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Abstract Eucalyptus grandis is a hardwood tree used worldwide as pure species or hybrid partner to breed fast-growing plantation forestry crops that serve as feedstocks of timber and lignocellulosic biomass for pulp, paper, biomaterials, and biorefinery products. The current v2.0 genome reference for the species served as the first reference for the genus and has helped drive the development of molecular breeding tools for eucalypts. Using PacBio HiFi long reads and Omni-C proximity ligation sequencing, we produced an improved, haplotype-phased assembly (v4.0) for TAG0014, an early-generation selection of E. grandis. The 2 haplotypes are 571 Mbp (HAP1) and 552 Mbp (HAP2) in size and consist of 37 and 46 contigs scaffolded onto 11 chromosomes (contig N50 of 28.9 and 16.7 Mbp), respectively. These haplotype assemblies are 70–90 Mbp smaller than the diploid v2.0 assembly but capture all except one of the 22 telomeres, suggesting that substantial redundant sequence was included in the previous assembly. A total of 35,929 (HAP1) and 35,583 (HAP2) gene models were annotated, of which 438 and 472 contain long introns (>10 kbp) in gene models previously (v2.0) identified as multiple smaller genes. These and other improvements have increased gene annotation completeness levels from 93.8 to 99.4% in the v4.0 assembly. We found that 6,493 and 6,346 genes are within tandem duplicate arrays (HAP1 and HAP2, respectively, 18.4 and 17.8% of the total) and >43.8% of the haplotype assemblies consists of repeat elements. Analysis of synteny between the haplotypes and the E. grandis v2.0 reference genome revealed extensive regions of collinearity, but also some major rearrangements, and provided a preview of population and pangenome variation in the species. 

Abstract Research in Arabidopsis thaliana has a powerful influence on our understanding of gene functions and pathways. However, not everything translates from Arabidopsis to crops and other plants. Here, a group of experts consider instances where translation has been lost and why such translation is not possible or is challenging. First, despite great efforts, floral dip transformation has not succeeded in other species outside Brassicaceae. Second, due to gene duplications and losses throughout evolution, it can be complex to establish which genes are orthologs of Arabidopsis genes. Third, during evolution Arabidopsis has lost arbuscular mycorrhizal symbiosis. Fourth, other plants have evolved specialized cell types that are not present in Arabidopsis. Fifth, similarly, C4 photosynthesis cannot be studied in Arabidopsis, which is a C3 plant. Sixth, many other plant species have larger genomes, which has given rise to innovations in transcriptional regulation that are not present in Arabidopsis. Seventh, phenotypes such as acclimation to water stress can be challenging to translate due to different measurement strategies. And eighth, while the circadian oscillator is conserved, there are important nuances in the roles of circadian regulators in crop plants. A key theme emerging across these vignettes is that even when translation is lost, insights can still be gained through comparison with Arabidopsis. 

Abstract Ancient whole-genome duplications (WGDs) are believed to facilitate novelty and adaptation by providing the raw fuel for new genes. However, it is unclear how recent WGDs may contribute to evolvability within recent polyploids. Hybridization accompanying some WGDs may combine divergent gene content among diploid species. Some theory and evidence suggest that polyploids have a greater accumulation and tolerance of gene presence-absence and genomic structural variation, but it is unclear to what extent either is true. To test how recent polyploidy may influence pangenomic variation, we sequenced, assembled, and annotated twelve complete, chromosome-scale genomes of Camelina sativa, an allohexaploid biofuel crop with three distinct subgenomes. Using pangenomic comparative analyses, we characterized gene presence-absence and genomic structural variation both within and between the subgenomes. We found over 75% of ortholog gene clusters are core in Camelina sativa and <10% of sequence space was affected by genomic structural rearrangements. In contrast, 19% of gene clusters were unique to one subgenome, and the majority of these were Camelina-specific (no ortholog in Arabidopsis). We identified an inversion that may contribute to vernalization requirements in winter-type Camelina, and an enrichment of Camelina-specific genes with enzymatic processes related to seed oil quality and Camelina’s unique glucosinolate profile. Genes related to these traits exhibited little presence-absence variation. Our results reveal minimal pangenomic variation in this species, and instead show how hybridization accompanied by WGD may benefit polyploids by merging diverged gene content of different species. 

Abstract Cotton (Gossypium hirsutumL.) is the key renewable fibre crop worldwide, yet its yield and fibre quality show high variability due to genotype-specific traits and complex interactions among cultivars, management practices and environmental factors. Modern breeding practices may limit future yield gains due to a narrow founding gene pool. Precision breeding and biotechnological approaches offer potential solutions, contingent on accurate cultivar-specific data. Here we address this need by generating high-quality reference genomes for three modern cotton cultivars (‘UGA230’, ‘UA48’ and ‘CSX8308’) and updating the ‘TM-1’ cotton genetic standard reference. Despite hypothesized genetic uniformity, considerable sequence and structural variation was observed among the four genomes, which overlap with ancient and ongoing genomic introgressions from ‘Pima’ cotton, gene regulatory mechanisms and phenotypic trait divergence. Differentially expressed genes across fibre development correlate with fibre production, potentially contributing to the distinctive fibre quality traits observed in modern cotton cultivars. These genomes and comparative analyses provide a valuable foundation for future genetic endeavours to enhance global cotton yield and sustainability. 

Leaf fungal microbiomes can be fundamental drivers of host plant success, as they contain pathogens that devastate crop plants and taxa that enhance nutrient uptake, discourage herbivory, and antagonize pathogens. We measured leaf fungal diversity with amplicon sequencing across an entire growing season in a diversity panel of switchgrass ( Panicum virgatum ). We also sampled a replicated subset of genotypes across 3 additional sites to compare the importance of time, space, ecology, and genetics. We found a strong successional pattern in the microbiome shaped both by host genetics and environmental factors. Further, we used genome-wide association (GWA) mapping and RNA sequencing to show that 3 cysteine-rich receptor-like kinases (crRLKs) were linked to a genetic locus associated with microbiome structure. We confirmed GWAS results in an independent set of genotypes for both the internal transcribed spacer (ITS) and large subunit (LSU) ribosomal DNA markers. Fungal pathogens were central to microbial covariance networks, and genotypes susceptible to pathogens differed in their expression of the 3 crRLKs, suggesting that host immune genes are a principal means of controlling the entire leaf microbiome. 

Abstract Peatlands are crucial sinks for atmospheric carbon but are critically threatened due to warming climates.Sphagnum(peat moss) species are keystone members of peatland communities where they actively engineer hyperacidic conditions, which improves their competitive advantage and accelerates ecosystem-level carbon sequestration. To dissect the molecular and physiological sources of this unique biology, we generated chromosome-scale genomes of twoSphagnumspecies:S. divinumandS. angustifolium.Sphagnumgenomes show no gene colinearity with any other reference genome to date, demonstrating thatSphagnumrepresents an unsampled lineage of land plant evolution. The genomes also revealed an average recombination rate an order of magnitude higher than vascular land plants and short putative U/V sex chromosomes. These newly described sex chromosomes interact with autosomal loci that significantly impact growth across diverse pH conditions. This discovery demonstrates that the ability ofSphagnumto sequester carbon in acidic peat bogs is mediated by interactions between sex, autosomes and environment. 

Water shortages caused by droughts lead to crop losses that affect billions of people around the world each year. By discovering how wild plants adapt to drought, it may be possible to identify traits and genes that help to improve the growth of crop plants when water is scarce. It has been suggested that plants have adapted to droughts by flowering at times of the year when droughts are less likely to occur. For example, if droughts are more likely to happen in spring, the plants may delay flowering until the summer. Arabidopsis thaliana is a small plant that is found across Eurasia, Africa and North America, including in areas that are prone to drought at different times of the year. Individual plants of the same species may carry different versions of the same gene (known as alleles). Some of these alleles may not work properly and are referred to as loss-of-function alleles. Monroe et al. investigated whether A. thaliana plants carry any loss-of-function alleles that are associated with droughts happening in the spring or summer, and whether they are linked to when those plants will flower. Monroe et al. analyzed satellite images collected over the last 30 years to measure when droughts have occurred. Next, they searched genome sequences of Arabidopsis thaliana for alleles that might help the plants to adapt to droughts in the spring or summer. Combining the two approaches revealed that loss-of-function alleles associated with spring droughts were strongly predicted to be associated with the plants flowering later in the year. Similarly, loss-of-function alleles associated with summer droughts were predicted to be associated with the plants flowering earlier in the year. These findings support the idea that plants can adapt to drought by changing when they produce flowers, and suggest that loss-of-function alleles play a major role in this process. New techniques for editing genes mean it is easier than ever to generate new loss-of-function alleles in specific genes. Therefore, the results presented by Monroe et al. may help researchers to develop new varieties of crop plants that are better adapted to droughts. 

Abstract The large size and complexity of most fern genomes have hampered efforts to elucidate fundamental aspects of fern biology and land plant evolution through genome-enabled research. Here we present a chromosomal genome assembly and associated methylome, transcriptome and metabolome analyses for the model fern species Ceratopteris richardii . The assembly reveals a history of remarkably dynamic genome evolution including rapid changes in genome content and structure following the most recent whole-genome duplication approximately 60 million years ago. These changes include massive gene loss, rampant tandem duplications and multiple horizontal gene transfers from bacteria, contributing to the diversification of defence-related gene families. The insertion of transposable elements into introns has led to the large size of the Ceratopteris genome and to exceptionally long genes relative to other plants. Gene family analyses indicate that genes directing seed development were co-opted from those controlling the development of fern sporangia, providing insights into seed plant evolution. Our findings and annotated genome assembly extend the utility of Ceratopteris as a model for investigating and teaching plant biology.