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Genomics02:02

Genomics

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Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
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Genomic Imprinting and Inheritance02:30

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Diploid organisms inherit genetic material through chromosomes from both parents. Copies of the same gene are known as alleles. In most cases, both alleles are simultaneously expressed and allow various cellular processes to function optimally. If one of the alleles is missing or mutated, the expression of the other allele can compensate; however, this is not true for all genes.
The expression of some genes depends on which parent passed the gene to the offspring, through a phenomenon known as...
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Genome Size and the Evolution of New Genes03:21

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While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.
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Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes02:16

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The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...
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Microtubule Associated Proteins (MAPs)01:42

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Microtubule function and architecture are regulated by an array of specialized proteins called microtubule-associated proteins or MAPs. These proteins are widespread across different organisms and have conserved protein motifs, like the multi-TOG domain for tubulin binding found in the CLASP family of MAPs. Some MAPs are lineage-specific based on their conserved domains. Their functions depend upon the cytoskeletal architecture and cell type they are located within. In-plant cells, a specific...
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Plotting of Topographic Maps01:29

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Topographic maps represent the Earth's surface features using contour lines, which connect points of equal elevation to create a two-dimensional representation of three-dimensional terrain. Creating a topographic map requires a systematic approach.Begin by plotting a scaled grid and marking intersections corresponding to the survey's elevation data points. Assign elevation values at these intersections to build the base map. Next, determine contour levels using a consistent contour interval,...
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Updated: Jan 29, 2026

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
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Metabotyping as a Stopover in Genome-to-Phenome Mapping.

Pubudu P Handakumbura1, Bryan Stanfill2, Albert Rivas-Ubach3

  • 1The Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Washington, WA, 99352, USA. pubudupinipa.handakumbura@pnnl.gov.

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Summary

Researchers developed a two-step method to predict plant traits from genetic data. This approach uses metabolite profiles (metabotypes) to link genotype to phenotype, improving predictions in model grass.

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Area of Science:

  • Genomics
  • Metabolomics
  • Plant Biology

Background:

  • Predicting phenotypic traits from genomic and environmental data remains a significant challenge in biology.
  • Linking genotype to phenotype is crucial for applications in medicine, nutrition, and agriculture.
  • Current methods struggle to fully integrate complex genotype-phenotype interactions.

Purpose of the Study:

  • To propose and validate a two-step procedure for bridging the genome-to-phenome gap.
  • To investigate the role of internal phenotypes (metabotypes) in predicting external traits.
  • To establish correlative models for predicting plant phenotypes using genomic and metabolite data.

Main Methods:

  • Utilized the model grass *Brachypodium distachyon* with diverse genotypes.
  • Measured external phenotypes: biomass accumulation and shoot-root allometry.
  • Developed correlative models linking genotypes to metabolite profiles (metabotypes) and metabotypes to external phenotypes under varying watering regimes.

Main Results:

  • Established significant correlations between genotypes and their corresponding metabotypes.
  • Demonstrated strong associations between metabotypes and external phenotypic traits.
  • Showcased the predictive power of metabotypes under different environmental conditions (watering regimes).

Conclusions:

  • Metabolite profiles (metabotypes) can serve as effective integrators for predicting external phenotypes.
  • The proposed two-step approach successfully bridges the genome-to-phenome gap.
  • This strategy holds potential for advancing genome-informed disciplines like plant breeding and personalized agriculture.