Biology subjects

Fechete, L. I.

Publications and source records attributed to Fechete, L. I..

6 recordsLinked to original sources

bioRxiv2026

Specialised root hair cells facilitate rhizobial infection

Legumes establish symbiotic partnerships with soil bacteria that convert atmospheric nitrogen into plant-available forms. Symbiotic bacteria enter through root hairs following recognition by cell surface receptors that help identify compatible symbionts. However, many root hairs express these receptors, and it has long remained unclear why only a small fraction become infected. Here, we use single-cell transcriptomics to show that legumes pre-specify a rare root hair population for infection before bacterial contact. These susceptible root hairs represent less than one percent of the total, express infection-associated genes prior to encountering symbionts and are conserved in distantly related legumes. Their abundance is regulated by the hormone ethylene and correlates with infection capacity. Our findings reveal that root hair cells do not respond uniformly to symbionts but are instead transcriptionally specialised in advance to control infection entry points. This pre-specification provides a mechanism to balance symbiotic benefits against pathogen infection risks and may exemplify a more general strategy used by multicellular hosts to spatially restrict microbial access.

plant biology↗

bioRxiv2025

A high-quality genome assembly and integrative data portal (Phabase) for the Mesoamerican black bean (Phaseolus vulgaris cv. Negro Jamapa)

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 statementIn 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.

plant biology↗

bioRxiv2025

RHD6LA regulates root hair responses to both symbionts and commensals

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 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 new mechanisms for microbial discrimination in rhizobium-responsive root hairs.

molecular biology↗

bioRxiv2022

Single-cell analysis maps distinct cellular responses to rhizobia and identifies the novel infection regulator SYMRKL1 in Lotus japonicus

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.

plant biology↗

bioRxiv2022

The giant diploid faba genome unlocks variation in a global protein crop

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.

plant biology↗

bioRxiv2022

Genetic analysis of global faba bean germplasm maps agronomic traits and identifies strong selection signatures for geographical origin

Faba bean (Vicia faba L.) is a high-protein grain legume crop with great potential for further cultivation. However, little is known about the genetics underlying trait diversity. In this study, we use 21,345 high-quality SNP markers to genetically characterise 2,678 faba bean genotypes. We perform genome-wide association studies of key agronomic traits using a Seven-parent-MAGIC population and detect 238 significant marker-trait associations linked to 12 traits of agronomic importance, with 65 of these being stable across multiple environments. Using a non-redundant diversity panel of 685 accessions from 52 countries, we identify 3 subpopulations differentiated by geographical origin and 33 genomic regions subject to strong diversifying selection between subpopulations. We find that SNP markers associated with the differentiation of northern and southern accessions were able to explain a significant proportion of agronomic trait variance in the Seven-parent-MAGIC population, suggesting that some of these traits have played an important role in breeding. Altogether, our findings point to genomic regions associated with important agronomic traits and selection in faba bean, which can be used for breeding purposes. Key MessageWe identified marker-trait associations for key faba bean agronomic traits and genomic signatures of selection within a global germplasm collection.

genetics↗