Biology subjects

Werle Noe, I.

Publications and source records attributed to Werle Noe, I..

2 recordsLinked to original sources

bioRxiv2026

Chromosome-level genome assemblies and annotations of Amaranthus spinosus, Amaranthus acanthochiton, Amaranthus arenicola, and Amaranthus floridanus

Amaranthus L. spans aggressive agricultural weeds, ornamentals, and ancient pseudocereals. Species within the genus vary in morphology, environmental tolerance, and sexual systems, making them well-suited for studying reproductive evolution and plant adaptation. To investigate sex chromosome architecture within the genus, we generated chromosome-level assemblies of a monoecious amaranth (Amaranthus spinosus) and three dioecious species (A. acanthochiton, A. arenicola, and A. floridanus) using PacBio high-fidelity (HiFi) long reads. We paired these data with Dovetail Genomics Omni-C sequencing to achieve haplotype resolution for A. spinosus and A. acanthochiton, and we used reference-guided scaffolding for the remaining two species. The assemblies are highly contiguous, with sizes ranging from 394.24 to 607.10 Mbp, contig N50 from 0.63 to 8.76 Mbp, and scaffold N50 from 22.44 to 37.97 Mbp. Evaluation of the assemblies and annotations revealed 96.3 to 97.6%, and 97.6 to 98.3% BUSCO completeness, respectively. Comparative genomic analysis revealed that the Chromosome 1 inversions and Robertsonian fusion previously reported in A. tuberculatus are conserved in A. acanthochiton and consistent with the architecture of A. arenicola and A. floridanus, suggesting that the evolution of dioecy in this clade predates subsequent speciation. In parallel, multiple homologs of Rf1 on Chromosome 3 of A. spinosus, a monoecious species that exhibits spatial separation of male and female flowers and is closely related to the dioecious A. palmeri, were identified. Together, this study provides foundational resources for advancing evolutionary, ecological, and agronomic research across the genus, including herbicide resistance evolution and weediness traits.

genomics↗

bioRxiv2026

Resistance to protoporphyrinogen oxidase inhibitor herbicides in giant ragweed (Ambrosia trifida) is associated with a novel R98Q target-site mutation in PPO2

BACKGROUNDReduced control of giant ragweed (Ambrosia trifida L.) with protoporphyrinogen oxidase (PPO)-inhibiting herbicides was recently reported in two southern Illinois populations, VRC and TMS. The objectives of this study were to assess resistance to postemergence-applied PPO inhibitors in VRC and TMS, evaluate VRC response to acetolactate synthase (ALS)- and enolpyruvyl shikimate phosphate synthase (EPSPS)-inhibiting herbicides, and identify target-site mechanisms associated with PPO-inhibitor resistance. RESULTSBased on LD estimates, VRC resistance ratios ranged from 1.1- to 3.7-fold for lactofen and 2.2- to 6.9-fold for fomesafen relative to PPO-sensitive populations SIU and DSO. In TMS, LD estimates were 257.4 g ai ha {superscript 1} for lactofen and 318.4 g ai ha {superscript 1} for fomesafen. Glyphosate LD estimates exceeded three times the labeled field rate in VRC, SIU, and DSO, whereas VRC and SIU had higher cloransulam-methyl LD estimates than DSO. Whole-transcriptome sequencing identified polymorphisms in PPX1 and PPX2; however, only PPO2 R98Q altered a catalytic-domain binding-pocket residue and was considered likely to contribute to resistance in VRC. R98Q was absent in TMS, and PPX1 and PPX2 expression did not differ among populations. CONCLUSIONVRC and TMS have evolved resistance to lactofen and fomesafen, and VRC also exhibited reduced sensitivity to cloransulam-methyl and glyphosate. PPO2 R98Q is novel in A. trifida and, to our knowledge, represents the first report of this mutation associated with PPO-inhibitor resistance in plants. The absence of target-site alterations in TMS suggests a potential non-target-site basis for resistance. These findings highlight the need for integrated, diversified management to further reduce herbicide selection pressure.

plant biology↗