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PloS one2017; 12(8); e0180359; doi: 10.1371/journal.pone.0180359

A curated catalog of canine and equine keratin genes.

Abstract: Keratins represent a large protein family with essential structural and functional roles in epithelial cells of skin, hair follicles, and other organs. During evolution the genes encoding keratins have undergone multiple rounds of duplication and humans have two clusters with a total of 55 functional keratin genes in their genomes. Due to the high similarity between different keratin paralogs and species-specific differences in gene content, the currently available keratin gene annotation in species with draft genome assemblies such as dog and horse is still imperfect. We compared the National Center for Biotechnology Information (NCBI) (dog annotation release 103, horse annotation release 101) and Ensembl (release 87) gene predictions for the canine and equine keratin gene clusters to RNA-seq data that were generated from adult skin of five dogs and two horses and from adult hair follicle tissue of one dog. Taking into consideration the knowledge on the conserved exon/intron structure of keratin genes, we annotated 61 putatively functional keratin genes in both the dog and horse, respectively. Subsequently, curators in the RefSeq group at NCBI reviewed their annotation of keratin genes in the dog and horse genomes (Annotation Release 104 and Annotation Release 102, respectively) and updated annotation and gene nomenclature of several keratin genes. The updates are now available in the NCBI Gene database (https://www.ncbi.nlm.nih.gov/gene).
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Publication Date: 2017-08-28 PubMed ID: 28846680PubMed Central: PMC5573215DOI: 10.1371/journal.pone.0180359Google Scholar: Lookup
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  • Journal Article

Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

The research article is about creating a definitive catalog of keratin genes in dogs and horses, which was achieved by comparing gene predictions with RNA-seq data from various adult skin and hair follicle tissues. The study significantly improved the keratin gene annotation in these species.

Objective of the Study

  • The study aims to improve the annotation of keratin genes in dogs and horses. Keratins are an important family of proteins in epithelial cells, and understanding their genetic background can be crucial for genetics and medical research.

Methodology

  • The researchers utilized the latest gene predictions from the National Center for Biotechnology Information (NCBI) and compared these to RNA-seq data that was generated from the skin of five dogs and two horses, plus hair follicle tissue from one dog.
  • Through careful annotation by taking into account the known exon/intron structure of keratin genes, 61 likely functional keratin genes were annotated both in the dog and horse.

Review and Updates

  • Post annotation, the RefSeq group at NCBI reviewed and updated their annotation of keratin genes in the genomes of dogs and horses, contributing to a more accurate and reliable database of such genes.
  • This updated information is now available in the NCBI Gene database, serving as a comprehensive resource for vetereinary and genetic scientists.

Significance of the Study

  • This study provides a more accurate, curated catalog of keratin genes in dogs and horses. It addresses the former imperfections and species-specific differences in gene content.
  • It significantly contributes to the broader scientific community’s understanding of keratin gene structure in animals, and especially in animals like dogs and horses that are common subjects in medical research.

Cite This Article

APA
Balmer P, Bauer A, Pujar S, McGarvey KM, Welle M, Galichet A, Müller EJ, Pruitt KD, Leeb T, Jagannathan V. (2017). A curated catalog of canine and equine keratin genes. PLoS One, 12(8), e0180359. https://doi.org/10.1371/journal.pone.0180359

Publication

PloS one
ISSN: 1932-6203
NlmUniqueID: 101285081
Country: United States
Language: English
Volume: 12
Issue: 8
Pages: e0180359
PII: e0180359

Researcher Affiliations

Balmer, Pierre
  • Division of Clinical Dermatology, Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
  • Dermfocus, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
Bauer, Anina
  • Dermfocus, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
  • Institute of Genetics, Vetsuisse Faculty, University of Bern,Bern, Switzerland.
Pujar, Shashikant
  • National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States of America.
McGarvey, Kelly M
  • National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States of America.
Welle, Monika
  • Dermfocus, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
  • Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
Galichet, Arnaud
  • Dermfocus, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
  • Department of Clinical Research, Molecular Dermatology and Stem Cell Research, University of Bern, Bern, Switzerland.
Müller, Eliane J
  • Dermfocus, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
  • Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
  • Department of Clinical Research, Molecular Dermatology and Stem Cell Research, University of Bern, Bern, Switzerland.
  • Clinic for Dermatology, Inselspital, Bern University Hospital, Bern, Switzerland.
Pruitt, Kim D
  • National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States of America.
Leeb, Tosso
  • Dermfocus, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
  • Institute of Genetics, Vetsuisse Faculty, University of Bern,Bern, Switzerland.
Jagannathan, Vidhya
  • Dermfocus, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
  • Institute of Genetics, Vetsuisse Faculty, University of Bern,Bern, Switzerland.

MeSH Terms

  • Animals
  • Databases, Genetic
  • Dogs / genetics
  • Exons
  • Genome
  • Horses / genetics
  • Introns
  • Keratins / genetics
  • Molecular Sequence Annotation
  • Species Specificity

Conflict of Interest Statement

The authors have declared that no competing interests exist.

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