Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Genome Annotation and Assembly

Genome Annotation and Assembly

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.

Genome Size and the Evolution of New Genes

Genome Size and the Evolution of New Genes

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.

Genome Size and the Evolution of New Genes

Genome Size and the Evolution of New Genes

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.

Genomics

Genomics

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...

Next-generation Sequencing

Next-generation Sequencing

The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.

Genome-wide Association Studies-GWAS

Genome-wide Association Studies-GWAS

Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

A single-cell blueprint for cellular diversity in the Green Lineage.

Current biology : CB·2026

Same author

Genotype imputation improves SNP density and genetic analysis accuracy in slash pine.

Yi chuan = Hereditas·2026

Same author

Alternatively Spliced Dual-Coding Regions Contribute to the Human Gene Regulatory Program.

bioRxiv : the preprint server for biology·2026

Same author

Physiological and Yield Responses of Peanut (<i>Arachis hypogaea</i> L.) Genotypes Under Well-Watered and Water-Stressed Conditions.

Plants (Basel, Switzerland)·2026

Same author

Adoption of Standard Reference SNP Identifiers in Agricultural Genomics for Interoperability and Data Reuse.

Scientific data·2026

Same author

A chromosome-level genome assembly of Platycladus orientalis and comparative genomics reveal pivotal roles of transposable elements in gene duplication and pseudogenization across gymnosperm giga-genomes.

Plant communications·2026

Same journal

Correction to 'scSuperAnnotator: A platform for benchmarking comparison and visualizing automated cellular annotation methods for scRNA-seq data'.

Nucleic acids research·2026

Same journal

Correction to 'Differentiable partition function calculation for RNA'.

Nucleic acids research·2026

Same journal

Deployment of non-canonical splicing in tunicate genomes is mediated by divergent U2AF function and changing m6A modification in U1 and U6 snRNA.

Nucleic acids research·2026

Same journal

Bacillus subtilis DnaB forms multiple protein-protein interactions essential for DNA replication initiation.

Nucleic acids research·2026

Same journal

Multiple forms of protein-protein and DNA binding are exhibited by BrxC from the BREX phage restriction system.

Nucleic acids research·2026

Same journal

Biosynthesis of glycosylated 5-hydroxycytosine in the DNA of diverse viruses.

Nucleic acids research·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Jun 6, 2026

Development of Compendium for Esophageal Squamous Cell Carcinoma

Development of Compendium for Esophageal Squamous Cell Carcinoma

Published on: April 12, 2024

Gramene database in 2010: updates and extensions.

Ken Youens-Clark¹, Ed Buckler, Terry Casstevens

¹Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA. kclark@cshl.edu

Nucleic Acids Research

|November 16, 2010

Summary

This summary is machine-generated.

The Gramene database has expanded over 10 years to include numerous plant genomes, offering diverse genomics data and web services for researchers. This resource supports plant science by integrating genetic information and providing advanced tools.

More Related Videos

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Published on: December 22, 2017

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

Published on: May 22, 2018

Related Experiment Videos

Last Updated: Jun 6, 2026

Development of Compendium for Esophageal Squamous Cell Carcinoma

Development of Compendium for Esophageal Squamous Cell Carcinoma

Published on: April 12, 2024

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Published on: December 22, 2017

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

Published on: May 22, 2018

Area of Science:

Plant Genomics
Bioinformatics
Database Development

Background:

Gramene database initiated with a focus on rice, the first fully-sequenced grass genome.
The database has expanded to encompass major model and crop plants, including Arabidopsis, maize, and sorghum.
It has been operational for 10 years, evolving into a comprehensive plant genomics resource.

Purpose of the Study:

To detail the evolution and current capabilities of the Gramene database.
To highlight the expansion of plant species covered and data types hosted.
To showcase the integrated tools and web services available to the scientific community.

Main Methods:

Integration of diverse datasets: quantitative trait loci (QTL), metabolic pathways, genetic diversity, genes, proteins, germplasm, literature, and ontologies.
Development of a structured markers and sequences database linked with genome browsers and maps.
Implementation of web services such as Distributed Annotation Server (DAS) and BLAST, alongside a public MySQL database.

Main Results:

Gramene now serves as a resource for multiple plant species beyond rice, including Arabidopsis, Brachypodium, maize, sorghum, poplar, and grape.
The database hosts a wide array of integrated data types and provides advanced bioinformatics tools.
Regular database builds and interim releases ensure data and software updates.

Conclusions:

Gramene has matured into a robust, multi-species plant genomics database over its 10-year history.
The comprehensive data integration and web services offered by Gramene significantly support plant science research.
The database's ongoing development and release cycle ensure its continued relevance and utility.