large genome sizes with the addition of nitrogen, and nitrogen plus phosphorus. This drives an asymmetric competition for light, causing a decline in species richness mainly in species with small genome sizes. This dynamic is likely to be caused by the nutrient demands of the nucleus and/or the scaling effects of nuclear size on cell size which impact water use efficiency. The model will help inform the best management approaches to reverse the rapid and unprecedented degradation of grasslands globally.

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., We thank Natural Environment Research Council (NE/G020256/1), the Czech Academy of Sciences (RVO:60077344) and Ramón y Cajal Fellowship (RYC-2017-2274) funded by the Ministerio de Ciencia y Tecnología (Gobierno de España) for support. We also thank Natural Environment Research Council for funding a studentship to S.D. and the China Scholarship Council for funding W.W., Main Methods Data availability Code availability References Acknowledgements Author information Ethics declarations Additional information Extended data Supplementary information Rights and permissions About this article Further reading

Nicotiana section Suaveolentes is the largest section of Nicotiana and is a monophyletic group of allotetraploid species. Most of the species are endemic to Australia, but three species occur on islands in the South Pacific as far east as French Polynesia and one species is native to Namibia. Here, we present phylogenetic results based on genome skimming, with near-complete taxon sampling and multiple accessions sampled for several species. These represent the first phylogenetic results for the section that include most recognized taxa, using wild-sourced material wherever possible. Despite known chromosome number and genome size changes in the section, there is little divergence in the ribosomal DNA operon (26S, 18.S and 5.8S plus associated spacers) and plastid genomes, with little to no taxonomic signal in plastome phylogenetic results and clear plastid-nuclear discordance. These results contrast with strong morphological differentiation (both floral and vegetative) between most of the core Australian taxa and obvious differences in ecological preferences. Together, these initial results portray Nicotiana section Suaveolentes as experiencing recent and ongoing radiation in the arid zone of Australia.

The bluebells Hyacinthoides hispanica (Mill.) Rothm. and H. non-scripta (L.) Chouard ex Rothm. form a hybrid zone in Spain and represent a natural experiment for the study of gene flow between species. The results of this study provide not only important insights to obtain empirical evidence regarding the mechanisms of gene flow enabled by hybridization but also to improve conservation assessment of the anthropogenic hybridization zone amongst bluebells occurring in Britain. We developed genome-wide genetic markers for amplicon-based resequencing from individuals across the hybrid zone, mapped morphological changes across the zone and determined the fitness of hybrids in laboratory crosses. We revealed significant clines across the zone at 61% of single nucleotide polymorphisms of the nuclear genes, most of which have a relatively shallow slope (mean slope 0.051 km–1, mean width of 78.4 km). In contrast, there was a rapid change in organellar haplotypes (slope = 0.238 km–1, mean width of 16.78 km). Thirteen nuclear genes had clines coincident with the organellar transition, and a subset had products directly involved in cyto-nuclear interactions. The location of this hybrid zone, the wide transitions in morphology and allele frequency all suggest that the zone is long established, and probably formed after the last glacial maximum. The high fitness of interspecific crosses is consistent with ongoing gene flow across the zone, although cyto-nuclear incompatibilities appear to prevent the movement of some alleles and coordinated activity between cellular compartments.

Genome size varies 2400-fold across plants, influencing their evolution through changes in cell size and cell division rates which impact plants' environmental stress tolerance. Repetitive element expansion explains much genome size diversity, and the processes structuring repeat "communities" are analogous to those structuring ecological communities. However, which environmental stressors influence repeat community dynamics has not yet been examined from an ecological perspective. We measured genome size and leveraged climatic data for 91% of genera within the ecologically diverse palm family (Arecaceae). We then generated genomic repeat profiles for 141 palm species, and analysed repeats using phylogenetically informed linear models to explore relationships between repeat dynamics and environmental factors. We show that palm genome size and repeat "community" composition are best explained by aridity. Specifically, Ty3-gypsy and TIR elements were more abundant in palm species from wetter environments, which generally had larger genomes, suggesting amplification. By contrast, Ty1-copia and LINE elements were more abundant in drier environments. Our results suggest that water stress inhibits repeat expansion through selection on upper genome size limits. However, elements that may associate with stress-response genes (e.g. Ty1-copia) have amplified in arid-adapted palm species. Overall, we provide novel evidence of climate influencing the assembly of repeat "communities"., JP was supported by a Ramón y Cajal Fellowship (RYC-2017-2274) funded by MCIN/AEI/10.13039/501100011033 and by ‘ESF Investing in your future’. SB was funded by a Garfield Weston Foundation postdoctoral fellowship. PN and JM were supported by the ELIXIR CZ Research Infrastructure Project (Czech Ministry of Education, Youth and Sports; grant no. LM2018131)., IntroductionMaterials and Methods Plant material collection and genome size measurement Phylogenetic, environmental and genomic data collection Modelling relationships between genome size and environmental variables DNA repeat profiling Assessing repeat dynamics in palm genomesResults Palm genome size variation Aridity preferences of palm species help explain genome size variation Ecological metrics of palm repeat ‘communities’ vary with genome size Repeat abundances correlate with genome size Aridity preferences of palm species explain abundances of certain repeat lineagesDiscussion Palm genome size variation Aridity thresholds best explain palm genome size diversity The ‘community ecology’ of repeats correlates with genome size Repeat dynamics may be modulated by aridityConclusionsAcknowledgementsAuthor contributions

Background and Aims The extent to which genome size and chromosome numbers evolve in concert is little understood, particularly after polyploidy (whole-genome duplication), when a genome returns to a diploid-like condition (diploidization). We study this phenomenon in 46 species of allotetraploid Nicotiana section Suaveolentes (Solanaceae), which formed Methods We analysed newly assessed genome sizes and chromosome numbers within the context of a restriction site-associated nuclear DNA (RADseq) phylogenetic framework. Key Results RADseq generated a well-supported phylogenetic tree, in which multiple accessions from each species formed unique genetic clusters. Chromosome numbers and genome sizes vary from n = 2x = 15 to 24 and 2.7 to 5.8 pg/1C nucleus, respectively. Decreases in both genome size and chromosome number occur, although neither consistently nor in parallel. Species with the lowest chromosome numbers (n = 15–18) do not possess the smallest genome sizes and, although N. heterantha has retained the ancestral chromosome complement, n = 2x = 24, it nonetheless has the smallest genome size, even smaller than that of the modern representatives of ancestral diploids. Conclusions The results indicate that decreases in genome size and chromosome number occur in parallel down to a chromosome number threshold, n = 20, below which genome size increases, a phenomenon potentially explained by decreasing rates of recombination over fewer chromosomes. We hypothesize that, more generally in plants, major decreases in genome size post-polyploidization take place while chromosome numbers are still high because in these stages elimination of retrotransposons and other repetitive elements is more efficient. Once such major genome size change has been accomplished, then dysploid chromosome reductions take place to reorganize these smaller genomes, producing species with small genomes and low chromosome numbers such as those observed in many annual angiosperms, including Arabidopsis.

Whole-genome duplication, in particular allopolyploidy, has shaped the evolution of angiosperms and other organisms. Structural reorganization of chromosomes and repatterning of gene expression is frequently observed in early generation allopolyploids, with potential ecological consequences. The relative contributions of environmental and intrinsic drivers to these changes are unknown. We show here that in marsh orchids (Dactylorhiza, Orchidaceae), recurrently-formed allopolyploids are characterized by distinct eco-physiologies matching their respective environments, providing us with an excellent study system to address this question. Here we integrate eco-physiological and transcriptomic comparative studies to reveal a complex suite of intertwined, pronounced differences between sibling allopolyploids. We show that Dactylorhiza majalis that is distributed in Central and Southern Europe favors meadows with mesic soils. Its sibling allopolyploid D. traunsteineri occurs in fens, characterized by soils depleted by macro- and micronutrients, mainly in previously glaciated European areas. We further uncover distinct features in their nutrient transport, leaf elemental chemistry, light-harvesting, photoprotection, and stomata activity, that appear all linked to their distinct ecologies, in particular soil chemistry differences at their native sites. Recurrent polyploidization hence enriches biodiversity through eco-physiological diversification, providing the opportunity for sibling allopolyploids to evolve as distinct evolutionary units, despite pervasive interspecific gene flow.Significance StatementWhole-genome duplication resulting in polyploidy has underpinned the evolution of flowering plants and other organisms, and is important for many crops. However, the ecological implications of polyploidy remain little understood. Here, we demonstrate that two sibling allopolyploid marsh orchid species prefer distinct habitats, and have evolved a suite of distinctive ecophysiological characters (e.g. nutrient transport, energy harvesting and photoprotection). We argue that the divergence of these characters in the nascent polyploids drove adaptation into distinct ecological niches (low nutrient fens versus meadows with mesic soils), generating ecological barriers that maintains distinct, independent lineages, even in the presence of interspecific gene flow.

High-speed real-time wavelength conversion at key data centre network nodes is an emerging fundamental functionality requirement for transparent content resolution, wavelength assignment and routing towards better utilization of network resources under dynamic traffic patterns. In this paper, we experimentally demonstrate the first vertical cavity surface emitting laser (VCSEL)-based broadband wavelength converter for ultra-wide wavelength routing in Datacom. An 850 nm multimode VCSEL is directly modulated with 8.5 Gbps data and successfully transmitted error-free over 100 m OM3 multimode fibre (MMF) with a receiver sensitivity of −16.04 dBm, and a total transmission penalty of 1.14 dB. The received data is then used to run two cascaded single mode VCSELs at 1550 nm within the network integration node, therefore achieving the first reported real-time inter-band wavelength converter to C-band. By exploiting VCSEL wavelength tuneability with changing bias current, we show that the converted wavelengths can be routed over 3.2 nm spectra range for integration into ITU-T 50 GHz flexible grid and beyond. The newly converted wavelengths are successfully transmitted over 24.7 km of G 655 single mode fibre, achieving a minimum receiver sensitivity of −14.28 dBm, with a maximum transmission penalty of 2.72 dB. This work offers a viable enabling development technology for broadband wavelength converters for real-time wavelength routing in optical interconnects to address content resolution and wavelength assignment problem for current and future Datacom.

Short-reach optical interconnects among massive serves in data centers have attracted extensive research recently. Increasing capacity, cost and power efficiency as well as wavelength switching between data center network nodes are still key challenges for current optical interconnects. In this work, we experimentally demonstrate the real-time inter-mode optical wavelength switching technique, for high-speed wavelength flexible data center interconnects. A 10 Gbit/s 1 550 nm single mode vertical cavity surface emitting laser (VCSEL) is optically injected and used to control a 10 Gbit/s multimode VCSEL carrier at 850 nm. Results show that a clearly open eye diagram is achieved at back-to-back analysis, implying a successful wavelength switch and error-free operation at 10 Gbit/s. A fully optical wavelength conversion of a multimode VCSEL operation at 850 nm using a single mode VCSEL subject to external optical injection at 1 550 nm is reported. This work opens new perspectives towards the development of a cost effective high-speed real-time inter-band wavelength switching technique between servers and network devices operating at different transmission windows at network nodes, for current and future optical interconnects.

All-optical wavelength reuse is a viable approach for realization of low cost colourless ONUs. We experimentally demonstrate a novel all-optical wavelength reuse technique with simultaneous upstrea...

To improve the time and frequency reference standards used for radio astronomy and high precision atomic physics applications, we describe a novel stable frequency transmission technique. The approach uses a vertical-cavity surface- emitting laser (VCSEL) based phase correction actuator. Using a frequency mixing process for feedback control, the phase noise induced along the 26 km G.655 optical fibre link was actively reduced. This was achieved by using a 1 310 nm dither controlled VCSEL phase error correction actuator together with the inherent chromatic dispersion properties of the fibre. The technique corrects phase noise and optical signal drift along the fibre at the transmission end. Fractional frequency instabilities across the G.655 fibre link of 4.44×10−12 at 1 s and 4.86×10−14 at 104 s are successfully reported.

Accurate time transfer and synchronization between different network nodes is a key functional requirement in digital communication. Developments in optical fiber-based frequency dissemination techniques have improved optical frequency stability over time to much lower levels. In this work, we experimentally present the reference frequency transfer employing 850 nm vertical cavity surface emitting laser (VCSEL) over 100.3 m OM3 multimode fiber for synchronization of clocks on networked devices such as servers and racks/pod at different data center network nodes. A low-cost power-efficient multimode VCSEL with central wavelength at 844.26 nm is directly modulated with a 2 GHz reference frequency (RF) clock signal, and transferred over 100.3 m of OM3 multimode fiber. The single side band (SSB) phase noise of -104.62 dBc/Hz and −100.70 dBc/Hz is experimentally measured at back-to-back (B2B) and 100.3 m OM3 multimode fiber transmission respectively at a 1 kHz frequency offset. The jitter stability of 0.14 ps and 0.15 ps is experimentally achieved at B2B and 100.3 m fiber transmission, respectively. This work provides an alternative viable approach for the development of time keeping devices in high-speed short-reach optical communication systems.

This work experimentally demonstrates the potential of multi-level pulse amplitude modulation with direct detection to maximize carrier spectral efficiency and double the Gigabit passive optical networks (G-PON) network data rate. Three scenarios have experimentally been exploited. First, a 1310 nm vertical surface-emitting laser (VCSEL) has directly been modulated with a 10 Gbps OOK data. A receiver sensitivity of −19.11 dBm is attained, and a successful error free transmission over 22 km SMF fibre achieved, with a transmission penalty of 0.46 dB. To maximize carrier spectral efficiency, 2/4 PAM modulation formats are adopted respectively. A receiver sensitivity of −14.64 and −11.63 dBm is attained for 2-PAM and 4-PAM formats respectively. However, a 3.21 km fibre transmission introduces a penalty of 0.64 and 3.30 dB for 2-PAM and 4-PAM formarts respectively. 2/4-PAM modulation formats significantly increase the aggregated data rate at different ONUs within the G-PON without expensive optics inve...

In this paper, we propose and experimentally demonstrate a vertical cavity surface emitting laser (VCSEL)-based simultaneous 45.2 Gbit/s (2×22.6 Gbit/s) 4-PAM data and 8 GHz (2×4 GHz) phase modulated reference frequency (RF) clock signal transmission dense wavelength division multiplexing (DWDM) system for optical interconnects. Two low-cost power-efficient 10 G VCSEL channels with central wavelengths at 1 550.71 nm and 1 551.11 nm are separately modulated with 22.6 Gbit/s 4-PAM data, therefore doubling the channel bit rate. Carrier spectral efficiency per channel is further maximized by exploiting the phase attribute in transmission of a 4 Hz RF clock signal. To further maximize the network capacity, the two VCSEL channels are densely multiplexed at 0.4 nm spacing. We therefore experimentally achieve the network data rate of 45.2 Gbit/s with 8 GHz phase modulated RF clock signal. The results show that receiver sensitivities of −11.02 dBm and −9.98 dBm are experimentally achieved for VCSEL channels of 1 550.71 nm and 1 551.11 nm respectively without the phase modulated RF clock signal. However, the introduction of a phase modulated clock signal contributes to a maximum interference penalty of 0.57 dBm and 0.41 dBm for the considered channels respectively. Simultaneous distribution of transmission data and reference clock signal over shared network structure maximizes the carrier spectral efficiency and network capacity with low cost.