May 1, 2025 - Plant Systems Biology. Rebecca Dewhirst, a postdoc at LBNL, studies leaf water potential of poplar trees in response to an experimental drought. [Courtesy LBNL]The Genomic Science Program (GSP) recognizes that gene function determination has not kept pace with omics data acquisition and that this incongruence represents an ascending challenge for the research community.

The Plant Genome is an open access journal providing the latest advances and breakthroughs in plant genomics research, including genome analyses and engineering.

In particular, we look at the extent ... evolution of gene families. ... Plant genomes span several orders of magnitude in size, vary in levels of ploidy and heterozygosity, and contain old and recent bursts of transposable elements, which render them challenging but interesting ...

January 4, 2024 - The Plant GDB Genome Browser displays current gene structure models and transcript evidence from spliced alignments of EST and cDNA sequences. If applicable, matched GSS contigs, community annotations, similar proteins, and microarray probes ...

University of California at Davis' genome center devoted to studying cotton. French Plant Genomics Resource Center This link opens in a new window

These technologies will generate enormous amount of sequencing data, which will be beneficial to understand the basic physiology of plants. This issue of Current Genomics is a compilation of review articles on various facets of plant genomics written by experts.

Explore the complexity of plant genomes! Discover insights on polyploidy, genome duplication, and advanced sequencing for sustainable agriculture.

Furthermore, whole genomes can now be sequenced. This review addresses these issues and also discusses ways to extract biological meaning from DNA data. Although genomic issuesare addressed from a plant perspective, this review provides insights into the genomic analyses of other organisms. Key terms: genomics, Arabidopsis thaliana, Oryza sativa, plant breeding, gene discovery ... Until very recently, the molecular analysis of plants often focused on the single gene level.

PlantGDB (http://www.plantgdb.org/) is a database of molecular sequence data for all plant species with significant sequencing efforts. The database organizes EST sequences into contigs that represent tentative unique genes. Contigs are annotated ...

October 19, 2020 - The plant DNA C-values database (release 7.1): An updated online repository of plant genome size data for comparative studies. New Phytologist, 226, 301–305. https://doi.org/10.1111/nph.16261 ... Pteridophyte Phylogeny Group (PPG) (2016). A community-derived classification for extant lycophytes and ferns. Journal of Systematics and Evolution, 54, 563–603. ... Puttick, M. N., Clark, J. W., & Donoghue, P. C. J. (2015). Size is not everything: Rates of genome size evolution, not C-value, correlate with speciation in angiosperms.

Here, the authors report the genome assemblies of three Curcuma species and find that terpene synthase genes quite often become pseudogenes inside an inversion, indicating inversions act as a counteracting force against gene tandem duplication. ... A chromosome-level genome assembly for Angelica sinensis var. Qinggui1 combined with metabolomic and transcriptomic analyses provides insight into the pathways involved in the biosynthesis of pharmaceutically important compounds in roots of this plant.

May 8, 2026 - More Bioinformatics Resources This link opens in a new window · Crop Protection Compendium This link opens in a new window · Compiles and presents scientific information on all aspects of global crop protection by integrating text, images, maps, and databases in an encyclopedic portal.

December 29, 2025 - Whether you’re working on drought tolerance, disease resistance, or yield optimization, PlantArray offers the precision, throughput, and reliability needed to translate genomic insights into agricultural innovation. Discover how PlantArray can transform your research program and help you develop the climate-resilient crops the world needs.

Recent technological advancements have substantially expanded our ability to analyze and understand plant genomes and to reduce the gap existing between genotype and phenotype. The fast evolving field of genomics allows scientists to analyze thousand of genes in parallel, to understand the ...

[8] summarizes recent developments in plant genomics and their application, with an emphasis on cereal crops. They discuss genome sequencing approaches, quantitative trait loci (QTL) mapping and genome-wide association (GWAS) studies, directed mutagenesis, plant non-coding RNAs, gene editing using CRISPR-Cas9, and complementation of crop genotyping by crop phenotyping. Noncoding RNAs (ncRNAs) modulate mRNA or protein profiles. ncRNAs are essential for growth and development in plants and have emerged as key players in guarding plants during stress conditions.

With the JGI Plant Flagship Pangenomes, driven by DOE science needs, this program is expanding JGI Plant Flagship genomes into pangenomes, which capture much greater diversity for these species. The pangenomes enable the exploration and identification of small and large structural variation — this variation drives major phenotypic differences in plants and will accelerate gene discovery. BrachyPan on Phytozome (see Brachypodium Resources below)

Check which features are supported on each species here; if you would like to request a new species please email Helpdesk. The new Ensembl provides access to over 4700 genomes: http://beta.ensembl.org · There are over 4100 animal, 470 plant, and 100 fungal genomes ready to explore.

Experimental evolution in maize ... two plant-height-associated regions ... Experimental evolution studies are common in agricultural research, where they are often deemed “long-term selection.” These are often used to perform selection mapping, which involves identifying markers that were putatively under selection based on finding signals of selection left in the genome...

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Identifying the causal mutation of a phenotype can be accelerated by combining genetic mapping with whole genome sequencing, in a process termed mapping-by-sequencing, and James et al. [9] describe important new guidelines for mapping-by-sequencing in Arabidopsis. They generate a Perl-based simulation tool called Pop-seq, which simulates mapping populations to determine the number of plants and the sequencing depth required to identify candidate mutations in outcrossed and backcrossed mapping populations.