Increasing the proportion of locally produced plant protein in currently meat-rich diets could substantially reduce greenhouse gas emissions and loss of biodiversity¹. However, plant protein production is hampered by the lack of a cool-season legume equivalent to soybean in agronomic value². Faba bean (Vicia fabaL.) has a high yield potential and is well suited for cultivation in temperate regions, but genomic resources are scarce. Here, we report a high-quality chromosome-scale assembly of the faba bean genome and show that it has expanded to a massive 13 Gb in size through an imbalance between the rates of amplification and elimination of retrotransposons and satellite repeats. Genes and recombination events are evenly dispersed across chromosomes and the gene space is remarkably compact considering the genome size, although with substantial copy number variation driven by tandem duplication. Demonstrating practical application of the genome sequence, we develop a targeted genotyping assay and use high-resolution genome-wide association analysis to dissect the genetic basis of seed size and hilum colour. The resources presented constitute a genomics-based breeding platform for faba bean, enabling breeders and geneticists to accelerate the improvement of sustainable protein production across the Mediterranean, subtropical and northern temperate agroecological zones.

Legume-rhizobium signaling during establishment of symbiotic nitrogen fixation restricts rhizobium colonization to specific cells. A limited number of root hair cells allow infection threads to form, and only a fraction of the epidermal infection threads progress to cortical layers to establish functional nodules. Here we use single-cell analysis to define the epidermal and cortical cell populations that respond to and facilitate rhizobium infection. We then identify high-confidence nodulation gene candidates based on their specific expression in these populations, pinpointing genes stably associated with infection across genotypes and time points. We show that one of these, which we name SYMRKL1, encodes a protein with an ectodomain predicted to be nearly identical to that of SYMRK and is required for normal infection thread formation. Our work disentangles cellular processes and transcriptional modules that were previously confounded due to lack of cellular resolution, providing a more detailed understanding of symbiotic interactions.

Allotetraploid white clover (Trifolium repens) formed during the last glaciation through hybridisation of two European diploid progenitors from restricted niches: one coastal, the other alpine. Here, we examine which hybridisation‐derived molecular events may have underpinned white clover's postglacial niche expansion. We compared the transcriptomic frost responses of white clovers (an inbred line and an alpine‐adapted ecotype), extant descendants of its progenitor species and a resynthesised white clover neopolyploid to identify genes that were exclusively frost‐induced in the alpine progenitor and its derived subgenomes. From these analyses we identified galactinol synthase, the rate‐limiting enzyme in biosynthesis of the cryoprotectant raffinose, and found that the extant descendants of the alpine progenitor as well as the neopolyploid white clover rapidly accumulated significantly more galactinol and raffinose than the coastal progenitor under cold stress. The frost‐induced galactinol synthase expression and rapid raffinose accumulation derived from the alpine progenitor likely provided an advantage during early postglacial colonisation for white clover compared to its coastal progenitor.

Increasing the proportion of locally produced plant protein in currently meat-rich diets could substantially reduce greenhouse gas emission and loss of biodiversity. However, plant protein production is hampered by the lack of a cool-season legume equivalent to soybean in agronomic value. Faba bean ( Vicia faba L.) has a high yield potential and is well-suited for cultivation in temperate regions, but genomic resources are scarce. Here, we report a high-quality chromosome-scale assembly of the faba bean genome and show that it has grown to a massive 13 Gb in size through an imbalance between the rates of amplification and elimination of retrotransposons and satellite repeats. Genes and recombination events are evenly dispersed across chromosomes and the gene space is remarkably compact considering the genome size, though with significant copy number variation driven by tandem duplication. Demonstrating practical application of the genome sequence, we develop a targeted genotyping assay and use high-resolution genome-wide association (GWA) analysis to dissect the genetic basis of hilum colour. The resources presented constitute a genomics-based breeding platform for faba bean, enabling breeders and geneticists to accelerate improvement of sustainable protein production across Mediterranean, subtropical, and northern temperate agro-ecological zones.

While intracellular symbiosis with rhizobia relies on Nod factor signaling through the conserved common symbiosis signaling pathway (CSSP), it remains unclear how legumes simultaneously manage interactions with commensal soil microbes. Using single cell RNA-sequencing, we show that commensal soil bacteria induce a Nod factor-independent transcriptional response in specific root hairs. This response is similar to the rhizobium response in the CSSP-deficient cyclops mutant, which is unable to accommodate rhizobia in root hair infection threads. Both responses include the nodulation gene NODULATION SIGNALING PATHWAY 2 ( NSP2 ) and a transcription factor, which we name ROOT HAIR DEFECTIVE 6 LIKE A ( RHD6LA ). We show that RHD6LA is required for facilitating infection thread formation in response to rhizobia and for preventing exaggerated root hair responses to commensal soil bacteria. The overlap between commensal and symbiotic signaling highlights the complexity of legume-microbe interactions at the root hair interface and suggests additional mechanisms for microbial discrimination in rhizobium-responsive root hairs.

Summary: Common bean ( Phaseolus vulgaris L.) is one of the major legume crops worldwide, constituting a fundamental part of the diet in several countries. In central and south Mexico, the Mesoamerican Negro Jamapa variety is the one of most widely consumed cultivar, and it has notably served as a working model for functional genomics to address the molecular responses to stresses and during the nitrogen-fixing symbiosis with rhizobia. Despite this, the genome sequence of this landrace is not yet available, and the transcriptomic data generated by different research groups on this species are scattered. This prompted us to carry out a de novo sequencing, assembly and gene prediction for Negro Jamapa genome, using Hi-Fi PacBio technology and advanced genomic tools, respectively. Herein, we present a high-quality genome assembly for Negro Jamapa at chromosome level. The assembled genome is 522 Mb length, with an N50 of 45Mb, 89X coverage and BUSCO completeness of 98.4%, parameters that are considerably better than the available Mesoamerican reference genome. In parallel, we built an expression atlas of P. vulgaris from various tissues and growth conditions, by re-mapping publicly available RNA-seq and small RNA-seq data produced in recent years by distinct research groups. This analysis is available for the scientific community in the new user-friendly portal developed in this study, Phabase ( https://phabase.ccg.unam.mx/ ). This portal includes several tools such as BLAST, gene and microRNA expression atlas, JBrowse, download section and integration with other Phaseolus spp. genomes. Significance statement: In this study we report the first genome sequence of Phaseolus vulgaris Negro Jamapa, one of the most widely consumed bean varieties and a key experimental model for multiple research groups. We also developed Phabase (Phabase), an integrated database hosting this genome together with BLAST, JBrowse, and a comprehensive expression atlas. This resource enables functional genomics, comparative analyses, and accelerated breeding of common bean.