Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Genome Annotation and Assembly03:36

Genome Annotation and Assembly

21.3K
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.
21.3K
RNA-seq03:21

RNA-seq

12.3K
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...
12.3K

You might also read

Related Articles

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

Sort by
Same author

Impact of Socio-demographic Variables, Surgical Techniques and Risk Factors on the Outcome of Coronary Artery Bypass Graft Surgery among Bangladeshi Population.

Mymensingh medical journal : MMJ·2024
Same author

A 15 Year's Experience with Minimally Invasive Mitral Valve Replacement in Bangladesh.

Mymensingh medical journal : MMJ·2020
Same author

Fast Tract Anesthesia Using Isoflurane and Propofol During Off-pump Coronary Artery Bypass Graft Surgery.

Mymensingh medical journal : MMJ·2019
Same author

Pregnancy Outcome with Prosthetic Heart Valve in Bangladesh: A Retrospective Cohort Study.

Mymensingh medical journal : MMJ·2019
Same author

Single-molecule sequencing and Hi-C-based proximity-guided assembly of amaranth (Amaranthus hypochondriacus) chromosomes provide insights into genome evolution.

BMC biology·2017
Same author

The Evolution of HD2 Proteins in Green Plants.

Trends in plant science·2016
Same journal

Validation of the International Weed Genomics Consortium genome annotation pipeline through reannotation of the model species Arabidopsis thaliana.

The plant genome·2026
Same journal

High-density mutation tracks are associated with proton-beam irradiation patterns in Sorghum bicolor.

The plant genome·2026
Same journal

Application of deep learning in crop research: From genomics to phenomics.

The plant genome·2026
Same journal

Haplotype‑resolved comparison of transcription factor superfamilies between wild and cultivated autotetraploid green jujube and prioritization of candidate transcription factors via machine learning.

The plant genome·2026
Same journal

A public mid-density genotyping platform for pecan [Carya illinoinensis (Wangenh.) K. Koch].

The plant genome·2026
Same journal

Missing comparability: When genomic selection faces field variability. A case study in soybeans.

The plant genome·2026
See all related articles

Related Experiment Video

Updated: Mar 11, 2026

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine
10:40

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

11.0K

The Amaranth Genome: Genome, Transcriptome, and Physical Map Assembly.

J W Clouse, D Adhikary, J T Page

    The Plant Genome
    |November 30, 2016
    PubMed
    Summary
    This summary is machine-generated.

    A high-quality draft genome sequence of grain amaranth was generated, revealing its genetic makeup and evolutionary history. This research provides a foundation for understanding amaranth

    More Related Videos

    Fluorescence-microscopy Screening and Next-generation Sequencing: Useful Tools for the Identification of Genes Involved in Organelle Integrity
    12:42

    Fluorescence-microscopy Screening and Next-generation Sequencing: Useful Tools for the Identification of Genes Involved in Organelle Integrity

    Published on: April 13, 2012

    12.8K
    Isolation and Transcriptome Analysis of Plant Cell Types
    08:53

    Isolation and Transcriptome Analysis of Plant Cell Types

    Published on: April 7, 2023

    2.2K

    Related Experiment Videos

    Last Updated: Mar 11, 2026

    Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine
    10:40

    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

    11.0K
    Fluorescence-microscopy Screening and Next-generation Sequencing: Useful Tools for the Identification of Genes Involved in Organelle Integrity
    12:42

    Fluorescence-microscopy Screening and Next-generation Sequencing: Useful Tools for the Identification of Genes Involved in Organelle Integrity

    Published on: April 13, 2012

    12.8K
    Isolation and Transcriptome Analysis of Plant Cell Types
    08:53

    Isolation and Transcriptome Analysis of Plant Cell Types

    Published on: April 7, 2023

    2.2K

    Area of Science:

    • Genomics
    • Plant Science
    • Nutritional Science

    Background:

    • Amaranth ( L.) is a nutrient-rich pseudocereal gaining attention for its high lysine content.
    • It is an ancient paleopolyploid with disomic inheritance (2n = 32) and a genome size of approximately 466 Mb.

    Purpose of the Study:

    • To present a high-quality draft genome sequence of grain amaranth.
    • To analyze the genome's structure, repetitive elements, and gene content.
    • To investigate the evolutionary relationships among grain amaranths and identify the progenitor species.

    Main Methods:

    • Genome sequencing and assembly (377 Mb in 3518 scaffolds).
    • Repetitive element analysis and de novo transcriptome assembly (66,370 contigs).
    • Protein-coding gene annotation (23,059 genes).
    • Resequencing of seven grain amaranths and progenitor species for SNP phylogeny.
    • De novo physical map generation using BioNano Genomics' Genome Mapping platform.
    • Synteny analysis with sugar beet ( L.) and estimation of polyploidization event age.

    Main Results:

    • A draft genome assembly of 377 Mb with an N50 of 371 kb was produced.
    • Approximately 48% of the genome consists of repeat sequences, with -like elements being the most common retrotransposon.
    • A de novo transcriptome yielded 66,370 contigs.
    • Annotation identified 23,059 protein-coding genes.
    • SNP phylogeny identified as the progenitor of grain amaranths.
    • A physical map spanning 340 Mb improved the hybrid assembly N50 to 697 kb.
    • Synteny analysis provided insights into the timing of polyploidization.

    Conclusions:

    • The high-quality draft genome sequence provides a valuable resource for amaranth research.
    • Understanding amaranth's genome structure and evolution can aid in crop improvement.
    • This study clarifies the evolutionary history and progenitor of grain amaranths.