Biology subjects

Montiel, J.

Publications and source records attributed to Montiel, J..

6 recordsLinked to original sources

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

The Lotus japonicus alpha Expansin EXPA1 is recruited during intracellular and intercellular rhizobial colonization

Most legumes establish a mutualistic association with rhizobia, a group of nitrogen-fixing bacteria. In Lotus japonicus, the symbiotic colonization occurs intracellularly, via root-hair infection threads by Mesorhizobium loti, or intercellularly, with Agrobacterium pusense IRBG74. In both mechanisms, cell wall remodeling is presumably an essential process. In plants, alpha-Expansins (EXPA) promote cell wall loosening by non-enzymatically triggering a pH-dependent relaxation. In this study, we show that LjEXPA1, is critical for the intracellular and intercellular symbiotic program in L. japonicus. Promoter activity and subcellular localization analyses revealed that EXPA1 is recruited at essential compartments and structures of epidermal and cortical cells in both mechanisms of rhizobial infection, such as the infection chambers, infection pockets and transcellular infection threads. Additionally, EXPA1-YFP abundantly accumulated in dividing cortical cells during nodule formation. The expression profile of EXPA1 correlates with the symbiotic phenotype observed in homozygous mutants disrupted in the EXPA1 gene (expA1-1 and expA1-2). Infection thread formation and intercellular colonization was drastically reduced in expA1-1 and expA1-2 mutants, respect to wild type plants. Similarly, nodule formation was significantly reduced in these mutants after M. loti or IRBG74 inoculation. Our results indicate that non-enzymatic cell wall remodeling by the alpha Expansin EXPA1 is crucial for the successful establishment of Lotus-rhizobia symbiosis, regardless of the infection mechanism.

plant 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

Aromatic amino acid biosynthesis by a Lotus Aldolase impacts root hair development and symbiotic associations

O_LILegume roots can be symbiotically colonized by arbuscular mycorrhizal (AM) fungi and nitrogen-fixing bacteria. In Lotus japonicus, the latter occurs intracellularly by the cognate rhizobial partner Mesorhizobium loti or intercellularly with the Agrobacterium pusense IRBG74 strain. Although these symbiotic programs show distinctive cellular and transcriptome signatures, some molecular components are shared. C_LIO_LIIn this study, we demonstrate that Aldolase1, the first enzyme in the biosynthetic pathway of aromatic amino acids (AAA), plays a critical role in root hair development and for AM and rhizobial symbioses in Lotus. C_LIO_LITwo homozygous mutants affected in Aldolase1 (ald1-1 and ald1-2) show drastic alterations in the root hair morphology, associated with a progressive disruption of the actin cytoskeleton. The altered root hair structure was prevented by chemical and genetic complementation. C_LIO_LIBoth ald1-1 and ald1-2 show significant reductions in rhizobial infection (intracellular and intercellular), nodule organogenesis and AM colonization. RNAseq analysis of ald1-2 roots suggested that these phenotypes are associated with downregulation of several cell wall related genes, and with an attenuated symbiotic signalling. This work provides robust evidence that links AAA metabolism to root hair development and successful symbiotic associations. C_LI

plant biology↗

bioRxiv2021

A promiscuity locus confers Lotus burttii nodulation with rhizobia from five different genera

Legumes acquire access to atmospheric nitrogen through nitrogen fixation by rhizobia in root nodules. Rhizobia are soil dwelling organisms and there is a tremendous diversity of rhizobial species in different habitats. From the legume perspective, host range is a compromise between the ability to colonize new habitats, where the preferred symbiotic partner may be absent, and guarding against infection by suboptimal nitrogen fixers. Here, we investigate natural variation in rhizobial host range across Lotus species. We find that Lotus burttii is considerably more promiscuous than Lotus japonicus, represented by the Gifu accession, in its interactions with rhizobia. This promiscuity allows Lotus burttii to form nodules with Mesorhizobium, Rhizobium, Sinorhizobium, Bradyrhizobium, and Allorhizobium species that represent five distinct genera. Using recombinant inbred lines, we have mapped the Gifu/burttii promiscuity QTL to the same genetic locus regardless of rhizobial genus, suggesting a general genetic mechanism for host-range expansion. The Gifu/burttii QTL now provides an opportunity for genetic and mechanistic understanding of promiscuous legume-rhizobia interactions.

plant biology↗

bioRxiv2020

Distinct signalling routes mediates intercellular and intracellular rhizobial infection in Lotus japonicus

Rhizobial infection of legume roots during development of nitrogen fixing root nodules occurs either intracellularly though plant derived infection threads traversing the epidermal and cortical cell layers to deliver the bacteria or intercellularly via bacterial entry between epidermal plant cells. Although, around 25% of all legume genera are postulated to be intercellularly infected, the pathways and mechanisms supporting this process has remained virtually unexplored due to lack of genetically amenable legumes that have this infection mode. In this study, we report that the model legume Lotus japonicus is infected intercellularly by Rhizobium sp. IRBG74 and demonstrate that the resources available in Lotus enable insight into the genetic requirements and the fine-tuning of the pathway governing intercellular infection. Inoculation of Lotus mutants shows that Ern1 and RinRK1 are dispensable for intercellular infection in contrast to intracellular infection. Other symbiotic genes, including Nfr5, SymRK, CCaMK, Epr3, Cyclops, Nin, Nsp1, Nsp2, Cbs and Vpy1 are equally important for both entry modes. Comparative RNAseq analysis of roots inoculated with IRBG74 revealed a distinctive transcriptome response compared to intracellular colonization. In particular, a number of cytokinin-related genes were differentially regulated. Corroborating this observation cyp735A and ipt4 cytokinin biosynthesis mutants were significantly affected in their nodulation with IRBG74 while lhk1 cytokinin receptor mutants did not form any nodules. These results indicate that a differential requirement for cytokinin signalling conditions intercellular rhizobial entry and highlight the distinct modalities of the inter- and intra-cellular infection mechanisms.

plant biology↗