Crab-eating macaques (Macaca fascicularis) are one of the most frequently used and studied species for biomedical research . Due to the broad range of habitats, they have various common names including crab-eating macaque, cynomolgus macaque, Philippine monkey, and long-tailed macaque. Numerous wild crab-eating macaques are distributed in Southeast Asia, including Indonesia, Philippines, Myanmar, Vietnam, and Thailand . They inhabit various habitats including primary, secondary, coastal, mangrove, and riverine forests and areas near villages. Diurnal and arboreal crab-eating macaques belong to the infraorder Catarrhini, superfamily Carecopithecoidea, family Cercopithecidae, and genus Macaca.
With the aid of fossil records and comparative DNA sequence analysis, genus macaques and humans have diverged from a common ancestor between 25 and 31 million years ago . This evolutionary relationship has made this primate as a more suitable experimental animal model than rodents, dogs, and pigs and may lead to its widespread use for the translational studies for drug testing . Among the genus Macaca, Rhesus and crab-eating macaque is representative species which were widely used as a non-human primate model for biomedical research. However, the rhesus macaque is the most frequently used primate as a non-human primate model . In the United States, more than 60% of monkeys housed in National Institutes of Health (NIH)-supported facilities are rhesus macaques . Furthermore, 65% of the monkeys used for experimental research each year are rhesus macaques. In 2007, first draft genome sequences of rhesus macaque genome was published . These worldwide trends in use and accumulated genome information data may lead to the assumption that the rhesus macaque is the ideal non-human primate model. However, the event of “export ban of rhesus monkey from India in 1977” had restricted the usage of Indian subspecies of the rhesus macaque and accelerate the building of self-sustaining breeding colonies in the US. Therefore, researchers who want to have a research with rhesus monkey in the outside of US have some problems, they have concerned the chinese-origin rhesus macaque and crab-eating macaque from south asia . Furthermore, the crab-eating macaque has important advantages, including (1) easy handling derived from a smaller body size (♂ 412–648 mm, ♀ 385–503 mm vs. ♂ 483–635 mm, ♀ 470–531 mm), weight (♂ 4.7–8.3 kg, ♀ 2.5–5.7 kg vs. ♂ 5.6–10.9 kg, ♀ 4.4–10.9 kg) and longer tails than rhesus macaques ; (2) low cost and easy availability for experimental use; and (3) lack of seasonal fertility, which may affect efficient experiments and scheduling in the large-scale housing of experimental monkeys . Finally, abundant gene information is available for the crab-eating macaque. Greater numbers of EST and full-length cDNA library sequences are available in the NCBI database for crab-eating macaque [9–15]. And recently their draft genome sequences also available in the EBI database [6, 16]. Therefore, crab-eating macaque could be a excellent experimental primate animal models for biomedical studies.
In an in-depth examination of the published papers from 2010 to 2011 indicated that pharmacology field for safety and toxicity testing of newly developed drugs was the most frequently encountered [17–20]. In particular, the crab-eating macaque was used predominantly in brain research, the neurosciences, and clinical research [21–24]. Furthermore, experimental primate model have been developed by four different ways of simple replacement, induced, infection, and surgical. The induced method involved treatment with specific chemicals (e.g., 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) or streptozotocin (STZ)[25–27], whereas the surgical method (e.g., middle cerebral artery occlusion model for ischemia) were created through specific types of surgery . The infection method was simpler than previously described since humans and the crab-eating macaque have numerous “anthroponosis” (the opposite of “zoonosis”), including influenza, tuberculosis, and hepatitis . Lastly, simple replacement method was the usage of natural crab-eating monkey for specific purpose (e.g., drug safety or efficacy testing) .
From now, numerous disease models, including aging, alcohol abuse, Alzheimer’s disease, amenorrhea, asthma, diabetes, epilepsy, menopause, obesity, osteoporosis, Parkinson’s disease, plague, variola, vascular disease, and various infection disease models, have been developed and used [31–46] However, small amount of transcript sequences of crab-eating macaque could be a weak point to be a good experimental animals for biomedical application. If we have abundant transcript sequences for crab-eating macaque, we could design the whole gene probe sequences for microarray analyses. And also, due to the insufficient transcript sequences, we could not analyze the alternatively spliced transcripts in different tissues. Recent accumulated transcriptome information underlined that AS event is an important molecular mechanism since it can generate different functional units for transcriptome and proteome diversity using limited genetic sources[47–49]. And also human transcriptome studies with different human tissues show different AS patterns derived by tissue-specific alternative promoters and polyadenylation [50–52]. However, sometimes aberrant changes in alternative splicing could occur the human disease (e.g. retinitis pigmentosa or cystic fibrosis) [53, 54]. And A few number of papers have reviewed the association between alternative splicing and disease [55–58]. Among the different AS mechanism, TE exonization is intriguing AS events . Specifically, small amount of TEs show the tissue specific and species specific characters . That means that TE exonization event could be a one of the important AS events. Therefore, AS is not a simple molecular aspect of RNA transcription, rather it represents a highly controlled and evolved molecular mechanism for generating genetic diversity using limited DNA resources. And also AS control mechanism are major growing topics in biomedical researches. Hence, the investigation of the AS events in specific genes is another means of novel gene or disease gene identification and characterization steps. However, these kinds of applications with crab-eating macaque for advanced biomedical research could be achieved by the massive amount of transcript sequences and information.
In this study, we carried out a whole-transcriptome sequencing analysis of 16 tissues from Macaca fascicularis using GS FLX sequencing to generate massive transcript information for the improvement of biomedical use. More than 4 million raw reads were created and assembled, resulting in 35,524 isogroups, 44,458 isotigs, 54,858 contigs, and 348,160 singletons. Additionally, we identified and experimentally validated differentially expressed gene (DEG) transcripts. Finally, using the numerous transcript sequences, we analyze the AS and TE events of crab-eating macaque.