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.

RNA-seq

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...

You might also read

Related Articles

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

Sort by

Same author

Genetic blueprint of herbaceous peony floral scent: evidence from terpene synthase, Nudix hydrolase, and prenyltransferase.

Horticulture research·2026

Same author

Accurate Identification of <i>Ilex</i> (Aquifoliaceae) Taxa Based on Leaf Morphology Using Deep Learning.

Plants (Basel, Switzerland)·2026

Same author

Pangenomic analyses of rose uncover widespread structure variation and empower genomics-directed breeding.

Nature genetics·2026

Same author

The Mitochondrial Genome of <i>Curcuma longa</i>: A Large and Structurally Complex Genome with Extensive Intracellular DNA Transfer.

Genes·2026

Same author

A distorter-restorer system drives quantitative reproductive isolation in rice.

Nature plants·2026

Same author

A chromosomal haplotype-resolved genome assembly of Cuphea hookeriana.

Scientific data·2026

Same journal

AcGLK2 involves anthocyanin biosynthesis via bidirectionally modulating expression of MYB transcription factors in <i>Actinidia chinensis</i>.

Horticulture research·2026

Same journal

LpCbDR1 regulates leaf senescence and drought tolerance by activating the chlorophyll b reductase gene and stress-related genes in perennial ryegrass.

Horticulture research·2026

Same journal

T2T reference genome assembly provides insights into anthocyanin accumulation in broccoli.

Horticulture research·2026

Same journal

A small-scale CRISPR mutant library in rapeseed of commercial cultivar Zhongshuang 11.

Horticulture research·2026

Same journal

Deciphering flavonoids and terpenoids biosynthesis through chromosomal-level genome, metabolome, and transcriptome integration in <i>Spuriopimpinella brachycarpa</i>.

Horticulture research·2026

Same journal

Evolution and diversification of PAL-mediated salicylic acid biosynthesis in Rosaceae.

Horticulture research·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Jul 1, 2025

Optimization and Comparative Analysis of Plant Organellar DNA Enrichment Methods Suitable for Next-generation Sequencing

Optimization and Comparative Analysis of Plant Organellar DNA Enrichment Methods Suitable for Next-generation Sequencing

Published on: July 28, 2017

PMAT: an efficient plant mitogenome assembly toolkit using low-coverage HiFi sequencing data.

Changwei Bi^1,2, Fei Shen³, Fuchuan Han⁴

¹State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Tree Genetics and Biotechnology of Educational Department of China, Key Laboratory of Tree Genetics and Silvicultural Sciences of Jiangsu Province, Nanjing Forestry University, Nanjing 210037, China.

Horticulture Research

|March 12, 2024

Summary

This summary is machine-generated.

A new toolkit, PMAT, efficiently assembles complete plant mitochondrial genomes (mitogenomes) using low-coverage HiFi sequencing data. This advances plant evolution studies and breeding applications by overcoming previous assembly challenges.

More Related Videos

Robust DNA Isolation and High-throughput Sequencing Library Construction for Herbarium Specimens

Robust DNA Isolation and High-throughput Sequencing Library Construction for Herbarium Specimens

Published on: March 8, 2018

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

Published on: August 20, 2021

Related Experiment Videos

Last Updated: Jul 1, 2025

Optimization and Comparative Analysis of Plant Organellar DNA Enrichment Methods Suitable for Next-generation Sequencing

Optimization and Comparative Analysis of Plant Organellar DNA Enrichment Methods Suitable for Next-generation Sequencing

Published on: July 28, 2017

Robust DNA Isolation and High-throughput Sequencing Library Construction for Herbarium Specimens

Robust DNA Isolation and High-throughput Sequencing Library Construction for Herbarium Specimens

Published on: March 8, 2018

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

Published on: August 20, 2021

Area of Science:

Genomics
Plant Science
Bioinformatics

Background:

Plant mitochondrial genomes (mitogenomes) are crucial for understanding plant biology, evolution, and breeding.
Assembling complete plant mitogenomes is difficult due to recombination and gene transfer.
Existing sequencing methods face limitations in accuracy, completeness, and cost.

Purpose of the Study:

To develop an efficient toolkit for de novo assembly of plant mitogenomes.
To utilize low-coverage HiFi sequencing data for improved mitogenome assembly.
To overcome the limitations of current plant mitogenome assembly approaches.

Main Methods:

Development of the Plant Mitogenome Assembly Toolkit (PMAT).
Application of PMAT for de novo assembly of 13 diverse plant mitogenomes.
Evaluation of PMAT's performance against existing organelle genome assemblers.

Main Results:

PMAT achieved superior assembly accuracy and completeness compared to existing tools.
Complete plant mitogenomes were obtained using only 1x HiFi sequencing data.
The toolkit demonstrated efficiency with low-coverage sequencing data.

Conclusions:

PMAT provides an efficient and accurate method for plant mitogenome assembly.
The toolkit enables high-quality mitogenome assembly with minimal sequencing data.
PMAT will accelerate research in plant evolutionary variation and breeding applications.