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While prokaryotic pan-genomes have been shown to contain many more genes than any individual organism, the prevalence and functional significance of differentially present genes in eukaryotes remains poorly understood. Whole-genome de novo assembly and annotation of 54 lines of the grass Brachypodium distachyon yield a pan-genome containing nearly twice the number of genes found in any individual genome. Genes present in all lines are enriched for essential biological functions, while genes present in only some lines are enriched for conditionally beneficial functions (e.g., defense and development), display faster evolutionary rates, lie closer to transposable elements and are less likely to be syntenic with orthologous genes in other grasses. Our data suggest that differentially present genes contribute substantially to phenotypic variation within a eukaryote species, these genes have a major influence in population genetics, and transposable elements play a key role in pan-genome evolution.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5736591 | PMC |
http://dx.doi.org/10.1038/s41467-017-02292-8 | DOI Listing |
Int J Mol Sci
December 2024
The Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou 571158, China.
The basic helix-loop-helix () transcription factor (TF) family, the second-largest among eukaryotes, is known for its evolutionary and functional diversity across plant species. However, genes have not yet been characterized in . In this study, we identified 76 genes, which exhibit a variety of physicochemical properties.
View Article and Find Full Text PDFEnviron Sci Technol
December 2024
Grupo MOSS, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS, CSIC), Av. Reina Mercedes, 10, Sevilla 4012, Spain.
Protoplasma
December 2024
Laboratory of Extremophile Plants, Centre of Biotechnology of Borj-Cedria, Hammam-Lif, Tunisia.
Phosphorus (P) is a macronutrient that plays a crucial role in critical plant functions. Phosphate transporters (PHTs) ensure the acquisition and translocation of Pi in the plant, thereby playing a key role in maintaining normal plant growth under Pi deficiency conditions. In Brachypodium distachyon, the grass model system, the function of individual PHT genes, remains largely unknown.
View Article and Find Full Text PDFPlant J
December 2024
Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, 99164, USA.
Root systems are uniquely adapted to fluctuations in external nutrient availability. In response to suboptimal nitrogen conditions, plants adopt a root foraging strategy that favors a deeper and more branched root architecture, enabling them to explore and acquire soil resources. This response is gradually suppressed as nitrogen conditions improve.
View Article and Find Full Text PDFNew Phytol
January 2025
Department of Biology, University of Massachusetts, 611 N. Pleasant St, Amherst, MA, 01002, USA.
Replicated trait evolution can provide insights into the mechanisms underlying the evolution of biodiversity. One example of replicated evolution is the awn, an organ elaboration in grass inflorescences. Awns are likely homologous to leaf blades.
View Article and Find Full Text PDFEnter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!