Todd P. Michael
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View article: Domoic acid biosynthesis and genome expansion in <i>Nitzschia navis-varingica</i>
Domoic acid biosynthesis and genome expansion in <i>Nitzschia navis-varingica</i> Open
Production of the neurotoxin domoic acid (DA) by benthic diatom Nitzschia navis-varingica poses considerable health and economic concerns. In this study, we employed whole genome sequencing and transcriptomic analyses of regionally distinc…
View article: Hybridization and low-light adaptability in California eelgrass (Zostera spp.)
Hybridization and low-light adaptability in California eelgrass (Zostera spp.) Open
The temperate seagrass Zostera marina is a foundational marine species that provides critical habitat in bays and estuaries throughout the Northern Hemisphere. Human activities and climatic events have necessitated Z. marina restoration, f…
View article: FT-like genes in Cannabis and hops: sex specific expression and copy-number variation may explain flowering time variation
FT-like genes in Cannabis and hops: sex specific expression and copy-number variation may explain flowering time variation Open
Cannabis sativa is a fascinating, yet under-researched, species. To facilitate the global expansion of C. sativa cultivation a greater understanding of flowering time control is crucial. The PEBP gene family consists of universal promoters…
View article: Pangenome of U.S. ex-PVP and Wild Sorghum Reveals Structural Variants and Selective Sweeps Shaping Adaptation and Trait Improvement
Pangenome of U.S. ex-PVP and Wild Sorghum Reveals Structural Variants and Selective Sweeps Shaping Adaptation and Trait Improvement Open
Sorghum is a cereal crop grown for food, feed, and biofuel, yet the genomic diversity of elite commercial lines remains underexplored. Here, we assembled a sorghum pangenome from long-read sequences of 46 U.S. ex-Plant Variety Protection A…
View article: Centromere divergence and allopolyploidy reshape carnivorous sundew genomes
Centromere divergence and allopolyploidy reshape carnivorous sundew genomes Open
Centromeres are essential for chromosome function, yet their role in shaping genome evolution in polyploid plants, together with their highly variable forms across angiosperms, remains unresolved in the context of plant diversification. Al…
View article: Culture-independent meta-pangenomics enabled by long-read metagenomics reveals associations with pediatric undernutrition
Culture-independent meta-pangenomics enabled by long-read metagenomics reveals associations with pediatric undernutrition Open
The human gut microbiome is linked to child malnutrition, yet traditional microbiome approaches lack resolution. We hypothesized that complete metagenome-assembled genomes (cMAGs), recovered through long-read (LR) DNA sequencing, would ena…
View article: Population Genomics Reveals Panmixia in Pacific Sardine (<i>Sardinops sagax</i>) of the North Pacific
Population Genomics Reveals Panmixia in Pacific Sardine (<i>Sardinops sagax</i>) of the North Pacific Open
The spatial structure and dynamics of populations are important considerations when defining management units in organisms that are harvested as natural resources. In the Eastern Pacific, Pacific Sardine range from Chile to Alaska, the nor…
View article: Targeted deletions of large syntenic regions in <i>Arabidopsis thaliana</i>
Targeted deletions of large syntenic regions in <i>Arabidopsis thaliana</i> Open
Plant genomes have undergone multiple rounds of whole-genome duplication (WGD) throughout their evolutionary history. As a result, many species, including Arabidopsis thaliana , retain duplicated genomic segments, or syntenic regions, whic…
View article: Developing future resilience from signatures of adaptation across the sorghum pangenome
Developing future resilience from signatures of adaptation across the sorghum pangenome Open
While the green revolution adapted a handful of crops to homogenous and high-input industrialized agriculture, much of the global population still relies on local food production from low-input smallholder farms that grow highly variable c…
View article: Pangenome of U.S. ex-PVP and Wild Sorghum Reveals Structural Variants and Selective Sweeps Shaping Adaptation and Trait Improvement
Pangenome of U.S. ex-PVP and Wild Sorghum Reveals Structural Variants and Selective Sweeps Shaping Adaptation and Trait Improvement Open
Sorghum is a cereal crop grown for food, feed, and biofuel, yet the genomic diversity of elite commercial lines remains underexplored. Here, we assembled a sorghum pangenome from long-read sequences of 46 U.S. ex-Plant Variety Protection A…
View article: Transcriptomic stress responses in <i>Vaccinium</i> spp. F1 hybrids: Implications for temperature-resilient cranberry breeding using a crop wild relative
Transcriptomic stress responses in <i>Vaccinium</i> spp. F1 hybrids: Implications for temperature-resilient cranberry breeding using a crop wild relative Open
Summary Cranberry ( Vaccinium macrocarpon ) is an important North American fruit crop with vulnerability to temperature extremes and a relatively recent domestication history. Hybridization with a cold-adapted crop wild relative (CWR), V. …
View article: Designing a nitrogen-efficient cold-tolerant maize for modern agricultural systems
Designing a nitrogen-efficient cold-tolerant maize for modern agricultural systems Open
Maize (Zea mays L.) is the world's most productive grain crop and a cornerstone of global food supply. However, in temperate agricultural systems, maize exhibits 2 key anomalies. First, as a tropical species, maize cannot be planted in the…
View article: Genome-wide association study reveals influence of cell-specific gene networks on Soybean root system architecture
Genome-wide association study reveals influence of cell-specific gene networks on Soybean root system architecture Open
Root system architecture (RSA), the three-dimensional arrangement of roots in soil, is a critical determinant of plant productivity, resource use efficiency, and resilience to environmental stress. Despite its agronomic importance, RSA rem…
View article: Domesticated cannabinoid synthases amid a wild mosaic cannabis pangenome
Domesticated cannabinoid synthases amid a wild mosaic cannabis pangenome Open
Cannabis sativa is a globally important seed oil, fibre and drug-producing plant species. However, a century of prohibition has severely restricted development of breeding and germplasm resources, leaving potential hemp-based nutritional a…
View article: Domoic acid biosynthesis and genome expansion in <i>Nitzschia navis-varingica</i>
Domoic acid biosynthesis and genome expansion in <i>Nitzschia navis-varingica</i> Open
Production of the neurotoxin domoic acid (DA) by benthic diatom Nitzschia navis-varingica poses considerable health and economic concerns. In this study, we employed whole genome sequencing and transcriptomic analyses of regionally distinc…
View article: Soil depth determines the microbial communities in <i>Sorghum bicolor</i> fields within a uniform regional environment
Soil depth determines the microbial communities in <i>Sorghum bicolor</i> fields within a uniform regional environment Open
Sorghum bicolor, an important global crop, adapted to thrive in hotter and drier conditions than maize or rice, has deep roots that interact with a stratified soil microbiome that plays a crucial role in plant health, growth, and carbon st…
View article: Duckweed genomes and epigenomes underlie triploid hybridization and clonal reproduction
Duckweed genomes and epigenomes underlie triploid hybridization and clonal reproduction Open
View article: Triploidy is prominent in the duckweed <i>Lemna minor</i> complex
Triploidy is prominent in the duckweed <i>Lemna minor</i> complex Open
Duckweeds (Lemnaceae Martinov) are aquatic monocotyledonous flowering plants comprising five genera and 35 recognized species, known for being the smallest and fastest-growing flowering plants on Earth. Many species are morphologically ind…
View article: A single-nuclei transcriptome census of the Arabidopsis maturing root identifies that MYB67 controls phellem cell maturation
A single-nuclei transcriptome census of the Arabidopsis maturing root identifies that MYB67 controls phellem cell maturation Open
The periderm provides a protective barrier in many seed plant species. The development of the suberized phellem, which forms the outermost layer of this important tissue, has become a trait of interest for enhancing both plant resilience t…
View article: Trait Development and CRISPR-Enabled Improvement in the African Orphan Crop Fonio (Digitaria exilis)
Trait Development and CRISPR-Enabled Improvement in the African Orphan Crop Fonio (Digitaria exilis) Open
Fonio (Digitaria exilis), known as the "grain of life," is a vital food security crop grown by smallholder farmers across West Africa. Renowned for its short maturity period of 6-8 weeks, fonio provides essential harvests during periods of…
View article: Can a plant biologist fix a thermostat?
Can a plant biologist fix a thermostat? Open
Summary The shift to reductionist biology at the dawn of the genome era yielded a ‘parts list’ of plant genes and a nascent understanding of complex biological processes. Today, with the genomics era in full swing, advances in high‐definit…
View article: THE BIOLOGICAL SECTION (23 AUGUST 2024) WITHIN THE XXIV GAMOW INTERNATIONAL ASTRONOMICAL CONFERENCE “ASTRONOMY AND BEYOND: ASTROPHYSICS, COSMOLOGY AND GRAVITATION, ASTROPARTICLE PHYSICS, RADIO ASTRONOMY, ASTROBIOLOGY AND GENETICS”, HELD ON 19–23 AUGUST 2024 AT ODESA I. I. MECHNIKOV NATIONAL UNIVERSITY, ODESA CITY, UKRAINE
THE BIOLOGICAL SECTION (23 AUGUST 2024) WITHIN THE XXIV GAMOW INTERNATIONAL ASTRONOMICAL CONFERENCE “ASTRONOMY AND BEYOND: ASTROPHYSICS, COSMOLOGY AND GRAVITATION, ASTROPARTICLE PHYSICS, RADIO ASTRONOMY, ASTROBIOLOGY AND GENETICS”, HELD ON 19–23 AUGUST 2024 AT ODESA I. I. MECHNIKOV NATIONAL UNIVERSITY, ODESA CITY, UKRAINE Open
It was the sixth session of the Biological Section within the Gamow International Astronomical Conference that took place on 23 August 2024. The Biological Section was traditionally held under the title “Importance of G. Gamov’s Ideas for …
View article: OrthoBrowser: gene family analysis and visualization
OrthoBrowser: gene family analysis and visualization Open
Motivation The analysis of gene families across diverse species is pivotal in elucidating evolutionary dynamics and functional genomic landscapes. Typical analysis approaches often require significant computational expertise and user time.…
View article: ARABLE CROP FARMERS’ PERCEPTION OF ORGANIC FARMING PRACTICES IN EKITI STATE
ARABLE CROP FARMERS’ PERCEPTION OF ORGANIC FARMING PRACTICES IN EKITI STATE Open
This study assessed the arable crop farmers’ perception of organic farming practices in Ekiti state, Nigeria. The objectives of the study were to: describe the socio-economic characteristics of arable crop farmers; examine the level of awa…
View article: An X-linked sex determination mechanism in cannabis and hop
An X-linked sex determination mechanism in cannabis and hop Open
Sex chromosomes in cannabis and hop were identified a century ago because of their obvious visible differences in size (heteromorphy). However, we know little about the genes they contain that control the development of the inflorescences.…
View article: Crossing the Pacific: Genomics Reveals the Presence of Japanese Sardine (<i>Sardinops melanosticta</i>) in the California Current Large Marine Ecosystem
Crossing the Pacific: Genomics Reveals the Presence of Japanese Sardine (<i>Sardinops melanosticta</i>) in the California Current Large Marine Ecosystem Open
Recent increases in frequency and intensity of warm water anomalies and marine heatwaves have led to shifts in species ranges and assemblages. Genomic tools can be instrumental in detecting such shifts. In the early stages of a project ass…
View article: The genome sequence of Inga oerstediana Benth.
The genome sequence of Inga oerstediana Benth. Open
We present a genome assembly from an individual of Inga oerstediana (Streptophyta; Magnoliopsida; Fabales; Fabaceae). The genome sequence has a total length of 970.60 megabases. Most of the assembly is scaffolded into 13 chromosomal pseudo…
View article: The genome sequence of Inga leiocalycina Benth.
The genome sequence of Inga leiocalycina Benth. Open
We present a genome assembly from an individual of Inga leiocalycina (Streptophyta; Magnoliopsida; Fabales; Fabaceae). The genome sequence has a total length of 948.00 megabases. Most of the assembly is scaffolded into 13 chromosomal pseud…
View article: Assembly of Mitochondrial Genomes Using Nanopore Long‐Read Technology in Three Sea Chubs (Teleostei: Kyphosidae)
Assembly of Mitochondrial Genomes Using Nanopore Long‐Read Technology in Three Sea Chubs (Teleostei: Kyphosidae) Open
Complete mitochondrial genomes have become markers of choice to explore phylogenetic relationships at multiple taxonomic levels and they are often assembled using whole genome short‐read sequencing. Herein, using three species of sea chubs…
View article: Chromosome-level baobab genome illuminates its evolutionary trajectory and environmental adaptation
Chromosome-level baobab genome illuminates its evolutionary trajectory and environmental adaptation Open