Generation of a de novo Transcriptome Assembly from Equine Lamellar Tissue

The equine hoof is a specialized structure in which the entire skeleton is suspended within the capsule entirely by interdigitated structures known as laminae. Inflammation of this tissue, known as laminitis, is a devastating disease that is the second leading cause of both lameness and euthanasia. Current research on the laminitic transcriptome focuses on the expression of known genes. However, as this tissue is quite unique and equine annotation is largely based on other species, there are likely yet uncharacterized transcripts expressed in the laminae that may be involved in the etiology of laminitis. To discover these unique transcripts, we performed whole transcriptome sequencing of sagittal lamellar sections from one control and two laminitis affected. The control animal presented with no evidence of lameness upon veterinary examination and no gross pathological evidence at necropsy. The selected cases represented two different disease states of laminitis, with one acute case (secondary to enterocolitis) and one chronic case (repeat episodes related to Equine Metabolic Syndrome). The control sample was selected for an initial analysis to assess the feasibility of generating a de novo transcriptome from short reads. Assembly of 36 million 100bp reads resulted in around 80,000 putative transcripts. Of these, around 38,000 thousand could be mapped to proteins in NCBI's NR database. Inclusion of the additional samples into the assembly pipeline and screening for novel transcripts is currently on-going. Sequencing the hoof transcriptome represents a powerful tool to expand on equine transcriptome annotation and potentially identify novel loci of the equine laminae.