Todd P. Michael

This paper presents a near telomere-to-telomere, haplotype-resolved genome assembly of Vellozia tubiflora, a desiccation-tolerant plant, providing genomic resources for evolutionary and comparative studies.

The paper shows that genomic ancestry explains more of the dominant expression axis in Arabidopsis thaliana than environmental factors, and identifies a heritable proliferation module linked to growth phenotypes.

This study uses dual transcriptomics to compare parasitism strategies between two Rafflesiaceae species and their hosts, revealing molecular parallels to gall formation and a potential role for fungal symbionts.

The paper analyzes duckweed clones to resolve taxonomic relationships and finds triploidy is common, with implications for classification and evolution.

The paper uses whole-genome phylogenomic and synteny data to resolve the evolutionary origin of flatfish body asymmetry, finding strong support for a single origin.

The paper identifies an X-linked sex determination mechanism in cannabis and hop, showing that an X-linked gene involved in ethylene biosynthesis controls female inflorescence development, while the Y chromosome lacks clear sex-determining genes.

The paper uses genomic data to determine whether flatfish asymmetry evolved once or multiple times, finding strong support for a single origin.

This study evaluates genomic prediction and GWAS in an expanded rice NAM population, finding that prediction accuracy plateaus at moderate marker density and training size, while GWAS benefits from higher density.

This study examines transcriptomic responses in cranberry hybrids under heat and cold stress, identifying potential for cold tolerance through introgression from a wild relative.

The paper introduces a coefficient of variation-based filter for RNAseq data to retain low-variation genes, enabling better identification of cell populations in Arabidopsis snRNAseq data.

The paper resolves the molecular architecture of 5S rDNA loci in Spirodela polyrhiza using long-read sequencing and fluorescence in situ hybridization, revealing structural and regulatory differences between loci.

This study shows ELF3, a circadian clock component, restricts lateral root development by maintaining rhythmic gene expression and interacting with hormonal signals in Arabidopsis.

This study identifies an expanded domoic acid biosynthesis gene cluster in Nitzschia navis-varingica through genome sequencing and biochemical validation, revealing its unique organization and evolutionary significance.

The paper characterizes the PEBP gene family in Cannabis sativa and H. lupulus, identifying copy-number variation and sex-specific expression that may explain flowering time differences.

This paper constructs a sorghum pangenome and identifies trait-associated variants to inform climate-aware genome-enabled breeding strategies.

The paper constructs a sorghum pangenome from ex-PVP cultivars and a wild accession, identifying structural variants and selective sweeps linked to adaptation and trait improvement.

This study constructs a chromosome-scale cannabis pangenome to explore genomic diversity and evolution, revealing low diversity in cannabinoid synthase genes and high diversity in other regions.

The paper investigates soil depth's effect on microbial communities in Sorghum bicolor fields, finding significant changes in composition and diversity with depth.

This study presents a chromosome-level genome assembly of Pinguicula gigantea and performs phylogenomic analysis to explore the evolution of carnivory in this species.

This paper introduces VIGS in Ephedra tweedieana to study gene function in gymnosperms, achieving efficient gene silencing and observable phenotypes.

OrthoBrowser provides a user-friendly interface for visualizing and exploring gene family data across species, enhancing the usability of phylogenetic and orthology analysis tools.

This study presents a chromosome-level genome of baobab, revealing its evolutionary history, genomic features, and population structure, with insights into its longevity mechanisms.

The paper estimates telomere length in plants using long-read sequencing and finds that gymnosperms have shorter telomeres than eudicots and monocots, while clonally maintained species have longer telomeres.

The paper uses a new root phenotyping system to conduct a GWAS on soybean root system architecture, identifying SNPs and gene networks associated with specific root traits.

PanKmer provides a reference-free toolkit for pangenome analysis using k-mer decomposition to explore genetic variation across multiple genomes.

The paper demonstrates that 95% ethanol preserves fish blood and plant tissue for high-quality genome assembly using Nanopore sequencing.

The paper compares the genomes of cranberry and its wild relative to identify genomic regions associated with domestication and breeding traits.

Ultra-long-read sequencing resolves Arabidopsis centromeres, revealing their genetic and epigenetic structure and dynamics.

The paper assembles and resolves two haplotypes of a cassava line using multiple sequencing technologies, revealing over 5,000 large structural variants.

The paper generates a genome and single nuclei transcriptome of Lemna minuta to trace all developmental and terminal cell types across the entire plant.