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We present a genome assembly from an individual Medicago arabica (the spotted medick; Tracheophyta; Magnoliopsida; Fabales; Fabaceae). The genome sequence is 515.5 megabases in span. Most of the assembly is scaffolded into 8 chromosomal pseudomolecules. The mitochondrial and plastid genome assemblies have lengths of 324.47 kilobases and 125.07 kilobases in length, respectively. Gene annotation of this assembly on Ensembl identified 24,619 protein-coding genes.

We present a genome assembly from an individual Phragmites australis (the common reed; Streptophyta; Magnoliopsida; Poales; Poaceae). The genome sequence has a total length of 848.70 megabases. Most of the assembly is scaffolded into 24 chromosomal pseudomolecules, supporting the specimen being an allotetraploid (2n = 4x = 48). The three mitochondrial assemblies had lengths of 304.58, 92.24, and 76.54 kilobases and the plastid genome assembly had a length of 137.67 kilobases. Gene annotation of this assembly on Ensembl identified 47,513 protein-coding genes.

We present a genome assembly from an individual Trifolium dubium (lesser trefoil; Tracheophyta; Magnoliopsida; Fabales; Fabaceae) as part of a collaboration between the Darwin Tree of Life and the European Reference Genome Atlas. The genome sequence is 679.1 megabases in span. Most of the assembly is scaffolded into 15 chromosomal pseudomolecules. The two mitochondrial genomes have lengths of 133.86 kb and 182.32 kb, and the plastid genome assembly has a length of 126.22 kilobases.

We present a genome assembly from an individual Chamaenerion angustifolium (fireweed; Tracheophyta; Magnoliopsida; Myrtales; Onagraceae). The genome sequence is 655.9 megabases in span. Most of the assembly is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial and plastid genome assemblies have lengths of 495.18 kilobases and 160.41 kilobases in length, respectively.

We present a genome assembly from an individual Ilex aquifolium (the English holly; Eudicot; Magnoliopsida; Aquifoliales; Aquifoliaceae). The genome sequence is 800.0 megabases in span. Most of the assembly is scaffolded into 20 chromosomal pseudomolecules. The assembled mitochondrial and plastid genomes have lengths of 538.43 kilobases and 157.52 kilobases in length, respectively.

Abstract Estimating effective population size (Ne) is important for theoretical and practical applications in evolutionary biology and conservation. Nevertheless, estimates of Ne in organisms with complex life‐history traits remain scarce because of the challenges associated with estimation methods. Partially clonal plants capable of both vegetative (clonal) growth and sexual reproduction are a common group of organisms for which the discrepancy between the apparent number of individuals (ramets) and the number of genetic individuals (genets) can be striking, and it is unclear how this discrepancy relates to Ne. In this study, we analysed two populations of the orchid Cypripedium calceolus to understand how the rate of clonal versus sexual reproduction affected Ne. We genotyped >1000 ramets at microsatellite and SNP loci, and estimated contemporary Ne with the linkage disequilibrium method, starting from the theoretical expectation that variance in reproductive success among individuals caused by clonal reproduction and by constraints on sexual reproduction would lower Ne. We considered factors potentially affecting our estimates, including different marker types and sampling strategies, and the influence of pseudoreplication in genomic data sets on Ne confidence intervals. The magnitude of Ne/Nramets and Ne/Ngenets ratios we provide may be used as reference points for other species with similar life‐history traits. Our findings demonstrate that Ne in partially clonal plants cannot be predicted based on the number of genets generated by sexual reproduction, because demographic changes over time can strongly influence Ne. This is especially relevant in species of conservation concern in which population declines may not be detected by only ascertaining the number of genets.

We present a genome assembly from an individual Pulicaria dysenterica (common fleabane; Tracheophyta; Magnoliopsida; Asterales; Asteraceae). The genome sequence is 833.2 megabases in span. Most of the assembly is scaffolded into 9 chromosomal pseudomolecules. The mitochondrial and plastid genomes were assembled and have lengths of 375.47 kilobases and 150.94 kilobases respectively.

We present a genome assembly from a specimen of Ballota nigra (black horehound; Tracheophyta; Magnoliopsida; Lamiales; Lamiaceae). The genome sequence is 1186.8 megabases in span. Most of the assembly is scaffolded into 11 chromosomal pseudomolecules. Three mitochondrial chromosomes were assembled, with lengths of 148,17, 121,67 and 125,74 kilobases. The chloroplast genome has been assembled and is 151.91 kilobases in length.

Glioblastoma is a highly aggressive disease with poor survival outcomes. An emerging body of literature links the role of the renin–angiotensin system (RAS), well-known for its function in the cardiovascular system, to the progression of cancers. We studied the expression of RAS-related genes (ATP6AP2, AGTR1, AGTR2, ACE, AGT, and REN) in The Cancer Genome Atlas (TCGA) glioblastoma cohort, their relationship to patient survival, and association with tumour microenvironment pathways. The expression of RAS genes was then examined in 12 patient-derived glioblastoma cell lines treated with chemoradiation. In cases of glioblastoma within the TCGA, ATP6AP2, AGTR1, ACE, and AGT had consistent expressions across samples, while AGTR2 and REN were lowly expressed. High expression of AGTR1 was independently associated with lower progression-free survival (PFS) (p = 0.01) and had a non-significant trend for overall survival (OS) after multivariate analysis (p = 0.095). The combined expression of RAS receptors (ATP6AP2, AGTR1, and AGTR2) was positively associated with gene pathways involved in hypoxia, microvasculature, stem cell plasticity, and the molecular characterisation of glioblastoma subtypes. In patient-derived glioblastoma cell lines, ATP6AP2 and AGTR1 were upregulated after chemoradiotherapy and correlated with an increase in HIF1A expression. This data suggests the RAS is correlated with changes in the tumour microenvironment and associated with glioblastoma survival outcomes.

Societal Impact Statement Digitized molecular data are vital to numerous aspects of scientific research and genetic resource use. The Convention on Biological Diversity currently refers to this as “Digital Sequence Information” (DSI), a term not widely adopted by science and lacking a clear definition. There are concerns over the access to genetic resources and absence of benefit sharing by provider countries. Open access to DSI might exacerbate this, which is leading to increasing policy interventions and restricted access to genetic resources and DSI. We analyze current international debate and proposed solutions and provide case studies of DSI use producing tangible benefits for the provider countries and scientific research, demonstrating the importance of open access DSI to achieving conservation goals. Summary Substantial advances in DNA sequencing over the last decades hold great potential to enhance food security and sustainable use of global biodiversity, benefiting the world's poorest people. Digital Sequence Information (DSI) plays a crucial role in catalyzing research applications that can contribute to international societal and biodiversity conservation targets. However, benefit sharing relating to DSI is difficult to identify and hindered by the lack of clear international governance and legislation, which in turn has led to a reluctance to make DSI publicly and freely available. Critically, no precise definition exists under the Convention on Biological Diversity (CBD), the Nagoya Protocol (NP), or the International Treaty for Plant Genetic Resources for Food and Agriculture (ITPGRFA). The key difference between DSI and biological resources, for which access and use are highly regulated under those frameworks, is that information is nonphysical. Information can be replicated and used without movement of, or access to, physical specimens. Thus, regulating the use of DSI is extremely challenging and remains controversial. Here, we review the regulation of DSI and the possible future steps by the international community, in the context of the benefit‐sharing obligations of the CBD, NP, and ITPGRFA. We highlight how multilateral agreements work in practice and are a solution to this impasse. We provide case studies demonstrating how the Royal Botanic Gardens, Kew, and its collaborators address the uncertainty surrounding the use of DSI, illustrating tangible and equitable benefits that have arisen from such use. We conclude that open access to DSI is needed for scientific research and international policy.

Societal Impact Statement We rely on plants and fungi for most aspects of our lives. Yet plants and fungi are under threat, and we risk losing species before we know their identity, roles, and potential uses. Knowing names, distributions, and threats are first steps toward effective conservation action. Accessible products like field guides and online resources engage society, harnessing collective support for conservation. Here, we review current knowledge of the plants and fungi of the UK and UK Overseas Territories, highlighting gaps to help direct future research efforts toward conserving these vital elements of biodiversity. Summary This review summarizes current knowledge of the status and threats to the plants and fungi of Great Britain and the UK Overseas Territories (UKOTs). Although the body of knowledge is considerable, the distribution of information varies substantially, and we highlight knowledge gaps. The UK vascular flora is the most well studied and we have a relatively clear picture of its 9,001 native and alien taxa. We have seedbanked 72% of the native and archaeophyte angiosperm taxa and 78% of threatened taxa. Knowledge of the UKOTs flora varies across territories and we report a UKOTs flora comprising 4,093 native and alien taxa. We have conserved 27% of the native flora and 51% of the threatened vascular plants in Kew's Millennium Seed Bank, UK. We need a better understanding of the conservation status of plants in the wild, and progress toward completion or updating national red lists varies. Site‐based protection of key plant assemblages is outlined, and progress in identifying Important Plant Areas analyzed. Knowledge of the non‐vascular flora, especially seaweeds remains patchy, particularly in many UKOTs. The biggest gaps overall are in fungi, particularly non‐lichenized fungi. Considerable investment is needed to fill these knowledge gaps and instigate effective conservation strategies.

Abstract The split between conservation science and real‐world application is an ongoing issue despite several calls for unification. Researchers are empowered to partially bridge the research‐implementation gap by making their findings more accessible. Cypripedium calceolus is the most recognizable orchid of the European flora, and is currently facing habitat change and fragmentation, in addition to threats from collectors and illegal traders. Although several studies have focused on the ecological and genetic features of the species, a comprehensive account of how such aspects can be translated into concrete conservation recommendations is still missing. In this study, we describe microsatellite genetic variation in 188 individuals from different Italian populations of C. calceolus. Our results indicate the need for immediate conservation action for the most isolated populations in the Central Apennines and north‐western Italy. Although our genetic findings are specific to the Italian populations, our aim is to review ecological and population genetic aspects in C. calceolus and their implications for conservation against the existing threats. Therefore, our detailed guidelines for translocation, habitat management and post‐translocation monitoring can be used to inform conservation strategies in threatened populations of C. calceolus across its range.

Plant genomes are highly diverse in size and repetitive DNA composition. In the absence of polyploidy, the dynamics of repetitive elements, which make up the bulk of the genome in many species, are the main drivers underpinning changes in genome size and the overall evolution of the genomic landscape. The advent of high-throughput sequencing technologies has enabled investigation of genome evolutionary dynamics beyond model plants to provide exciting new insights in species across the biodiversity of life. Here we analyze the evolution of repetitive DNA in two closely related species of Heloniopsis (Melanthiaceae), which despite having the same chromosome number differ nearly twofold in genome size [i.e., H. umbellata (1C = 4,680 Mb), and H. koreana (1C = 2,480 Mb)]. Low-coverage genome skimming and the RepeatExplorer2 pipeline were used to identify the main repeat families responsible for the significant differences in genome sizes. Patterns of repeat evolution were found to correlate with genome size with the main classes of transposable elements identified being twice as abundant in the larger genome of H. umbellata compared with H. koreana. In addition, among the satellite DNA families recovered, a single shared satellite (HeloSAT) was shown to have contributed significantly to the genome expansion of H. umbellata. Evolutionary changes in repetitive DNA composition and genome size indicate that the differences in genome size between these species have been underpinned by the activity of several distinct repeat lineages.

Coffea arabica (Arabica) and C. canephora (robusta) almost entirely dominate global coffee production. Various challenges at the production (farm) level, including the increasing prevalence and severity of disease and pests and climate change, indicate that the coffee crop portfolio needs to be substantially diversified in order to ensure resilience and sustainability. In this study, we use a multidisciplinary approach (herbarium and literature review, fieldwork and DNA sequencing) to elucidate the identity, whereabouts, and potential attributes, of two poorly known coffee crop species: C. affinis and C. stenophylla. We show that despite widespread (albeit small-scale) use as a coffee crop species across Upper West Africa and further afield more than 100 years ago, these species are now extremely rare in the wild and are not being farmed. Fieldwork enabled us to rediscover C. stenophylla in Sierra Leone, which previously had not been recorded in the wild there since 1954. We confirm that C. stenophylla is an indigenous species in Guinea, Sierra Leone, and Ivory Coast. Coffea affinis was discovered in the wild in Sierra Leone for the first time, having previously been found only in Guinea and Ivory Coast. Prior to our rediscovery, C. affinis was last seen in the wild in 1941, although sampling of an unidentified herbarium specimen reveals that it was collected in Guinea-Conakry in 2015. DNA sequencing using plastid and ITS markers was used to: (1) confirm the identity of museum and field collected samples of C. stenophylla; (2) identify new accessions of C. affinis; (3) refute hybrid status for C. affinis; (4) identify accessions confused with C. affinis; (5) show that C. affinis and C. stenophylla are closely related, and possibly a single species; (6) substantiate the hybrid C. stenophylla × C. liberica; (7) demonstrate the use of plastid and nuclear markers as a simple means of identifying F1 and early-generation interspecific hybrids in Coffea; (8) infer that C. liberica is not monophyletic; and (9) show that hybridization is possible across all the major groups of key Africa Coffea species (Coffee Crop Wild Relative Priority Groups I and II). Coffea affinis and C. stenophylla may possess useful traits for coffee crop plant development, including taste differentiation, disease resistance, and climate resilience. These attributes would be best accessed via breeding programs, although the species may have niche-market potential via minimal domestication.

Abstract 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.

Abstract With c. 28,000 species, orchids are one of the largest families of flowering plants, and they are also one of the most threatened, in part due to their complex life history strategies. Threats include habitat destruction and climate change, but many orchids are also threatened by unsustainable (often illegal and/or undocumented) harvest for horticulture, food or medicine. The level of these threats now outstrips our abilities to combat them at a species-by-species basis for all species in such a large group as Orchidaceae; if we are to be successful in conserving orchids for the future, we will need to develop approaches that allow us to address the threats on a broader scale to complement focused approaches for the species that are identified as being at the highest risk.

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