Biology subjects

Amiri, K. M.

Publications and source records attributed to Amiri, K. M..

4 recordsLinked to original sources

bioRxiv2026

Ommochrome pathway knockout via CRISPR/Cas9 reveals sex-linked eye pigmentation and establishes a heritable genome-editing platform in Rhynchophorus ferrugineus

The red palm weevil, Rhynchophorus ferrugineus, is the most economically destructive palm pest worldwide, threatening livelihoods, food security, and ecosystems across 49 countries. Weevil management currently relies predominantly on chemical insecticides, raising significant environmental and public health concerns. Despite its global agricultural importance, genetic approaches to pest management and the mechanistic basis of genome-editing strategies in Rhynchophorus remain largely unexplored. Here, we employed CRISPR/Cas9 genome editing to disrupt the R. ferrugineus ommochrome biosynthetic pathway -- a multi-enzymatic metabolic cascade that converts tryptophan into ommochrome pigments, including brown, yellow, and red pigments. We targeted two key pathway components: the ATP-binding cassette transporter white and the heme peroxidase cardinal. Both genes were ubiquitously expressed, with peak expression levels in the gut, fat body, and head. Elevated transcript levels were observed across early, mid, and late pupal stages and in 0-, 1-, and 2-day-old adult males and females, consistent with the progression of eye pigmentation throughout the R. ferrugineus life cycle. Embryonic microinjection of a single guide RNA (sgRNA)-Cas9 ribonucleoprotein complex targeting white produced in the Generation-0 (G0) adults with a distinct, white-eyed phenotype with a brownish outer margin, in contrast to the black eyes of wild-type adults. Genome-edited cardinal mutant adults displayed a translucent, brownish-white-eyed phenotype, with white streaks that gradually transitioned to a persistent translucent reddish-brown eye coloration. Mutations in both genes were confirmed in G0 adults by genomic DNA sequencing. Mutant adults were crossed to generate heterozygous G1 (+/-), G2 (-/-, -/+, and +/+), and G3 lines (-/-) with genotypes verified as carrying 2-, 3-, 9-, and 13-nucleotide deletions. A stable, heritable eye-color phenotype was established in homozygous knockout (-/-) G3 lines for both white and cardinal, confirmed by unambiguous indel (insertions/deletions) genotyping. Inheritance analysis revealed that both genes are X-linked, following a classical Mendelian sex-linked pattern: paternal alleles are transmitted exclusively to daughters, while maternal alleles are inherited equally by both daughters and sons. This study establishes the first fully homozygous knockout strain in R. ferrugineus and, by characterizing sex-linked inheritance in a coleopteran system, advances our understanding of how CRISPR/Cas9 can be efficiently applied to destructive palm weevil species. The present study represents the first report of CRISPR/Cas9 genome editing in any weevil (Curculionidae), using white and cardinal as marker genes. These findings provide a valuable platform for functional genomics and genome engineering in R. ferrugineus and offer a translational framework for genome editing in the invasive South American palm weevil, R. palmarum, laying a solid foundation for the development of gene-drive strategies aimed at sustainable palm weevil population control.

zoology↗

bioRxiv2026

Reversible chromatin remodeling enables Prosopis cineraria survival under recurrent heat extremes.

Recurrent seasonal heat and drought raise fundamental questions about how long-lived desert plants sustain physiological function across temperature extremes. We have used seasonal profiling at six time points with multilayered omics studies (Hi-C, transcriptomic, histone marks, and DNA methylation) to understand how Prosopis cineraria, a native Arabian desert legume tree, responds to different temperatures and the underlying mechanisms. A clear pattern emerges during peak heat. chromatin boundaries are selectively weakened, and candidate topological domains merge, activating clusters of heat-protective genes that gain active promoter and enhancer marks (H3K4me3 and H3K27ac). In the cool season, immune and developmental gene regulation is coupled with flowering, consistent with a temporal risk-strategy that shifts reproduction away from lethal heat. At the same time, promoter CHH methylation near transposable elements, together with reduced active promoter and enhancer marks (H3K4me3/H3K27ac), points to a proactive developmental phase rather than just surviving the stress. Integrating physiological data, we connect chromatin activation to an SA-ABA reciprocal seasonal profile, MIZ1-associated hydrotropism, and Stay-Green-mediated delayed senescence through chlorophyll retention. With Landscape genomics and phylogenetics, we further identified a housekeeping PEPC with a high predicted melting temperature that could sustain a malate-derived carbon supply, buffering metabolism under heat. Together, these findings reveal that reversible epigenetic gating enables desert trees to survive and recover from extreme seasonal stress.

plant biology↗

bioRxiv2026

Desert Cucurbit Microbiomes: Spatiotemporal Dynamics and Functional Adaptations

BackgroundPlant microbiomes can contribute to host adaptation in extreme environments, particularly deserts where high temperatures, intense radiation, water limitation, and nutrient-poor soils constrain plant survival. Citrullus colocynthis is a desert-adapted cucurbit with medicinal and agricultural relevance, yet integrated understanding of its microbiome across seasons, tissues, habitats, and functional traits remains limited. Here, we asked whether spatiotemporal microbiome dynamics in C. colocynthis are linked to microbial functional potential and cultivable traits relevant to persistence under arid conditions. ResultsTo address this, we profiled the microbiome of C. colocynthis across two sites, two seasons, and multiple compartments using 16S rRNA amplicon screening, shotgun metagenomics, culture-based phenotyping, and genome analysis. Amplicon profiling provided an exploratory framework and showed that plant-associated bacterial communities were shaped primarily by season and tissue type, with roots emerging as the most season-responsive compartment. Shotgun metagenomics confirmed stronger seasonal restructuring in root bacterial communities than in leaves and extended taxonomic profiling to fungal and archaeal fractions, which were interpreted descriptively because of low read representation. Summer root communities were enriched in actinobacterial genera, including Saccharopolyspora, Amycolatopsis, Pseudonocardia, and Nonomuraea, while functional profiling indicated coordinated shifts in central metabolism, cofactor salvage, exopolysaccharide-related pathways, and redox-associated functions. Twenty-four cultured bacterial isolates exhibited diverse stress-tolerance and plant growth-promoting traits, and whole-genome analyses identified biosynthetic, osmoprotective, oxidative-stress, and phytohormone-related gene content. Pangenome analysis of Pseudomonas orientalis revealed an open pangenome and lifestyle-associated accessory genes linked to host-associated functions. ConclusionsTogether, these findings connect seasonal bacterial community turnover, metagenomic functional potential, and cultivable microbial traits in a desert plant holobiont, highlighting desert-native bacteria and pathways relevant to microbiome-guided strategies for arid agriculture.

microbiology↗

bioRxiv2022

The multifaceted roles of R2R3 transcription factor HlMYB7 in the regulation of flavonoid and bitter acids pathways, development and biotic stress in hop (Humulus lupulus L.)

Hop (Humulus lupulus) biosynthesizes the highly economically valuable secondary metabolites, which include flavonoids, bitter acids, polyphenols and essential oils. These compounds have important pharmacological properties and are widely implicated in the brewing industry owing to bittering flavor, floral aroma and preservative activity. Our previous studies documented that ternary MYB-bHLH-WD40 (MBW) and binary WRKY1-WD40 (WW) protein complexes transcriptionally regulate the accumulation of bitter acid (BA) and prenylflavonoids (PF). In the present study, we investigated the regulatory functions of the R2R3-MYB repressor HlMYB7 transcription factor, which contains a conserved N-terminal domain along with the repressive motif EAR, in regulating the PF- and BA-biosynthetic pathway and their accumulation in hop. Constitutive expression of HlMYB7 resulted in transcriptional repression of structural genes involved in the terminal steps of biosynthesis of PF and BA, as well as stunted growth, delayed flowering, and reduced tolerance to viroid infection in hop. Furthermore, yeast two-hybrid and transient reporter assays revealed that HlMYB7 targets both PF and BA pathway genes and suppresses MBW and WW protein complexes. Heterologous expression of HlMYB7 leads to down-regulation of structural genes of flavonoid pathway in Arabidopsis thaliana, including a decrease in anthocyanin content in Nicotiana tabacum. The combined results from functional and transcriptomic analyses highlight the important role of HlMYB7 in fine-tuning and balancing the accumulation of secondary metabolites at the transcriptional level, thus offer a plausible target for metabolic engineering in hop.

plant biology↗