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

Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

321
Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
321
Karyotyping01:17

Karyotyping

65.0K
Overview
65.0K
  1. Home
  3. Research Domains
  5. Agricultural, Veterinary And Food Sciences
  7. Horticultural Production
  9. Horticultural Crop Improvement (incl. Selection And Breeding)
  11. A Haplotype-resolved, Chromosome-scale Genome For Malus Domestica Borkh. 'wa 38'

A Haplotype-resolved, Chromosome-scale Genome for Malus domestica Borkh. 'WA 38'

Huiting Zhang1,2, Itsuhiro Ko3,4, Abigail Eaker3,4

  • 1Department of Horticulture, Washington State University, Pullman, WA, 99164, USA.

G3 (Bethesda, Md.)
|September 17, 2024

Related Experiment Videos

Protocols for CRISPR/Cas9 Mutagenesis of the Oriental Fruit Fly Bactrocera dorsalis
08:19

Protocols for CRISPR/Cas9 Mutagenesis of the Oriental Fruit Fly Bactrocera dorsalis

Published on: September 28, 2022

2.3K
Determination of Self- and Inter-incompatibility Relationships in Apricot Combining Hand-Pollination, Microscopy and Genetic Analyses
08:08

Determination of Self- and Inter-incompatibility Relationships in Apricot Combining Hand-Pollination, Microscopy and Genetic Analyses

Published on: June 16, 2020

7.2K
High-throughput Physical Mapping of Chromosomes using Automated in situ Hybridization
08:48

High-throughput Physical Mapping of Chromosomes using Automated in situ Hybridization

Published on: June 28, 2012

11.6K

View abstract on PubMed

Summary
This summary is machine-generated.

We present the first haplotype-phased, chromosomal-level genome assembly for the apple cultivar Cosmic Crisp® (Malus domestica

Area of Science:

  • Plant genomics
  • Agricultural science
  • Bioinformatics

Background:

  • Genome sequencing advances Rosaceous crops, providing insights into traits like fruit quality and disease resistance.
  • Understanding apple cultivar genomes is crucial for breeding and improving postharvest storage.

Purpose of the Study:

  • To present the first haplotype-phased, chromosomal-level genome assembly for Malus domestica 'WA 38' (Cosmic Crisp®).
  • To enable detailed genome-scale comparisons with other apple cultivars.
  • To provide a reproducible and transparent genome assembly and annotation workflow.

Main Methods:

  • Utilized short and long read sequencing data with a k-mer based approach for assembly.
  • Assembled and segregated parental chromosomes into distinct haplomes (HapA from 'Honeycrisp', HapB from 'Enterprise').
Keywords:
Malus domestica ‘WA 38’Apple genomicscomparative genomicsgenome annotation

Related Experiment Videos

Protocols for CRISPR/Cas9 Mutagenesis of the Oriental Fruit Fly Bactrocera dorsalis
08:19

Protocols for CRISPR/Cas9 Mutagenesis of the Oriental Fruit Fly Bactrocera dorsalis

Published on: September 28, 2022

2.3K
Determination of Self- and Inter-incompatibility Relationships in Apricot Combining Hand-Pollination, Microscopy and Genetic Analyses
08:08

Determination of Self- and Inter-incompatibility Relationships in Apricot Combining Hand-Pollination, Microscopy and Genetic Analyses

Published on: June 16, 2020

7.2K
High-throughput Physical Mapping of Chromosomes using Automated in situ Hybridization
08:48

High-throughput Physical Mapping of Chromosomes using Automated in situ Hybridization

Published on: June 28, 2012

11.6K
  • Employed BUSCO for assessing genome completeness and annotated gene content.

    • Main Results:

    • Successfully generated two 650 Mb haplome assemblies (HapA and HapB) with 98.7% BUSCO completeness.
    • Annotated 53,028 genes in HapA and 54,235 genes in HapB.
    • Identified significant genome structure and gene family differences compared to 'Gala' and 'Honeycrisp' cultivars.

    Conclusions:

    • This is the first pome fruit genome fully phased into parental haplotypes, offering unprecedented detail.
    • The genome assembly and annotation provide valuable resources for apple breeding and research.
    • The shared, containerized workflow ensures transparency and reproducibility for future genome projects.
    genome sequence
    haplotype-resolved assembly
    plant genomics