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Related Concept Videos

Genome Annotation and Assembly03:36

Genome Annotation and Assembly

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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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Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies
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First Draft Genome Assembly of Root-Lesion Nematode Pratylenchus scribneri Generated Using Long-Read Sequencing.

Deepika Arora1, Alvaro G Hernandez2, Kimberly K O Walden2

  • 1Department of Plant Pathology, North Dakota State University, Fargo, ND 58105, USA.

International Journal of Molecular Sciences
|April 28, 2023
PubMed
Summary
This summary is machine-generated.

Researchers have sequenced the draft genome of the root-lesion nematode, *Pratylenchus scribneri*. This provides crucial genomic data for understanding plant-parasitic nematodes and improving crop protection strategies.

Keywords:
BUSCOcontigsdiploidgenomeroot-lesion nematodesequencingultra-low DNA input

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Area of Science:

  • Nematology
  • Genomics
  • Plant Pathology

Background:

  • Root-lesion nematodes (genus *Pratylenchus*) are significant plant-parasitic nematodes (PPNs) with a global presence.
  • Despite their economic importance, genomic data for the *Pratylenchus* genus is limited.
  • This study addresses the scarcity of genomic information for this key PPN group.

Purpose of the Study:

  • To generate a draft genome assembly for *Pratylenchus scribneri*.
  • To provide foundational genomic resources for *Pratylenchus* research.
  • To enable future molecular studies on plant-nematode interactions.

Main Methods:

  • PacBio Sequel IIe System with ultra-low DNA input HiFi sequencing workflow.
  • Draft genome assembly using 500 *P. scribneri* individuals.
  • Benchmarking Universal Single-Copy Ortholog (BUSCO) analysis and GenomeScope2/Smudgeplots for genome characterization.

Main Results:

  • A draft genome assembly of 227.24 Mb with 276 contigs and an N50 of 1.72 Mb.
  • 51,146 predicted protein sequences were identified.
  • BUSCO analysis indicated 65.4% complete BUSCOs, and genome analysis suggested a diploid genome for *P. scribneri*.

Conclusions:

  • The generated draft genome assembly of *Pratylenchus scribneri* is a valuable resource.
  • This genomic data will advance research into host plant-nematode interactions.
  • Facilitates the development of novel molecular strategies for crop protection against root-lesion nematodes.