title: Generation of a de novo transcriptome from equine lamellar tissue.
abstract: BACKGROUND
  Laminitis, the structural failure of interdigitated tissue that suspends the distal skeleton within the hoof capsule, is a devastating disease that is the second leading cause of both lameness and euthanasia in the horse. Current transcriptomic research focuses on the expression of known genes. However, as this tissue is quite unique and equine gene annotation is largely derived from computational predictions, there are likely yet uncharacterized transcripts that may be involved in the etiology of laminitis. In order to create a novel annotation resource, we performed whole transcriptome sequencing of sagittal lamellar sections from one control and two laminitis affected horses.
  
  
  RESULTS
  Whole transcriptome sequencing of the three samples resulted in 113 million reads. Overall, 88 % of the reads mapped to the equCab2 reference genome, allowing for the identification of 119,430 SNPs. The de novo assembly generated around 75,000 transcripts, of which 36,000 corresponded to known annotations. Annotated transcript models are hosted in a public data repository and thus can be easily accessed or loaded into genome browsers. RT-PCR of 12 selected assemblies confirmed structure and expression in lamellar tissue.
  
  
  CONCLUSIONS
  Transcriptome sequencing represents a powerful tool to expand on equine annotation and identify novel targets for further laminitis research.
authors.affiliation: Department of Animal Sciences, University of Florida, Gainesville, FL, 32611, USA. heather.holl@ufl.edu.
authors.forename: Heather M
authors.initials: HM
authors.lastname: Holl
authors.affiliation: Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, 14853, USA. wng.peter@gmail.com.
authors.forename: Shan
authors.initials: S
authors.lastname: Gao
authors.affiliation: Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, 14853, USA. zf25@cornell.edu.
authors.forename: Zhangjun
authors.initials: Z
authors.lastname: Fei
authors.affiliation: Laboratory of Molecular Immunoregulation, National Cancer Institute, Bethesda, MD, 20892, USA. candrewsdvm@gmail.com.
authors.forename: Caroline
authors.initials: C
authors.lastname: Andrews
authors.affiliation: Department of Animal Sciences, University of Florida, Gainesville, FL, 32611, USA. samantha.brooks@ufl.edu.
authors.forename: Samantha A
authors.initials: SA
authors.lastname: Brooks
mesh_terms: D000818:Animals; D019295:Computational Biology; D018076:DNA, Complementary / Q000737:chemistry / Q000235:genetics; D030541:Databases, Genetic; D005091:Exons; D020869:Gene Expression Profiling; D056426:Genetic Loci; D059014:High-Throughput Nucleotide Sequencing; D006736:Horses; D058977:Molecular Sequence Annotation; D009928:Organ Specificity / Q000235:genetics; D010641:Phenotype; D015203:Reproducibility of Results; D059467:Transcriptome
chemical_list: D018076:DNA, Complementary