Sequencing and de novo analysis of the Chinese Sika deer antler-tip transcriptome during the ossification stage using Illumina RNA-Seq technology

Abstract

Deer antlers are the only mammalian appendages capable of repeated rounds of regeneration. Every year, deer antlers are shed and regrown from blastema into large branched structures of cartilage and bone. Little is known about the genes involved in antler development particularly during the later stages of ossification. We have produced more than 39 million sequencing reads in a single run using the Illumina sequencing platform. These were assembled into 138,642 unique sequences (mean size: 405bp) representing 50 times the number of Sika deer sequences previously available in the NCBI database (as of Nov 2, 2011). Based on a similarity search of a database of known proteins, we identified 43,937 sequences with a cut-off E-value of 10(-5). Assembled sequences were annotated using Gene Ontology terms, Clusters of Orthologous Groups classifications and Kyoto Encyclopedia of Genes and Genomes pathways. A number of highly expressed genes involved in the regulation of Sika deer antler ossification, including growth factors, transcription factors and extracellular matrix components were found. This is the most comprehensive sequence resource available for the deer antler and provides a basis for the molecular genetics and functional genomics of deer antler.