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Societal Impact Statement Cherimoya has been an important food source since Pre‐Columbian times in the Americas. Although it is currently considered an underutilized fruit crop, it is still important at the local level in several regions of Central and South America, and has a clear niche for expansion in regions with subtropical climates. However, the availability of genomic resources to facilitate breeding programs and improve the understanding of Annonaceae genetic diversity is limited. In this work, we provide an important resource to fill this knowledge gap, with the hope that it will ultimately increase this crop's resilience under different climate change scenarios, which will increase food security in regions with subtropical climates. Summary Cherimoya (Annona cherimola Mill.) is a perennial fruit tree crop native to the Neotropics valued since pre‐Columbian times by different native American civilizations. It belongs to the Annonaceae, the largest family of the Magnoliid clade, sister to the eudicot and monocot clades of angiosperms. Despite its excellent organoleptic and nutritive qualities, this crop remains underutilized, although it has a clear niche for expansion in regions with subtropical climates. To date, no previous significant genomic information is available for this species, which would be a key tool to optimize breeding programs and advance in the study and conservation of its extant genetic diversity. A combination of different sequencing technologies (Illumina, Pacific Biosciences) has been implemented in order to assemble a chromosome‐level reference genome of A. cherimola. The final reference genome resulted in an assembly of 1.13 Gb and N50 of 170.86 Mb, anchored into seven pseudomolecules and with a completeness of 95.6%. A total of 41,413 protein‐coding genes were identified, many of which were related to secondary metabolism, defense mechanisms, stress response, and development. The results of this study provide novel significant genomic resources not only for cherimoya and other species of the Annonaceae but also for understanding the evolution of the earlier divergent angiosperms. Alternative language Societal Impact Statements El chirimoyo ha sido muy apreciado como alimento desde tiempos precolombinos por diferentes culturas de las Américas. Es actualmente considerado un cultivo infrautilizado, aunque es importante a nivel local en diferentes países de Centro y Sudamérica, y tiene un claro nicho de expansión en regiones subtropicales. Sin embargo, la disponibilidad de recursos genómicos para facilitar los programas de mejora e incrementar el conocimiento de la diversidad genética de las Annonaceae es limitada. En este trabajo proporcionamos un importante recurso con el fin de reducir esta brecha, con la esperanza de que en última instancia permita una mejor adaptación de este cultivo a los desafíos planteados por el cambio climático y, por tanto, facilite la seguridad alimentaria en regiones subtropicales. Cherimoya has been an important food source since Pre‐Columbian times in the Americas. Although it is currently considered an underutilized fruit crop, it is still important at the local level in several regions of Central and South America, and has a clear niche for expansion in regions with subtropical climates. However, the availability of genomic resources to facilitate breeding programs and improve the understanding of Annonaceae genetic diversity is limited. In this work, we provide an important resource to fill this knowledge gap, with the hope that it will ultimately increase this crop's resilience under different climate change scenarios, which will increase food security in regions with subtropical climates.

Key message Bryophytes as models to study the male germ line: loss-of-function mutants of epigenetic regulators HAG1 and SWI3a/b demonstrate conserved function in sexual reproduction. With the water-to-land transition, land plants evolved a peculiar haplodiplontic life cycle in which both the haploid gametophyte and the diploid sporophyte are multicellular. The switch between these phases was coined alternation of generations. Several key regulators that control the bauplan of either generation are already known. Analyses of such regulators in flowering plants are difficult due to the highly reduced gametophytic generation, and the fact that loss of function of such genes often is embryo lethal in homozygous plants. Here we set out to determine gene function and conservation via studies in bryophytes. Bryophytes are sister to vascular plants and hence allow evolutionary inferences. Moreover, embryo lethal mutants can be grown and vegetatively propagated due to the dominance of the bryophyte gametophytic generation. We determined candidates by selecting single copy orthologs that are involved in transcriptional control, and of which flowering plant mutants show defects during sexual reproduction, with a focus on the under-studied male germ line. We selected two orthologs, SWI3a/b and HAG1 , and analyzed loss-of-function mutants in the moss P. patens . In both mutants, due to lack of fertile spermatozoids, fertilization and hence the switch to the diploid generation do not occur. Pp hag1 additionally shows arrested male and impaired female gametangia development. We analyzed HAG1 in the dioecious liverwort M. polymorpha and found that in Mp hag1 the development of gametangiophores is impaired. Taken together, we find that involvement of both regulators in sexual reproduction is conserved since the earliest divergence of land plants.

Tomato ( Solanum lycopersicum ) is an established model for studying fruit biology; however, most studies of tomato fruit growth and ripening are based on homogenized pericarp, and do not consider the internal tissues, or the expression signatures of individual cell and tissue types. We present a spatiotemporally resolved transcriptome analysis of tomato fruit ontogeny, using laser microdissection (LM) or hand dissection coupled with RNA-Seq analysis. Regulatory and structural gene networks, including families of transcription factors and hormone synthesis and signaling pathways, are defined across tissue and developmental spectra. The ripening program is revealed as comprising gradients of gene expression, initiating in internal tissues then radiating outward, and basipetally along a latitudinal axis. We also identify spatial variations in the patterns of epigenetic control superimposed on ripening gradients. Functional studies elucidate previously masked regulatory phenomena and relationships, including those associated with fruit quality traits, such as texture, color, aroma, and metabolite profiles. Cell-type transcriptome profiling greatly elucidate organismal development. Here, the authors report a spatiotemporally resolved comprehensive transcriptome analysis of tomato fruit ontogeny and suggest a new model of fruit maturation which initiates in internal tissues then radiates outwards.

Land plants have been intimately associated with fungi over the course of their evolution. Because of their lack of sophisticated protective structures, early land plants would conceivably have required additional defense strategies against microbial pathogens, including various fungi. On the other hand, a symbiotic association between plants and fungi is instrumental to plant adaptation to terrestrial environments (Selosse & Le Tacon, 1998; Bidartondo et al., 2011; Martin et al., 2017). The crucial role of this partnership is further evidenced by the widespread occurrence of mycorrhiza (root–fungi association) in vascular plants, as well as mycorrhiza-like fungal associations (MFAs hereafter) in nonvascular plants, such as liverworts and hornworts (Wang & Qiu, 2006; Pressel et al., 2014). Surprisingly, although fungal symbiosis is commonly considered to be an ancestral trait for land plants (Wang & Qiu, 2006; Delaux et al., 2015), with the possible exception of the genus Takakia (Boullard, 1988; Grosche et al., 2018), no MFAs have been confirmed in other mosses (Pressel et al., 2014; Field et al., 2015), the most diverse group of nonvascular land plants.Here, we report two genomic regions in the nuclear genome of the moss Physcomitrium patens, previously Physcomitrella patens (Medina et al., 2019; Rensing et al., 2020), that contain mostly fungi-specific genes and mobile genetic elements. These two regions were identified in our genome screening for horizontally acquired genes in P. patens. Available evidence indicates that these fungi-specific genes are probably involved in the interaction between mosses and fungi. We discuss how these fungi-specific genes might have contributed to the defense against fungal and other microbial pathogens, as well as the loss of MFAs in mosses.

Mango (Mangifera indica L.) (2n = 40) is a member of the Anacardiaceae family, which was domesticated at least 4000 years ago in Asia. Mangoes are delicious fruits with great nutritional value. They are one of the major fruit crops worldwide, cultivated in more than 100 countries, with a production of more than 40 million tons. Recently the genome sequences of several mango varieties have been released, but there are no bioinformatics platforms dedicated to mango genomics and breeding to host mango omics data. Here, we present MangoBase, a web portal dedicated to mango genomics, which provides multiple interactive bioinformatics tools, sequences, and annotations to analyze, visualize, and download omics data related to mango. Additionally, MangoBase includes a gene expression atlas with 12 datasets and 80 experiments representing some of the most significant mango RNA-seq experiments published to this date. These experiments study mango fruit ripening in several cultivars with different pulp firmness and sweetness or peel coloration, and other experiments also study hot water postharvest treatment, infection with C. gloeosporioides, and the main mango tree organ tissues.

Introduction: Physcomitrium patens (Hedw.) Mitten (previously known as Physcomitrella patens ) was collected by H.L.K. Whitehouse in Gransden Wood (Huntingdonshire, United Kingdom) in 1962 and distributed across the globe starting in 1974. Hence, the Gransden accession has been cultured in vitro in laboratories for half a century. Today, there are more than 13 different pedigrees derived from the original accession. Additionally, accessions from other sites worldwide were collected during the last decades.Methods and Results: In this study, 250 high throughput RNA sequencing (RNA-seq) samples and 25 gDNA samples were used to detect single nucleotide polymorphisms (SNPs). Analyses were performed using five different P. patens accessions and 13 different Gransden pedigrees. SNPs were overlaid with metadata and known phenotypic variations. Unique SNPs defining Gransden pedigrees and accessions were identified and experimentally confirmed. They can be successfully employed for PCR-based identification.Conclusion: We show independent mutations in different Gransden laboratory pedigrees, demonstrating that somatic mutations occur and accumulate during in vitro culture. The frequency of such mutations is similar to those observed in naturally occurring populations. We present evidence that vegetative propagation leads to accumulation of deleterious mutations, and that sexual reproduction purges those. Unique SNP sets for five different P. patens accessions were isolated and can be used to determine individual accessions as well as Gransden pedigrees. Based on that, laboratory methods to easily determine P. patens accessions and Gransden pedigrees are presented.

The transition from germinating seeds to emerging seedlings is one of the most vulnerable plant life cycle stages. Heteromorphic diaspores (seed and fruit dispersal units) are an adaptive bet-hedging strategy to cope with spatiotemporally variable environments. While the roles and mechanisms of seedling traits have been studied in monomorphic species, which produce one type of diaspore, very little is known about seedlings in heteromorphic species. Using the dimorphic diaspore model Aethionema arabicum (Brassicaceae), we identified contrasting mechanisms in the germination responses to different temperatures of the mucilaginous seeds (M + seed morphs), the dispersed indehiscent fruits (IND fruit morphs), and the bare non-mucilaginous M − seeds obtained from IND fruits by pericarp (fruit coat) removal. What follows the completion of germination is the pre-emergence seedling growth phase, which we investigated by comparative growth assays of early seedlings derived from the M + seeds, bare M − seeds, and IND fruits. The dimorphic seedlings derived from M + and M − seeds did not differ in their responses to ambient temperature and water potential. The phenotype of seedlings derived from IND fruits differed in that they had bent hypocotyls and their shoot and root growth was slower, but the biomechanical hypocotyl properties of 15-day-old seedlings did not differ between seedlings derived from germinated M + seeds, M − seeds, or IND fruits. Comparison of the transcriptomes of the natural dimorphic diaspores, M + seeds and IND fruits, identified 2,682 differentially expressed genes (DEGs) during late germination. During the subsequent 3 days of seedling pre-emergence growth, the number of DEGs was reduced 10-fold to 277 root DEGs and 16-fold to 164 shoot DEGs. Among the DEGs in early seedlings were hormonal regulators, in particular for auxin, ethylene, and gibberellins. Furthermore, DEGs were identified for water and ion transporters, nitrate transporter and assimilation enzymes, and cell wall remodeling protein genes encoding enzymes targeting xyloglucan and pectin. We conclude that the transcriptomes of seedlings derived from the dimorphic diaspores, M + seeds and IND fruits, undergo transcriptional resetting during the post-germination pre-emergence growth transition phase from germinated diaspores to growing seedlings.

Background RNA-sequencing analysis is increasingly utilized to study gene expression in non-model organisms without sequenced genomes. Aethionema arabicum (Brassicaceae) exhibits seed dimorphism as a bet-hedging strategy – producing both a less dormant mucilaginous (M + ) seed morph and a more dormant non-mucilaginous (NM) seed morph. Here, we compared de novo and reference-genome based transcriptome assemblies to investigate Ae. arabicum seed dimorphism and to evaluate the reference-free versus -dependent approach for identifying differentially expressed genes (DEGs). Results A de novo transcriptome assembly was generated using sequences from M + and NM Ae. arabicum dry seed morphs. The transcripts of the de novo assembly contained 63.1% complete Benchmarking Universal Single-Copy Orthologs (BUSCO) compared to 90.9% for the transcripts of the reference genome. DEG detection used the strict consensus of three methods (DESeq2, edgeR and NOISeq). Only 37% of 1533 differentially expressed de novo assembled transcripts paired with 1876 genome-derived DEGs. Gene Ontology (GO) terms distinguished the seed morphs: the terms translation and nucleosome assembly were overrepresented in DEGs higher in abundance in M + dry seeds, whereas terms related to mRNA processing and transcription were overrepresented in DEGs higher in abundance in NM dry seeds. DEGs amongst these GO terms included ribosomal proteins and histones (higher in M + ), RNA polymerase II subunits and related transcription and elongation factors (higher in NM). Expression of the inferred DEGs and other genes associated with seed maturation (e.g. those encoding late embryogenesis abundant proteins and transcription factors regulating seed development and maturation such as ABI3, FUS3, LEC1 and WRI1 homologs) were put in context with Arabidopsis thaliana seed maturation and indicated that M + seeds may desiccate and mature faster than NM. The 1901 transcriptomic DEG set GO-terms had almost 90% overlap with the 2191 genome-derived DEG GO-terms. Conclusions Whilst there was only modest overlap of DEGs identified in reference-free versus -dependent approaches, the resulting GO analysis was concordant in both approaches. The identified differences in dry seed transcriptomes suggest mechanisms underpinning previously identified contrasts between morphology and germination behaviour of M + and NM seeds.

The olive (Olea europaea L.) is an ancient crop of great importance in the Mediterranean basin due to the production of olive oil and table olives, which are important sources of fat and have benefits for human health. This crop is expanding and increasing its production worldwide and five olive genomes have recently been sequenced, representing a wild olive and important cultivars in terms of olive oil production, intensive agriculture, and adaptation to the East Asian climate. However, few bioinformatic and genomic resources are available to assist olive research and breeding, and there are no platforms to query olive gene expression data. Here, we present OliveAtlas, an interactive gene expression atlas for olive with multiple bioinformatics tools and visualization methods, enabling multiple gene comparison, replicate inspection, gene set enrichment, and data downloading. It contains 70 RNA-seq experiments, organized in 10 data sets representing the main olive plant organs, the pollen germination and pollen tube elongation process, and the response to a collection of biotic and abiotic stresses, among other experimental conditions. OliveAtlas is a web tool based on easyGDB with expression data based on the ‘Picual’ genome reference and gene annotation.

The pollen tube is a key innovation of land plants that is essential for successful fertilisation. Its development and growth have been profusely studied in model organisms, but in spite of the economic impact of olive trees, little is known regarding the genome-wide events underlying pollen hydration and growth in this species. To fill this gap, triplicate mRNA samples at 0, 1, 3, and 6 h of in vitro germination of olive cultivar Picual pollen were analysed by RNA-seq. A bioinformatics R workflow called RSeqFlow was developed contemplating the best practices described in the literature, covering from expression data filtering to differential expression and clustering, to finally propose hub genes. The resulting olive pollen transcriptome consisted of 22,418 reliable transcripts, where 5364 were differentially expressed, out of which 173 have no orthologue in plants and up to 3 of them might be pollen-specific transcription factors. Functional enrichment revealed a deep transcriptional reprogramming in mature olive pollen that is also dependent on protein stability and turnover to allow pollen tube emergence, with many hub genes related to heat shock proteins and F-box-containing proteins. Reprogramming extends to the first 3 h of growth, including processes consistent with studies performed in other plant species, such as global down-regulation of biosynthetic processes, vesicle/organelle trafficking and cytoskeleton remodelling. In the last stages, growth should be maintained from persistent transcripts. Mature pollen is equipped with transcripts to successfully cope with adverse environments, even though the in vitro growth seems to induce several stress responses. Finally, pollen-specific transcription factors were proposed as probable drivers of pollen germination in olive trees, which also shows an overall increased number of pollen-specific gene isoforms relative to other plants.