Annotation of the domestic dog genome sequence: finding the missing genes.

Mammalian Genome : Official Journal of the International Mammalian Genome Society
Thomas DerrienChristophe Hitte

Abstract

There are over 350 genetically distinct breeds of domestic dog that present considerable variation in morphology, physiology, and disease susceptibility. The genome sequence of the domestic dog was assembled and released in 2005, providing an estimated 20,000 protein-coding genes that are a great asset to the scientific community that uses the dog system as a genetic biomedical model and for comparative and evolutionary studies. Although the canine gene set had been predicted using a combination of ab initio methods, homology studies, motif analysis, and similarity-based programs, it still requires a deep annotation of noncoding genes, alternative splicing, pseudogenes, regulatory regions, and gain and loss events. Such analyses could benefit from new sequencing technologies (RNA-Seq) to better exploit the advantages of the canine genetic system in tracking disease genes. Here, we review the catalog of canine protein-coding genes and the search for missing genes, and we propose rationales for an accurate identification of noncoding genes though next-generation sequencing.

References

Aug 1, 1993·Nature Genetics·M S BoguskiC M Tolstoshev
Jun 1, 1997·Computer Applications in the Biosciences : CABIOS·S TiwariR Ramaswamy
Nov 21, 1997·Computer Applications in the Biosciences : CABIOS·Z Yang
Oct 12, 2002·Bioinformatics·Irmtraud M Meyer, Richard Durbin
Apr 18, 2003·Proceedings of the National Academy of Sciences of the United States of America·Richard GuyonElaine A Ostrander
Sep 27, 2003·Science·Ewen F KirknessJ Craig Venter
May 5, 2004·Genome Research·Ewan BirneyRichard Durbin
May 8, 2004·Nature Reviews. Genetics·Laurence D HurstMartin J Lercher
May 25, 2004·Science·Heidi G ParkerLeonid Kruglyak
Sep 15, 2004·BMC Genomics·Matthew BreenElaine A Ostrander
Dec 2, 2004·Nature Reviews. Genetics·Nathan B Sutter, Elaine A Ostrander
Jul 14, 2005·Nature Reviews. Genetics·Christophe HitteFrancis Galibert
Sep 6, 2005·Science·P CarninciUNKNOWN RIKEN Genome Exploration Research Group and Genome Science Group (Genome Network Project Core Group)
Dec 13, 2005·Nature·Kerstin Lindblad-TohEric S Lander
Feb 21, 2006·Nature Methods·Rimantas KodziusPiero Carninci
Jun 8, 2006·Molecular Biology and Evolution·Marie Sémon, Laurent Duret
Oct 3, 2006·PLoS Computational Biology·Leo Goodstadt, Chris P Ponting
Jan 24, 2007·Bioinformatics·T FarautT Schiex
Jun 15, 2007·Genome Research·Thomas R Gingeras
Jun 16, 2007·The Journal of Biological Chemistry·Yunli ZhouAnne Klibanski
Nov 14, 2007·PLoS Computational Biology·Max A Alekseyev, Pavel A Pevzner
Apr 23, 2008·Current Protocols in Bioinformatics·Enrique BlancoRoderic Guigó
Jul 17, 2008·Methods in Molecular Biology·Christophe HitteFrancis Galibert
Aug 30, 2008·Genome Dynamics·F Galibert, C André
Sep 13, 2008·Science·Cord DrögemüllerTosso Leeb
Nov 4, 2008·Nature·Eric T WangChristopher B Burge
Nov 19, 2008·Nature Reviews. Genetics·Zhong WangMichael Snyder
Dec 18, 2008·Genome Biology·France DenoeudFrançois Artiguenave
Feb 6, 2009·BMC Genomics·Thomas DerrienChristophe Hitte
Apr 25, 2009·PLoS Genetics·John S Mattick
May 29, 2009·Proceedings of the National Academy of Sciences of the United States of America·Lucia A HindorffTeri A Manolio
Jul 3, 2009·Proceedings of the National Academy of Sciences of the United States of America·Ahmad M KhalilJohn L Rinn

❮ Previous
Next ❯

Citations

Nov 10, 2013·Mammalian Genome : Official Journal of the International Mammalian Genome Society·Meenakshi RoyRobert Wayne
Aug 17, 2012·The New England Journal of Medicine·Elaine A Ostrander
Dec 22, 2019·Animals : an Open Access Journal From MDPI·Victoria L ShouldiceJ Andrew B Robinson

❮ Previous
Next ❯

Related Concepts

Related Feeds

Alternative splicing

Alternative splicing a regulated gene expression process that allows a single genetic sequence to code for multiple proteins. Here is that latest research.