Author

David Kopecký

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Open access Sep 2026

Chromosome-level, haplotype-resolved genome assembly of the tanniferous forage legume big trefoil (Lotus pedunculatus Cav.) using CiFi

Big trefoil (Lotus pedunculatus Cav.) is a perennial forage legume that thrives on acidic, low-fertility soils and produces condensed tannins that reduce enteric methanogenesis in ruminants. Despite this agronomic potential, genomic resources for the species remain scarce, and the existing haploid assembly does not resolve the two haplotypes of this outcrossing diploid species. Here we present a haplotype-resolved, chromosome-level reference genome for L. pedunculatus genotype Lusitano29 – the first plant genome assembled using CiFi, a long-read chromosome conformation capture method. We combined PacBio HiFi long reads with CiFi concatemers produced from DpnII and Hind III libraries; in silico digestion and combinatorial pairing of the resulting monomers yielded 790.3 M and 10.3 M pseudo-paired contacts, respectively, enabling scaffolding and manual curation to chromosome level. The 991.1 Mb assembly resolves two phased haplotypes of 500 and 491 Mb, with 96.6% of the sequence anchored in twelve pseudo-chromosomes (six per haplotype). Telomeric repeats were detected at 19 of 24 pseudo-chromosome ends, and no structural errors were detected (scaffold N50 73.8 Mb; consensus QV 64.7; k-mer completeness 99.4%; genome-mode BUSCO completeness 97.0%; CRAQ S-AQI 100.0). Annotation supported by PacBio Iso-Seq full-length transcripts predicted 38,069 and 36,484 protein-coding genes in haplotypes 1 and 2, respectively (protein-mode BUSCO completeness 96.5%), indicating a high completeness of annotated genes. This genome assembly provides a foundation for allele-aware trait dissection of proanthocyanidin biosynthesis, comparative genomics in Lotus, and population genomics and genomics-assisted breeding in L. pedunculatus.

Alexander T. Pettersson, Yu-Tang Chen, Tim Davalan et al. · bioRxiv · 0 citations

Open access Aug 2026

The afterlife of a horizontally transferred gene: Expansion and functional diversification of a C1A peptidase in wild Hordeum species

Abstract Horizontal gene transfer (HGT) can accelerate plant adaptation, but the evolutionary fate of newly acquired nuclear genes is often unclear. Here, we analyzed a papain‐like cysteine peptidase horizontally transferred from Panicoideae to wild Hordeum (Poaceae). Using chromosome‐level assemblies of 21 diploid Hordeum species, we assessed presence/absence, copy‐number variation, coding diversity, selection, predicted protein functionality, and expression. To infer donor relationships, we screened 77 Panicoideae accessions (48 species, 20 genera) by polymerase chain reaction and sequenced positive amplicons with Nanopore. The transferred locus, likely acquired as part of a larger panicoid DNA segment, is retained across Hordeum sect. Stenostachys but shows strong post‐transfer diversification, with 1–8 copies per species, extensive transposable‐element insertions, and numerous coding‐sequence variants. Close homologs in Panicoideae were rare and restricted to Panicum and Paspalum; gene trees identified Panicum bergii as the closest sampled relative. Selection analyses indicated heterogeneous constraints and episodic positive selection in some Hordeum lineages. Only a minority of copies retained an intact catalytic triad, whereas most were predicted to be pseudopeptidases. Transcripts were detected across species and tissues. These results indicate that an HGT‐derived DNA block can persist, amplify, and diversify in recipient genomes, generating raw material for later functional evolution.

V. Mahelka, P. Caklová, R. Čegan et al. · The Plant Genome · 0 citations