Veeckman, E. | Search bioRxiv

bioRxiv2026

Plant LETM1 homologs are required for fungus-induced antibiotic resistance and biostimulation

Our findings confirm that CIRA15A / LEUCINE ZIPPER-EF-HAND CONTAINING TRANSMEMBRANE PROTEIN1 (LETM1) is critical for Trichoderma-induced growth biostimulation in sugar beet and the Cellulase-Induced Resistance to Alamethicin (CIRA) response in Arabidopsis. Notably, this plant homolog of a gene associated with human disease plays a vital role in both defense against Trichoderma antimicrobial peptides and the biostimulation of plant growth. We identified AtCIRA15A/LETM1 and AtCIRA15B/LETM2 as key genetic determinants of CIRA through Arabidopsis analysis and comparative studies of sugar beet inbred lines. BvLETM1 allelic variations correlated with differential biostimulation responses, and complementation confirmed functional LETM1 alleles restore CIRA in Arabidopsis mutants. These findings highlight LETM1 as a crucial factor in Trichoderma-plant interactions, with potential applications in breeding for enhanced microbial-induced plant biostimulation and agricultural productivity.

plant biology↗

bioRxiv2022

Stack Mapping Anchor Points (SMAP): a versatile suite of tools for read-backed haplotyping

Here we present SMAP, a software package that implements a suite of computational tools to extract multi-allelic haplotypes using read-backed haplotyping. SMAP tools first perform accurate read processing and analyze read mapping distributions across sample sets. Then, two complementary modules can be invoked for haplotype calling: SMAP haplotype-sites combines known Single Nucleotide Polymorphisms (SNPs) and/or read mapping position polymorphisms (SMAPs) to reconstruct compressed, read-reference-encoded haplotype strings. In contrast, SMAP haplotype-window works independent of prior knowledge of polymorphisms, groups reads by locus, defines a window enclosed between two custom border sequences, and retains the entire corresponding DNA sequence as haplotype. Haplotype-window is, among many applications, especially useful for high-throughput CRISPR/Cas mutation screens. Either way, SMAP creates a single integrated haplotype call table across all loci and samples. SMAP haplotyping is extremely versatile and can be applied to highly multiplex amplicon sequencing (HiPlex), Shotgun (e.g. whole genome shotgun (WGS) sequencing, probe capture and RNA-Seq), or Genotyping-by-Sequencing (GBS) data; and to Illumina short reads, PacBio and MinION long reads. SMAP creates discrete genotype calls for individuals of any ploidy or quantitative haplotype frequency spectra for Pool-Seq data, and can scale from tens to thousands of loci and/or samples. SMAP, including the source code written in Python is available at https://gitlab.com/truttink/smap, and a detailed user manual and guidelines for accurate read processing is available at https://ngs-smap.readthedocs.io/, under the GNU Affero General Public License v3.0.

genomics↗