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Biotechnology Letters

, Volume 34, Issue 5, pp 813–822 | Cite as

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

  • Baojin Yao
  • Yu ZhaoEmail author
  • Haishan Zhang
  • Mei Zhang
  • Meichen Liu
  • Hailong Liu
  • Juan LiEmail author
Original Research Paper

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: 405 bp) 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.

Keywords

Antler tip Chinese Sika deer Gene expression Ossification Transcriptome 

Notes

Acknowledgments

This work was supported by the National Key Technology Research and Development Program of the Ministry of Science and Technology of China (Grant No. 2011BAI03B00) and by the National Science and Technology Major Project of the Ministry of Science and Technology of China (Grant No. 2011ZX09401-305-09).

Supplementary material

10529_2011_841_MOESM1_ESM.pdf (3.1 mb)
Fig. S1 Graph of de novo assembly results at different k-mer sizes. The x-axis indicates different k-mer sizes. The y-axis indicates the number of assembly sequences under different k-mer sizes. (PDF 3174 kb)
10529_2011_841_MOESM2_ESM.pdf (1.1 mb)
Fig. S2 Ratio distribution of the gap’s length to the length of assembled unigenes. The x-axis indicates the ratio of the gap’s length to the length of assembled unigenes. The y-axis indicates the number of unigenes containing gaps. (PDF 1117 kb)
10529_2011_841_MOESM3_ESM.pdf (2.3 mb)
Fig. S3 Random distribution of Illumina sequencing reads in the assembled unigenes. The x-axis indicates the relative position of sequencing reads in the assembled unigenes. The orientation of unigene is from 5′ end to 3′ end. (PDF 2325 kb)
10529_2011_841_MOESM4_ESM.pdf (3.2 mb)
Fig. S4 Validation of candidate genes in Sika deer transcriptome by qPCR. The left y-axis indicates the relative abundance of candidate genes in Sika deer antler resulting from qPCR. The right y-axis indicates gene expression levels of candidate genes according to RPKM calculation. (PDF 3306 kb)
10529_2011_841_MOESM5_ESM.pdf (78 kb)
Supplementary material 5 (PDF 78 kb)
10529_2011_841_MOESM6_ESM.pdf (41 kb)
Supplementary material 6 (PDF 41 kb)

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Copyright information

© Springer Science+Business Media B.V. 2011

Authors and Affiliations

  1. 1.School of Public HealthJilin UniversityChangchunChina
  2. 2.Center for New Medicine ResearchChangchun University of Chinese MedicineChangchunChina
  3. 3.Department of Colorectal SurgeryChina-Japan Union Hospital, Jilin UniversityChangchunChina

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