Open Access Highly Accessed Research article

Large-scale transcriptome sequencing and gene analyses in the crab-eating macaque (Macaca fascicularis) for biomedical research

Jae-Won Huh1†, Young-Hyun Kim3†, Sang-Je Park2†, Dae-Soo Kim4, Sang-Rae Lee1, Kyoung-Min Kim1,3, Kang-Jin Jeong1, Ji-Su Kim1, Bong-Seok Song1, Bo-Woong Sim1, Sun-Uk Kim1, Sang-Hyun Kim1 and Kyu-Tae Chang1,3*

Author Affiliations

1 National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Ochang, Chungbuk, 363-883, Republic of Korea

2 Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan, 609-735, Republic of Korea

3 University of Science & Technology, National Primate Research Center, KRIBB, Daejeon, 305-806, Republic of Korea

4 Genome Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 305-806, Republic of Korea

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BMC Genomics 2012, 13:163 doi:10.1186/1471-2164-13-163

Published: 4 May 2012

Abstract

Background

As a human replacement, the crab-eating macaque (Macaca fascicularis) is an invaluable non-human primate model for biomedical research, but the lack of genetic information on this primate has represented a significant obstacle for its broader use.

Results

Here, we sequenced the transcriptome of 16 tissues originated from two individuals of crab-eating macaque (male and female), and identified genes to resolve the main obstacles for understanding the biological response of the crab-eating macaque. From 4 million reads with 1.4 billion base sequences, 31,786 isotigs containing genes similar to those of humans, 12,672 novel isotigs, and 348,160 singletons were identified using the GS FLX sequencing method. Approximately 86% of human genes were represented among the genes sequenced in this study. Additionally, 175 tissue-specific transcripts were identified, 81 of which were experimentally validated. In total, 4,314 alternative splicing (AS) events were identified and analyzed. Intriguingly, 10.4% of AS events were associated with transposable element (TE) insertions. Finally, investigation of TE exonization events and evolutionary analysis were conducted, revealing interesting phenomena of human-specific amplified trends in TE exonization events.

Conclusions

This report represents the first large-scale transcriptome sequencing and genetic analyses of M. fascicularis and could contribute to its utility for biomedical research and basic biology.