Scripps VIVO scripps research logo

  • Index
  • Log in
  • Home
  • People
  • Organizations
  • Research
  • Events
Search form

Fugu genome does not contain mitochondrial pseudogenes

Academic Article
uri icon
  • Overview
  • Research
  • Identity
  • Additional Document Info
  • View All
scroll to property group menus

Overview

authors

  • Venkatesh, B.
  • Dandona, N.
  • Brenner, Sydney

publication date

  • February 2006

journal

  • Genomics  Journal

abstract

  • Contrary to previous observations that fish genomes are devoid of nuclear mitochondrial pseudogenes, a genome-wide survey identified a large number of "recent" and "ancient" nuclear mitochondrial DNA fragments (Numts) in the whole-genome sequences of the fugu (Takifugu rubripes), Tetraodon nigroviridis, and zebrafish (Danio rerio). We have analyzed the latest assembly (v4.0) of the fugu genome and show that, like the Anopheles genome, the fugu nuclear genome does not contain mitochondrial pseudogenes. Fugu assembly v4.0 contains a single scaffold representing the near complete sequence of the fugu mitochondria. The "recent" Numts identified by the previous study in fugu assembly v2.0 are in fact shotgun sequences of mitochondrial DNA that were misassembled with the nuclear sequences, whereas the "ancient" Numts appear to be the result of spurious matches. It is likely that the Numts identified in the genomes of Tetraodon and zebrafish are also similar artifacts. Shotgun sequences of whole genomes often include some mitochondrial sequences. Therefore, any Numts identified in shotgun-sequence assemblies should be verified by Southern hybridization or PCR amplification.

subject areas

  • Animals
  • DNA, Mitochondrial
  • Genome
  • Pseudogenes
  • Takifugu
  • Zebrafish
scroll to property group menus

Research

keywords

  • Numt
  • fugu
  • mitochondrial pseudogene
  • teleost fish
  • whole-genome shotgun sequencing
scroll to property group menus

Identity

International Standard Serial Number (ISSN)

  • 0888-7543

Digital Object Identifier (DOI)

  • 10.1016/j.ygeno.2005.11.007

PubMed ID

  • 16386876
scroll to property group menus

Additional Document Info

start page

  • 307

end page

  • 310

volume

  • 87

issue

  • 2

©2021 The Scripps Research Institute | Terms of Use | Powered by VIVO

  • About
  • Contact Us
  • Support