Ten new high-quality genome assemblies for diverse bioenergy sorghum genotypes.

Introduction: Sorghum ( (L.) Moench) is an agriculturally and economically important staple crop that has immense potential as a bioenergy feedstock due to its relatively high productivity on marginal lands. To capitalize on and further improve sorghum as a potential source of sustainable biofuel, it is essential to understand the genomic mechanisms underlying complex traits related to yield, composition, and environmental adaptations.

Evidence of glucosinolates translocation from inflorescences to stems during postharvest storage of broccoli.

Broccoli is a vegetable appreciated by consumers for its nutritional properties, particularly for its high glucosinolate (GLS) content. However, broccoli shows a high rate of senescence during postharvest and the GLS content in inflorescences decreases sharply. Usually, postharvest studies on broccoli focus on inflorescences, ignoring the other tissues harvested such as the stems and main stalk.

Era of gapless plant genomes: innovations in sequencing and mapping technologies revolutionize genomics and breeding.

Whole-genome sequencing and assembly have revolutionized plant genetics and molecular biology over the last two decades. However, significant shortcomings in first- and second-generation technology resulted in imperfect reference genomes: numerous and large gaps of low quality or undeterminable sequence in areas of highly repetitive DNA along with limited chromosomal phasing restricted the ability of researchers to characterize regulatory noncoding elements and genic regions that underwent recent duplication events. Recently, advances in long-read sequencing have resulted in the first gapless, telomere-to-telomere (T2T) assemblies of plant genomes.

A chromosome-scale genome assembly of Artemisia argyi reveals unbiased subgenome evolution and key contributions of gene duplication to volatile terpenoid diversity.

Artemisia argyi Lévl. et Vant., a perennial Artemisia herb with an intense fragrance, is widely used in traditional medicine in China and many other Asian countries.

Domestication and selection footprints in Persian walnuts (Juglans regia).

Walnut (Juglans) species are economically important hardwood trees cultivated worldwide for both edible nuts and high-quality wood. Broad-scale assessments of species diversity, evolutionary history, and domestication are needed to improve walnut breeding. In this study, we sequenced 309 walnut accessions from around the world, including 55 Juglans relatives, 98 wild Persian walnuts (J.

Iron counteracts zinc-induced toxicity in soybeans.

Zinc (Zn) and iron (Fe) are essential micronutrients for all living organisms and the major targets for crop biofortification. However, when acquired in excess quantities, Zn and Fe can be toxic to plants. In this study, we examined the interaction between Zn and Fe in soybean plants under various Zn and Fe treatments.

Characterization and response of two potato receptor-like kinases to cyst nematode infection.

Plant-parasitic cyst nematodes ( and spp.) secrete CLAVATA3/EMBRYO SURROUNDING REGION-RELATED (CLE) effector proteins, which act as ligand mimics of plant CLE peptides to promote successful nematode infection. Previous studies of the Arabidopsis-beet cyst nematode (BCN; ) pathosystem showed that Arabidopsis CLE receptors including CLAVATA1 (CLV1), CLV2, and RECEPTOR-LIKE PROTEIN KINASE 2 (RPK2) are required for BCN CLE signaling.

Pan-genome and multi-parental framework for high-resolution trait dissection in melon (Cucumis melo).

Linking genotype with phenotype is a fundamental goal in biology and requires robust data for both. Recent advances in plant-genome sequencing have expedited comparisons among multiple-related individuals. The abundance of structural genomic within-species variation that has been discovered indicates that a single reference genome cannot represent the complete sequence diversity of a species, leading to the expansion of the pan-genome concept.

A key virulence effector from cyst nematodes targets host autophagy to promote nematode parasitism.

Autophagy, an intracellular degradation system conserved in eukaryotes, has been increasingly recognized as a key battlefield in plant-pathogen interactions. However, the role of plant autophagy in nematode parasitism is mostly unknown. We report here the identification of a novel and conserved effector, Nematode Manipulator of Autophagy System 1 (NMAS1), from plant-parasitic cyst nematodes (Heterodera and Globodera spp.

CuGenDBv2: an updated database for cucurbit genomics.

The Cucurbitaceae (cucurbit) family consists of about 1,000 species in 95 genera, including many economically important and popular fruit and vegetable crops. During the past several years, reference genomes have been generated for >20 cucurbit species, and variome and transcriptome profiling data have been rapidly accumulated for cucurbits. To efficiently mine, analyze and disseminate these large-scale datasets, we have developed an updated version of Cucurbit Genomics Database.

Parsimonious genotype by environment interaction covariance models for cassava ().

The assessment of cassava clones across multiple environments is often carried out at the uniform yield trial, a late evaluation stage, before variety release. This is to assess the differential response of the varieties across the testing environments, a phenomenon referred to as genotype-by-environment interaction (GEI). This phenomenon is considered a critical challenge confronted by plant breeders in developing crop varieties.

Toward a data infrastructure for the Plant Cell Atlas.

We review how a data infrastructure for the Plant Cell Atlas might be built using existing infrastructure and platforms. The Human Cell Atlas has developed an extensive infrastructure for human and mouse single cell data, while the European Bioinformatics Institute has developed a Single Cell Expression Atlas, that currently houses several plant data sets. We discuss issues related to appropriate ontologies for describing a plant single cell experiment.

Spatiotemporal dynamics of the tomato fruit transcriptome under prolonged water stress.

Water availability influences all aspects of plant growth and development; however, most studies of plant responses to drought have focused on vegetative organs, notably roots and leaves. Far less is known about the molecular bases of drought acclimation responses in fruits, which are complex organs with distinct tissue types. To obtain a more comprehensive picture of the molecular mechanisms governing fruit development under drought, we profiled the transcriptomes of a spectrum of fruit tissues from tomato (Solanum lycopersicum), spanning early growth through ripening and collected from plants grown under varying intensities of water stress.

Clonostachys spp., natural mosquito antagonists, and their prospects for biological control of Aedes aegypti.

Aedes aegypti (Linnaeus, 1762) is an important vector of arboviruses in the tropics and subtropics. New control strategies based on natural enemies such as entomopathogenic fungi are of utmost importance, and the present study reports the first isolation of Clonostachys spp. (Hypocreales: Bionectriaceae) from mosquitoes and their activity against A.

Laboratory studies assessing the microbial biocontrol potential of diverse strains of Beauveria bassiana isolated from coffee berry borer, with emphasis on strains from Hawai'i Island and comparisons to commercial strain GHA.

A series of experiments investigated genetically diverse strains of Beauveria bassiana (Bb) isolated from coffee berry borer (CBB). Objectives included assessment of their biocontrol potential, particularly in comparison to Bb commercial strain GHA currently applied for CBB control, and identification of various attributes potentially contributing to their comparatively greater epizootic potential in CBB populations. Bioassays identified one strain from Hawai'i Island and one from Puerto Rico with virulence greater than GHA based on equal weights of unformulated conidial powder (CP); however, the greater potency of the CPs was ultimately explained by their 2.

Occurrence of entomopathogenic hypocrealean fungi in mosquitoes and their larval habitats in Central Brazil, and activity against Aedes aegypti.

Collecting entomopathogenic fungi associated with mosquitoes and studies on their activity against mosquito developmental stages will improve the understanding of their potential as agents to control important mosquito vectors. Twenty-one strains of entomopathogenic fungi affecting mosquitoes in Central Brazil were studied: 7 of Beauveria bassiana, 7 of Metarhizium humberi, 3 of M. anisopliae, 2 of Cordyceps sp.

Genome Sequencing of up to 6,000-Year-Old Citrullus Seeds Reveals Use of a Bitter-Fleshed Species Prior to Watermelon Domestication.

Iconographic evidence from Egypt suggests that watermelon pulp was consumed there as a dessert by 4,360 BP. Earlier archaeobotanical evidence comes from seeds from Neolithic settlements in Libya, but whether these were watermelons with sweet pulp or other forms is unknown. We generated genome sequences from 6,000- and 3,300-year-old seeds from Libya and Sudan, and from worldwide herbarium collections made between 1824 and 2019, and analyzed these data together with resequenced genomes from important germplasm collections for a total of 131 accessions.

Protein-protein interaction techniques to investigate post-translational regulation of carotenogenesis.

Carotenoids are indispensable to plants. The regulatory mechanisms underlying carotenoid metabolism have been subjected to intensive investigation. Post-translational regulation is critically important to rapidly modulate enzyme protein level and activity in fine-tuning carotenoid production in living organisms.

Golden Rice-Lessons learned for inspiring future metabolic engineering strategies and synthetic biology solutions.

Golden Rice is a genetically modified rice variety that accumulates carotenoids with provitamin A activity in its endosperm. This biofortified crop was developed to fight provitamin A deficiency prevailing in countries with a diet based on rice as the major staple. Since its first version in 2000, Golden Rice was continuously developed to increase endosperm carotenoids, to achieve regulatory compliance, and to introgress the trait into regional rice varieties.

Laser capture of tomato pericarp tissues for microscale carotenoid analysis by supercritical fluid chromatography.

Plant organs and tissues are comprised of an array of cell types often superimposed on a gradient of developmental stages. As a result, the ability to analyze and understand the synthesis, metabolism, and accumulation of plant biomolecules requires improved methods for cell- and tissue-specific analysis. Tomato (Solanum lycopersicum) is the world's most valuable fruit crop and is an important source of health-promoting dietary compounds, including carotenoids.

An apple somatic mutation of delayed fruit maturation date is primarily caused by a retrotransposon insertion-associated large deletion.

Somatic mutations may alter important traits in tree fruits, such as fruit color, size and maturation date. Autumn Gala (AGala), a somatic mutation from apple cultivar Gala, matures 4 weeks later than Gala. To understand the mechanisms underlying the delayed maturation, RNA-seq analyses were conducted with fruit sampled at 13 (Gala) and 16 (AGala) time-points during their growth and development.

Strongwellsea selandia and Strongwellsea gefion (Entomophthorales: Entomophthoraceae), two new species infecting adult flies from genus Helina (Diptera: Muscidae).

Two new species from the genus Strongwellsea (Entomophthorales: Entomophthoraceae) that infect adult flies from the genus Helina (Muscidae) are described: Strongwellsea selandia Eilenberg & Humber infecting adult Helina evecta (Harris), and Strongwellsea gefion Eilenberg & Humber infecting adult Helina reversio (Harris). The descriptions are based on pathobiological, phenotypical and genotypical characters. The new species differ from other described members from the genus Strongwellsea by a) pathobiology as revealed by natural host species, b) morphology of primary conidia, c) color of resting spores, and d) genotypical clustering based on analysis of ITS2.

Combined nature and human selections reshaped peach fruit metabolome.

Background: Plant metabolites reshaped by nature and human beings are crucial for both their lives and human health. However, which metabolites respond most strongly to selection pressure at different evolutionary stages and what roles they undertake on perennial fruit crops such as peach remain unclear.

Results: Here, we report 18,052 significant locus-trait associations, 12,691 expression-metabolite correlations, and 294,676 expression quantitative trait loci (eQTLs) for peach.

Loss of function of the bHLH transcription factor Nrd1 in tomato enhances resistance to Pseudomonas syringae.

Basic helix-loop-helix (bHLH) transcription factors constitute a superfamily in eukaryotes, but their roles in plant immunity remain largely uncharacterized. We found that the transcript abundance in tomato (Solanum lycopersicum) leaves of one bHLH transcription factor-encoding gene, negative regulator of resistance to DC3000 1 (Nrd1), increased significantly after treatment with the immunity-inducing flgII-28 peptide. Plants carrying a loss-of-function mutation in Nrd1 (Δnrd1) showed enhanced resistance to Pseudomonas syringae pv.