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The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
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Transmission electron microscopy (TEM) can be used to determine the 3D structure of biological samples with the help of techniques such as electron microscope tomography and single-particle reconstruction. While single-particle reconstruction can examine macromolecules and macromolecular complexes in vitro conditions only, tomography permits the study of cell components or small cells in vivo.
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Related Experiment Video

Updated: Mar 8, 2026

Tomato Analyzer: A Useful Software Application to Collect Accurate and Detailed Morphological and Colorimetric Data from Two-dimensional Objects
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TOMATOMICS: A Web Database for Integrated Omics Information in Tomato.

Toru Kudo1, Masaaki Kobayashi1, Shin Terashima1

  • 1Bioinformatics Laboratory, School of Agriculture, Meiji University,Higashi-mita, Tama-ku, Kawasaki, Kanagawa, Japan.

Plant & Cell Physiology
|January 24, 2017
PubMed
Summary
This summary is machine-generated.

This study integrates tomato genetic resources and genome data to create TOMATOMICS, a web database for enhanced omics information discovery. This resource aids researchers in understanding tomato biology and accelerating functional analyses.

Keywords:
DatabaseGenomeMicro-TomSolanum lycopersicum (tomato)Transcriptome

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Area of Science:

  • Plant Biology
  • Genomics
  • Bioinformatics

Background:

  • Solanum lycopersicum (tomato) is a vital crop and model organism for fruit research.
  • Existing genetic resources like mutant lines and cDNA clones from Micro-Tom, alongside genome data from Heinz 1706, are crucial for tomato research.
  • Efficient acquisition and integration of omics data are essential for advancing tomato biology.

Purpose of the Study:

  • To integrate existing Micro-Tom experimental resources with the Heinz 1706 genome sequence.
  • To infer gene structures by comparing genome and transcriptome data.
  • To develop a centralized web database, TOMATOMICS, for streamlined access to comprehensive tomato omics information.

Main Methods:

  • Integration of Micro-Tom genetic resources and Heinz 1706 genome sequence data.
  • Inference of gene structures through comparative analysis of Heinz 1706 genome and Micro-Tom/Heinz 1706 transcriptome data (cDNAs and RNA-seq).
  • Development and maintenance of the TOMATOMICS web database, incorporating search functions and a genome browser.

Main Results:

  • Successful integration of diverse tomato omics data, including cDNA clones, full-length mRNA sequences, and RNA-seq data.
  • Inferred gene structures based on comparative genomic and transcriptomic analyses.
  • Establishment of TOMATOMICS, providing intuitive access to genetic resources, gene structures, expression profiles, and functional annotations.

Conclusions:

  • The integrated approach and the TOMATOMICS database significantly enhance the efficiency of acquiring and utilizing omics information for tomato research.
  • TOMATOMICS serves as a valuable platform for comprehensive functional analyses and accelerating discoveries in tomato biology.
  • Streamlined connectivity and user-friendly access to data empower researchers in the field of plant genomics.