The Baboon Kidney Transcriptome: Analysis of Transcript Sequence, Splice Variants, and Abundance

Kimberly D. Spradling, Jeremy P. Glenn, Roy Garcia, Robert E. Shade, Laura A. Cox

Research output: Contribution to journalArticle

7 Citations (Scopus)

Abstract

The baboon is an invaluable model for the study of human health and disease, including many complex diseases of the kidney. Although scientists have made great progress in developing this animal as a model for numerous areas of biomedical research, genomic resources for the baboon, such as a quality annotated genome, are still lacking. To this end, we characterized the baboon kidney transcriptome using high-throughput cDNA sequencing (RNA-Seq) to identify genes, gene variants, single nucleotide polymorphisms (SNPs), insertion-deletion polymorphisms (InDels), cellular functions, and key pathways in the baboon kidney to provide a genomic resource for the baboon. Analysis of our sequencing data revealed 45,499 high-confidence SNPs and 29,813 InDels comparing baboon cDNA sequences with the human hg18 reference assembly and identified 35,900 cDNAs in the baboon kidney, including 35,150 transcripts representing 15,369 genic genes that are novel for the baboon. Gene ontology analysis of our sequencing dataset also identified numerous biological functions and canonical pathways that were significant in the baboon kidney, including a large number of metabolic pathways that support known functions of the kidney. The results presented in this study catalogues the transcribed mRNAs, noncoding RNAs, and hypothetical proteins in the baboon kidney and establishes a genomic resource for scientists using the baboon as an experimental model.

Original languageEnglish (US)
Article numbere57563
JournalPLoS One
Volume8
Issue number4
DOIs
StatePublished - Apr 23 2013
Externally publishedYes

Fingerprint

Papio
Gene Expression Profiling
transcriptomics
Polymorphism
Genes
kidneys
Kidney
Complementary DNA
Nucleotides
Untranslated RNA
genomics
Ontology
single nucleotide polymorphism
Animals
Single Nucleotide Polymorphism
Throughput
Health
genes
RNA
genetic polymorphism

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Spradling, K. D., Glenn, J. P., Garcia, R., Shade, R. E., & Cox, L. A. (2013). The Baboon Kidney Transcriptome: Analysis of Transcript Sequence, Splice Variants, and Abundance. PLoS One, 8(4), [e57563]. https://doi.org/10.1371/journal.pone.0057563

The Baboon Kidney Transcriptome : Analysis of Transcript Sequence, Splice Variants, and Abundance. / Spradling, Kimberly D.; Glenn, Jeremy P.; Garcia, Roy; Shade, Robert E.; Cox, Laura A.

In: PLoS One, Vol. 8, No. 4, e57563, 23.04.2013.

Research output: Contribution to journalArticle

Spradling, Kimberly D. ; Glenn, Jeremy P. ; Garcia, Roy ; Shade, Robert E. ; Cox, Laura A. / The Baboon Kidney Transcriptome : Analysis of Transcript Sequence, Splice Variants, and Abundance. In: PLoS One. 2013 ; Vol. 8, No. 4.
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