MATHLOUTHI, N. E. H. | Search bioRxiv

bioRxiv2026

First high-quality genome assemblies with chromosome-scale contiguity of Tunisian durum wheat (Triticum turgidum subsp. durum) landraces Chili and Mahmoudi

Durum wheat (Triticum turgidum subsp. durum) is a globally important crop for pasta and couscous production. Chili and Mahmoudi are historically significant Tunisian landraces valued for exceptional grain quality, high protein content, and adaptation to arid Mediterranean climates, yet no high-quality reference genome assemblies were available for either variety before this work. We assembled both genomes using publicly available PacBio HiFi long reads and Illumina Hi-C proximity ligation data (NCBI BioProject PRJNA1420514), with hifiasm v0.25.0 in primary mode and YaHS v1.2a.2 for Hi-C scaffolding. Assembly quality was assessed with QUAST v5.3.0 and BUSCO v5.8.0 (embryophyta_odb10 lineage). The Chili assembly spans 10.84 Gbp (scaffold N50 756.2 Mbp, BUSCO 99.4%) and Mahmoudi spans 10.70 Gbp (scaffold N50 756.8 Mbp, BUSCO 99.3%). Merqury v1.3 confirmed high base accuracy (QV 68.0 and 68.3, respectively) and k-mer completeness exceeding 98% for both. Independent validation with wfmash yielded 98.6% mean alignment identity across 11,172 chromosome-to-reference alignments. Post-assembly characterization encompassed GC profiling, centromere architecture, ribosomal DNA arrays, and structural variation. Both assemblies substantially exceed the contiguity of existing durum wheat references and represent the first chromosome-scale genomic resources for North African durum wheat landraces. Automated Hi-C scaffolding produced a small number of scaffolds spanning multiple chromosomes, which we resolved by alignment-guided splitting against the Svevo v2 reference, yielding 14 chromosome-scale pseudomolecules per landrace (largest 858.7 Mbp Chili, 868.1 Mbp Mahmoudi). Assemblies and pseudomolecules are available from Zenodo (10.5281/zenodo.20366290). The entire workflow was executed reproducibly on the public Galaxy Europe platform, demonstrating that reference-quality plant genome assembly is achievable without local HPC infrastructure. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=151 HEIGHT=200 SRC="FIGDIR/small/727644v4_ufig1.gif" ALT="Figure 1"> View larger version (52K): org.highwire.dtl.DTLVardef@d6f244org.highwire.dtl.DTLVardef@1bb8a49org.highwire.dtl.DTLVardef@173e577org.highwire.dtl.DTLVardef@1ddea6c_HPS_FORMAT_FIGEXP M_FIG C_FIG Key messageFirst chromosome-scale genome assemblies of the Tunisian durum wheat landraces Chili and Mahmoudi, with comprehensive structural characterization, an alignment-guided chromosome-resolution step that delivers 14 pseudomolecules per landrace, and k-mer-based polyploid assignment on consumer hardware.

genomics↗

bioRxiv2026

Unlocking Open-Access Genomic and Transcriptomic Data: The First Bioinformatic Exploitation of Tunisian Durum Wheat Landraces Chili and Mahmoudi, Pioneering Data-Driven Research in North Africa

Durum wheat (Triticum turgidum subsp. durum) is a Mediterranean dietary staple threatened by accelerating climate change, yet the genomic basis of adaptation in North African landraces remains poorly characterised. We present the first integrated whole-genome sequencing (WGS) and RNA-seq study of two contrasting Tunisian landraces: humid-adapted Chili and arid-adapted Mahmoudi. From 27,777 high-confidence SNPs, permutation-based F[~]ST[~] outlier analysis (1,000 shuffles) identified 46 selection hotspots across six chromosomes, with a peak signal on chromosome 6B (F[~]ST[~] = 0.833; p = 0.013). Constitutive transcriptome profiling (38,159 expressed genes) revealed 406 expression-divergent observations (|log{square}FC|{square}>{square}1) between landraces. Physical co-localisation analysis confirmed that 99.5% of expression-divergent observations are independent of selection hotspots, implicating trans-regulatory rewiring as the dominant adaptive mechanism. Trans-regulated genes are significantly enriched for disease-resistance (NBS-LRR, RLK, PR; FDR = 1.4 x 10{square}{square}) and ubiquitin-proteasome components (FDR = 0.049). Mahmoudi constitutively upregulates ROS-scavenging and dehydrin networks ("store-and-protect"), while Chili elevates aquaporins and transcription factors ("acquire-and-distribute"). These findings identify six chromosomal breeding targets, establish chromosome 6B as a priority fine-mapping locus, and demonstrate that arid-zone adaptation is orchestrated primarily through trans-regulatory stress-network rewiring.

bioinformatics↗